Crystal Structure of the Middle East Respiratory Syndrome Coronavirus (MERS-CoV) Papain-like Protease Bound to Ubiquitin Facilitates Targeted Disruption of Deubiquitinating Activity to Demonstrate Its Role in Innate Immune Suppression*
Identifieur interne : 000D86 ( Pmc/Corpus ); précédent : 000D85; suivant : 000D87Crystal Structure of the Middle East Respiratory Syndrome Coronavirus (MERS-CoV) Papain-like Protease Bound to Ubiquitin Facilitates Targeted Disruption of Deubiquitinating Activity to Demonstrate Its Role in Innate Immune Suppression*
Auteurs : Ben A. Bailey-Elkin ; Robert C. M. Knaap ; Garrett G. Johnson ; Tim J. Dalebout ; Dennis K. Ninaber ; Puck B. Van Kasteren ; Peter J. Bredenbeek ; Eric J. Snijder ; Marjolein Kikkert ; Brian L. MarkSource :
- The Journal of Biological Chemistry [ 0021-9258 ] ; 2014.
Abstract
Url:
DOI: 10.1074/jbc.M114.609644
PubMed: 25320088
PubMed Central: 4263872
Links to Exploration step
PMC:4263872Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Crystal Structure of the Middle East Respiratory Syndrome Coronavirus
(MERS-CoV) Papain-like Protease Bound to Ubiquitin Facilitates Targeted
Disruption of Deubiquitinating Activity to Demonstrate Its Role in Innate Immune
Suppression<xref ref-type="fn" rid="FN1">*</xref></title><author><name sortKey="Bailey Elkin, Ben A" sort="Bailey Elkin, Ben A" uniqKey="Bailey Elkin B" first="Ben A." last="Bailey-Elkin">Ben A. Bailey-Elkin</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Knaap, Robert C M" sort="Knaap, Robert C M" uniqKey="Knaap R" first="Robert C. M." last="Knaap">Robert C. M. Knaap</name><affiliation><nlm:aff id="aff2"></nlm:aff></affiliation></author><author><name sortKey="Johnson, Garrett G" sort="Johnson, Garrett G" uniqKey="Johnson G" first="Garrett G." last="Johnson">Garrett G. Johnson</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Dalebout, Tim J" sort="Dalebout, Tim J" uniqKey="Dalebout T" first="Tim J." last="Dalebout">Tim J. Dalebout</name><affiliation><nlm:aff id="aff2"></nlm:aff></affiliation></author><author><name sortKey="Ninaber, Dennis K" sort="Ninaber, Dennis K" uniqKey="Ninaber D" first="Dennis K." last="Ninaber">Dennis K. Ninaber</name><affiliation><nlm:aff id="aff2"></nlm:aff></affiliation></author><author><name sortKey="Van Kasteren, Puck B" sort="Van Kasteren, Puck B" uniqKey="Van Kasteren P" first="Puck B." last="Van Kasteren">Puck B. Van Kasteren</name><affiliation><nlm:aff id="aff2"></nlm:aff></affiliation></author><author><name sortKey="Bredenbeek, Peter J" sort="Bredenbeek, Peter J" uniqKey="Bredenbeek P" first="Peter J." last="Bredenbeek">Peter J. Bredenbeek</name><affiliation><nlm:aff id="aff2"></nlm:aff></affiliation></author><author><name sortKey="Snijder, Eric J" sort="Snijder, Eric J" uniqKey="Snijder E" first="Eric J." last="Snijder">Eric J. Snijder</name><affiliation><nlm:aff id="aff2"></nlm:aff></affiliation></author><author><name sortKey="Kikkert, Marjolein" sort="Kikkert, Marjolein" uniqKey="Kikkert M" first="Marjolein" last="Kikkert">Marjolein Kikkert</name><affiliation><nlm:aff id="aff2"></nlm:aff></affiliation></author><author><name sortKey="Mark, Brian L" sort="Mark, Brian L" uniqKey="Mark B" first="Brian L." last="Mark">Brian L. Mark</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">25320088</idno><idno type="pmc">4263872</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4263872</idno><idno type="RBID">PMC:4263872</idno><idno type="doi">10.1074/jbc.M114.609644</idno><date when="2014">2014</date><idno type="wicri:Area/Pmc/Corpus">000D86</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">000D86</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Crystal Structure of the Middle East Respiratory Syndrome Coronavirus
(MERS-CoV) Papain-like Protease Bound to Ubiquitin Facilitates Targeted
Disruption of Deubiquitinating Activity to Demonstrate Its Role in Innate Immune
Suppression<xref ref-type="fn" rid="FN1">*</xref></title><author><name sortKey="Bailey Elkin, Ben A" sort="Bailey Elkin, Ben A" uniqKey="Bailey Elkin B" first="Ben A." last="Bailey-Elkin">Ben A. Bailey-Elkin</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Knaap, Robert C M" sort="Knaap, Robert C M" uniqKey="Knaap R" first="Robert C. M." last="Knaap">Robert C. M. Knaap</name><affiliation><nlm:aff id="aff2"></nlm:aff></affiliation></author><author><name sortKey="Johnson, Garrett G" sort="Johnson, Garrett G" uniqKey="Johnson G" first="Garrett G." last="Johnson">Garrett G. Johnson</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Dalebout, Tim J" sort="Dalebout, Tim J" uniqKey="Dalebout T" first="Tim J." last="Dalebout">Tim J. Dalebout</name><affiliation><nlm:aff id="aff2"></nlm:aff></affiliation></author><author><name sortKey="Ninaber, Dennis K" sort="Ninaber, Dennis K" uniqKey="Ninaber D" first="Dennis K." last="Ninaber">Dennis K. Ninaber</name><affiliation><nlm:aff id="aff2"></nlm:aff></affiliation></author><author><name sortKey="Van Kasteren, Puck B" sort="Van Kasteren, Puck B" uniqKey="Van Kasteren P" first="Puck B." last="Van Kasteren">Puck B. Van Kasteren</name><affiliation><nlm:aff id="aff2"></nlm:aff></affiliation></author><author><name sortKey="Bredenbeek, Peter J" sort="Bredenbeek, Peter J" uniqKey="Bredenbeek P" first="Peter J." last="Bredenbeek">Peter J. Bredenbeek</name><affiliation><nlm:aff id="aff2"></nlm:aff></affiliation></author><author><name sortKey="Snijder, Eric J" sort="Snijder, Eric J" uniqKey="Snijder E" first="Eric J." last="Snijder">Eric J. Snijder</name><affiliation><nlm:aff id="aff2"></nlm:aff></affiliation></author><author><name sortKey="Kikkert, Marjolein" sort="Kikkert, Marjolein" uniqKey="Kikkert M" first="Marjolein" last="Kikkert">Marjolein Kikkert</name><affiliation><nlm:aff id="aff2"></nlm:aff></affiliation></author><author><name sortKey="Mark, Brian L" sort="Mark, Brian L" uniqKey="Mark B" first="Brian L." last="Mark">Brian L. Mark</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author></analytic><series><title level="j">The Journal of Biological Chemistry</title><idno type="ISSN">0021-9258</idno><idno type="eISSN">1083-351X</idno><imprint><date when="2014">2014</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p><bold>Background:</bold> MERS-CoV papain-like protease (PL<sup>pro</sup>)
processes viral polyproteins and has deubiquitinating activity.</p><p><bold>Results:</bold> A crystal structure of MERS-CoV PL<sup>pro</sup> bound to
ubiquitin guided mutagenesis to disrupt PL<sup>pro</sup> deubiquitinating
activity without affecting polyprotein cleavage.</p><p><bold>Conclusion:</bold> The deubiquitinating activity of MERS-CoV
PL<sup>pro</sup> suppresses the induction of interferon-β
expression.</p><p><bold>Significance:</bold> Our strategy to selectively disable PL<sup>pro</sup>deubiquitinating activity enables the study of its specific functions in
infection.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Zaki, A M" uniqKey="Zaki A">A. M. Zaki</name></author><author><name sortKey="Van Boheemen, S" uniqKey="Van Boheemen S">S. van Boheemen</name></author><author><name sortKey="Bestebroer, T M" uniqKey="Bestebroer T">T. M. Bestebroer</name></author><author><name sortKey="Osterhaus, A D M E" uniqKey="Osterhaus A">A. D. M. E. Osterhaus</name></author><author><name sortKey="Fouchier, R A M" uniqKey="Fouchier R">R. A. M. Fouchier</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Azhar, E I" uniqKey="Azhar E">E. I. Azhar</name></author><author><name sortKey="El Kafrawy, S A" uniqKey="El Kafrawy S">S. A. El-Kafrawy</name></author><author><name sortKey="Farraj, S A" uniqKey="Farraj S">S. A. Farraj</name></author><author><name sortKey="Hassan, A M" uniqKey="Hassan A">A. M. Hassan</name></author><author><name sortKey="Al Saeed, M S" uniqKey="Al Saeed M">M. S. Al-Saeed</name></author><author><name sortKey="Hashem, A M" uniqKey="Hashem A">A. M. Hashem</name></author><author><name sortKey="Madani, T A" uniqKey="Madani T">T. A. Madani</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Reusken, C B" uniqKey="Reusken C">C. B. Reusken</name></author><author><name sortKey="Farag, E A" uniqKey="Farag E">E. A. Farag</name></author><author><name sortKey="Jonges, M" uniqKey="Jonges M">M. Jonges</name></author><author><name sortKey="Godeke, G J" uniqKey="Godeke G">G. J. Godeke</name></author><author><name sortKey="El Sayed, A M" uniqKey="El Sayed A">A. M. El-Sayed</name></author><author><name sortKey="Pas, S D" uniqKey="Pas S">S. D. Pas</name></author><author><name sortKey="Raj, V S" uniqKey="Raj V">V. S. Raj</name></author><author><name sortKey="Mohran, K J" uniqKey="Mohran K">K. J. Mohran</name></author><author><name sortKey="Moussa, H A" uniqKey="Moussa H">H. A. Moussa</name></author><author><name sortKey="Ghobashy, H" uniqKey="Ghobashy H">H. Ghobashy</name></author><author><name sortKey="Alhajri, F" uniqKey="Alhajri F">F. Alhajri</name></author><author><name sortKey="Ibrahim, A K" uniqKey="Ibrahim A">A. K. Ibrahim</name></author><author><name sortKey="Bosch, B J" uniqKey="Bosch B">B. J. Bosch</name></author><author><name sortKey="Pasha, S K" uniqKey="Pasha S">S. K. Pasha</name></author><author><name sortKey="Al Romaihi, H E" uniqKey="Al Romaihi H">H. E. Al-Romaihi</name></author><author><name sortKey="Al Thani, M" uniqKey="Al Thani M">M. Al-Thani</name></author><author><name sortKey="Al Marri, S A" uniqKey="Al Marri S">S. A. Al-Marri</name></author><author><name sortKey="Alhajri, M M" uniqKey="Alhajri M">M. M. AlHajri</name></author><author><name sortKey="Haagmans, B L" uniqKey="Haagmans B">B. L. Haagmans</name></author><author><name sortKey="Koopmans, M P" uniqKey="Koopmans M">M. P. Koopmans</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Van Boheemen, S" uniqKey="Van Boheemen S">S. van Boheemen</name></author><author><name sortKey="De Graaf, M" uniqKey="De Graaf M">M. de Graaf</name></author><author><name sortKey="Lauber, C" uniqKey="Lauber C">C. Lauber</name></author><author><name sortKey="Bestebroer, T M" uniqKey="Bestebroer T">T. M. Bestebroer</name></author><author><name sortKey="Raj, V S" uniqKey="Raj V">V. S. Raj</name></author><author><name sortKey="Zaki, A M" uniqKey="Zaki A">A. M. Zaki</name></author><author><name sortKey="Osterhaus, A D" uniqKey="Osterhaus A">A. D. Osterhaus</name></author><author><name sortKey="Haagmans, B L" uniqKey="Haagmans B">B. L. Haagmans</name></author><author><name sortKey="Gorbalenya, A E" uniqKey="Gorbalenya A">A. E. Gorbalenya</name></author><author><name sortKey="Snijder, E J" uniqKey="Snijder E">E. J. Snijder</name></author><author><name sortKey="Fouchier, R A" uniqKey="Fouchier R">R. A. Fouchier</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Firth, A E" uniqKey="Firth A">A. E. Firth</name></author><author><name sortKey="Brierley, I" uniqKey="Brierley I">I. Brierley</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Perlman, S" uniqKey="Perlman S">S. Perlman</name></author><author><name sortKey="Netland, J" uniqKey="Netland J">J. Netland</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Yang, X" uniqKey="Yang X">X. Yang</name></author><author><name sortKey="Chen, X" uniqKey="Chen X">X. Chen</name></author><author><name sortKey="Bian, G" uniqKey="Bian G">G. Bian</name></author><author><name sortKey="Tu, J" uniqKey="Tu J">J. Tu</name></author><author><name sortKey="Xing, Y" uniqKey="Xing Y">Y. Xing</name></author><author><name sortKey="Wang, Y" uniqKey="Wang Y">Y. Wang</name></author><author><name sortKey="Chen, Z" uniqKey="Chen Z">Z. Chen</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Kilianski, A" uniqKey="Kilianski A">A. Kilianski</name></author><author><name sortKey="Mielech, A M" uniqKey="Mielech A">A. M. Mielech</name></author><author><name sortKey="Deng, X" uniqKey="Deng X">X. Deng</name></author><author><name sortKey="Baker, S C" uniqKey="Baker S">S. C. Baker</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Komander, D" uniqKey="Komander D">D. Komander</name></author><author><name sortKey="Rape, M" uniqKey="Rape M">M. Rape</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Komander, D" uniqKey="Komander D">D. Komander</name></author><author><name sortKey="Clague, M J" uniqKey="Clague M">M. J. Clague</name></author><author><name sortKey="Urbe, S" uniqKey="Urbe S">S. Urbé</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Frieman, M" uniqKey="Frieman M">M. Frieman</name></author><author><name sortKey="Ratia, K" uniqKey="Ratia K">K. Ratia</name></author><author><name sortKey="Johnston, R E" uniqKey="Johnston R">R. E. Johnston</name></author><author><name sortKey="Mesecar, A D" uniqKey="Mesecar A">A. D. Mesecar</name></author><author><name sortKey="Baric, R S" uniqKey="Baric R">R. S. Baric</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Barretto, N" uniqKey="Barretto N">N. Barretto</name></author><author><name sortKey="Jukneliene, D" uniqKey="Jukneliene D">D. Jukneliene</name></author><author><name sortKey="Ratia, K" uniqKey="Ratia K">K. Ratia</name></author><author><name sortKey="Chen, Z" uniqKey="Chen Z">Z. Chen</name></author><author><name sortKey="Mesecar, A D" uniqKey="Mesecar A">A. D. Mesecar</name></author><author><name sortKey="Baker, S C" uniqKey="Baker S">S. C. Baker</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Clementz, M A" uniqKey="Clementz M">M. A. Clementz</name></author><author><name sortKey="Chen, Z" uniqKey="Chen Z">Z. Chen</name></author><author><name sortKey="Banach, B S" uniqKey="Banach B">B. S. Banach</name></author><author><name sortKey="Wang, Y" uniqKey="Wang Y">Y. Wang</name></author><author><name sortKey="Sun, L" uniqKey="Sun L">L. Sun</name></author><author><name sortKey="Ratia, K" uniqKey="Ratia K">K. Ratia</name></author><author><name sortKey="Baez Santos, Y M" uniqKey="Baez Santos Y">Y. M. Baez-Santos</name></author><author><name sortKey="Wang, J" uniqKey="Wang J">J. Wang</name></author><author><name sortKey="Takayama, J" uniqKey="Takayama J">J. Takayama</name></author><author><name sortKey="Ghosh, A K" uniqKey="Ghosh A">A. K. Ghosh</name></author><author><name sortKey="Li, K" uniqKey="Li K">K. Li</name></author><author><name sortKey="Mesecar, A D" uniqKey="Mesecar A">A. D. Mesecar</name></author><author><name sortKey="Baker, S C" uniqKey="Baker S">S. C. Baker</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Mielech, A M" uniqKey="Mielech A">A. M. Mielech</name></author><author><name sortKey="Kilianski, A" uniqKey="Kilianski A">A. Kilianski</name></author><author><name sortKey="Baez Santos, Y M" uniqKey="Baez Santos Y">Y. M. Baez-Santos</name></author><author><name sortKey="Mesecar, A D" uniqKey="Mesecar A">A. D. Mesecar</name></author><author><name sortKey="Baker, S C" uniqKey="Baker S">S. C. Baker</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Lindner, H A" uniqKey="Lindner H">H. A. Lindner</name></author><author><name sortKey="Fotouhi Ardakani, N" uniqKey="Fotouhi Ardakani N">N. Fotouhi-Ardakani</name></author><author><name sortKey="Lytvyn, V" uniqKey="Lytvyn V">V. Lytvyn</name></author><author><name sortKey="Lachance, P" uniqKey="Lachance P">P. Lachance</name></author><author><name sortKey="Sulea, T" uniqKey="Sulea T">T. Sulea</name></author><author><name sortKey="Menard, R" uniqKey="Menard R">R. Ménard</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Lindner, H A" uniqKey="Lindner H">H. A. Lindner</name></author><author><name sortKey="Lytvyn, V" uniqKey="Lytvyn V">V. Lytvyn</name></author><author><name sortKey="Qi, H" uniqKey="Qi H">H. Qi</name></author><author><name sortKey="Lachance, P" uniqKey="Lachance P">P. Lachance</name></author><author><name sortKey="Ziomek, E" uniqKey="Ziomek E">E. Ziomek</name></author><author><name sortKey="Menard, R" uniqKey="Menard R">R. Ménard</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Mielech, A M" uniqKey="Mielech A">A. M. Mielech</name></author><author><name sortKey="Chen, Y" uniqKey="Chen Y">Y. Chen</name></author><author><name sortKey="Mesecar, A D" uniqKey="Mesecar A">A. D. Mesecar</name></author><author><name sortKey="Baker, S C" uniqKey="Baker S">S. C. Baker</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Jensen, S" uniqKey="Jensen S">S. Jensen</name></author><author><name sortKey="Thomsen, A R" uniqKey="Thomsen A">A. R. Thomsen</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Goubau, D" uniqKey="Goubau D">D. Goubau</name></author><author><name sortKey="Schlee, M" uniqKey="Schlee M">M. Schlee</name></author><author><name sortKey="Deddouche, S" uniqKey="Deddouche S">S. Deddouche</name></author><author><name sortKey="Pruijssers, A J" uniqKey="Pruijssers A">A. J. Pruijssers</name></author><author><name sortKey="Zillinger, T" uniqKey="Zillinger T">T. Zillinger</name></author><author><name sortKey="Goldeck, M" uniqKey="Goldeck M">M. Goldeck</name></author><author><name sortKey="Schuberth, C" uniqKey="Schuberth C">C. Schuberth</name></author><author><name sortKey="Van Der Veen, A G" uniqKey="Van Der Veen A">A. G. Van der Veen</name></author><author><name sortKey="Fujimura, T" uniqKey="Fujimura T">T. Fujimura</name></author><author><name sortKey="Rehwinkel, J" uniqKey="Rehwinkel J">J. Rehwinkel</name></author><author><name sortKey="Iskarpatyoti, J A" uniqKey="Iskarpatyoti J">J. A. Iskarpatyoti</name></author><author><name sortKey="Barchet, W" uniqKey="Barchet W">W. Barchet</name></author><author><name sortKey="Ludwig, J" uniqKey="Ludwig J">J. Ludwig</name></author><author><name sortKey="Dermody, T S" uniqKey="Dermody T">T. S. Dermody</name></author><author><name sortKey="Hartmann, G" uniqKey="Hartmann G">G. Hartmann</name></author><author><name sortKey="Sousa, C R" uniqKey="Sousa C">C. R. Sousa</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Jiang, X" uniqKey="Jiang X">X. Jiang</name></author><author><name sortKey="Chen, Z J" uniqKey="Chen Z">Z. J. Chen</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Devaraj, S G" uniqKey="Devaraj S">S. G. Devaraj</name></author><author><name sortKey="Wang, N" uniqKey="Wang N">N. Wang</name></author><author><name sortKey="Chen, Z" uniqKey="Chen Z">Z. Chen</name></author><author><name sortKey="Chen, Z" uniqKey="Chen Z">Z. Chen</name></author><author><name sortKey="Tseng, M" uniqKey="Tseng M">M. Tseng</name></author><author><name sortKey="Barretto, N" uniqKey="Barretto N">N. Barretto</name></author><author><name sortKey="Lin, R" uniqKey="Lin R">R. Lin</name></author><author><name sortKey="Peters, C J" uniqKey="Peters C">C. J. Peters</name></author><author><name sortKey="Tseng, C T K" uniqKey="Tseng C">C.-T. K. Tseng</name></author><author><name sortKey="Baker, S C" uniqKey="Baker S">S. C. Baker</name></author><author><name sortKey="Li, K" uniqKey="Li K">K. Li</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Spiegel, M" uniqKey="Spiegel M">M. Spiegel</name></author><author><name sortKey="Pichlmair, A" uniqKey="Pichlmair A">A. Pichlmair</name></author><author><name sortKey="Martinez Sobrido, L" uniqKey="Martinez Sobrido L">L. Martínez-Sobrido</name></author><author><name sortKey="Cros, J" uniqKey="Cros J">J. Cros</name></author><author><name sortKey="Garcia Sastre, A" uniqKey="Garcia Sastre A">A. García-Sastre</name></author><author><name sortKey="Haller, O" uniqKey="Haller O">O. Haller</name></author><author><name sortKey="Weber, F" uniqKey="Weber F">F. Weber</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Spiegel, M" uniqKey="Spiegel M">M. Spiegel</name></author><author><name sortKey="Weber, F" uniqKey="Weber F">F. Weber</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Cheung, C Y" uniqKey="Cheung C">C. Y. Cheung</name></author><author><name sortKey="Poon, L L M" uniqKey="Poon L">L. L. M. Poon</name></author><author><name sortKey="Ng, I H Y" uniqKey="Ng I">I. H. Y. Ng</name></author><author><name sortKey="Luk, W" uniqKey="Luk W">W. Luk</name></author><author><name sortKey="Sia, S F" uniqKey="Sia S">S.-F. Sia</name></author><author><name sortKey="Wu, M H S" uniqKey="Wu M">M. H. S. Wu</name></author><author><name sortKey="Chan, K H" uniqKey="Chan K">K.-H. Chan</name></author><author><name sortKey="Yuen, K Y" uniqKey="Yuen K">K.-Y. Yuen</name></author><author><name sortKey="Gordon, S" uniqKey="Gordon S">S. Gordon</name></author><author><name sortKey="Guan, Y" uniqKey="Guan Y">Y. Guan</name></author><author><name sortKey="Peiris, J S M" uniqKey="Peiris J">J. S. M. Peiris</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Chu, H" uniqKey="Chu H">H. Chu</name></author><author><name sortKey="Zhou, J" uniqKey="Zhou J">J. Zhou</name></author><author><name sortKey="Ho Yin Wong, B" uniqKey="Ho Yin Wong B">B. Ho-Yin Wong</name></author><author><name sortKey="Li, C" uniqKey="Li C">C. Li</name></author><author><name sortKey="Cheng, Z S" uniqKey="Cheng Z">Z.-S. Cheng</name></author><author><name sortKey="Lin, X" uniqKey="Lin X">X. Lin</name></author><author><name sortKey="Kwok Man Poon, V" uniqKey="Kwok Man Poon V">V. Kwok-Man Poon</name></author><author><name sortKey="Sun, T" uniqKey="Sun T">T. Sun</name></author><author><name sortKey="Choi Yi Lau, C" uniqKey="Choi Yi Lau C">C. Choi-Yi Lau</name></author><author><name sortKey="Fuk Woo Chan, J" uniqKey="Fuk Woo Chan J">J. Fuk-Woo Chan</name></author><author><name sortKey="Kai Wang To, K" uniqKey="Kai Wang To K">K. Kai-Wang To</name></author><author><name sortKey="Chan, K H" uniqKey="Chan K">K.-H. Chan</name></author><author><name sortKey="Lu, L" uniqKey="Lu L">L. Lu</name></author><author><name sortKey="Zheng, B J" uniqKey="Zheng B">B.-J. Zheng</name></author><author><name sortKey="Yuen, K Y" uniqKey="Yuen K">K.-Y. Yuen</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Chan, R W Y" uniqKey="Chan R">R. W. Y. Chan</name></author><author><name sortKey="Chan, M C W" uniqKey="Chan M">M. C. W. Chan</name></author><author><name sortKey="Agnihothram, S" uniqKey="Agnihothram S">S. Agnihothram</name></author><author><name sortKey="Chan, L L Y" uniqKey="Chan L">L. L. Y. Chan</name></author><author><name sortKey="Kuok, D I T" uniqKey="Kuok D">D. I. T. Kuok</name></author><author><name sortKey="Fong, J H M" uniqKey="Fong J">J. H. M. Fong</name></author><author><name sortKey="Guan, Y" uniqKey="Guan Y">Y. Guan</name></author><author><name sortKey="Poon, L L M" uniqKey="Poon L">L. L. M. Poon</name></author><author><name sortKey="Baric, R S" uniqKey="Baric R">R. S. Baric</name></author><author><name sortKey="Nicholls, J M" uniqKey="Nicholls J">J. M. Nicholls</name></author><author><name sortKey="Peiris, J S M" uniqKey="Peiris J">J. S. M. Peiris</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Lau, S K" uniqKey="Lau S">S. K. Lau</name></author><author><name sortKey="Lau, C C" uniqKey="Lau C">C. C. Lau</name></author><author><name sortKey="Chan, K H" uniqKey="Chan K">K. H. Chan</name></author><author><name sortKey="Li, C P" uniqKey="Li C">C. P. Li</name></author><author><name sortKey="Chen, H" uniqKey="Chen H">H. Chen</name></author><author><name sortKey="Jin, D Y" uniqKey="Jin D">D. Y. Jin</name></author><author><name sortKey="Chan, J F" uniqKey="Chan J">J. F. Chan</name></author><author><name sortKey="Woo, P C" uniqKey="Woo P">P. C. Woo</name></author><author><name sortKey="Yuen, K Y" uniqKey="Yuen K">K. Y. Yuen</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Van Kasteren, P B" uniqKey="Van Kasteren P">P. B. van Kasteren</name></author><author><name sortKey="Beugeling, C" uniqKey="Beugeling C">C. Beugeling</name></author><author><name sortKey="Ninaber, D K" uniqKey="Ninaber D">D. K. Ninaber</name></author><author><name sortKey="Frias Staheli, N" uniqKey="Frias Staheli N">N. Frias-Staheli</name></author><author><name sortKey="Van Boheemen, S" uniqKey="Van Boheemen S">S. van Boheemen</name></author><author><name sortKey="Garcia Sastre, A" uniqKey="Garcia Sastre A">A. García-Sastre</name></author><author><name sortKey="Snijder, E J" uniqKey="Snijder E">E. J. Snijder</name></author><author><name sortKey="Kikkert, M" uniqKey="Kikkert M">M. Kikkert</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Te Velthuis, A J" uniqKey="Te Velthuis A">A. J. te Velthuis</name></author><author><name sortKey="Arnold, J J" uniqKey="Arnold J">J. J. Arnold</name></author><author><name sortKey="Cameron, C E" uniqKey="Cameron C">C. E. Cameron</name></author><author><name sortKey="Van Den Worm, S H" uniqKey="Van Den Worm S">S. H. van den Worm</name></author><author><name sortKey="Snijder, E J" uniqKey="Snijder E">E. J. Snijder</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Gack, M U" uniqKey="Gack M">M. U. Gack</name></author><author><name sortKey="Albrecht, R A" uniqKey="Albrecht R">R. A. Albrecht</name></author><author><name sortKey="Urano, T" uniqKey="Urano T">T. Urano</name></author><author><name sortKey="Inn, K S" uniqKey="Inn K">K. S. Inn</name></author><author><name sortKey="Huang, I C" uniqKey="Huang I">I. C. Huang</name></author><author><name sortKey="Carnero, E" uniqKey="Carnero E">E. Carnero</name></author><author><name sortKey="Farzan, M" uniqKey="Farzan M">M. Farzan</name></author><author><name sortKey="Inoue, S" uniqKey="Inoue S">S. Inoue</name></author><author><name sortKey="Jung, J U" uniqKey="Jung J">J. U. Jung</name></author><author><name sortKey="Garcia Sastre, A" uniqKey="Garcia Sastre A">A. García-Sastre</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Fitzgerald, K A" uniqKey="Fitzgerald K">K. A. Fitzgerald</name></author><author><name sortKey="Mcwhirter, S M" uniqKey="Mcwhirter S">S. M. McWhirter</name></author><author><name sortKey="Faia, K L" uniqKey="Faia K">K. L. Faia</name></author><author><name sortKey="Rowe, D C" uniqKey="Rowe D">D. C. Rowe</name></author><author><name sortKey="Latz, E" uniqKey="Latz E">E. Latz</name></author><author><name sortKey="Golenbock, D T" uniqKey="Golenbock D">D. T. Golenbock</name></author><author><name sortKey="Coyle, A J" uniqKey="Coyle A">A. J. Coyle</name></author><author><name sortKey="Liao, S M" uniqKey="Liao S">S. M. Liao</name></author><author><name sortKey="Maniatis, T" uniqKey="Maniatis T">T. Maniatis</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Gack, M U" uniqKey="Gack M">M. U. Gack</name></author><author><name sortKey="Shin, Y C" uniqKey="Shin Y">Y. C. Shin</name></author><author><name sortKey="Joo, C H" uniqKey="Joo C">C. H. Joo</name></author><author><name sortKey="Urano, T" uniqKey="Urano T">T. Urano</name></author><author><name sortKey="Liang, C" uniqKey="Liang C">C. Liang</name></author><author><name sortKey="Sun, L" uniqKey="Sun L">L. Sun</name></author><author><name sortKey="Takeuchi, O" uniqKey="Takeuchi O">O. Takeuchi</name></author><author><name sortKey="Akira, S" uniqKey="Akira S">S. Akira</name></author><author><name sortKey="Chen, Z" uniqKey="Chen Z">Z. Chen</name></author><author><name sortKey="Inoue, S" uniqKey="Inoue S">S. Inoue</name></author><author><name sortKey="Jung, J U" uniqKey="Jung J">J. U. Jung</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Seth, R B" uniqKey="Seth R">R. B. Seth</name></author><author><name sortKey="Sun, L" uniqKey="Sun L">L. Sun</name></author><author><name sortKey="Ea, C K" uniqKey="Ea C">C. K. Ea</name></author><author><name sortKey="Chen, Z J" uniqKey="Chen Z">Z. J. Chen</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Lin, R" uniqKey="Lin R">R. Lin</name></author><author><name sortKey="Heylbroeck, C" uniqKey="Heylbroeck C">C. Heylbroeck</name></author><author><name sortKey="Pitha, P M" uniqKey="Pitha P">P. M. Pitha</name></author><author><name sortKey="Hiscott, J" uniqKey="Hiscott J">J. Hiscott</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Gohara, D W" uniqKey="Gohara D">D. W. Gohara</name></author><author><name sortKey="Ha, C S" uniqKey="Ha C">C. S. Ha</name></author><author><name sortKey="Kumar, S" uniqKey="Kumar S">S. Kumar</name></author><author><name sortKey="Ghosh, B" uniqKey="Ghosh B">B. Ghosh</name></author><author><name sortKey="Arnold, J J" uniqKey="Arnold J">J. J. Arnold</name></author><author><name sortKey="Wisniewski, T J" uniqKey="Wisniewski T">T. J. Wisniewski</name></author><author><name sortKey="Cameron, C E" uniqKey="Cameron C">C. E. Cameron</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Messick, T E" uniqKey="Messick T">T. E. Messick</name></author><author><name sortKey="Russell, N S" uniqKey="Russell N">N. S. Russell</name></author><author><name sortKey="Iwata, A J" uniqKey="Iwata A">A. J. Iwata</name></author><author><name sortKey="Sarachan, K L" uniqKey="Sarachan K">K. L. Sarachan</name></author><author><name sortKey="Shiekhattar, R" uniqKey="Shiekhattar R">R. Shiekhattar</name></author><author><name sortKey="Shanks, J R" uniqKey="Shanks J">J. R. Shanks</name></author><author><name sortKey="Reyes Turcu, F E" uniqKey="Reyes Turcu F">F. E. Reyes-Turcu</name></author><author><name sortKey="Wilkinson, K D" uniqKey="Wilkinson K">K. D. Wilkinson</name></author><author><name sortKey="Marmorstein, R" uniqKey="Marmorstein R">R. Marmorstein</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Borodovsky, A" uniqKey="Borodovsky A">A. Borodovsky</name></author><author><name sortKey="Ovaa, H" uniqKey="Ovaa H">H. Ovaa</name></author><author><name sortKey="Kolli, N" uniqKey="Kolli N">N. Kolli</name></author><author><name sortKey="Gan Erdene, T" uniqKey="Gan Erdene T">T. Gan-Erdene</name></author><author><name sortKey="Wilkinson, K D" uniqKey="Wilkinson K">K. D. Wilkinson</name></author><author><name sortKey="Ploegh, H L" uniqKey="Ploegh H">H. L. Ploegh</name></author><author><name sortKey="Kessler, B M" uniqKey="Kessler B">B. M. Kessler</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Kabsch, W" uniqKey="Kabsch W">W. Kabsch</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Evans, P" uniqKey="Evans P">P. Evans</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Grosse Kunstleve, R W" uniqKey="Grosse Kunstleve R">R. W. Grosse-Kunstleve</name></author><author><name sortKey="Adams, P D" uniqKey="Adams P">P. D. Adams</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Terwilliger, T C" uniqKey="Terwilliger T">T. C. Terwilliger</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Terwilliger, T C" uniqKey="Terwilliger T">T. C. Terwilliger</name></author><author><name sortKey="Adams, P D" uniqKey="Adams P">P. D. Adams</name></author><author><name sortKey="Read, R J" uniqKey="Read R">R. J. Read</name></author><author><name sortKey="Mccoy, A J" uniqKey="Mccoy A">A. J. McCoy</name></author><author><name sortKey="Moriarty, N W" uniqKey="Moriarty N">N. W. Moriarty</name></author><author><name sortKey="Grosse Kunstleve, R W" uniqKey="Grosse Kunstleve R">R. W. Grosse-Kunstleve</name></author><author><name sortKey="Afonine, P V" uniqKey="Afonine P">P. V. Afonine</name></author><author><name sortKey="Zwart, P H" uniqKey="Zwart P">P. H. Zwart</name></author><author><name sortKey="Hung, L W" uniqKey="Hung L">L. W. Hung</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Emsley, P" uniqKey="Emsley P">P. Emsley</name></author><author><name sortKey="Lohkamp, B" uniqKey="Lohkamp B">B. Lohkamp</name></author><author><name sortKey="Scott, W G" uniqKey="Scott W">W. G. Scott</name></author><author><name sortKey="Cowtan, K" uniqKey="Cowtan K">K. Cowtan</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Afonine, P V" uniqKey="Afonine P">P. V. Afonine</name></author><author><name sortKey="Grosse Kunstleve, R W" uniqKey="Grosse Kunstleve R">R. W. Grosse-Kunstleve</name></author><author><name sortKey="Echols, N" uniqKey="Echols N">N. Echols</name></author><author><name sortKey="Headd, J J" uniqKey="Headd J">J. J. Headd</name></author><author><name sortKey="Moriarty, N W" uniqKey="Moriarty N">N. W. Moriarty</name></author><author><name sortKey="Mustyakimov, M" uniqKey="Mustyakimov M">M. Mustyakimov</name></author><author><name sortKey="Terwilliger, T C" uniqKey="Terwilliger T">T. C. Terwilliger</name></author><author><name sortKey="Urzhumtsev, A" uniqKey="Urzhumtsev A">A. Urzhumtsev</name></author><author><name sortKey="Zwart, P H" uniqKey="Zwart P">P. H. Zwart</name></author><author><name sortKey="Adams, P D" uniqKey="Adams P">P. D. Adams</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Graham, F L" uniqKey="Graham F">F. L. Graham</name></author><author><name sortKey="Van Der Eb, A J" uniqKey="Van Der Eb A">A. J. van der Eb</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Lin, M H" uniqKey="Lin M">M. H. Lin</name></author><author><name sortKey="Chuang, S J" uniqKey="Chuang S">S. J. Chuang</name></author><author><name sortKey="Chen, C C" uniqKey="Chen C">C. C. Chen</name></author><author><name sortKey="Cheng, S C" uniqKey="Cheng S">S. C. Cheng</name></author><author><name sortKey="Cheng, K W" uniqKey="Cheng K">K. W. Cheng</name></author><author><name sortKey="Lin, C H" uniqKey="Lin C">C. H. Lin</name></author><author><name sortKey="Sun, C Y" uniqKey="Sun C">C. Y. Sun</name></author><author><name sortKey="Chou, C Y" uniqKey="Chou C">C. Y. Chou</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Lei, J" uniqKey="Lei J">J. Lei</name></author><author><name sortKey="Mesters, J R" uniqKey="Mesters J">J. R. Mesters</name></author><author><name sortKey="Drosten, C" uniqKey="Drosten C">C. Drosten</name></author><author><name sortKey="Anemuller, S" uniqKey="Anemuller S">S. Anemüller</name></author><author><name sortKey="Ma, Q" uniqKey="Ma Q">Q. Ma</name></author><author><name sortKey="Hilgenfeld, R" uniqKey="Hilgenfeld R">R. Hilgenfeld</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Baez Santos, Y M" uniqKey="Baez Santos Y">Y. M. Báez-Santos</name></author><author><name sortKey="Mielech, A M" uniqKey="Mielech A">A. M. Mielech</name></author><author><name sortKey="Deng, X" uniqKey="Deng X">X. Deng</name></author><author><name sortKey="Baker, S" uniqKey="Baker S">S. Baker</name></author><author><name sortKey="Mesecar, A D" uniqKey="Mesecar A">A. D. Mesecar</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Ratia, K" uniqKey="Ratia K">K. Ratia</name></author><author><name sortKey="Saikatendu, K S" uniqKey="Saikatendu K">K. S. Saikatendu</name></author><author><name sortKey="Santarsiero, B D" uniqKey="Santarsiero B">B. D. Santarsiero</name></author><author><name sortKey="Barretto, N" uniqKey="Barretto N">N. Barretto</name></author><author><name sortKey="Baker, S C" uniqKey="Baker S">S. C. Baker</name></author><author><name sortKey="Stevens, R C" uniqKey="Stevens R">R. C. Stevens</name></author><author><name sortKey="Mesecar, A D" uniqKey="Mesecar A">A. D. Mesecar</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Faesen, A C" uniqKey="Faesen A">A. C. Faesen</name></author><author><name sortKey="Luna Vargas, M P" uniqKey="Luna Vargas M">M. P. Luna-Vargas</name></author><author><name sortKey="Sixma, T K" uniqKey="Sixma T">T. K. Sixma</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Rawlings, N D" uniqKey="Rawlings N">N. D. Rawlings</name></author><author><name sortKey="Waller, M" uniqKey="Waller M">M. Waller</name></author><author><name sortKey="Barrett, A J" uniqKey="Barrett A">A. J. Barrett</name></author><author><name sortKey="Bateman, A" uniqKey="Bateman A">A. Bateman</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Krishna, S S" uniqKey="Krishna S">S. S. Krishna</name></author><author><name sortKey="Majumdar, I" uniqKey="Majumdar I">I. Majumdar</name></author><author><name sortKey="Grishin, N V" uniqKey="Grishin N">N. V. Grishin</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Wojdyla, J A" uniqKey="Wojdyla J">J. A. Wojdyla</name></author><author><name sortKey="Manolaridis, I" uniqKey="Manolaridis I">I. Manolaridis</name></author><author><name sortKey="Van Kasteren, P B" uniqKey="Van Kasteren P">P. B. van Kasteren</name></author><author><name sortKey="Kikkert, M" uniqKey="Kikkert M">M. Kikkert</name></author><author><name sortKey="Snijder, E J" uniqKey="Snijder E">E. J. Snijder</name></author><author><name sortKey="Gorbalenya, A E" uniqKey="Gorbalenya A">A. E. Gorbalenya</name></author><author><name sortKey="Tucker, P A" uniqKey="Tucker P">P. A. Tucker</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Renatus, M" uniqKey="Renatus M">M. Renatus</name></author><author><name sortKey="Parrado, S G" uniqKey="Parrado S">S. G. Parrado</name></author><author><name sortKey="D Arcy, A" uniqKey="D Arcy A">A. D'Arcy</name></author><author><name sortKey="Eidhoff, U" uniqKey="Eidhoff U">U. Eidhoff</name></author><author><name sortKey="Gerhartz, B" uniqKey="Gerhartz B">B. Gerhartz</name></author><author><name sortKey="Hassiepen, U" uniqKey="Hassiepen U">U. Hassiepen</name></author><author><name sortKey="Pierrat, B" uniqKey="Pierrat B">B. Pierrat</name></author><author><name sortKey="Riedl, R" uniqKey="Riedl R">R. Riedl</name></author><author><name sortKey="Vinzenz, D" uniqKey="Vinzenz D">D. Vinzenz</name></author><author><name sortKey="Worpenberg, S" uniqKey="Worpenberg S">S. Worpenberg</name></author><author><name sortKey="Kroemer, M" uniqKey="Kroemer M">M. Kroemer</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Ye, Y" uniqKey="Ye Y">Y. Ye</name></author><author><name sortKey="Akutsu, M" uniqKey="Akutsu M">M. Akutsu</name></author><author><name sortKey="Reyes Turcu, F" uniqKey="Reyes Turcu F">F. Reyes-Turcu</name></author><author><name sortKey="Enchev, R I" uniqKey="Enchev R">R. I. Enchev</name></author><author><name sortKey="Wilkinson, K D" uniqKey="Wilkinson K">K. D. Wilkinson</name></author><author><name sortKey="Komander, D" uniqKey="Komander D">D. Komander</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Chou, C Y" uniqKey="Chou C">C. Y. Chou</name></author><author><name sortKey="Lai, H Y" uniqKey="Lai H">H. Y. Lai</name></author><author><name sortKey="Chen, H Y" uniqKey="Chen H">H. Y. Chen</name></author><author><name sortKey="Cheng, S C" uniqKey="Cheng S">S. C. Cheng</name></author><author><name sortKey="Cheng, K W" uniqKey="Cheng K">K. W. Cheng</name></author><author><name sortKey="Chou, Y W" uniqKey="Chou Y">Y. W. Chou</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Hu, M" uniqKey="Hu M">M. Hu</name></author><author><name sortKey="Li, P" uniqKey="Li P">P. Li</name></author><author><name sortKey="Song, L" uniqKey="Song L">L. Song</name></author><author><name sortKey="Jeffrey, P D" uniqKey="Jeffrey P">P. D. Jeffrey</name></author><author><name sortKey="Chenova, T A" uniqKey="Chenova T">T. A. Chenova</name></author><author><name sortKey="Wilkinson, K D" uniqKey="Wilkinson K">K. D. Wilkinson</name></author><author><name sortKey="Cohen, R E" uniqKey="Cohen R">R. E. Cohen</name></author><author><name sortKey="Shi, Y" uniqKey="Shi Y">Y. Shi</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Bailey Elkin, B A" uniqKey="Bailey Elkin B">B. A. Bailey-Elkin</name></author><author><name sortKey="Van Kasteren, P B" uniqKey="Van Kasteren P">P. B. van Kasteren</name></author><author><name sortKey="Snijder, E J" uniqKey="Snijder E">E. J. Snijder</name></author><author><name sortKey="Kikkert, M" uniqKey="Kikkert M">M. Kikkert</name></author><author><name sortKey="Mark, B L" uniqKey="Mark B">B. L. Mark</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Van Kasteren, P B" uniqKey="Van Kasteren P">P. B. van Kasteren</name></author><author><name sortKey="Bailey Elkin, B A" uniqKey="Bailey Elkin B">B. A. Bailey-Elkin</name></author><author><name sortKey="James, T W" uniqKey="James T">T. W. James</name></author><author><name sortKey="Ninaber, D K" uniqKey="Ninaber D">D. K. Ninaber</name></author><author><name sortKey="Beugeling, C" uniqKey="Beugeling C">C. Beugeling</name></author><author><name sortKey="Khajehpour, M" uniqKey="Khajehpour M">M. Khajehpour</name></author><author><name sortKey="Snijder, E J" uniqKey="Snijder E">E. J. Snijder</name></author><author><name sortKey="Mark, B L" uniqKey="Mark B">B. L. Mark</name></author><author><name sortKey="Kikkert, M" uniqKey="Kikkert M">M. Kikkert</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Ratia, K" uniqKey="Ratia K">K. Ratia</name></author><author><name sortKey="Kilianski, A" uniqKey="Kilianski A">A. Kilianski</name></author><author><name sortKey="Baez Santos, Y M" uniqKey="Baez Santos Y">Y. M. Baez-Santos</name></author><author><name sortKey="Baker, S C" uniqKey="Baker S">S. C. Baker</name></author><author><name sortKey="Mesecar, A" uniqKey="Mesecar A">A. Mesecar</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Dikic, I" uniqKey="Dikic I">I. Dikic</name></author><author><name sortKey="Wakatsuki, S" uniqKey="Wakatsuki S">S. Wakatsuki</name></author><author><name sortKey="Walters, K J" uniqKey="Walters K">K. J. Walters</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Eletr, Z M" uniqKey="Eletr Z">Z. M. Eletr</name></author><author><name sortKey="Wilkinson, K D" uniqKey="Wilkinson K">K. D. Wilkinson</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Sun, Z" uniqKey="Sun Z">Z. Sun</name></author><author><name sortKey="Chen, Z" uniqKey="Chen Z">Z. Chen</name></author><author><name sortKey="Lawson, S R" uniqKey="Lawson S">S. R. Lawson</name></author><author><name sortKey="Fang, Y" uniqKey="Fang Y">Y. Fang</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Zheng, D" uniqKey="Zheng D">D. Zheng</name></author><author><name sortKey="Chen, G" uniqKey="Chen G">G. Chen</name></author><author><name sortKey="Guo, B" uniqKey="Guo B">B. Guo</name></author><author><name sortKey="Cheng, G" uniqKey="Cheng G">G. Cheng</name></author><author><name sortKey="Tang, H" uniqKey="Tang H">H. Tang</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Xing, Y" uniqKey="Xing Y">Y. Xing</name></author><author><name sortKey="Chen, J" uniqKey="Chen J">J. Chen</name></author><author><name sortKey="Tu, J" uniqKey="Tu J">J. Tu</name></author><author><name sortKey="Zhang, B" uniqKey="Zhang B">B. Zhang</name></author><author><name sortKey="Chen, X" uniqKey="Chen X">X. Chen</name></author><author><name sortKey="Shi, H" uniqKey="Shi H">H. Shi</name></author><author><name sortKey="Baker, S C" uniqKey="Baker S">S. C. Baker</name></author><author><name sortKey="Feng, L" uniqKey="Feng L">L. Feng</name></author><author><name sortKey="Chen, Z" uniqKey="Chen Z">Z. Chen</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Randow, F" uniqKey="Randow F">F. Randow</name></author><author><name sortKey="Lehner, P J" uniqKey="Lehner P">P. J. Lehner</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Hadari, T" uniqKey="Hadari T">T. Hadari</name></author><author><name sortKey="Warms, J V" uniqKey="Warms J">J. V. Warms</name></author><author><name sortKey="Rose, I A" uniqKey="Rose I">I. A. Rose</name></author><author><name sortKey="Hershko, A" uniqKey="Hershko A">A. Hershko</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Delano, W L" uniqKey="Delano W">W. L. DeLano</name></author></analytic></biblStruct></listBibl></div1></back></TEI><pmc article-type="research-article"><pmc-dir>properties open_access</pmc-dir>
<front><journal-meta><journal-id journal-id-type="nlm-ta">J Biol Chem</journal-id><journal-id journal-id-type="iso-abbrev">J. Biol. Chem</journal-id><journal-id journal-id-type="publisher-id">J. Biol. Chem</journal-id><journal-id journal-id-type="hwp">jbc</journal-id><journal-id journal-id-type="pmc">jbc</journal-id><journal-id journal-id-type="publisher-id">JBC</journal-id><journal-title-group><journal-title>The Journal of Biological Chemistry</journal-title></journal-title-group><issn pub-type="ppub">0021-9258</issn><issn pub-type="epub">1083-351X</issn><publisher><publisher-name>American Society for Biochemistry and Molecular
Biology</publisher-name><publisher-loc>9650 Rockville Pike, Bethesda, MD 20814, U.S.A.</publisher-loc></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">25320088</article-id><article-id pub-id-type="pmc">4263872</article-id><article-id pub-id-type="publisher-id">M114.609644</article-id><article-id pub-id-type="doi">10.1074/jbc.M114.609644</article-id><article-categories><subj-group subj-group-type="heading"><subject>Microbiology</subject></subj-group></article-categories><title-group><article-title>Crystal Structure of the Middle East Respiratory Syndrome Coronavirus
(MERS-CoV) Papain-like Protease Bound to Ubiquitin Facilitates Targeted
Disruption of Deubiquitinating Activity to Demonstrate Its Role in Innate Immune
Suppression<xref ref-type="fn" rid="FN1">*</xref></article-title><alt-title alt-title-type="short">MERS-CoV PL<sup>pro</sup>·Ub Crystal
Structure and Immune Antagonism</alt-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Bailey-Elkin</surname><given-names>Ben A.</given-names></name><xref ref-type="aff" rid="aff1"><sup>‡</sup></xref><xref ref-type="author-notes" rid="FN2"><sup>1</sup></xref><xref ref-type="author-notes" rid="FN3"><sup>2</sup></xref></contrib><contrib contrib-type="author"><name><surname>Knaap</surname><given-names>Robert C. M.</given-names></name><xref ref-type="aff" rid="aff2"><sup>§</sup></xref><xref ref-type="author-notes" rid="FN3"><sup>2</sup></xref></contrib><contrib contrib-type="author"><name><surname>Johnson</surname><given-names>Garrett G.</given-names></name><xref ref-type="aff" rid="aff1"><sup>‡</sup></xref></contrib><contrib contrib-type="author"><name><surname>Dalebout</surname><given-names>Tim J.</given-names></name><xref ref-type="aff" rid="aff2"><sup>§</sup></xref></contrib><contrib contrib-type="author"><name><surname>Ninaber</surname><given-names>Dennis K.</given-names></name><xref ref-type="aff" rid="aff2"><sup>§</sup></xref></contrib><contrib contrib-type="author"><name><surname>van Kasteren</surname><given-names>Puck B.</given-names></name><xref ref-type="aff" rid="aff2"><sup>§</sup></xref></contrib><contrib contrib-type="author"><name><surname>Bredenbeek</surname><given-names>Peter J.</given-names></name><xref ref-type="aff" rid="aff2"><sup>§</sup></xref></contrib><contrib contrib-type="author"><name><surname>Snijder</surname><given-names>Eric J.</given-names></name><xref ref-type="aff" rid="aff2"><sup>§</sup></xref></contrib><contrib contrib-type="author"><name><surname>Kikkert</surname><given-names>Marjolein</given-names></name><xref ref-type="aff" rid="aff2"><sup>§</sup></xref><xref ref-type="author-notes" rid="FN4"><sup>3</sup></xref><xref ref-type="corresp" rid="cor1"><sup>4</sup></xref></contrib><contrib contrib-type="author"><name><surname>Mark</surname><given-names>Brian L.</given-names></name><xref ref-type="aff" rid="aff1"><sup>‡</sup></xref><xref ref-type="author-notes" rid="FN4"><sup>3</sup></xref><xref ref-type="corresp" rid="cor2"><sup>5</sup></xref></contrib><aff id="aff1">From the<label>‡</label>Department of Microbiology, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada and</aff><aff id="aff2">the<label>§</label>Molecular Virology Laboratory, Department of Medical Microbiology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands</aff></contrib-group><author-notes><corresp id="cor1"><label>4</label> To whom correspondence may be addressed. Tel.:
<phone>31-71-526-1442</phone>; Fax: <fax>31-71-526-6981</fax>; E-mail:
<email>m.kikkert@lumc.nl</email>.</corresp><corresp id="cor2"><label>5</label> Holder of a Manitoba Research Chair award. To
whom correspondence may be addressed. Tel.: <phone>204-480-1430</phone>; Fax:
<fax>204-474-7603</fax>; E-mail:
<email>brian.mark@umanitoba.ca</email>.</corresp><fn fn-type="other" id="FN2"><label>1</label><p>Recipient of a Research Manitoba Studentship.</p></fn><fn fn-type="equal" id="FN3"><label>2</label><p>Both authors contributed equally to this work.</p></fn><fn fn-type="equal" id="FN4"><label>3</label><p>Both authors contributed equally to this work.</p></fn></author-notes><pub-date pub-type="ppub"><day>12</day><month>12</month><year>2014</year></pub-date><pub-date pub-type="epub"><day>15</day><month>10</month><year>2014</year></pub-date><volume>289</volume><issue>50</issue><fpage>34667</fpage><lpage>34682</lpage><history><date date-type="received"><day>3</day><month>9</month><year>2014</year></date><date date-type="rev-recd"><day>30</day><month>9</month><year>2014</year></date></history><permissions><copyright-statement>© 2014 by The American Society for Biochemistry and
Molecular Biology, Inc.</copyright-statement><copyright-year>2014</copyright-year><license><license-p>This article is made available via the PMC Open Access Subset for
unrestricted re-use and analyses in any form or by any means with
acknowledgement of the original source. These permissions are granted for
the duration of the COVID-19 pandemic or until permissions are revoked in
writing. Upon expiration of these permissions, PMC is granted a perpetual
license to make this article available via PMC and Europe PMC, consistent
with existing copyright protections.</license-p></license></permissions><self-uri xlink:title="pdf" xlink:type="simple" xlink:href="zbc05014034667.pdf"></self-uri><abstract abstract-type="teaser"><p><bold>Background:</bold> MERS-CoV papain-like protease (PL<sup>pro</sup>)
processes viral polyproteins and has deubiquitinating activity.</p><p><bold>Results:</bold> A crystal structure of MERS-CoV PL<sup>pro</sup> bound to
ubiquitin guided mutagenesis to disrupt PL<sup>pro</sup> deubiquitinating
activity without affecting polyprotein cleavage.</p><p><bold>Conclusion:</bold> The deubiquitinating activity of MERS-CoV
PL<sup>pro</sup> suppresses the induction of interferon-β
expression.</p><p><bold>Significance:</bold> Our strategy to selectively disable PL<sup>pro</sup>deubiquitinating activity enables the study of its specific functions in
infection.</p></abstract><abstract><p>Middle East respiratory syndrome coronavirus (MERS-CoV) is a newly emerging human
pathogen that was first isolated in 2012. MERS-CoV replication depends in part
on a virus-encoded papain-like protease (PL<sup>pro</sup>) that cleaves the
viral replicase polyproteins at three sites releasing non-structural protein 1
(nsp1), nsp2, and nsp3. In addition to this replicative function, MERS-CoV
PL<sup>pro</sup> was recently shown to be a deubiquitinating enzyme (DUB)
and to possess deISGylating activity, as previously reported for other
coronaviral PL<sup>pro</sup> domains, including that of severe acute respiratory
syndrome coronavirus. These activities have been suggested to suppress host
antiviral responses during infection. To understand the molecular basis for
ubiquitin (Ub) recognition and deconjugation by MERS-CoV PL<sup>pro</sup>, we
determined its crystal structure in complex with Ub. Guided by this structure,
mutations were introduced into PL<sup>pro</sup> to specifically disrupt Ub
binding without affecting viral polyprotein cleavage, as determined using an in
<italic>trans</italic> nsp3↓4 cleavage assay. Having developed a
strategy to selectively disable PL<sup>pro</sup> DUB activity, we were able to
specifically examine the effects of this activity on the innate immune response.
Whereas the wild-type PL<sup>pro</sup> domain was found to suppress
IFN-β promoter activation, PL<sup>pro</sup> variants specifically
lacking DUB activity were no longer able to do so. These findings directly
implicate the DUB function of PL<sup>pro</sup>, and not its proteolytic activity
<italic>per se</italic>, in the inhibition of IFN-β promoter
activity. The ability to decouple the DUB activity of PL<sup>pro</sup> from its
role in viral polyprotein processing now provides an approach to further dissect
the role(s) of PL<sup>pro</sup> as a viral DUB during MERS-CoV infection.</p></abstract><kwd-group><kwd>Cysteine Protease</kwd><kwd>Deubiquitylation (Deubiquitination)</kwd><kwd>Innate Immunity</kwd><kwd>Structural Biology</kwd><kwd>Viral Immunology</kwd><kwd>X-ray Crystallography</kwd><kwd>Middle East Respiratory Syndrome Coronavirus</kwd><kwd>PLpro</kwd></kwd-group></article-meta></front><body><sec sec-type="intro"><title>Introduction</title><p>The Middle East respiratory syndrome coronavirus (MERS-CoV)<xref ref-type="fn" rid="FN5"><sup>6</sup></xref> was first isolated in June 2012 from a patient in
Saudi Arabia who had died from progressive respiratory and renal failure (<xref rid="B1" ref-type="bibr">1</xref>). Since then, over 800 cases have been
reported, with a case fatality rate surpassing 30% (<xref rid="B2" ref-type="bibr">2</xref>). The progression and severity of the symptoms observed in MERS
patients resemble the severe acute respiratory syndrome (SARS) observed in patients
infected with SARS-CoV, which caused a global pandemic in 2003, resulting in over
8000 cases, with a case fatality rate of ∼10% (<xref rid="B3" ref-type="bibr">3</xref>). Whereas the SARS-CoV outbreak was contained within
months, MERS cases continue to occur 2 years after the emergence of MERS-CoV in the
human population. Currently, dromedary camels are suspected to be one of the direct
reservoirs for the zoonotic transmission of MERS-CoV, although the exact chain of
transmission remains to be explored in more detail (<xref rid="B4" ref-type="bibr">4</xref>, <xref rid="B5" ref-type="bibr">5</xref>).</p><p>MERS-CoV and SARS-CoV are enveloped, positive-sense single-stranded RNA (+RNA)
viruses that belong to the <italic>Betacoronavirus</italic> genus in the family
Coronaviridae of the Nidovirales order (<xref rid="B6" ref-type="bibr">6</xref>).
The CoV non-structural proteins (nsps), which drive viral genome replication and
subgenomic RNA synthesis, are encoded within a large replicase gene that encompasses
the 5′-proximal three-quarters of the CoV genome. The replicase gene
contains two open reading frames, ORF1a and ORF1b. Translation of ORF1a yields
polyprotein 1a (pp1a), and −1 ribosomal frameshifting facilitates
translation of ORF1b to yield pp1ab (<xref rid="B7" ref-type="bibr">7</xref>). The
pp1a and pp1ab precursors are co- and post-translationally processed into functional
nsps by multiple ORF1a-encoded protease domains. CoVs employ either one or two
papain-like proteases (PL<sup>pro</sup>s), depending on the virus species, to
release nsp1, nsp2, and nsp3 and a chymotrypsin-like protease (3CL<sup>pro</sup>)
that cleaves all junctions downstream of nsp4 (reviewed in Ref. <xref rid="B8" ref-type="bibr">8</xref>). Comparative sequence analysis of the MERS-CoV genome
and proteome allowed for the prediction and annotation of 16 nsps, along with the
location of the probable proteolytic cleavage sites (<xref rid="B6" ref-type="bibr">6</xref>). The MERS-CoV PL<sup>pro</sup> domain, which resides in nsp3, has
recently been confirmed to recognize and cleave after the sequence
L<italic>X</italic>GG at the nsp1↓2 and nsp2↓3 junctions, as
defined previously for other CoV PL<sup>pro</sup>s, as well as an
I<italic>X</italic>GG sequence, which constitutes the nsp3↓4 cleavage
site (<xref rid="B9" ref-type="bibr">9</xref>, <xref rid="B10" ref-type="bibr">10</xref>).</p><p>These recognition sequences within pp1a/pp1ab resemble the C-terminal LRGG motif of
ubiquitin (Ub), an 8.5-kDa protein that can be conjugated to lysine residues or the
N terminus of target proteins as a form of post-translational modification through
the action of the cellular E1/2/3 ligase system (reviewed in Ref. <xref rid="B11" ref-type="bibr">11</xref>). Additional Ub molecules can be linked to any of the
7 lysine residues in Ub itself or to its N terminus to generate polyubiquitin
(poly-Ub) chains of various linkage types (<xref rid="B11" ref-type="bibr">11</xref>). The best-studied linkages are the ones occurring at Lys<sup>48</sup> of
Ub, which results in the targeting of the tagged substrate to the 26 S proteasome
for degradation, and at Lys<sup>63</sup>, which generates a scaffold for the
recruitment of cellular proteins to activate numerous signaling cascades, including
critical antiviral and proinflammatory pathways (<xref rid="B11" ref-type="bibr">11</xref>). The C terminus of Ub can be recognized by deubiquitinating enzymes
(DUBs), which catalyze the deconjugation of Ub, thus reversing the effects of
ubiquitination (<xref rid="B12" ref-type="bibr">12</xref>). Interestingly, CoV
PL<sup>pro</sup>s, including those of MERS- and SARS-CoV, have been suggested to
act as multifunctional proteases that not only cleave the viral polyproteins at
internal L<italic>X</italic>GG cleavage sites but also remove Ub and the antiviral
Ub-like molecule interferon-stimulated gene 15 (ISG15) from cellular proteins,
presumably to suppress host antiviral pathways (<xref rid="B9" ref-type="bibr">9</xref>, <xref rid="B13" ref-type="bibr">13</xref><xref ref-type="bibr" rid="B14">–</xref><xref rid="B19" ref-type="bibr">19</xref>).</p><p>Activation of antiviral and proinflammatory pathways is a critical first line of
defense against virus infections, including those caused by nidoviruses. Viral RNA
molecules are recognized by pattern recognition receptors, such as the cytoplasmic
RIG-I-like receptors (RLRs) RIG-I and MDA5, which are activated by intracellular
viral RNA transcripts bearing 5′ tri- and diphosphates and double-stranded
RNA (dsRNA) replication intermediates, respectively (<xref rid="B20" ref-type="bibr">20</xref>, <xref rid="B21" ref-type="bibr">21</xref>). Upon their stimulation,
RLRs signal through the mitochondrial antiviral signaling protein (MAVS), leading to
the formation of a signaling complex at the mitochondrial membrane and ultimately to
the activation of transcription factors IRF-3 and NF-κB. These transcription
factors in turn regulate the expression of antiviral type 1 interferons (IFN),
including IFN-β, which acts through autocrine and paracrine
receptor-mediated signaling pathways to induce the transcription of numerous
interferon-stimulated genes (ISGs) that will interfere with virus replication as
well as proinflammatory cytokines, such as IL-6, IL-8, and TNF-α. Regulation
of the antiviral and proinflammatory pathways is largely Ub-dependent, because
multiple factors in the innate immune cascade are ubiquitinated, including RIG-I,
which is critical for downstream signaling. Cellular DUBs function to prevent
excessive inflammation and immune responses during infection by removal of Ub from
innate immune factors (reviewed in Ref. <xref rid="B22" ref-type="bibr">22</xref>).</p><p>The DUB activities of MERS- and SARS-CoV PL<sup>pro</sup> have been implicated in the
suppression of host antiviral pathways because these proteases can suppress
IFN-β induction upon their ectopic expression (<xref rid="B9" ref-type="bibr">9</xref>, <xref rid="B13" ref-type="bibr">13</xref>, <xref rid="B15" ref-type="bibr">15</xref>, <xref rid="B16" ref-type="bibr">16</xref>,
<xref rid="B19" ref-type="bibr">19</xref>, <xref rid="B23" ref-type="bibr">23</xref>). Previous work has shown that during infection, SARS-CoV indeed
suppresses the host's antiviral responses by preventing the induction of
IFN-β expression in cell culture (<xref rid="B24" ref-type="bibr">24</xref><xref ref-type="bibr" rid="B25">–</xref><xref rid="B26" ref-type="bibr">26</xref>). Similarly, MERS-CoV infection has been found to
elicit a poor type-1 IFN response in cultured monocyte-derived dendritic cells
(<xref rid="B27" ref-type="bibr">27</xref>) and alveolar epithelial A549 cells
(<xref rid="B28" ref-type="bibr">28</xref>) as well as <italic>ex vivo</italic>in bronchial and lung tissue samples (<xref rid="B28" ref-type="bibr">28</xref>).
Furthermore, delayed induction of proinflammatory cytokines in human airway
epithelial cells infected with MERS-CoV has been reported (<xref rid="B29" ref-type="bibr">29</xref>).</p><p>Although the above observations suggest that MERS- and SARS-CoV actively suppress
antiviral responses, such as IFN-β production and inflammation, they do not
directly implicate the DUB activity of PL<sup>pro</sup> as being responsible for
(part of) this suppression. Due to the dependence of MERS-CoV replication on the
ability of PL<sup>pro</sup> to cleave the nsp1–nsp3 region of the replicase
polyproteins, studying the role of PL<sup>pro</sup> DUB activity, specifically in
the suppression of the cellular innate immune response, is difficult because both
activities depend on the same enzyme active site. Selective inactivation of only the
DUB activity of PL<sup>pro</sup> would enable the study of how this activity alone
affects cellular signaling; however, achieving this requires detailed information on
the structural basis of Ub recognition and deconjugation by PL<sup>pro</sup>. To
this end, we determined the crystal structure of MERS-CoV PL<sup>pro</sup> bound to
Ub to elucidate the molecular determinants of Ub recognition. Based on the structure
of this complex, mutations were introduced that selectively disrupted Ub recognition
by targeting regions of the Ub-binding site on PL<sup>pro</sup> that were
sufficiently distant from the active site of the protease. Using this approach, we
were able to remove the DUB activity from PL<sup>pro</sup> without affecting its
ability to cleave the nsp3↓4 cleavage site <italic>in trans</italic>. This
enabled us, for the first time, to demonstrate that the DUB activity of MERS-CoV
PL<sup>pro</sup> can suppress the MAVS-mediated induction of IFN-β
expression.</p></sec><sec sec-type="methods"><title>EXPERIMENTAL PROCEDURES</title><sec><title></title><sec><title></title><sec><title>Cells, Antibodies, and Plasmids</title><p>HEK293T cells were cultured in Dulbecco's modified Eagle's medium (DMEM)
supplemented with 10% fetal calf serum (FCS; Bodinco BV), 100 units/ml
penicillin, 100 units/ml streptomycin, and 2 m<sc>m</sc><sc>l</sc>-glutamine (cell culture medium and supplements were obtained
from Lonza).</p><p>Primary antibodies used were mouse anti-HA (ab18181; Abcam), mouse
anti-V5 (37-7500; Invitrogen), mouse anti-β-actin (A5316;
Sigma-Aldrich), mouse anti-FLAG (F3165; Sigma-Aldrich), and rabbit
anti-GFP (<xref rid="B30" ref-type="bibr">30</xref>). As secondary
antibodies, horseradish peroxidase (HRP)-conjugated antibodies were used
(P0447 and P0217; Dako).</p><p>The following plasmids were described elsewhere: pASK3 (<xref rid="B31" ref-type="bibr">31</xref>), pcDNA-eGFP (<xref rid="B30" ref-type="bibr">30</xref>), pCMV-FLAG-Ub (<xref rid="B32" ref-type="bibr">32</xref>), pLuc-IFN-β (<xref rid="B33" ref-type="bibr">33</xref>), pEBG-RIG-I<sub>(2CARD)</sub> (<xref rid="B34" ref-type="bibr">34</xref>), pcDNA-FLAG-MAVS (<xref rid="B35" ref-type="bibr">35</xref>), and
pEGFP-C1-IRF3<sub>(5D)</sub> (<xref rid="B36" ref-type="bibr">36</xref>).</p></sec><sec><title>Construction of MERS-CoV PL<sup>pro</sup> Expression Plasmids</title><p>A cDNA fragment encoding the PL<sup>pro</sup> domain (amino acids
1479–1803 of the MERS-CoV pp1a/pp1ab polyprotein (NCBI ID:
JX869059); pp1a/pp1ab amino acid numbering is used throughout the rest
of this work) was cloned into bacterial expression vector pASK3 in-frame
with N-terminal Ub and a C-terminal His<sub>6</sub> purification tag to
produce pASK-MERS-CoV-PL<sup>pro</sup>.</p><p>Using standard methodologies, the sequence encoding amino acids
1480–1803 of MERS-CoV pp1a/pp1ab was PCR-amplified, cloned
downstream of the T7 promoter of expression vector pE-SUMO
(LifeSensors), and used to transform <italic>Escherichia coli</italic>BL21 (DE3) GOLD cells (Stratagene) grown under kanamycin selection (35
μg/ml). Recombinant expression plasmid
(pE-SUMO-PL<sup>pro</sup>) was isolated from a single colony, and DNA
sequencing confirmed the expected sequence of the PL<sup>pro</sup>domain and the in-frame fusion of the 5′-end to a sequence
encoding a His<sub>6</sub>-SUMO purification tag, which facilitated
purification of the product by immobilized metal (nickel) affinity
chromatography as described below.</p><p>To obtain high expression in eukaryotic cells, the sequence of MERS-CoV
nsp3–4 (amino acids 854–3246) flanked by an N-terminal
HA tag and a C-terminal V5 tag was optimized based on the human codon
usage frequency, and potential splice sites and polyadenylation signals
were removed. This sequence was synthesized (Invitrogen) and
subsequently cloned into the pCAGGS vector (Addgene) using standard
methodologies. The following expression constructs were generated:
pCAGGS-HA-nsp3-4-V5 (amino acids 854–3246), pCAGGS-HA-nsp3C-4-V5
(amino acids 1820–3246, which does not include the
PL<sup>pro</sup> domain), and pCAGGS-HA-nsp3-Myc (amino acids
854–2739). The sequence encoding MERS-CoV PL<sup>pro</sup>(amino acids 1479–1803) was PCR-amplified using synthetic
plasmid DNA as a template and cloned in frame with a C-terminal V5 tag
in the pcDNA3.1(−) vector (Invitrogen). The
pASK-MERS-CoV-PL<sup>pro</sup> and
pcDNA3.1-MERS-CoV-PL<sup>pro</sup>expression constructs served as
templates for site-directed mutagenesis using the QuikChange strategy
with <italic>Pfu</italic> DNA polymerase (Agilent). All constructs were
verified by sequencing. The sequences of the constructs and primers used
in this study are available upon request.</p></sec><sec><title>Purification of MERS-CoV PL<sup>pro</sup> and in Vitro DUB Activity
Assay</title><p><italic>In vitro</italic> DUB activity assays were performed with
recombinant MERS-CoV PL<sup>pro</sup> batch-purified from lysates of
<italic>E. coli</italic> strain C2523. Cells transformed with
pASK-MERS-CoV-PL<sup>pro</sup> were cultured to an
<italic>A</italic><sub>600</sub> of 0.6 in lysogeny broth at 37
°C. Protein expression was then induced with 200 ng/ml
anhydrotetracycline for 16 h at 20 °C. The cells were pelleted,
resuspended in lysis buffer (20 m<sc>m</sc> HEPES, pH 7.0, 200
m<sc>m</sc> NaCl, 10% (v/v) glycerol, and 0.1 mg/ml lysozyme), and
lysed for 1 h at 4 °C, followed by sonication. The lysate was
clarified by centrifugation at 20,000 × <italic>g</italic> for
20 min at 4 °C, and the soluble fraction was applied to Talon
resin (GE Healthcare) pre-equilibrated with lysis buffer. After a 2-h
rolling incubation at 4 °C, the beads were washed four times
with wash buffer (20 m<sc>m</sc> HEPES, pH 7.0, 200 m<sc>m</sc> NaCl,
10% (v/v) glycerol, and 20 m<sc>m</sc> imidazole), followed by the
elution of the protein with elution buffer (20 m<sc>m</sc> HEPES, pH
7.0, 200 m<sc>m</sc> NaCl, 10% (v/v) glycerol, and 250 m<sc>m</sc>imidazole). Eluted protein was dialyzed against storage buffer (20
m<sc>m</sc> HEPES, pH 7.0, 100 m<sc>m</sc> NaCl, 50% (v/v) glycerol,
2 m<sc>m</sc> dithiothreitol (DTT)) and stored at −80
°C. N-terminal Ub is cleaved from the
Ub-PL<sup>pro</sup>-His<sub>6</sub> fusion protein by the
PL<sup>pro</sup> domain itself during expression. To achieve removal
of the Ub from mutated and/or inactive PL<sup>pro</sup>, <italic>E.
coli</italic> strain C2523 containing pCG1, expressing the
ubiquitin-specific processing protease 1 (Ubp1), was used (<xref rid="B37" ref-type="bibr">37</xref>).</p><p><italic>In vitro</italic> DUB activity assays were performed as described
by van Kasteren <italic>et al</italic>. (<xref rid="B30" ref-type="bibr">30</xref>). Briefly, the indicated amounts of purified MERS-CoV
PL<sup>pro</sup> wild type or active site mutant (C1592A) were
incubated with 2.5 μg of either Lys<sup>48</sup>-linked poly-Ub
chains or Lys<sup>63</sup>-linked poly-Ub chains (Boston Biochem) in a
final volume of 10 μl. Isopeptidase T (Boston Biochem) served as
a positive control. After a 2-h incubation at 37 °C, the
reaction was stopped by the addition of 4× Laemmli sample buffer
(4× LSB; 500 m<sc>m</sc> Tris, 4% SDS, 40% glycerol, 0.02%
bromphenol blue, 2 m<sc>m</sc> DTT, pH 6.8). SDS-polyacrylamide gels
were stained with Coomassie Brilliant Blue (Sigma-Aldrich) and scanned
using a GS-800 calibrated densitometer (Bio-Rad).</p></sec><sec><title>Expression and Purification of MERS-CoV PL<sup>pro</sup> for
Crystallization</title><p><italic>E. coli</italic> BL21(DE3) GOLD cells harboring
pE-SUMO-PL<sup>pro</sup> were grown at 37 °C with aeration
in 500 ml of lysogeny broth containing kanamycin (35 μg/ml) to
an <italic>A</italic><sub>600</sub> of 0.6–0.8. Expression of
the His<sub>6</sub>-SUMO-PL<sup>pro</sup> fusion protein was then
induced by the addition 1 m<sc>m</sc> isopropyl
β-<sc>d</sc>-1-thiogalactopyranoside for 18 h at 16 °C
with aeration. Cells were pelleted by centrifugation and stored at
−80 °C.</p><p>Cell pellets were resuspended in ice-cold lysis buffer (150 m<sc>m</sc>Tris, pH 8.5, 1 <sc>m</sc> NaCl, 0.1 m<sc>m</sc> phenylmethanesulfonyl
fluoride (PMSF), 2 m<sc>m</sc> DTT) and lysed using a French pressure
cell (AMINCO). Cell lysate was clarified by centrifugation (17,211
× <italic>g</italic> at 4 °C), and the supernatant
containing the His<sub>6</sub>-SUMO-PL<sup>pro</sup> fusion was applied
to a column containing nickel-nitrilotriacetic acid affinity resin
(Qiagen). The column was washed with 10 column volumes of lysis buffer
supplemented with 25 m<sc>m</sc> imidazole, followed by elution of the
fusion protein with lysis buffer containing 250 m<sc>m</sc> imidazole.
The His<sub>6</sub>-SUMO tag was then removed from PL<sup>pro</sup> by
adding His<sub>6</sub>-tagged Ulp1 SUMO protease to the eluted
SUMO-PL<sup>pro</sup> fusion, followed by dialysis of the protein
mixture overnight against 2 liters of cleavage buffer (150 m<sc>m</sc>NaCl, 50 m<sc>m</sc> Tris, pH 8.0, 1 m<sc>m</sc> DTT) at 4 °C.
Tag-free PL<sup>pro</sup> was separated from His<sub>6</sub>-SUMO and
the His<sub>6</sub>-Ulp1 SUMO protease by passing the dialyzed protein
mix through a nickel-nitrilotriacetic acid gravity column. The
flow-through contained purified PL<sup>pro</sup> that was subsequently
dialyzed against 20 m<sc>m</sc> Tris, pH 8.5, 150 m<sc>m</sc> NaCl, 2
m<sc>m</sc> DTT and further purified by gel filtration using a
Superdex 75 (GE Healthcare) gel filtration column.</p></sec><sec><title>Covalent Coupling of Ub to PL<sup>pro</sup></title><p>Ub(1–75)-3-bromopropylamine (Ub-3Br) is a modified form of Ub
with a reactive C terminus that forms an irreversible covalent linkage
to the active site cysteine of DUBs and was prepared according to
Messick <italic>et al.</italic> (<xref rid="B38" ref-type="bibr">38</xref>) and Borodovsky <italic>et al.</italic> (<xref rid="B39" ref-type="bibr">39</xref>). Purified PL<sup>pro</sup> was incubated
with a 2-fold molar excess of Ub-3Br and incubated for 1 h at room
temperature with end-over-end mixing. The resulting
PL<sup>pro</sup>·Ub complex was dialyzed into 20 m<sc>m</sc>Tris, pH 8.5, 150 m<sc>m</sc> NaCl, 2 m<sc>m</sc> DTT, and excess Ub-3Br
was removed by gel filtration using a Superdex 75 column.</p></sec><sec><title>Crystallization of PL<sup>pro</sup> and PL<sup>pro</sup>·Ub
Complexes</title><p>The purified PL<sup>pro</sup>·Ub complex was concentrated and
crystallized at 20 °C in two different conditions using the
vapor diffusion method: 1) 20% PEG 4000, 0.1 <sc>m</sc> trisodium
citrate, pH 5.4, 20% isopropyl alcohol at 10 mg/ml, which yielded the
structure of open PL<sup>pro</sup>·Ub (see
“Results”), and 2) 1.80 <sc>m</sc> ammonium sulfate
(AmSO<sub>4</sub>) at 20 mg/ml, which yielded the structure of
closed PL<sup>pro</sup>·Ub (see “Results”).
Crystals of unliganded PL<sup>pro</sup> were also grown using the vapor
diffusion method in 18% PEG 4000, 0.1 <sc>m</sc> trisodium citrate, pH
5.6, 16% isopropyl alcohol after concentrating the protein to 12 mg/ml.
Immediately prior to crystallization, 1 <sc>m</sc> DTT was added to the
protein to a final concentration of 5 m<sc>m</sc>, which was found to
improve crystallization.</p><p>In preparation for x-ray data collection, single crystals of open
PL<sup>pro</sup>·Ub from condition 1 above were briefly
swept through a droplet of cryoprotectant composed of 22% PEG 4000, 0.1
<sc>m</sc> trisodium citrate, pH 5.6, 20% 1,2-propanediol before
flash cooling in liquid nitrogen. Similarly, single crystals of closed
PL<sup>pro</sup>·Ub from condition 2 above and unbound
PL<sup>pro</sup> were cryoprotected in 1.85 <sc>m</sc>AmSO<sub>4</sub>, 15% glycerol and 22% PEG 4000, 0.1 <sc>m</sc>trisodium citrate, pH 5.6, 10% 1,2-propanediol, respectively, before
flash cooling in liquid nitrogen.</p></sec><sec><title>Data Collection and Structure Determination</title><p>X-ray diffraction data were collected from all crystals at the Zn-K
absorption edge at beamline 08B1-1 of the Canadian Light Source and
integrated using XDS (<xref rid="B40" ref-type="bibr">40</xref>).
Integrated data were then scaled using Scala (<xref rid="B41" ref-type="bibr">41</xref>). Initial phase estimates for reflections
collected from unliganded and Ub-bound PL<sup>pro</sup> were determined
via a single wavelength anomalous dispersion experiment. The position of
the zinc anomalous scatterer was identified using HySS (<xref rid="B42" ref-type="bibr">42</xref>), and density modification was performed
with RESOLVE (<xref rid="B43" ref-type="bibr">43</xref>) within the
phenix.autosol pipeline (<xref rid="B44" ref-type="bibr">44</xref>).
Initial models were constructed using phenix.autobuild, and further
model building and refinement were carried out using Coot (<xref rid="B45" ref-type="bibr">45</xref>) and phenix.refine (<xref rid="B46" ref-type="bibr">46</xref>). Crystallographic statistics
for all structures are found in <xref rid="T1" ref-type="table">Table
1</xref>.</p><table-wrap id="T1" orientation="portrait" position="float"><label>TABLE 1</label><caption><p><bold>Crystallographic statistics for MERS-CoV PL<sup>pro</sup>and PL<sup>pro</sup>·Ub structures</bold></p></caption><table frame="hsides" rules="groups"><thead valign="bottom"><tr><th align="center" rowspan="1" colspan="1">Crystal</th><th align="center" rowspan="1" colspan="1">PL<sup>pro</sup></th><th align="center" rowspan="1" colspan="1">Open
PL<sup>pro</sup>·Ub</th><th align="center" rowspan="1" colspan="1">Closed
PL<sup>pro</sup>·Ub</th></tr></thead><tbody valign="top"><tr><td align="left" rowspan="1" colspan="1"><bold>Crystal
geometry</bold></td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1"></td></tr><tr><td align="left" rowspan="1" colspan="1"> Space group</td><td align="left" rowspan="1" colspan="1">P6<sub>3</sub></td><td align="left" rowspan="1" colspan="1">P6<sub>3</sub></td><td align="left" rowspan="1" colspan="1">P6<sub>5</sub>22</td></tr><tr><td align="left" rowspan="1" colspan="1"> Unit cell
(Å)</td><td align="left" rowspan="1" colspan="1"><italic>a</italic>= <italic>b</italic> = 137.94 <italic>c</italic> =
57.70; α = β = 90° γ =
120°</td><td align="left" rowspan="1" colspan="1"><italic>a</italic>= <italic>b</italic> = 136.77 <italic>c</italic> =
57.99; α = β = 90° γ =
120°</td><td align="left" rowspan="1" colspan="1"><italic>a</italic>= <italic>b</italic> = 176.92 <italic>c</italic> =
84.55; α = β = 90° γ =
120°</td></tr><tr><td colspan="4" rowspan="1"><hr></hr></td></tr><tr><td align="left" rowspan="1" colspan="1"><bold>Crystallographic data</bold></td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1"></td></tr><tr><td align="left" rowspan="1" colspan="1"> Wavelength
(Å)</td><td align="left" rowspan="1" colspan="1">1.28294</td><td align="left" rowspan="1" colspan="1">1.28280</td><td align="left" rowspan="1" colspan="1">1.28219</td></tr><tr><td align="left" rowspan="1" colspan="1"> Resolution range
(Å)</td><td align="left" rowspan="1" colspan="1">45.15–2.60
(2.90–2.80)<xref ref-type="table-fn" rid="TF1-1"><italic><sup>a</sup></italic></xref></td><td align="left" rowspan="1" colspan="1">44.23–2.15
(2.22–2.15)</td><td align="left" rowspan="1" colspan="1">44.24–2.60
(2.90–2.80)</td></tr><tr><td align="left" rowspan="1" colspan="1"> Total
observations</td><td align="left" rowspan="1" colspan="1">137,170
(13,780)</td><td align="left" rowspan="1" colspan="1">124,058
(12,315)</td><td align="left" rowspan="1" colspan="1">283,649
(28,118)</td></tr><tr><td align="left" rowspan="1" colspan="1"> Unique
reflections</td><td align="left" rowspan="1" colspan="1">15,683 (1566)</td><td align="left" rowspan="1" colspan="1">33,472 (3291)</td><td align="left" rowspan="1" colspan="1">19,694 (1918)</td></tr><tr><td align="left" rowspan="1" colspan="1"> Multiplicity</td><td align="left" rowspan="1" colspan="1">8.7 (8.8)</td><td align="left" rowspan="1" colspan="1">3.7 (3.7)</td><td align="left" rowspan="1" colspan="1">14.4 (14.7)</td></tr><tr><td align="left" rowspan="1" colspan="1"> Completeness
(%)</td><td align="left" rowspan="1" colspan="1">100.00
(100.00)</td><td align="left" rowspan="1" colspan="1">98.73 (98.12)</td><td align="left" rowspan="1" colspan="1">99.97 (100)</td></tr><tr><td align="left" rowspan="1" colspan="1"> Anomalous
completeness</td><td align="left" rowspan="1" colspan="1">99.4 (98.5)</td><td align="left" rowspan="1" colspan="1">92.4 (92.6)</td><td align="left" rowspan="1" colspan="1">100 (100)</td></tr><tr><td align="left" rowspan="1" colspan="1"> <italic>R</italic><sub>merge</sub></td><td align="left" rowspan="1" colspan="1">0.085 (0.76)</td><td align="left" rowspan="1" colspan="1">0.041 (0.79)</td><td align="left" rowspan="1" colspan="1">0.061 (0.78)</td></tr><tr><td align="left" rowspan="1" colspan="1"> CC1/2</td><td align="left" rowspan="1" colspan="1">0.99 (0.83)</td><td align="left" rowspan="1" colspan="1">0.99 (0.54)</td><td align="left" rowspan="1" colspan="1">1 (0.93)</td></tr><tr><td align="left" rowspan="1" colspan="1"> CC*</td><td align="left" rowspan="1" colspan="1">0.99 (0.95)</td><td align="left" rowspan="1" colspan="1">1 (0.84)</td><td align="left" rowspan="1" colspan="1">1 (0.98)</td></tr><tr><td align="left" rowspan="1" colspan="1"> <italic>I</italic>/σ<italic>I</italic></td><td align="left" rowspan="1" colspan="1">17.13 (3.42)</td><td align="left" rowspan="1" colspan="1">20.52 (1.97)</td><td align="left" rowspan="1" colspan="1">34.01 (3.69)</td></tr><tr><td align="left" rowspan="1" colspan="1"> Wilson
<italic>B</italic>-factor
(Å<sup>2</sup>)</td><td align="left" rowspan="1" colspan="1">75.15</td><td align="left" rowspan="1" colspan="1">46.79</td><td align="left" rowspan="1" colspan="1">74.96</td></tr><tr><td colspan="4" rowspan="1"><hr></hr></td></tr><tr><td align="left" rowspan="1" colspan="1"><bold>Phasing
statistics</bold></td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1"></td></tr><tr><td align="left" rowspan="1" colspan="1"> Figure of
merit</td><td align="left" rowspan="1" colspan="1">0.12</td><td align="left" rowspan="1" colspan="1">0.18</td><td align="left" rowspan="1" colspan="1">0.23</td></tr><tr><td align="left" rowspan="1" colspan="1"> Figure of merit
after RESOLVE</td><td align="left" rowspan="1" colspan="1">0.64</td><td align="left" rowspan="1" colspan="1">0.63</td><td align="left" rowspan="1" colspan="1">0.67</td></tr><tr><td colspan="4" rowspan="1"><hr></hr></td></tr><tr><td align="left" rowspan="1" colspan="1"><bold>Refinement
statistics</bold></td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1"></td></tr><tr><td align="left" rowspan="1" colspan="1"> Reflections in test
set</td><td align="left" rowspan="1" colspan="1">1570</td><td align="left" rowspan="1" colspan="1">1996</td><td align="left" rowspan="1" colspan="1">1609</td></tr><tr><td align="left" rowspan="1" colspan="1"> Protein atoms</td><td align="left" rowspan="1" colspan="1">2384</td><td align="left" rowspan="1" colspan="1">3020</td><td align="left" rowspan="1" colspan="1">3020</td></tr><tr><td align="left" rowspan="1" colspan="1"> Zinc atoms</td><td align="left" rowspan="1" colspan="1">1</td><td align="left" rowspan="1" colspan="1">1</td><td align="left" rowspan="1" colspan="1">1</td></tr><tr><td align="left" rowspan="1" colspan="1"> Solvent
molecules</td><td align="left" rowspan="1" colspan="1">26</td><td align="left" rowspan="1" colspan="1">205</td><td align="left" rowspan="1" colspan="1">65</td></tr><tr><td align="left" rowspan="1" colspan="1"> <italic>R</italic><sub>work</sub>(<italic>R</italic><sub>free</sub>)</td><td align="left" rowspan="1" colspan="1">0.23 (0.27)</td><td align="left" rowspan="1" colspan="1">0.20 (0.23)</td><td align="left" rowspan="1" colspan="1">0.24 (0.28)</td></tr><tr><td colspan="4" rowspan="1"><hr></hr></td></tr><tr><td align="left" rowspan="1" colspan="1"><bold>Root mean
square deviations</bold></td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1"></td></tr><tr><td align="left" rowspan="1" colspan="1"> Bond lengths/angles
(Å/degrees)</td><td align="left" rowspan="1" colspan="1">0.002/0.60</td><td align="left" rowspan="1" colspan="1">0.002/0.52</td><td align="left" rowspan="1" colspan="1">0.002/0.54</td></tr><tr><td colspan="4" rowspan="1"><hr></hr></td></tr><tr><td align="left" rowspan="1" colspan="1"><bold>Ramachandran
plot</bold></td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1"></td></tr><tr><td align="left" rowspan="1" colspan="1"> Favored/allowed
(%)</td><td align="left" rowspan="1" colspan="1">95/5</td><td align="left" rowspan="1" colspan="1">95/5</td><td align="left" rowspan="1" colspan="1">93/7</td></tr><tr><td align="left" rowspan="1" colspan="1"> Average
<italic>B</italic>-factor
(Å<sup>2</sup>)</td><td align="left" rowspan="1" colspan="1">76.70</td><td align="left" rowspan="1" colspan="1">66.80</td><td align="left" rowspan="1" colspan="1">86.50</td></tr><tr><td align="left" rowspan="1" colspan="1"> <italic>B</italic>-Factor
for macromolecules</td><td align="left" rowspan="1" colspan="1">76.70</td><td align="left" rowspan="1" colspan="1">69.20</td><td align="left" rowspan="1" colspan="1">86.60</td></tr><tr><td align="left" rowspan="1" colspan="1"> <italic>B</italic>-Factor
for solvent</td><td align="left" rowspan="1" colspan="1">76.65</td><td align="left" rowspan="1" colspan="1">65.40</td><td align="left" rowspan="1" colspan="1">84.20</td></tr></tbody></table><table-wrap-foot><fn id="TF1-1"><p><italic><sup>a</sup></italic> Values in parentheses refer to
the highest resolution shell.</p></fn></table-wrap-foot></table-wrap></sec><sec><title>Protease Activity Assays in Cell Culture</title><p>HEK293T cells, grown to 80% confluence in 12-well plates, were
transfected using the calcium phosphate transfection method (<xref rid="B47" ref-type="bibr">47</xref>). To determine the DUB activity
of MERS-CoV PL<sup>pro</sup>, plasmids encoding FLAG-tagged Ub (0.25
μg), GFP (0.25 μg), and MERS-CoV-PL<sup>pro</sup>-V5
(0.2 μg) were co-transfected. A combination of plasmids encoding
GFP (0.25 μg), HA-nsp3C-4-V5 (0.2 μg), and
MERS-CoV-PL<sup>pro</sup>-V5 (0.15 μg) were transfected to
assess the in <italic>trans</italic> cleavage activity of
MERS-CoV-PL<sup>pro</sup>. Total amounts of transfected DNA were
equalized to 2 μg by the addition of empty pcDNA vector. At 18 h
post-transfection, cells were lysed in 2× LSB. Proteins were
separated in an SDS-polyacrylamide gel and blotted onto Hybond-P (GE
Healthcare) using the Trans-blot turbo transfer system (Bio-Rad).
Aspecific binding to the membrane was blocked with dried milk powder
solution, and after antibody incubation, protein bands were visualized
using Pierce ECL 2 Western blotting substrate (Thermo Scientific).</p></sec><sec><title>Luciferase-based IFN-β Reporter Assay</title><p>Using the calcium phosphate method, 80% confluent HEK293T cells in
24-well plates were transfected with 5 ng of plasmid pRL-TK (Promega)
encoding <italic>Renilla</italic> luciferase; IFN-β-Luc firefly
reporter plasmid (25 ng); innate immune response inducer plasmids
encoding RIG-I<sub>(2CARD)</sub>, MAVS, or IRF3<sub>(5D)</sub> (25 ng);
and the indicated quantities of MERS-CoV PL<sup>pro</sup>- or MERS-CoV
nsp3-encoding expression plasmids. Total amounts of transfected DNA were
equalized to 1 μg by the addition of empty pcDNA vector. At 16 h
post-transfection, cells were lysed in 1× passive lysis buffer
(Promega). Firefly and <italic>Renilla</italic> luciferase activity was
measured using the Dual-Luciferase reporter assay system (Promega) on a
Mithras LB 940 multimode reader (Berthold Technologies). Experiments
were performed in triplicate and independently repeated at least four
times. Firefly luciferase activity was normalized to
<italic>Renilla</italic> luciferase, and statistical significance
was determined using an unpaired two-tailed Student's <italic>t</italic>test. Values of <0.05 were considered statistically significant.
4× LSB was added to the remaining lysates, and these samples
were analyzed by Western blotting as described above.</p></sec></sec></sec></sec><sec sec-type="results"><title>RESULTS</title><sec><title>DUB Activity of Recombinant MERS-CoV PL<sup>pro</sup></title><p>It was recently shown in cell culture experiments that ectopic expression of
MERS-CoV PL<sup>pro</sup> resulted in deconjugation of poly-Ub and ISG15 from
cellular targets (<xref rid="B9" ref-type="bibr">9</xref>, <xref rid="B16" ref-type="bibr">16</xref>). DUB activity of purified recombinant MERS-CoV
PL<sup>pro</sup> was also demonstrated using
Ub-7-amino-4-trifluoromethylcoumarin (<xref rid="B48" ref-type="bibr">48</xref>)
or Ub-7-amino-4-methylcoumarin (<xref rid="B49" ref-type="bibr">49</xref>) as a
substrate. To characterize the direct activity of recombinant MERS-CoV
PL<sup>pro</sup> toward poly-Ub, we purified the enzyme from <italic>E.
coli</italic> and incubated it with either Lys<sup>48</sup>- or
Lys<sup>63</sup>-linked poly-Ub chains. Wild-type PL<sup>pro</sup> degraded
both Lys<sup>48</sup>- and Lys<sup>63</sup>-linked chains in a
concentration-dependent manner, whereas mutating the active site nucleophile
(C1592A) severely reduced the activity of the enzyme toward both Ub linkage
types (<xref ref-type="fig" rid="F1">Fig. 1</xref>). No clear preference of the
enzyme for cleaving either the Lys<sup>63</sup> or the Lys<sup>48</sup> Ub
linkage was observed under the conditions used in this <italic>in vitro</italic>DUB assay (<xref ref-type="fig" rid="F1">Fig. 1</xref>, compare
<italic>A</italic> and <italic>B</italic>). This assay clearly demonstrated
that the protease domain used throughout this study for ectopic expression and
crystallization experiments possesses DUB activity toward Lys<sup>48</sup>- and
Lys<sup>63</sup>-linked Ub chains and that this activity does not require
other viral or cellular proteins. During the preparation of this manuscript, an
article by Báez-Santos <italic>et al.</italic> (<xref rid="B50" ref-type="bibr">50</xref>) was published in which similar results were
presented.</p><fig id="F1" orientation="portrait" position="float"><label>FIGURE 1.</label><caption><p><bold><italic>In vitro</italic> cleavage of Lys<sup>48</sup>- and
Lys<sup>63</sup>-linked poly-Ub chains by recombinant MERS-CoV
PL<sup>pro</sup>.</bold> Purified recombinant MERS-CoV
PL<sup>pro</sup> was incubated with 2.5 μg of
Lys<sup>48</sup>-linked (<italic>A</italic>) or
Lys<sup>63</sup>-linked (<italic>B</italic>) poly-Ub chains of different
length in each reaction for 2 h at 37 °C in a final volume of 10
μl. A range of 2-fold dilutions starting at 2
μ<sc>m</sc> MERS-CoV wild-type PL<sup>pro</sup> per reaction
was used. Activity of the PL<sup>pro</sup> active site mutant (C1592A)
was assessed at a concentration of 2 μ<sc>m</sc>. Isopeptidase T
(<italic>IsoT</italic>; 0.5 μg/reaction) served as a
positive control (<xref rid="B69" ref-type="bibr">69</xref>).</p></caption><graphic xlink:href="zbc0521402620001"></graphic></fig></sec><sec><title>Crystal Structures of MERS-CoV PL<sup>pro</sup> and
PL<sup>pro</sup>·Ub Complexes</title><sec><title></title><sec><title>MERS-CoV PL<sup>pro</sup></title><p>The crystal structure of PL<sup>pro</sup> was determined both on its own
and as a covalent complex with Ub (PL<sup>pro</sup>·Ub). The
PL<sup>pro</sup> domain crystallized in space group P6<sub>3</sub>,
and consistent with another recently determined crystal structure of
MERS-CoV PL<sup>pro</sup> (<xref rid="B49" ref-type="bibr">49</xref>),
we found the protease to adopt a fold consistent with DUBs of the
ubiquitin-specific protease (USP) family. The structure includes a
C-terminal catalytic domain containing a right-handed fingers, palm, and
thumb domain organization as well as an N-terminal Ub-like (Ubl) domain
found in many USPs, including that of SARS-CoV (<xref rid="B51" ref-type="bibr">51</xref>, <xref rid="B52" ref-type="bibr">52</xref>) (<xref ref-type="fig" rid="F2">Fig.
2</xref><italic>A</italic>). The packing of the palm and thumb
domains forms a cleft leading into the active site in a manner
consistent with the domain organization prototyped by the Clan CA group
of cysteine proteases (<xref rid="B53" ref-type="bibr">53</xref>). The
Ubl domain packs against the thumb domain composed of helices
α2–7, which in turn packs against the palm domain
composed of strands β6, β7, and β14–19.
Extending from the palm, the fingers domain is composed of strands
β10, β11, β13, β14, and β19 and
contains a C<sub>4</sub> zinc ribbon motif (<xref rid="B54" ref-type="bibr">54</xref>) coordinating a zinc atom via residues
Cys<sup>1672</sup>, Cys<sup>1675</sup>, Cys<sup>1707</sup>, and
Cys<sup>1709</sup> in tetrahedral geometry, similar to that of SARS
PL<sup>pro</sup>, transmissible gastroenteritis coronavirus
PL1<sup>pro</sup>, and cellular USP2 and USP21 (<xref rid="B51" ref-type="bibr">51</xref>, <xref rid="B55" ref-type="bibr">55</xref><xref ref-type="bibr" rid="B56">–</xref><xref rid="B57" ref-type="bibr">57</xref>).</p><fig id="F2" orientation="portrait" position="float"><label>FIGURE 2.</label><caption><p><bold>MERS-CoV PL<sup>pro</sup> and PL<sup>pro</sup>·Ub
structures.</bold><italic>A</italic>, structure of the MERS-CoV PL<sup>pro</sup>domain (2.15 Å resolution). The palm, thumb, fingers,
and N-terminal ubiquitin-like (Ubl) domains are indicated by
<italic>colored panels</italic>, and <italic>arrows</italic>indicate the active site and C<sub>4</sub> zinc ribbon motif.
The active site residues are depicted as <italic>sticks.
B</italic>, structure of the MERS-CoV PL<sup>pro</sup> bound
to Ub (2.8 Å resolution). PL<sup>pro</sup> is shown in
<italic>green</italic>, and the covalently bound Ub molecule
is <italic>orange</italic> and shown as <italic>tubes</italic>.
Active site residues are shown as <italic>sticks</italic> with
Gly<sup>75</sup> and the 3CN linker of Ub covalently linked
to Cys<sup>1592</sup> of PL<sup>pro</sup>. <italic>C</italic>,
superposition showing a ∼6.8-Å movement of the
zinc ribbon motif between the open (<italic>yellow</italic>) and
closed (<italic>green</italic>) PL<sup>pro</sup>·Ub
structures and a previously reported PL<sup>pro</sup> structure
(<italic>gray</italic>) (Protein Data Bank entry <ext-link ext-link-type="pdb" xlink:href="4P16">4P16</ext-link> (<xref rid="B49" ref-type="bibr">49</xref>)). Our PL<sup>pro</sup>structure is not shown because it is highly similar to the open
PL<sup>pro</sup>·Ub structure. Movement of the zinc
ribbon motif was determined by measuring the distance between
the zinc atom of the respective structures. Superpositions were
performed in Coot (<xref rid="B45" ref-type="bibr">45</xref>).
Ub was removed from the closed and open
PL<sup>pro</sup>·Ub structures for clarity. Figures were
created using PyMOL (<xref rid="B70" ref-type="bibr">70</xref>).</p></caption><graphic xlink:href="zbc0521402620002"></graphic></fig></sec><sec><title>PL<sup>pro</sup> Covalently Bound to Ub</title><p>The MERS-CoV PL<sup>pro</sup>·Ub complex crystallized in two
different space groups (P6<sub>3</sub> and P6<sub>5</sub>22), which
revealed a considerable level of conformational flexibility in the
protein. Electron density maps calculated using diffraction data
collected from PL<sup>pro</sup>·Ub complex that crystallized in
space group P6<sub>3</sub> revealed weak density for the covalently
bound Ub molecule. Although the entire bound Ub molecule could be
modeled within its binding site on PL<sup>pro</sup> in this crystal
form, high temperature factors for atoms comprising the modeled Ub
molecule suggested that it was not rigidly bound to the protease despite
being covalently linked to the active site cysteine. Further analysis of
the crystal packing revealed that the Ub molecule was fully exposed to
solvent and not involved in crystal contacts, which provided a degree of
mobility to Ub when bound to PL<sup>pro</sup> (<xref ref-type="fig" rid="F3">Fig. 3</xref><italic>A</italic>). This result encouraged us
to pursue additional crystallization conditions, which yielded crystals
of PL<sup>pro</sup>·Ub in space group P6<sub>5</sub>22 (<xref ref-type="fig" rid="F2">Figs. 2</xref><italic>B</italic> and <xref ref-type="fig" rid="F3">3</xref><italic>B</italic>). The crystal
packing in this space group allowed for multiple crystal contacts
between the bound Ub monomer and surrounding symmetry mates and resulted
in clear, well defined density for the Ub molecule (<xref ref-type="fig" rid="F3">Fig. 3</xref><italic>B</italic>). Interestingly, relative
to the P6<sub>3</sub> crystal forms of PL<sup>pro</sup>, the fingers
domain in this crystal form was moved toward Ub (<xref ref-type="fig" rid="F2">Fig. 2</xref><italic>C</italic>). In light of these
movements, the PL<sup>pro</sup>·Ub structure with the fingers
domain positioned away from Ub (space group P6<sub>3</sub>) will
hereafter be referred to as “open”
PL<sup>pro</sup>·Ub, whereas the structure with the fingers
domain shifted toward Ub (space group P6<sub>5</sub>22) will be referred
to as “closed” PL<sup>pro</sup>·Ub. An overlay
of the different PL<sup>pro</sup> crystal structures that have been
determined reveals that these structures vary in the position of the
zinc ribbon motif, further suggesting a high degree of mobility for this
region (<xref ref-type="fig" rid="F2">Fig. 2</xref><italic>C</italic>).
In line with this observation, movement of the fingers domain toward
bound Ub was also reported for the SARS-CoV PL<sup>pro</sup> domain,
which displayed a 3.8-Å movement of the zinc atom when comparing
the Ub-bound and unbound structures (<xref rid="B58" ref-type="bibr">58</xref>). Further comparison of the closed MERS-CoV
PL<sup>pro</sup>·Ub structure with the recently determined
SARS-CoV PL<sup>pro</sup>·Ub structure (<xref rid="B58" ref-type="bibr">58</xref>) revealed differences in the relative
orientation of the fingers domain of the two proteases. The MERS-CoV
PL<sup>pro</sup> fingers domain was found to be shifted
∼26° away from the palm domain compared with that of
SARS-CoV PL<sup>pro</sup>, resulting in a slight difference in the Ub
binding orientation, with the MERS-CoV PL<sup>pro</sup>-bound Ub being
positioned closer toward helix α7 of the palm domain (<xref ref-type="fig" rid="F4">Fig. 4</xref>).</p><fig id="F3" orientation="portrait" position="float"><label>FIGURE 3.</label><caption><p><bold>Crystal packing arrangement of the open and closed MERS-CoV
PL<sup>pro</sup>·Ub structures.</bold> The
contents of four unit cells are shown, with PL<sup>pro</sup> and
Ub depicted in <italic>gray</italic> and
<italic>orange</italic>, respectively. <italic>A</italic>, the
open PL<sup>pro</sup>·Ub structure crystallized in space
group P6<sub>3</sub>, where Ub was found to face the solvent,
uninvolved in crystal contacts. <italic>B</italic>, the closed
PL<sup>pro</sup>·Ub structure crystallized in space
group P6<sub>5</sub>22, where Ub no longer faces the solvent,
and is involved in crystal contacts. Images were created using
PyMOL (<xref rid="B70" ref-type="bibr">70</xref>).</p></caption><graphic xlink:href="zbc0521402620003"></graphic></fig><fig id="F4" orientation="portrait" position="float"><label>FIGURE 4.</label><caption><p><bold>Structural comparison of the SARS-CoV
PL<sup>pro</sup>·Ub and MERS-CoV
PL<sup>pro</sup>·Ub complexes.</bold><italic>A</italic>, superposition of the closed MERS-CoV
PL<sup>pro</sup>·Ub complex (<italic>green</italic>)
and the SARS-CoV PL<sup>pro</sup>·Ub complex
(<italic>purple</italic>; Protein Data Bank entry <ext-link ext-link-type="pdb" xlink:href="4M0W">4M0W</ext-link>) using
SSM superpose in Coot (<xref rid="B45" ref-type="bibr">45</xref>) (bound Ub molecules were ignored during the
superposition). The Ub molecules bound to the MERS-CoV
PL<sup>pro</sup> domain and SARS-CoV PL<sup>pro</sup> domain
are depicted as <italic>tubes</italic> in
<italic>orange</italic> and <italic>pale cyan</italic>,
respectively. The ∼26° shift in the fingers
domain between the two respective structures is indicated.
<italic>B</italic>, alternate orientation of the SARS-CoV
PL<sup>pro</sup>·Ub and MERS-CoV
PL<sup>pro</sup>·Ub superpositions highlighting the
difference in Ub binding. In the MERS-CoV
PL<sup>pro</sup>·Ub complex, Ub is found shifted toward
helix α7 compared with the SARS
PL<sup>pro</sup>·Ub complex. Helix α7 of
MERS-CoV PL<sup>pro</sup> is indicated with an
<italic>arrow</italic>. Images were created using PyMOL
(<xref rid="B70" ref-type="bibr">70</xref>).</p></caption><graphic xlink:href="zbc0521402620004"></graphic></fig></sec></sec></sec><sec><title>PL<sup>pro</sup> Active Site Organization and Interaction with the C-terminal
RLRGG Motif of Ub</title><p>The cleft formed between the palm and thumb domains of PL<sup>pro</sup> guides
the C-terminal <sup>72</sup>RLRGG<sup>76</sup> motif of Ub toward the protease
active site, and the interactions between the C-terminal motif of Ub and the
active site cleft are depicted in <xref ref-type="fig" rid="F5">Fig. 5</xref>(<italic>A</italic> and <italic>B</italic>). The PL<sup>pro</sup> active
site is composed of a Cys<sup>1592</sup>-His<sup>1759</sup>-Asp<sup>1774</sup>catalytic triad, which adopts a catalytically competent arrangement in both the
unliganded and Ub-bound structures of PL<sup>pro</sup> (<xref ref-type="fig" rid="F5">Fig. 5</xref><italic>C</italic>). The oxyanion hole of the
PL<sup>pro</sup> active site appears to be composed of backbone amides from
residues Asn<sup>1590</sup>, Asn<sup>1591</sup>, and Cys<sup>1592</sup>, which
appear suitably arranged to stabilize the negative charge that develops on the
carbonyl oxygen of the scissile bond during catalysis (<xref ref-type="fig" rid="F5">Fig. 5</xref><italic>C</italic>). Interestingly, as noted by Lei
<italic>et al.</italic> (<xref rid="B49" ref-type="bibr">49</xref>), the
MERS-CoV PL<sup>pro</sup> active site appears incomplete. In SARS-CoV
PL<sup>pro</sup>, Trp<sup>107</sup> (amino acid numbering according to the
structure of Protein Data Bank entry <ext-link ext-link-type="pdb" xlink:href="2FE8">2FE8</ext-link>) is positioned within the enzyme's active
site with the indole nitrogen of its side chain oriented such that it is
probably involved in forming part of the oxyanion hole (<xref rid="B51" ref-type="bibr">51</xref>). In the case of MERS-CoV PL<sup>pro</sup>, we and
others (<xref rid="B48" ref-type="bibr">48</xref>, <xref rid="B49" ref-type="bibr">49</xref>) have found the structurally equivalent residue in
MERS-CoV PL<sup>pro</sup> to be Leu<sup>1587</sup>, which would be unable to
participate in stabilizing the oxyanion during catalysis. Furthermore, it was
recently shown that MERS-CoV PL<sup>pro</sup> L1587W mutants show greater
catalytic efficiency than wild-type PL<sup>pro</sup> (<xref rid="B48" ref-type="bibr">48</xref>, <xref rid="B49" ref-type="bibr">49</xref>). Given
the effect this residue has on the catalytic rate of PL<sup>pro</sup>, it will
be very interesting to understand how this residue influences MERS-CoV
replication kinetics. It has been proposed that the decreased catalytic
efficiency may influence maturation of the MERS-CoV polyprotein (<xref rid="B48" ref-type="bibr">48</xref>) and could be involved in the recognition of
residues downstream of the scissile bond of the polyprotein cleavage sites or in
the modulation of PL<sup>pro</sup> DUB activity.</p><fig id="F5" orientation="portrait" position="float"><label>FIGURE 5.</label><caption><p><bold>Active site of MERS-CoV PL<sup>pro</sup> and interactions with the
C-terminal RLRGG motif of Ub.</bold> Interactions between open
PL<sup>pro</sup> (<italic>green</italic>) and the C-terminal RLRGG
motif of Ub (<italic>orange</italic>) are depicted in <italic>A</italic>and <italic>B. A</italic>, the main-chain amide of the 3CN linker, which
mimics Gly<sup>76</sup> of Ub, forms a hydrogen bond with the main chain
carbonyl of PL<sup>pro</sup> residue Gly<sup>1758</sup>. The main-chain
amide of Gly<sup>75</sup> of Ub forms a hydrogen bond with the carbonyl
group of PL<sup>pro</sup> Asp<sup>1645</sup>, and a hydrogen bonding
interaction occurs between the main-chain carbonyl of Arg<sup>74</sup>of Ub and the main-chain amide of Gly<sup>1758</sup> of
PL<sup>pro</sup>. The side-chain η-amino group of Ub residue
Arg<sup>74</sup> is hydrogen-bonded to the main-chain carbonyl group
of PL<sup>pro</sup> Thr<sup>1755</sup>. Hydrogen bonds also occur
between the side-chain ϵ- and η-amino groups of Ub
Arg<sup>72</sup> and the carboxylate of PL<sup>pro</sup>Asp<sup>1645</sup> as well as between the main-chain amide of Ub
residue Leu<sup>73</sup> and side chain PL<sup>pro</sup> residue
Asp<sup>1646</sup>. The BL2 loop between strands β15 and
β16 is indicated with an <italic>arrow. B</italic>, alternate
orientation of the PL<sup>pro</sup> active site showing a hydrogen
bonding interaction between the Ub Leu<sup>73</sup> main-chain amide
group and the side-chain carboxylate of PL<sup>pro</sup> residue
Asp<sup>1646</sup>. The side chain of Ub residue Leu<sup>63</sup>also undergoes hydrophobic interactions with PL<sup>pro</sup> residues
Phe<sup>1750</sup> and Pro<sup>1731</sup>. <italic>C</italic>, the
MERS-CoV PL<sup>pro</sup>Cys<sup>1592</sup>-His<sup>1759</sup>-Asp<sup>1774</sup> catalytic
triad residues are shown as well as residues Asn<sup>1590</sup> and
Asn<sup>1591</sup>, which together with Cys<sup>1592</sup> form the
oxyanion hole via their backbone amide groups. The covalent 3CN molecule
is shown linking the C terminus of Ub to the active site
Cys<sup>1592</sup> of PL<sup>pro</sup>. The active site
Leu<sup>1587</sup> residue, which is not involved in oxyanion hole
formation, is also shown. The electron density is a maximum likelihood
weighted 2<italic>F<sub>o</sub></italic> −
<italic>F<sub>c</sub></italic> map contoured at 1.0σ. Images
were created using PyMOL (<xref rid="B70" ref-type="bibr">70</xref>).</p></caption><graphic xlink:href="zbc0521402620005"></graphic></fig><p>Interestingly, differences were observed in the position of a loop on
PL<sup>pro</sup> connecting strands β15 and β16, which is
structurally analogous to the blocking loop (BL2) first described in the
structure of USP14 (<xref rid="B59" ref-type="bibr">59</xref>). This loop is
disordered in our unliganded PL<sup>pro</sup> structure and that previously
determined by others (<xref rid="B49" ref-type="bibr">49</xref>); however, in
both of our PL<sup>pro</sup>·Ub structures, we found this loop to be
fully resolved, supported by the main-chain hydrogen-bonding interactions
between Arg<sup>74</sup> of Ub and Gly<sup>1758</sup> of PL<sup>pro</sup>, as
well as a hydrophobic interaction between Val<sup>1757</sup> and
Pro<sup>1644</sup>, two PL<sup>pro</sup> residues present on opposite sides
of the active site cleft (<xref ref-type="fig" rid="F5">Fig.
5</xref><italic>A</italic>). The side-chain η-amino group of the Ub
residue Arg<sup>74</sup> is also hydrogen-bonded to the main-chain carbonyl
group of PL<sup>pro</sup> residue Thr<sup>1755</sup>; however, this interaction
is only seen in the open PL<sup>pro</sup>·Ub structure. The SARS-CoV
PL<sup>pro</sup> domain has also been crystallized both in the presence
(<xref rid="B51" ref-type="bibr">51</xref>) and absence (<xref rid="B58" ref-type="bibr">58</xref>) of Ub, and although the BL2 loop of unbound
SARS-CoV PL<sup>pro</sup> was resolved in two of three monomers of the
asymmetric unit, the third showed weak electron density for BL2 and high
temperature factors, indicating a high degree of mobility. In addition, in the
transmissible gastroenteritis coronavirus USP domain PL1<sup>pro</sup>, a
structurally analogous BL2 loop was found to be in an open conformation with
poorly defined electron density in the absence of substrate (<xref rid="B55" ref-type="bibr">55</xref>). It is interesting to note that all three
coronavirus USP DUBs crystallized to date (from MERS-CoV, SARS-CoV, and
transmissible gastroenteritis coronavirus) demonstrate a significant degree of
flexibility within the BL2 loop region in the absence of substrate and that none
of the structures determined in their unbound form demonstrate obstruction of
the active site via BL2.</p></sec><sec><title>Structure-guided Design of PL<sup>pro</sup> Mutants Defective in DUB
Activity</title><p>We previously demonstrated that the DUB activity of the papain-like protease 2
(PLP2) from equine arteritis virus (another member of the nidovirus order),
which resembles the ovarian tumor (OTU) domain-containing family of DUBs (<xref rid="B60" ref-type="bibr">60</xref>), could be selectively removed without
affecting its ability to process the equine arteritis virus replicase
polyprotein. This allowed us to establish that the DUB activity of PLP2 is
directly responsible for suppressing Ub-dependent antiviral pathways during
infection of primary host cells (<xref rid="B61" ref-type="bibr">61</xref>).
Subsequently, Ratia <italic>et al.</italic> (<xref rid="B62" ref-type="bibr">62</xref>) applied a similar strategy to the SARS-CoV PL<sup>pro</sup>domain in order to partially remove the DUB activity of PL<sup>pro</sup> while
maintaining the nsp2-3-processing function. We now used the crystal structure of
the USP-like MERS PL<sup>pro</sup>·Ub complex to guide the design of
mutations targeting the Ub-binding site on PL<sup>pro</sup> that would
completely disrupt Ub binding without affecting the structural integrity of the
active site. PL<sup>pro</sup> residues interacting directly with Ub were
replaced with larger, bulkier residues that would prevent Ub binding by altering
both shape and surface electrostatics of the Ub-binding site. Individual
mutation of eight different PL<sup>pro</sup> residues (Arg<sup>1649</sup>,
Thr<sup>1653</sup>, Ala<sup>1656</sup>, Asn<sup>1673</sup>,
Val<sup>1674</sup>, Val<sup>1691</sup>, Val<sup>1706</sup>, and
Gln<sup>1708</sup>) and combinations thereof were generated (<xref ref-type="fig" rid="F6">Fig. 6</xref>, <italic>A–D</italic>).
Importantly, these residues are located at a distance from the PL<sup>pro</sup>active site, and thus we hypothesized that they would only participate in DUB
activity and not polyprotein processing.</p><fig id="F6" orientation="portrait" position="float"><label>FIGURE 6.</label><caption><p><bold>Structure-guided mutagenesis of PL<sup>pro</sup> residues involved
in Ub recognition.</bold><italic>A</italic>, <italic>surface representation</italic> of the
closed MERS-CoV PL<sup>pro</sup>·Ub complex. PL<sup>pro</sup> is
shown in <italic>green</italic>, and Ub is shown in <italic>transparent
orange</italic>. Those residues that were mutated in order to
disrupt Ub binding are <italic>colored magenta</italic> and are
indicated with <italic>arrows. Colored boxes</italic> refer <italic>to
close-up views</italic> of the PL<sup>pro</sup>·Ub
interactions and are shown to the <italic>right. B</italic>, hydrophobic
interaction is shown between Val<sup>1691</sup> of PL<sup>pro</sup> and
Ile<sup>44</sup> of Ub. <italic>C</italic>, Thr<sup>1653</sup> of
PL<sup>pro</sup> is shown hydrogen-bonded to Gln<sup>49</sup> and
Glu<sup>51</sup> of Ub, and Arg<sup>1649</sup> of PL<sup>pro</sup>is shown interacting with Arg<sup>72</sup> of Ub. <italic>D</italic>,
hydrogen-bonding interactions are shown between Gln<sup>1708</sup> of
PL<sup>pro</sup> and Gln<sup>62</sup> of Ub, and a hydrophobic
interaction is shown between Val<sup>1706</sup> of PL<sup>pro</sup> and
Phe<sup>4</sup> of Ub. Asn<sup>1673</sup> and Val<sup>1674</sup> of
PL<sup>pro</sup>, which do not interact with Ub, are also displayed.
Images were created using PyMOL (<xref rid="B70" ref-type="bibr">70</xref>).</p></caption><graphic xlink:href="zbc0521402620006"></graphic></fig><p>Despite significant movement within the fingers domain of PL<sup>pro</sup>, most
interactions between the protease and Ub are consistent between the open and
closed Ub-bound complexes. Residue Ile<sup>44</sup> of Ub, which forms part of
the hydrophobic patch that is commonly recognized by Ub-binding proteins (<xref rid="B63" ref-type="bibr">63</xref>), interacts with the hydrophobic side
chain of Val<sup>1691</sup> of PL<sup>pro</sup> (<xref ref-type="fig" rid="F6">Fig. 6</xref><italic>B</italic>). Residues Gln<sup>49</sup> and
Glu<sup>51</sup> of Ub form hydrogen-bonding interactions with
Thr<sup>1653</sup> that is present on helix α7, which runs through
the center of PL<sup>pro</sup>. Two arginine residues, Arg<sup>1649</sup> of
PL<sup>pro</sup> and Arg<sup>72</sup> of Ub (the latter of which forms part
of the C-terminal tail of Ub that is bound in the PL<sup>pro</sup> active site
cleft) are oriented such that the guanidinium groups of these residues are
arranged in a stacked conformation (<xref ref-type="fig" rid="F6">Fig.
6</xref><italic>C</italic>). In addition, due to the inward movement toward
Ub of the closed PL<sup>pro</sup>·Ub fingers domain, a unique
hydrogen-bonding interaction between Gln<sup>62</sup> of Ub and
Gln<sup>1708</sup> of PL<sup>pro</sup> and a hydrophobic interaction between
Phe<sup>4</sup> of Ub and Val<sup>1706</sup> of PL<sup>pro</sup> were found
to occur in this complex (<xref ref-type="fig" rid="F6">Fig.
6</xref><italic>D</italic>). Residue Ala<sup>1656</sup> is positioned near
the C terminus of PL<sup>pro</sup> helix α7, and although it is not
directly involved in Ub binding, we believed that it was positioned such that
the introduction of larger residues (<italic>e.g.</italic> arginine or
phenylalanine) could disrupt Ub recognition, and thus this residue was targeted
for mutation (<xref ref-type="fig" rid="F6">Fig. 6</xref><italic>C</italic>).
Two residues on the solvent-facing region of the PL<sup>pro</sup> zinc ribbon
motif, Asn<sup>1673</sup> and Val<sup>1674</sup>, were also targeted for
mutagenesis. Although they do not bind Ub at the S1 binding site (the substrate
binding site on PL<sup>pro</sup> responsible for binding mono(Ub) in our
structure; see Ref. <xref rid="B64" ref-type="bibr">64</xref> for nomenclature),
we hypothesized that it may inhibit association with the distal Ub on
Lys<sup>63</sup> poly-Ub chains based on a superposition of a
Lys<sup>63</sup>-linked di-Ub model onto the PL<sup>pro</sup>-bound Ub
molecule of the closed PL<sup>pro</sup>·Ub complex structure determined
here (not shown). In addition, the crystal structure of USP21 bound to linear
di-Ub was recently determined and revealed that the tip of the fingers domain of
this DUB acts as an S2 recognition site, binding to the distal Ub of a linear
di-Ub molecule (<xref rid="B57" ref-type="bibr">57</xref>). Given the structural
similarity between Lys<sup>63</sup> di-Ub and linear di-Ub and the clear
activity we observed for MERS-CoV PL<sup>pro</sup> toward Lys<sup>63</sup>, we
hypothesized that mutating residues Asn<sup>1673</sup> and Val<sup>1674</sup>near the zinc ribbon may also disrupt Ub processing.</p></sec><sec><title>Targeted Mutations within the PL<sup>pro</sup>·Ub Binding Site
Disrupt Ub Processing but Not Proteolytic Cleavage of the nsp3↓4
Site</title><p>Using a previously described ectopic expression assay (<xref rid="B61" ref-type="bibr">61</xref>), we monitored the effects of amino acid
substitutions in PL<sup>pro</sup>, as described above, on overall levels of
Ub-conjugated proteins in HEK293T cells as well as the ability of these
PL<sup>pro</sup> variants to process the MERS-CoV nsp3↓4 polyprotein
cleavage site <italic>in trans</italic>. V5-tagged PL<sup>pro</sup> (wild type
and mutants) was co-expressed with N-terminally HA-tagged and C-terminally
V5-tagged MERS-CoV nsp3C-4 excluding the PL<sup>pro</sup> domain, hereafter
referred to as HA-nsp3C-4-V5. We assume that the successful processing of the
nsp3↓4 site in HA-nsp3C-4-V5 is indicative of unaltered proteolytic
cleavage capability of PL<sup>pro</sup>, which during infection facilitates the
release of nsp1, -2, and -3 from the viral polyproteins. Processing of
HA-nsp3C-4-V5 in <italic>trans</italic> by wild-type PL<sup>pro</sup> and our
panel of mutants was visualized via Western blotting (<xref ref-type="fig" rid="F7">Fig. 7</xref><italic>A</italic>). Whereas wild-type
PL<sup>pro</sup> was able to cleave HA-nsp3C-4-V5 substrate in
<italic>trans</italic>, the PL<sup>pro</sup> active site mutant C1592A was
unable to cleave the nsp3↓4 site (<xref ref-type="fig" rid="F7">Fig.
7</xref><italic>A</italic>, compare <italic>lanes 5</italic> and
<italic>6</italic> and <italic>lanes 19</italic> and <italic>20</italic>).
As expected, each of the substitutions in the Ub-binding site of
PL<sup>pro</sup> only minimally affected nsp3↓4 cleavage, with the
exception of the A1656R mutant that displayed a clearly reduced ability to
cleave HA-nsp3C-4-V5 compared with wild-type PL<sup>pro</sup> (<xref ref-type="fig" rid="F7">Fig. 7</xref><italic>A</italic>, compare
<italic>lanes 5</italic> and <italic>10</italic>). This suggests that
Ala<sup>1656</sup> of PL<sup>pro</sup> may be involved in recognizing and
binding sequences in the vicinity of the nsp3↓4 cleavage site. Most
double and triple substitutions tested were also slightly less efficient in
cleaving HA-nsp3C-4-V5 compared with the wild-type control.</p><fig id="F7" orientation="portrait" position="float"><label>FIGURE 7.</label><caption><p><bold>Effect of PL<sup>pro</sup> mutations on in <italic>trans</italic>cleavage of nsp3↓4 and on DUB activity.</bold><italic>A</italic>, HEK293T cells were co-transfected with plasmids
encoding HA-nsp3C-4-V5 (which does not contain PL<sup>pro</sup>),
PL<sup>pro</sup>-V5 (wild type and mutants), and GFP (as a
transfection control). As a control, plasmid encoding HA-nsp3-4-V5,
which includes the PL<sup>pro</sup> domain, was transfected
(<italic>lanes 1</italic> and <italic>15</italic>), and cleavage
resulted in the generation of full-length HA-tagged nsp3 and V5-tagged
nsp4. Cells were lysed 18 h post-transfection, and expressed proteins
were analyzed by Western blotting. Proteolytic cleavage was measured
from the generation of N-terminal HA-tagged nsp3C and C-terminal
V5-tagged nsp4. <italic>B</italic>, HEK293T cells were transfected with
a combination of plasmids encoding FLAG-Ub, PL<sup>pro</sup>-V5
(wild-type and mutants), and GFP (as a transfection control). Cells were
lysed 18 h post-transfection, and expressed proteins were analyzed by
Western blotting to visualize the deconjugation of FLAG-tagged Ub from a
wide range of cellular proteins by MERS-CoV PL<sup>pro</sup> wild-type
and mutants.</p></caption><graphic xlink:href="zbc0521402620007"></graphic></fig><p>In order to analyze the effect of the mutations on overall DUB activity,
PL<sup>pro</sup>-V5 was co-expressed with FLAG-Ub, and the levels of
FLAG-Ub-conjugated cellular proteins were visualized via Western blotting (<xref ref-type="fig" rid="F7">Fig. 7</xref><italic>B</italic>). Expression of
wild-type PL<sup>pro</sup> resulted in a strong decrease of the accumulation of
FLAG-Ub conjugates, whereas a negligible effect was observed upon expression of
active site mutant C1592A (<xref ref-type="fig" rid="F7">Fig.
7</xref><italic>B</italic>, compare <italic>lanes 3</italic> and
<italic>4</italic> and <italic>lanes 16</italic> and <italic>17</italic>).
Substitutions of residue Val<sup>1691</sup>, positioned on strand β12 of
PL<sup>pro</sup>, and Thr<sup>1653</sup> and Ala<sup>1656</sup>, residues
located on helix α7 (<xref ref-type="fig" rid="F6">Fig. 6</xref>,
<italic>B</italic> and <italic>C</italic>), displayed the clearest reduction
of PL<sup>pro</sup> DUB activity (<xref ref-type="fig" rid="F7">Fig.
7</xref><italic>B</italic>, <italic>lanes 5–8</italic>). The V1691R
mutation had the most pronounced effect, and a PL<sup>pro</sup> T1653R/V1691R
double mutant also displayed severely reduced DUB activity, comparable with that
seen for the active site mutant (<xref ref-type="fig" rid="F7">Fig.
7</xref><italic>B</italic>, compare <italic>lanes 4</italic> and
<italic>5</italic> and <italic>lanes 17</italic> and <italic>22</italic>).
Notably, a more conservative substitution at the same position, V1691L, had a
much less pronounced effect on DUB activity (<xref ref-type="fig" rid="F7">Fig.
7</xref><italic>B</italic>, <italic>lane 6</italic>). Substitution of
Val<sup>1674</sup> with either Ser or Arg impaired DUB activity but to a
much lesser extent than substitutions targeting Val<sup>1691</sup>,
Thr<sup>1653</sup>, and Ala<sup>1656</sup> (<xref ref-type="fig" rid="F7">Fig. 7</xref><italic>B</italic>, compare <italic>lanes
5–8</italic>, <italic>10</italic>, and <italic>11</italic>). The N1673R
substitution did not negatively affect DUB activity of PL<sup>pro</sup> at all,
whereas the N1673R/V1674S double substitution resulted in slightly greater DUB
activity (<xref ref-type="fig" rid="F7">Fig. 7</xref><italic>B</italic>,
<italic>lanes 9</italic> and <italic>20</italic>). These results do not
support our hypothesis based on modeling that Asn<sup>1673</sup> and
Val<sup>1674</sup> might form part of an S2 binding site that recognizes an
additional distal Ub within a Lys<sup>63</sup>-linked chain. Further structural
studies are needed to validate the role of these residues in binding Ub chains.
It should be noted, however, that these mutants may still be able to process
Lys<sup>63</sup>-linked poly-Ub chains by recognizing a single Ub monomer at
the end of a poly-Ub substrate, which may explain the ineffectiveness of these
mutations in disrupting DUB activity. Mutations at residues Val<sup>1706</sup>and Gln<sup>1708</sup> did not influence DUB activity of PL<sup>pro</sup> (<xref ref-type="fig" rid="F7">Fig. 7</xref><italic>B</italic>, <italic>lanes
18</italic> and <italic>19</italic>). Given that these residues were only
found to interact with Ub in our closed PL<sup>pro</sup> structure (<xref ref-type="fig" rid="F6">Fig. 6</xref><italic>A</italic>), their failure to
inhibit DUB activity in this cellular DUB assay is not surprising and indicates
that these residues are not essential for Ub recognition. Interestingly and
repeatedly observed, the R1649Y mutant was found to have even greater DUB
activity than wild-type PL<sup>pro</sup> (<xref ref-type="fig" rid="F7">Fig.
7</xref><italic>B</italic>, compare <italic>lanes 3</italic> and
<italic>12</italic>). This residue was found to interact with residue
Arg<sup>72</sup> of Ub, and although this result was unexpected, it is
possible that the R1649Y mutant retains the ability to interact with
Arg<sup>72</sup> of Ub via a cation-π interaction between the
aromatic tyrosine inserted into PL<sup>pro</sup> and the positively charged
arginine of Ub. Together, the findings from our mutagenesis study demonstrate
that it is possible to selectively decouple the DUB and polyprotein processing
activities of MERS-CoV PL<sup>pro</sup> through structure-guided site-directed
mutagenesis.</p></sec><sec><title>PL<sup>pro</sup> DUB Activity Suppresses the Innate Immune Response</title><p>Conjugation and deconjugation of Ub plays an important role in the regulation of
the innate immune response, and not surprisingly, pathogens have evolved
mechanisms to subvert these Ub-dependent pathways (reviewed in Ref. <xref rid="B22" ref-type="bibr">22</xref>). For arteriviruses, which are distant
relatives of CoVs within the nidovirus order, it has been shown that the DUB
activity of their PLP2 is involved in antagonizing IFN-β activation upon
ectopic expression, and for equine arteritis virus, this was confirmed during
infection in host cells (<xref rid="B61" ref-type="bibr">61</xref>, <xref rid="B65" ref-type="bibr">65</xref>). Coronavirus papain-like proteases have
been suggested to act as IFN-β and NF-κB antagonists as well
(<xref rid="B15" ref-type="bibr">15</xref>, <xref rid="B23" ref-type="bibr">23</xref>, <xref rid="B66" ref-type="bibr">66</xref>, <xref rid="B67" ref-type="bibr">67</xref>). MERS-CoV PL<sup>pro</sup> is thought to possess
these properties based on its capability to inhibit RIG-I-, MDA5-, and
MAVS-induced IFN-β promoter stimulation and to reduce
TNF-α-induced NF-κB reporter gene activity (<xref rid="B9" ref-type="bibr">9</xref>, <xref rid="B16" ref-type="bibr">16</xref>). We
therefore designed luciferase-based reporter gene assays to establish whether
the DUB activity of MERS-CoV PL<sup>pro</sup> alone suffices to antagonize the
IFN-β pathway. To this end, we first assessed at which level of this
innate immune signal transduction pathway MERS-CoV PL<sup>pro</sup> is most
active as a suppressor.</p><p>Innate immune signaling was induced in HEK293T cells by expression of one of
three signaling factors, RIG-I, MAVS, or IRF3, which stimulate the pathway
leading to IFN-β production at different levels. Because RIG-I and IRF3
normally need to be activated through post-translational modification
(ubiquitination and phosphorylation, respectively), constitutively active
variants were used (RIG-I<sub>(2CARD)</sub> and IRF3<sub>(5D)</sub>), which
efficiently induce downstream signaling independent of these activation steps.
Cells were co-transfected with plasmids encoding one of these innate immune
signaling proteins and wild-type PL<sup>pro</sup>, the PL<sup>pro</sup> active
site mutant C1592A, or full-length MERS-CoV nsp3 containing the PL<sup>pro</sup>domain. The inhibitory effect of the PL<sup>pro</sup> variants on the activation
of the IFN-β promotor by the different stimuli was measured via
co-expression of a firefly luciferase reporter gene under control of the
IFN-β promoter. Another co-transfected plasmid encoding
<italic>Renilla</italic> luciferase was included as an internal control in
order to be able to correct for variability in transfection efficiency. At 16 h
post-transfection, luciferase activities were measured, and activation of the
IFN-β promoter induced by expression of RIG-I<sub>(2CARD)</sub>, MAVS,
or IRF3<sub>(5D)</sub> was set at 100% (<xref ref-type="fig" rid="F8">Fig.
8</xref>). In accordance with Mielech <italic>et al.</italic> (<xref rid="B16" ref-type="bibr">16</xref>), we observed that MERS-CoV
PL<sup>pro</sup> significantly reduced the IFN-β promoter activation
that could be induced by expression of either RIG-I<sub>(2CARD)</sub> or MAVS.
This effect was concentration-dependent, whereas the PL<sup>pro</sup> active
site mutant was unable to block IFN-β promoter activation (<xref ref-type="fig" rid="F8">Fig. 8</xref>, <italic>A</italic> and
<italic>C</italic>). MERS-CoV nsp3 expression also inhibited RIG-I- and
MAVS-mediated IFN-β promoter induction (<xref ref-type="fig" rid="F8">Fig. 8</xref>, <italic>B</italic> and <italic>D</italic>), and together
this suggested that PL<sup>pro</sup> inhibits innate immune signaling at least
downstream of the MAVS adaptor and possibly also in the signaling between RIG-I
and MAVS. MERS-CoV PL<sup>pro</sup> also inhibited activation of the
IFN-β promoter after stimulation with IRF3<sub>(5D)</sub> in a
concentration-dependent manner, whereas the C1592A mutant did not reduce
IFN-β promoter activation (<xref ref-type="fig" rid="F8">Fig.
8</xref><italic>E</italic>). However, expression of full-length MERS-CoV
nsp3 did not significantly inhibit IFN-β promoter activation after
stimulation with IRF3<sub>(5D)</sub> (<xref ref-type="fig" rid="F8">Fig.
8</xref><italic>F</italic>). This suggests that the subcellular localization
of the protease, which in the case of full-length nsp3 is membrane-anchored and
in the case of the PL<sup>pro</sup> domain is presumably cytosolic, may be
important in determining its substrate specificity. Taken together, our results
suggest that MERS-CoV PL<sup>pro</sup> primarily interferes with the
IFN-β signaling pathway at the level between MAVS and IRF3.</p><fig id="F8" orientation="portrait" position="float"><label>FIGURE 8.</label><caption><p><bold>MERS-CoV PL<sup>pro</sup> inhibits RIG-I- and MAVS-induced
IFN-β promoter activity.</bold> HEK293T cells were
transfected with a combination of plasmids expressing a firefly
luciferase reporter gene under control of the IFN-β promoter,
<italic>Renilla</italic> luciferase; innate immune response inducers
RIG-I<sub>(2CARD)</sub>, MAVS, or IRF3<sub>(5D)</sub>; and
increasing amounts of MERS-CoV PL<sup>pro</sup> wild-type, active site
mutant C1592A (<italic>A</italic>, <italic>C</italic>, and
<italic>E</italic>), or full-length MERS-CoV nsp3
(<italic>B</italic>, <italic>D</italic>, and <italic>F</italic>).
Upon induction of the innate immune response with
RIG-I<sub>(2CARD)</sub> and IRF3<sub>(5D)</sub>, cells were
transfected with the PL<sup>pro</sup> (0, 150, 350, or 500 ng) or nsp3
(0, 350, 500, of 1000 ng) constructs. Upon induction with MAVS, cells
were transfected with the PL<sup>pro</sup> (0, 50, 75, 100 or 150 ng) or
nsp3 (0, 150, 350 or 500 ng) constructs. At 16 h post-transfection,
cells were lysed, and luciferase activity was measured. All experiments
were repeated independently at least four times. Significance was
evaluated using an unpaired two-tailed Student's <italic>t</italic>test; <italic>p</italic> values of <0.05 were considered
significant. <italic>Bars</italic>, mean; <italic>error bars</italic>,
S.D. Western blotting was used to verify expression of MERS-CoV
PL<sup>pro</sup> and nsp3.</p></caption><graphic xlink:href="zbc0521402620008"></graphic></fig><p>We therefore chose to use MAVS-mediated induction of IFN-β promoter
activation in subsequent experiments. This also resulted in the strongest
inhibition by PL<sup>pro</sup>, providing a maximum window to assess the effects
on IFN-β promoter inhibition by the PL<sup>pro</sup> mutants with
specifically inactivated DUB activity. Inhibition of IFN-β promoter
activation by wild-type and mutant PL<sup>pro</sup> was determined by
calculating the relative luciferase activity (<xref ref-type="fig" rid="F9">Fig.
9</xref>). Expression of wild-type PL<sup>pro</sup> reduced MAVS-induced
IFN-β promoter activity to ∼20% of the control, whereas active
site mutant C1592A reduced it by only a few percent compared with the untreated
control (<xref ref-type="fig" rid="F9">Fig. 9</xref>). Substitutions T1653R and
A1656R resulted in greatly impaired DUB activity (<xref ref-type="fig" rid="F7">Fig. 7</xref><italic>B</italic>, <italic>lanes 7</italic> and
<italic>8</italic>), and compared with wild-type PL<sup>pro</sup>,
expression of these mutants resulted in higher IFN-β promoter activity,
with relative luciferase values of ∼54 and 58% respectively (<xref ref-type="fig" rid="F9">Fig. 9</xref>). It should, however, be noted that
the A1656R mutant was also impaired in cleaving the nsp3↓4 site, and
therefore this mutation nonspecifically disrupted the two proteolytic functions
of PL<sup>pro</sup>. Strikingly, each mutant containing the V1691R substitution
was completely unable to inhibit IFN-β promoter activation, resulting in
relative luciferase activity levels similar to those seen with the active site
mutant (<xref ref-type="fig" rid="F9">Fig. 9</xref>, <italic>lanes 4</italic>,
<italic>16</italic>, and <italic>17</italic>). This strongly suggested that
the DUB activity of PL<sup>pro</sup>, which we found to be severely impaired in
V1691R mutants (<xref ref-type="fig" rid="F7">Fig. 7</xref><italic>B</italic>),
is responsible for suppressing MAVS-induced IFN-β promoter activity in
this assay. The level of reduction in DUB activity corresponded to the degree of
inhibition of IFN-β promoter activation for all PL<sup>pro</sup> mutants
tested, which strengthens this conclusion. In accordance with its increased DUB
activity, mutant R1649Y suppressed MAVS-induced IFN-β promoter activity
more effectively than wild-type PL<sup>pro</sup>.</p><fig id="F9" orientation="portrait" position="float"><label>FIGURE 9.</label><caption><p><bold>DUB activity is required for IFN-β promoter antagonism by
MERS-CoV PL<sup>pro</sup>.</bold> HEK293T cells were transfected
with plasmids encoding a firefly luciferase reporter gene under control
of the IFN-β promoter, <italic>Renilla</italic> luciferase,
innate immune response inducer MAVS (25 ng), and MERS-CoV
PL<sup>pro</sup> wild type and mutants (75 ng). At 16 h
post-transfection, cells were lysed, and luciferase activity was
measured. All experiments were repeated independently at least four
times. Significance relative to wild type was evaluated using an
unpaired two-tailed Student's <italic>t</italic> test; significant
values were indicated as follows: *, <italic>p</italic> < 0.05;
**, <italic>p</italic> < 0.01. <italic>Bars</italic>, mean;
<italic>error bars</italic>, S.D. Western blotting was used to
verify expression of MERS-CoV PL<sup>pro</sup>.</p></caption><graphic xlink:href="zbc0521402620009"></graphic></fig><p>Taken together, our data show that the DUB activity of MERS-CoV PL<sup>pro</sup>suffices to efficiently suppress MAVS-induced IFN-β promoter activation
and that this activity can be selectively disabled, without disrupting protease
activity toward the nsp3↓4 cleavage site, by targeting the Ub-binding
site of the enzyme. This demonstrates for the first time that the DUB activity
of MERS-CoV PL<sup>pro</sup> is specifically responsible for suppressing the
innate immune response.</p></sec></sec><sec sec-type="discussion"><title>DISCUSSION</title><p>Guided by the MERS PL<sup>pro</sup>·Ub crystal structures, we here describe
how the DUB activity of PL<sup>pro</sup> can be selectively disabled by introducing
mutations into the S1 binding pocket of the protease (<xref ref-type="fig" rid="F6">Fig. 6</xref>). Particularly, the substitution of Val<sup>1691</sup> with the
bulky and charged arginine residue severely impaired DUB activity in our cell
culture-based assays. In addition, our results demonstrate that the majority of the
mutations within the S1 Ub-binding site of PL<sup>pro</sup> that were tested do not
affect <italic>trans</italic> cleavage of the nsp3↓4 junction, with the
exception of an A1656R mutant that did disrupt cleavage of the nsp3↓4 site.
The latter result indicates that Ala<sup>1656</sup> resides in a region of
PL<sup>pro</sup> that recognizes both Ub and a region of the nsp3C-4 construct
that was used to test cleavage efficiency.</p><p>Our results demonstrate that the DUB activity of MERS-CoV PL<sup>pro</sup> inhibits
IFN-β promoter activation when innate immune signaling is induced by
co-expression of either RIG-I or MAVS. The fact that suppression of IFN-β
promoter activation was completely eliminated for several of our mutants (<xref ref-type="fig" rid="F9">Fig. 9</xref>) strongly suggests that the proteolytic
activity still present in those mutant enzymes has no additional role in the
suppression of this particular branch of the innate immune response
(<italic>e.g.</italic> by directly cleaving RIG-I or MAVS). A number of other
CoV papain-like proteases with DUB activity have also been implicated in
antagonizing the host innate immune response (<xref rid="B15" ref-type="bibr">15</xref>, <xref rid="B23" ref-type="bibr">23</xref>, <xref rid="B66" ref-type="bibr">66</xref>, <xref rid="B67" ref-type="bibr">67</xref>). In
agreement with our data, recent studies have demonstrated the ability of MERS-CoV
PL<sup>pro</sup> to inhibit RIG-I-, MDA5-, and MAVS-dependent IFN-β
promoter activation as well as to down-regulate the level of IFN-β mRNA
transcripts in MDA5-stimulated cells (<xref rid="B16" ref-type="bibr">16</xref>).
The current data support the hypothesis that all of these activities solely depend
on the deubiquitinating capacities of these coronavirus enzymes. Reports regarding
the dependence of MERS-CoV PL<sup>pro</sup>-mediated IFN-β antagonism on the
enzyme's protease activity have, however, varied thus far. Mielech <italic>et
al.</italic> (<xref rid="B16" ref-type="bibr">16</xref>) recently demonstrated
that a MERS-CoV nsp3 fragment containing PL<sup>pro</sup> but excluding the
transmembrane domain can inhibit MAVS-, RIG-I-, and MDA5-dependent IFN-β
promoter activation, and MDA5 mediated IFN-β mRNA transcription only with a
functional PL<sup>pro</sup> active site. Yang <italic>et al.</italic> (<xref rid="B9" ref-type="bibr">9</xref>) on the other hand used a MERS-CoV
PL<sup>pro</sup> expression product extending into the nsp3 transmembrane region
to demonstrate that down-regulation of RIG-I-stimulated IFN-β promoter
activity is seen even with an active site knock-out mutant. Here we show that
inhibition of RIG-I-, MAVS-, and IRF3-induced IFN-β promoter activity by the
MERS-CoV PL<sup>pro</sup> domain is clearly dependent on a functional active site
and that it is specifically the DUB activity of the protease that mediates this
inhibition. However, the possibility cannot be ruled out that other parts of nsp3
contain additional innate immune suppressing activities, which may be responsible
for the protease-independent effects reported with longer expression products.</p><p>Ubiquitination plays an important role in the regulation of pathways involved in
detecting and counteracting viral infections, and, not surprisingly, a number of
viruses of substantial diversity have been found to deploy DUBs that manipulate
these signaling processes by reversing the post-translational modification of
cellular proteins by Ub conjugation (<xref rid="B19" ref-type="bibr">19</xref>,
<xref rid="B68" ref-type="bibr">68</xref>). Some of these DUBs, specifically
those found in (+)RNA viruses, are also critical for viral replication by catalyzing
the proteolytic cleavage of specific sites in viral polyproteins, thus complicating
our ability to study the direct effects of the additional DUB activity of these
viral proteases. Ultimately, these effects need to be studied in the context of a
viral infection; however, a simple inactivation of the protease/DUB would not only
fail to prove the specific involvement of the DUB activity, it would also prevent
viral replication. The method described here selectively removed the DUB activity of
the MERS-CoV PL<sup>pro</sup> domain while leaving polyprotein processing activity
at the nsp3↓4 site unhindered, thus paving the way for the application of
these mutations to recombinant MERS-CoV and the direct study of the role of DUB
activity during infection.</p><p>We were able to show that Lys<sup>48</sup>- and Lys<sup>63</sup>-linked poly-Ub
chains are processed <italic>in vitro</italic> by MERS-CoV PL<sup>pro</sup> at
similar rates, which is in accordance with a recent report by Báez-Santos
<italic>et al.</italic> (<xref rid="B50" ref-type="bibr">50</xref>). In
contrast, SARS-CoV PL<sup>pro</sup> rapidly cleaves Lys<sup>48</sup>-linked poly-Ub
and displays only moderate activity for Lys<sup>63</sup> linkages in similar assays
(<xref rid="B62" ref-type="bibr">62</xref>). It has been suggested that SARS-CoV
PL<sup>pro</sup> may recognize Lys<sup>48</sup>-linked di-Ub via its S1 and S2
sites (<xref rid="B62" ref-type="bibr">62</xref>), although to date, no crystal
structures have been reported of SARS-CoV PL<sup>pro</sup> in complex with a di-Ub
substrate. Similarly, no such structural data have been obtained for MERS-CoV
PL<sup>pro</sup>, and thus future structural studies are necessary to determine
precisely how MERS-CoV PL<sup>pro</sup> recognizes poly-Ub substrates and whether
the preferences observed in expression systems can be confirmed in situations
representative of an infection.</p><p>In addition to deconjugating Ub, MERS- and SARS-CoV PL<sup>pro</sup> also recognize
the antiviral Ubl molecule ISG15 (<xref rid="B16" ref-type="bibr">16</xref>, <xref rid="B17" ref-type="bibr">17</xref>). In the absence of a crystal structure of a
DUB from the USP family in complex with ISG15, it is difficult to predict which
regions of PL<sup>pro</sup> may be specifically responsible for ISG15 binding.
However, it is interesting to note that both the palm and fingers domains of the
SARS-CoV PL<sup>pro</sup> domain (<xref rid="B62" ref-type="bibr">62</xref>) and the
cellular USP21 (<xref rid="B57" ref-type="bibr">57</xref>), respectively, have been
implicated in ISG15 recognition, probably through additional interactions between
PL<sup>pro</sup> and the N-terminal Ubl fold of ISG15. Future structural work is
necessary to identify the specific determinants of ISG15 recognition by MERS-CoV
PL<sup>pro</sup>. Structure-guided mutagenesis of MERS-CoV PL<sup>pro</sup> to
selectively disrupt deISGylation without affecting polyprotein cleavage would
further expand our insights into the role of this additional activity in coronaviral
immune evasion. The specific removal of DUB and potentially deISGylating activity
from viral proteases that suppress the host innate immune response may open new
avenues to engineer attenuated viruses for use as modified-live virus vaccines.</p></sec></body><back><fn-group><fn fn-type="supported-by" id="FN1"><label>*</label><p>This work was supported in part by Natural Sciences and Engineering Research
Council of Canada Grant 311775-2010 (to B. L. M.), the Division of Chemical
Sciences of the Netherlands Organization for Scientific Research (NWO-CW)
through ECHO grant 700.59.008 (to M. K. and E. J. S.), and the European Union
Seventh Framework Programme (FP7/2007–2013) under SILVER grant agreement
260644.</p></fn><fn fn-type="other"><p>The atomic coordinates and structure factors (codes <ext-link ext-link-type="uri" xlink:href="http://www.pdb.org/pdb/explore/explore.do?structureId=4REZ">4REZ</ext-link>, <ext-link ext-link-type="uri" xlink:href="http://www.pdb.org/pdb/explore/explore.do?structureId=4RF1">4RF1</ext-link>, and <ext-link ext-link-type="uri" xlink:href="http://www.pdb.org/pdb/explore/explore.do?structureId=4RF0">4RF0</ext-link>) have been deposited in the Protein Data Bank (<ext-link ext-link-type="uri" xlink:href="http://www.pdb.org/">http://wwpdb.org/</ext-link>).</p></fn></fn-group><fn-group content-type="abbreviations"><fn id="FN5"><label>6</label><p>The abbreviations used are: <def-list><def-item><term id="G1">MERS</term><def><p>Middle East respiratory syndrome</p></def></def-item><def-item><term id="G2">CoV</term><def><p>coronavirus</p></def></def-item><def-item><term id="G3">SARS</term><def><p>severe acute respiratory syndrome</p></def></def-item><def-item><term id="G4">nsp</term><def><p>non-structural protein</p></def></def-item><def-item><term id="G5">pp1a and pp1ab</term><def><p>polyprotein 1a and 1ab, respectively</p></def></def-item><def-item><term id="G6">PL<sup>pro</sup></term><def><p>papain-like protease</p></def></def-item><def-item><term id="G7">Ub</term><def><p>ubiquitin</p></def></def-item><def-item><term id="G8">DUB</term><def><p>deubiquitinating enzyme</p></def></def-item><def-item><term id="G9">ISG</term><def><p>interferon-stimulated gene</p></def></def-item><def-item><term id="G10">RLR</term><def><p>RIG-I-like receptor</p></def></def-item><def-item><term id="G11">MAVS</term><def><p>mitochondrial antiviral signaling protein</p></def></def-item><def-item><term id="G12">IFN</term><def><p>interferon(s)</p></def></def-item><def-item><term id="G13">LSB</term><def><p>Laemmli sample buffer</p></def></def-item><def-item><term id="G14">SUMO</term><def><p>small ubiquitin-like modifier</p></def></def-item><def-item><term id="G15">Ub-3Br</term><def><p>Ub(1–75)-3-bromopropylamine</p></def></def-item><def-item><term id="G16">USP</term><def><p>ubiquitin-specific protease.</p></def></def-item></def-list></p></fn></fn-group><ack><title>Acknowledgments</title><p>We are grateful to Diede Oudshoorn for generating MERS-CoV nsp3-4 expression
constructs and Kathleen C. Lehmann for excellent technical assistance. We kindly
thank the following people for providing reagents: John Hiscott, Craig E. Cameron,
Michaela U. Gack, and Adolfo García-Sastre. We thank Veronica Larmour for
technical assistance and Shaun Labiuk and the staff of the Canadian Light Source
(CLS) beamline 08B1-1 for assistance with data collection. The CLS is supported by
the Natural Sciences and Engineering Research Council of Canada, the National
Research Council, the Canadian Institutes of Health Research, and the University of
Saskatchewan.</p></ack><ref-list><title>REFERENCES</title><ref id="B1"><label>1.</label><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Zaki</surname><given-names>A. M.</given-names></name><name><surname>van Boheemen</surname><given-names>S.</given-names></name><name><surname>Bestebroer</surname><given-names>T. M.</given-names></name><name><surname>Osterhaus</surname><given-names>A. D. M. E.</given-names></name><name><surname>Fouchier</surname><given-names>R. A. M.</given-names></name></person-group> (<year>2012</year>) <article-title>Isolation of a
novel coronavirus from a man with pneumonia in Saudi Arabia</article-title>.
<source>N. Engl. J. Med</source>. <volume>367</volume>,
<fpage>1814</fpage>–<lpage>1820</lpage><pub-id pub-id-type="pmid">23075143</pub-id></mixed-citation></ref><ref id="B2"><label>2.</label><mixed-citation publication-type="book"><collab>World Health Organization</collab> (<year>2014</year>) <source>Middle
East Respiratory Syndrome Coronavirus (MERS-CoV): Update (United Arab
Emirates)</source>. <publisher-name>World Health
Organization</publisher-name>,
<publisher-loc>Geneva</publisher-loc></mixed-citation></ref><ref id="B3"><label>3.</label><mixed-citation publication-type="book"><collab>World Health Organization</collab> (<year>2003</year>) <source>Summary
of Probable SARS Cases with Onset of Illness from 1 November 2002 to 31 July
2003</source>. <publisher-name>World Health Organization</publisher-name>,
<publisher-loc>Geneva</publisher-loc></mixed-citation></ref><ref id="B4"><label>4.</label><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Azhar</surname><given-names>E. I.</given-names></name><name><surname>El-Kafrawy</surname><given-names>S. A.</given-names></name><name><surname>Farraj</surname><given-names>S. A.</given-names></name><name><surname>Hassan</surname><given-names>A. M.</given-names></name><name><surname>Al-Saeed</surname><given-names>M. S.</given-names></name><name><surname>Hashem</surname><given-names>A. M.</given-names></name><name><surname>Madani</surname><given-names>T. A.</given-names></name></person-group> (<year>2014</year>) <article-title>Evidence for
camel-to-human transmission of MERS coronavirus</article-title>. <source>N.
Engl. J. Med</source>. <volume>370</volume>,
<fpage>2499</fpage>–<lpage>2505</lpage><pub-id pub-id-type="pmid">24896817</pub-id></mixed-citation></ref><ref id="B5"><label>5.</label><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Reusken</surname><given-names>C. B.</given-names></name><name><surname>Farag</surname><given-names>E. A.</given-names></name><name><surname>Jonges</surname><given-names>M.</given-names></name><name><surname>Godeke</surname><given-names>G. J.</given-names></name><name><surname>El-Sayed</surname><given-names>A. M.</given-names></name><name><surname>Pas</surname><given-names>S. D.</given-names></name><name><surname>Raj</surname><given-names>V. S.</given-names></name><name><surname>Mohran</surname><given-names>K. J.</given-names></name><name><surname>Moussa</surname><given-names>H. A.</given-names></name><name><surname>Ghobashy</surname><given-names>H.</given-names></name><name><surname>Alhajri</surname><given-names>F.</given-names></name><name><surname>Ibrahim</surname><given-names>A. K.</given-names></name><name><surname>Bosch</surname><given-names>B. J.</given-names></name><name><surname>Pasha</surname><given-names>S. K.</given-names></name><name><surname>Al-Romaihi</surname><given-names>H. E.</given-names></name><name><surname>Al-Thani</surname><given-names>M.</given-names></name><name><surname>Al-Marri</surname><given-names>S. A.</given-names></name><name><surname>AlHajri</surname><given-names>M. M.</given-names></name><name><surname>Haagmans</surname><given-names>B. L.</given-names></name><name><surname>Koopmans</surname><given-names>M. P.</given-names></name></person-group> (<year>2014</year>) <article-title>Middle East
respiratory syndrome coronavirus (MERS-CoV) RNA and neutralising antibodies
in milk collected according to local customs from dromedary camels, Qatar,
April 2014</article-title>. <source>Euro Surveill</source>.
<volume>19</volume>, <fpage>20829</fpage><pub-id pub-id-type="pmid">24957745</pub-id></mixed-citation></ref><ref id="B6"><label>6.</label><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>van Boheemen</surname><given-names>S.</given-names></name><name><surname>de Graaf</surname><given-names>M.</given-names></name><name><surname>Lauber</surname><given-names>C.</given-names></name><name><surname>Bestebroer</surname><given-names>T. M.</given-names></name><name><surname>Raj</surname><given-names>V. S.</given-names></name><name><surname>Zaki</surname><given-names>A. M.</given-names></name><name><surname>Osterhaus</surname><given-names>A. D.</given-names></name><name><surname>Haagmans</surname><given-names>B. L.</given-names></name><name><surname>Gorbalenya</surname><given-names>A. E.</given-names></name><name><surname>Snijder</surname><given-names>E. J.</given-names></name><name><surname>Fouchier</surname><given-names>R. A.</given-names></name></person-group> (<year>2012</year>) <article-title>Genomic
characterization of a newly discovered coronavirus associated with acute
respiratory distress syndrome in humans</article-title>.
<source>MBio</source><pub-id pub-id-type="doi">10.1128/mBio.00473-12</pub-id></mixed-citation></ref><ref id="B7"><label>7.</label><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Firth</surname><given-names>A. E.</given-names></name><name><surname>Brierley</surname><given-names>I.</given-names></name></person-group> (<year>2012</year>) <article-title>Non-canonical
translation in RNA viruses</article-title>. <source>J. Gen. Virol</source>.
<volume>93</volume>, <fpage>1385</fpage>–<lpage>1409</lpage><pub-id pub-id-type="pmid">22535777</pub-id></mixed-citation></ref><ref id="B8"><label>8.</label><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Perlman</surname><given-names>S.</given-names></name><name><surname>Netland</surname><given-names>J.</given-names></name></person-group> (<year>2009</year>) <article-title>Coronaviruses
post-SARS: update on replication and pathogenesis</article-title>.
<source>Nat. Rev. Microbiol</source>. <volume>7</volume>,
<fpage>439</fpage>–<lpage>450</lpage><pub-id pub-id-type="pmid">19430490</pub-id></mixed-citation></ref><ref id="B9"><label>9.</label><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Yang</surname><given-names>X.</given-names></name><name><surname>Chen</surname><given-names>X.</given-names></name><name><surname>Bian</surname><given-names>G.</given-names></name><name><surname>Tu</surname><given-names>J.</given-names></name><name><surname>Xing</surname><given-names>Y.</given-names></name><name><surname>Wang</surname><given-names>Y.</given-names></name><name><surname>Chen</surname><given-names>Z.</given-names></name></person-group> (<year>2014</year>) <article-title>Proteolytic
processing, deubiquitinase and interferon antagonist activities of Middle
East respiratory syndrome coronavirus papain-like protease</article-title>.
<source>J. Gen. Virol</source>. <volume>95</volume>,
<fpage>614</fpage>–<lpage>626</lpage><pub-id pub-id-type="pmid">24362959</pub-id></mixed-citation></ref><ref id="B10"><label>10.</label><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Kilianski</surname><given-names>A.</given-names></name><name><surname>Mielech</surname><given-names>A. M.</given-names></name><name><surname>Deng</surname><given-names>X.</given-names></name><name><surname>Baker</surname><given-names>S. C.</given-names></name></person-group> (<year>2013</year>) <article-title>Assessing activity
and inhibition of Middle East respiratory syndrome coronavirus papain-like
and 3C-like proteases using luciferase-based biosensors</article-title>.
<source>J. Virol</source>. <volume>87</volume>,
<fpage>11955</fpage>–<lpage>11962</lpage><pub-id pub-id-type="pmid">23986593</pub-id></mixed-citation></ref><ref id="B11"><label>11.</label><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Komander</surname><given-names>D.</given-names></name><name><surname>Rape</surname><given-names>M.</given-names></name></person-group> (<year>2012</year>) <article-title>The ubiquitin
code</article-title>. <source>Annu. Rev. Biochem</source>.
<volume>81</volume>, <fpage>203</fpage>–<lpage>229</lpage><pub-id pub-id-type="pmid">22524316</pub-id></mixed-citation></ref><ref id="B12"><label>12.</label><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Komander</surname><given-names>D.</given-names></name><name><surname>Clague</surname><given-names>M. J.</given-names></name><name><surname>Urbé</surname><given-names>S.</given-names></name></person-group> (<year>2009</year>) <article-title>Breaking the
chains: structure and function of the deubiquitinases</article-title>.
<source>Nat. Rev. Mol. Cell Biol</source>. <volume>10</volume>,
<fpage>550</fpage>–<lpage>563</lpage><pub-id pub-id-type="pmid">19626045</pub-id></mixed-citation></ref><ref id="B13"><label>13.</label><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Frieman</surname><given-names>M.</given-names></name><name><surname>Ratia</surname><given-names>K.</given-names></name><name><surname>Johnston</surname><given-names>R. E.</given-names></name><name><surname>Mesecar</surname><given-names>A. D.</given-names></name><name><surname>Baric</surname><given-names>R. S.</given-names></name></person-group> (<year>2009</year>) <article-title>Severe acute
respiratory syndrome coronavirus papain-like protease ubiquitin-like domain
and catalytic domain regulate antagonism of IRF3 and NF-κB
signaling</article-title>. <source>J. Virol</source>. <volume>83</volume>,
<fpage>6689</fpage>–<lpage>6705</lpage><pub-id pub-id-type="pmid">19369340</pub-id></mixed-citation></ref><ref id="B14"><label>14.</label><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Barretto</surname><given-names>N.</given-names></name><name><surname>Jukneliene</surname><given-names>D.</given-names></name><name><surname>Ratia</surname><given-names>K.</given-names></name><name><surname>Chen</surname><given-names>Z.</given-names></name><name><surname>Mesecar</surname><given-names>A. D.</given-names></name><name><surname>Baker</surname><given-names>S. C.</given-names></name></person-group> (<year>2005</year>) <article-title>The papain-like
protease of severe acute respiratory syndrome coronavirus has
deubiquitinating activity</article-title>. <source>J. Virol</source>.
<volume>79</volume>,
<fpage>15189</fpage>–<lpage>15198</lpage><pub-id pub-id-type="pmid">16306590</pub-id></mixed-citation></ref><ref id="B15"><label>15.</label><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Clementz</surname><given-names>M. A.</given-names></name><name><surname>Chen</surname><given-names>Z.</given-names></name><name><surname>Banach</surname><given-names>B. S.</given-names></name><name><surname>Wang</surname><given-names>Y.</given-names></name><name><surname>Sun</surname><given-names>L.</given-names></name><name><surname>Ratia</surname><given-names>K.</given-names></name><name><surname>Baez-Santos</surname><given-names>Y. M.</given-names></name><name><surname>Wang</surname><given-names>J.</given-names></name><name><surname>Takayama</surname><given-names>J.</given-names></name><name><surname>Ghosh</surname><given-names>A. K.</given-names></name><name><surname>Li</surname><given-names>K.</given-names></name><name><surname>Mesecar</surname><given-names>A. D.</given-names></name><name><surname>Baker</surname><given-names>S. C.</given-names></name></person-group> (<year>2010</year>) <article-title>Deubiquitinating
and interferon antagonism activities of coronavirus papain-like
proteases</article-title>. <source>J. Virol</source>. <volume>84</volume>,
<fpage>4619</fpage>–<lpage>4629</lpage><pub-id pub-id-type="pmid">20181693</pub-id></mixed-citation></ref><ref id="B16"><label>16.</label><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Mielech</surname><given-names>A. M.</given-names></name><name><surname>Kilianski</surname><given-names>A.</given-names></name><name><surname>Baez-Santos</surname><given-names>Y. M.</given-names></name><name><surname>Mesecar</surname><given-names>A. D.</given-names></name><name><surname>Baker</surname><given-names>S. C.</given-names></name></person-group> (<year>2014</year>) <article-title>MERS-CoV
papain-like protease has deISGylating and deubiquitinating
activities</article-title>. <source>Virology</source><volume>450</volume>, <fpage>64</fpage>–<lpage>70</lpage><pub-id pub-id-type="pmid">24503068</pub-id></mixed-citation></ref><ref id="B17"><label>17.</label><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Lindner</surname><given-names>H. A.</given-names></name><name><surname>Fotouhi-Ardakani</surname><given-names>N.</given-names></name><name><surname>Lytvyn</surname><given-names>V.</given-names></name><name><surname>Lachance</surname><given-names>P.</given-names></name><name><surname>Sulea</surname><given-names>T.</given-names></name><name><surname>Ménard</surname><given-names>R.</given-names></name></person-group> (<year>2005</year>) <article-title>The papain-like
protease from the severe acute respiratory syndrome coronavirus is a
deubiquitinating enzyme</article-title>. <source>J. Virol</source>.
<volume>79</volume>,
<fpage>15199</fpage>–<lpage>15208</lpage><pub-id pub-id-type="pmid">16306591</pub-id></mixed-citation></ref><ref id="B18"><label>18.</label><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Lindner</surname><given-names>H. A.</given-names></name><name><surname>Lytvyn</surname><given-names>V.</given-names></name><name><surname>Qi</surname><given-names>H.</given-names></name><name><surname>Lachance</surname><given-names>P.</given-names></name><name><surname>Ziomek</surname><given-names>E.</given-names></name><name><surname>Ménard</surname><given-names>R.</given-names></name></person-group> (<year>2007</year>) <article-title>Selectivity in
ISG15 and ubiquitin recognition by the SARS coronavirus papain-like
protease</article-title>. <source>Arch. Biochem. Biophys</source>.
<volume>466</volume>, <fpage>8</fpage>–<lpage>14</lpage><pub-id pub-id-type="pmid">17692280</pub-id></mixed-citation></ref><ref id="B19"><label>19.</label><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Mielech</surname><given-names>A. M.</given-names></name><name><surname>Chen</surname><given-names>Y.</given-names></name><name><surname>Mesecar</surname><given-names>A. D.</given-names></name><name><surname>Baker</surname><given-names>S. C.</given-names></name></person-group> (<year>2014</year>) <article-title>Nidovirus
papain-like proteases: Multifunctional enzymes with protease,
deubiquitinating and deISGylating activities</article-title>. <source>Virus
Res</source>. <pub-id pub-id-type="doi">10.1016/j.virusres.2014.01.025</pub-id></mixed-citation></ref><ref id="B20"><label>20.</label><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Jensen</surname><given-names>S.</given-names></name><name><surname>Thomsen</surname><given-names>A. R.</given-names></name></person-group> (<year>2012</year>) <article-title>Sensing of RNA
viruses: a review of innate immune receptors involved in recognizing RNA
virus invasion</article-title>. <source>J. Virol</source>.
<volume>86</volume>, <fpage>2900</fpage>–<lpage>2910</lpage><pub-id pub-id-type="pmid">22258243</pub-id></mixed-citation></ref><ref id="B21"><label>21.</label><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Goubau</surname><given-names>D.</given-names></name><name><surname>Schlee</surname><given-names>M.</given-names></name><name><surname>Deddouche</surname><given-names>S.</given-names></name><name><surname>Pruijssers</surname><given-names>A. J.</given-names></name><name><surname>Zillinger</surname><given-names>T.</given-names></name><name><surname>Goldeck</surname><given-names>M.</given-names></name><name><surname>Schuberth</surname><given-names>C.</given-names></name><name><surname>Van der Veen</surname><given-names>A. G.</given-names></name><name><surname>Fujimura</surname><given-names>T.</given-names></name><name><surname>Rehwinkel</surname><given-names>J.</given-names></name><name><surname>Iskarpatyoti</surname><given-names>J. A.</given-names></name><name><surname>Barchet</surname><given-names>W.</given-names></name><name><surname>Ludwig</surname><given-names>J.</given-names></name><name><surname>Dermody</surname><given-names>T. S.</given-names></name><name><surname>Hartmann</surname><given-names>G.</given-names></name><name><surname>Sousa</surname><given-names>C. R.</given-names></name></person-group> (<year>2014</year>) <article-title>Antiviral immunity
via RIG-I-mediated recognition of RNA bearing
5′-diphosphates</article-title>. <source>Nature</source><pub-id pub-id-type="doi">10.1038/nature13590</pub-id></mixed-citation></ref><ref id="B22"><label>22.</label><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Jiang</surname><given-names>X.</given-names></name><name><surname>Chen</surname><given-names>Z. J.</given-names></name></person-group> (<year>2012</year>) <article-title>The role of
ubiquitylation in immune defence and pathogen evasion</article-title>.
<source>Nat. Rev. Immunol</source>. <volume>12</volume>,
<fpage>35</fpage>–<lpage>48</lpage><pub-id pub-id-type="pmid">22158412</pub-id></mixed-citation></ref><ref id="B23"><label>23.</label><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Devaraj</surname><given-names>S. G.</given-names></name><name><surname>Wang</surname><given-names>N.</given-names></name><name><surname>Chen</surname><given-names>Z.</given-names></name><name><surname>Chen</surname><given-names>Z.</given-names></name><name><surname>Tseng</surname><given-names>M.</given-names></name><name><surname>Barretto</surname><given-names>N.</given-names></name><name><surname>Lin</surname><given-names>R.</given-names></name><name><surname>Peters</surname><given-names>C. J.</given-names></name><name><surname>Tseng</surname><given-names>C.-T. K.</given-names></name><name><surname>Baker</surname><given-names>S. C.</given-names></name><name><surname>Li</surname><given-names>K.</given-names></name></person-group> (<year>2007</year>) <article-title>Regulation of
IRF-3-dependent innate immunity by the papain-like protease domain of the
severe acute respiratory syndrome coronavirus</article-title>. <source>J.
Biol. Chem</source>. <volume>282</volume>,
<fpage>32208</fpage>–<lpage>32221</lpage><pub-id pub-id-type="pmid">17761676</pub-id></mixed-citation></ref><ref id="B24"><label>24.</label><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Spiegel</surname><given-names>M.</given-names></name><name><surname>Pichlmair</surname><given-names>A.</given-names></name><name><surname>Martínez-Sobrido</surname><given-names>L.</given-names></name><name><surname>Cros</surname><given-names>J.</given-names></name><name><surname>García-Sastre</surname><given-names>A.</given-names></name><name><surname>Haller</surname><given-names>O.</given-names></name><name><surname>Weber</surname><given-names>F.</given-names></name></person-group> (<year>2005</year>) <article-title>Inhibition of
β interferon induction by severe acute respiratory syndrome
coronavirus suggests a two-step model for activation of interferon
regulatory factor 3</article-title>. <source>J. Virol</source>.
<volume>79</volume>, <fpage>2079</fpage>–<lpage>2086</lpage><pub-id pub-id-type="pmid">15681410</pub-id></mixed-citation></ref><ref id="B25"><label>25.</label><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Spiegel</surname><given-names>M.</given-names></name><name><surname>Weber</surname><given-names>F.</given-names></name></person-group> (<year>2006</year>) <article-title>Inhibition of
cytokine gene expression and induction of chemokine genes in non-lymphatic
cells infected with SARS coronavirus</article-title>. <source>Virol.
J</source>. <volume>3</volume>,
<fpage>17</fpage>–<lpage>17</lpage><pub-id pub-id-type="pmid">16571117</pub-id></mixed-citation></ref><ref id="B26"><label>26.</label><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Cheung</surname><given-names>C. Y.</given-names></name><name><surname>Poon</surname><given-names>L. L. M.</given-names></name><name><surname>Ng</surname><given-names>I. H. Y.</given-names></name><name><surname>Luk</surname><given-names>W.</given-names></name><name><surname>Sia</surname><given-names>S.-F.</given-names></name><name><surname>Wu</surname><given-names>M. H. S.</given-names></name><name><surname>Chan</surname><given-names>K.-H.</given-names></name><name><surname>Yuen</surname><given-names>K.-Y.</given-names></name><name><surname>Gordon</surname><given-names>S.</given-names></name><name><surname>Guan</surname><given-names>Y.</given-names></name><name><surname>Peiris</surname><given-names>J. S. M.</given-names></name></person-group> (<year>2005</year>) <article-title>Cytokine responses
in severe acute respiratory syndrome coronavirus-infected macrophages
<italic>in vitro</italic>: possible relevance to
pathogenesis</article-title>. <source>J. Virol</source>.
<volume>79</volume>, <fpage>7819</fpage>–<lpage>7826</lpage><pub-id pub-id-type="pmid">15919935</pub-id></mixed-citation></ref><ref id="B27"><label>27.</label><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Chu</surname><given-names>H.</given-names></name><name><surname>Zhou</surname><given-names>J.</given-names></name><name><surname>Ho-Yin Wong</surname><given-names>B.</given-names></name><name><surname>Li</surname><given-names>C.</given-names></name><name><surname>Cheng</surname><given-names>Z.-S.</given-names></name><name><surname>Lin</surname><given-names>X.</given-names></name><name><surname>Kwok-Man Poon</surname><given-names>V.</given-names></name><name><surname>Sun</surname><given-names>T.</given-names></name><name><surname>Choi-Yi Lau</surname><given-names>C.</given-names></name><name><surname>Fuk-Woo Chan</surname><given-names>J.</given-names></name><name><surname>Kai-Wang To</surname><given-names>K.</given-names></name><name><surname>Chan</surname><given-names>K.-H.</given-names></name><name><surname>Lu</surname><given-names>L.</given-names></name><name><surname>Zheng</surname><given-names>B.-J.</given-names></name><name><surname>Yuen</surname><given-names>K.-Y.</given-names></name></person-group> (<year>2014</year>) <article-title>Productive
replication of Middle East respiratory syndrome coronavirus in
monocyte-derived dendritic cells modulates innate immune
response</article-title>. <source>Virology</source><volume>454</volume>, <fpage>197</fpage>–<lpage>205</lpage><pub-id pub-id-type="pmid">24725946</pub-id></mixed-citation></ref><ref id="B28"><label>28.</label><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Chan</surname><given-names>R. W. Y.</given-names></name><name><surname>Chan</surname><given-names>M. C. W.</given-names></name><name><surname>Agnihothram</surname><given-names>S.</given-names></name><name><surname>Chan</surname><given-names>L. L. Y.</given-names></name><name><surname>Kuok</surname><given-names>D. I. T.</given-names></name><name><surname>Fong</surname><given-names>J. H. M.</given-names></name><name><surname>Guan</surname><given-names>Y.</given-names></name><name><surname>Poon</surname><given-names>L. L. M.</given-names></name><name><surname>Baric</surname><given-names>R. S.</given-names></name><name><surname>Nicholls</surname><given-names>J. M.</given-names></name><name><surname>Peiris</surname><given-names>J. S. M.</given-names></name></person-group> (<year>2013</year>) <article-title>Tropism of and
innate immune responses to the novel human betacoronavirus lineage C virus
in human <italic>ex vivo</italic> respiratory organ
cultures</article-title>. <source>J. Virol</source>. <volume>87</volume>,
<fpage>6604</fpage>–<lpage>6614</lpage><pub-id pub-id-type="pmid">23552422</pub-id></mixed-citation></ref><ref id="B29"><label>29.</label><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Lau</surname><given-names>S. K.</given-names></name><name><surname>Lau</surname><given-names>C. C.</given-names></name><name><surname>Chan</surname><given-names>K. H.</given-names></name><name><surname>Li</surname><given-names>C. P.</given-names></name><name><surname>Chen</surname><given-names>H.</given-names></name><name><surname>Jin</surname><given-names>D. Y.</given-names></name><name><surname>Chan</surname><given-names>J. F.</given-names></name><name><surname>Woo</surname><given-names>P. C.</given-names></name><name><surname>Yuen</surname><given-names>K. Y.</given-names></name></person-group> (<year>2013</year>) <article-title>Delayed induction
of proinflammatory cytokines and suppression of innate antiviral response by
the novel Middle East respiratory syndrome coronavirus: implications for
pathogenesis and treatment</article-title>. <source>J. Gen. Virol</source>.
<volume>94</volume>, <fpage>2679</fpage>–<lpage>2690</lpage><pub-id pub-id-type="pmid">24077366</pub-id></mixed-citation></ref><ref id="B30"><label>30.</label><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>van Kasteren</surname><given-names>P. B.</given-names></name><name><surname>Beugeling</surname><given-names>C.</given-names></name><name><surname>Ninaber</surname><given-names>D. K.</given-names></name><name><surname>Frias-Staheli</surname><given-names>N.</given-names></name><name><surname>van Boheemen</surname><given-names>S.</given-names></name><name><surname>García-Sastre</surname><given-names>A.</given-names></name><name><surname>Snijder</surname><given-names>E. J.</given-names></name><name><surname>Kikkert</surname><given-names>M.</given-names></name></person-group> (<year>2012</year>) <article-title>Arterivirus and
nairovirus ovarian tumor domain-containing Deubiquitinases target activated
RIG-I to control innate immune signaling</article-title>. <source>J.
Virol</source>. <volume>86</volume>,
<fpage>773</fpage>–<lpage>785</lpage><pub-id pub-id-type="pmid">22072774</pub-id></mixed-citation></ref><ref id="B31"><label>31.</label><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>te Velthuis</surname><given-names>A. J.</given-names></name><name><surname>Arnold</surname><given-names>J. J.</given-names></name><name><surname>Cameron</surname><given-names>C. E.</given-names></name><name><surname>van den Worm</surname><given-names>S. H.</given-names></name><name><surname>Snijder</surname><given-names>E. J.</given-names></name></person-group> (<year>2010</year>) <article-title>The RNA polymerase
activity of SARS-coronavirus nsp12 is primer dependent</article-title>.
<source>Nucleic Acids Res</source>. <volume>38</volume>,
<fpage>203</fpage>–<lpage>214</lpage><pub-id pub-id-type="pmid">19875418</pub-id></mixed-citation></ref><ref id="B32"><label>32.</label><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Gack</surname><given-names>M. U.</given-names></name><name><surname>Albrecht</surname><given-names>R. A.</given-names></name><name><surname>Urano</surname><given-names>T.</given-names></name><name><surname>Inn</surname><given-names>K. S.</given-names></name><name><surname>Huang</surname><given-names>I. C.</given-names></name><name><surname>Carnero</surname><given-names>E.</given-names></name><name><surname>Farzan</surname><given-names>M.</given-names></name><name><surname>Inoue</surname><given-names>S.</given-names></name><name><surname>Jung</surname><given-names>J. U.</given-names></name><name><surname>García-Sastre</surname><given-names>A.</given-names></name></person-group> (<year>2009</year>) <article-title>Influenza A virus
NS1 targets the ubiquitin ligase TRIM25 to evade recognition by the host
viral RNA sensor RIG-I</article-title>. <source>Cell Host Microbe</source><volume>5</volume>, <fpage>439</fpage>–<lpage>449</lpage><pub-id pub-id-type="pmid">19454348</pub-id></mixed-citation></ref><ref id="B33"><label>33.</label><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Fitzgerald</surname><given-names>K. A.</given-names></name><name><surname>McWhirter</surname><given-names>S. M.</given-names></name><name><surname>Faia</surname><given-names>K. L.</given-names></name><name><surname>Rowe</surname><given-names>D. C.</given-names></name><name><surname>Latz</surname><given-names>E.</given-names></name><name><surname>Golenbock</surname><given-names>D. T.</given-names></name><name><surname>Coyle</surname><given-names>A. J.</given-names></name><name><surname>Liao</surname><given-names>S. M.</given-names></name><name><surname>Maniatis</surname><given-names>T.</given-names></name></person-group> (<year>2003</year>) <article-title>IKKϵ and
TBK1 are essential components of the IRF3 signaling pathway</article-title>.
<source>Nat. Immunol</source>. <volume>4</volume>,
<fpage>491</fpage>–<lpage>496</lpage><pub-id pub-id-type="pmid">12692549</pub-id></mixed-citation></ref><ref id="B34"><label>34.</label><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Gack</surname><given-names>M. U.</given-names></name><name><surname>Shin</surname><given-names>Y. C.</given-names></name><name><surname>Joo</surname><given-names>C. H.</given-names></name><name><surname>Urano</surname><given-names>T.</given-names></name><name><surname>Liang</surname><given-names>C.</given-names></name><name><surname>Sun</surname><given-names>L.</given-names></name><name><surname>Takeuchi</surname><given-names>O.</given-names></name><name><surname>Akira</surname><given-names>S.</given-names></name><name><surname>Chen</surname><given-names>Z.</given-names></name><name><surname>Inoue</surname><given-names>S.</given-names></name><name><surname>Jung</surname><given-names>J. U.</given-names></name></person-group> (<year>2007</year>) <article-title>TRIM25 RING-finger
E3 ubiquitin ligase is essential for RIG-I-mediated antiviral
activity</article-title>. <source>Nature</source><volume>446</volume>, <fpage>916</fpage>–<lpage>920</lpage><pub-id pub-id-type="pmid">17392790</pub-id></mixed-citation></ref><ref id="B35"><label>35.</label><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Seth</surname><given-names>R. B.</given-names></name><name><surname>Sun</surname><given-names>L.</given-names></name><name><surname>Ea</surname><given-names>C. K.</given-names></name><name><surname>Chen</surname><given-names>Z. J.</given-names></name></person-group> (<year>2005</year>) <article-title>Identification and
characterization of MAVS, a mitochondrial antiviral signaling protein that
activates NF-κB and IRF 3</article-title>. <source>Cell</source><volume>122</volume>, <fpage>669</fpage>–<lpage>682</lpage><pub-id pub-id-type="pmid">16125763</pub-id></mixed-citation></ref><ref id="B36"><label>36.</label><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Lin</surname><given-names>R.</given-names></name><name><surname>Heylbroeck</surname><given-names>C.</given-names></name><name><surname>Pitha</surname><given-names>P. M.</given-names></name><name><surname>Hiscott</surname><given-names>J.</given-names></name></person-group> (<year>1998</year>) <article-title>Virus-dependent
phosphorylation of the IRF-3 transcription factor regulates nuclear
translocation, transactivation potential, and proteasome-mediated
degradation</article-title>. <source>Mol. Cell Biol</source>.
<volume>18</volume>, <fpage>2986</fpage>–<lpage>2996</lpage><pub-id pub-id-type="pmid">9566918</pub-id></mixed-citation></ref><ref id="B37"><label>37.</label><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Gohara</surname><given-names>D. W.</given-names></name><name><surname>Ha</surname><given-names>C. S.</given-names></name><name><surname>Kumar</surname><given-names>S.</given-names></name><name><surname>Ghosh</surname><given-names>B.</given-names></name><name><surname>Arnold</surname><given-names>J. J.</given-names></name><name><surname>Wisniewski</surname><given-names>T. J.</given-names></name><name><surname>Cameron</surname><given-names>C. E.</given-names></name></person-group> (<year>1999</year>) <article-title>Production of
“authentic” poliovirus RNA-dependent RNA polymerase
(3D(pol)) by ubiquitin-protease-mediated cleavage in <italic>Escherichia
coli</italic></article-title>. <source>Protein Expr. Purif</source>.
<volume>17</volume>, <fpage>128</fpage>–<lpage>138</lpage><pub-id pub-id-type="pmid">10497078</pub-id></mixed-citation></ref><ref id="B38"><label>38.</label><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Messick</surname><given-names>T. E.</given-names></name><name><surname>Russell</surname><given-names>N. S.</given-names></name><name><surname>Iwata</surname><given-names>A. J.</given-names></name><name><surname>Sarachan</surname><given-names>K. L.</given-names></name><name><surname>Shiekhattar</surname><given-names>R.</given-names></name><name><surname>Shanks</surname><given-names>J. R.</given-names></name><name><surname>Reyes-Turcu</surname><given-names>F. E.</given-names></name><name><surname>Wilkinson</surname><given-names>K. D.</given-names></name><name><surname>Marmorstein</surname><given-names>R.</given-names></name></person-group> (<year>2008</year>) <article-title>Structural basis
for ubiquitin recognition by the Otu1 ovarian tumor domain
protein</article-title>. <source>J. Biol. Chem</source>.
<volume>283</volume>,
<fpage>11038</fpage>–<lpage>11049</lpage><pub-id pub-id-type="pmid">18270205</pub-id></mixed-citation></ref><ref id="B39"><label>39.</label><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Borodovsky</surname><given-names>A.</given-names></name><name><surname>Ovaa</surname><given-names>H.</given-names></name><name><surname>Kolli</surname><given-names>N.</given-names></name><name><surname>Gan-Erdene</surname><given-names>T.</given-names></name><name><surname>Wilkinson</surname><given-names>K. D.</given-names></name><name><surname>Ploegh</surname><given-names>H. L.</given-names></name><name><surname>Kessler</surname><given-names>B. M.</given-names></name></person-group> (<year>2002</year>) <article-title>Chemistry-based
functional proteomics reveals novel members of the deubiquitinating enzyme
family</article-title>. <source>Chem. Biol</source>. <volume>9</volume>,
<fpage>1149</fpage>–<lpage>1159</lpage><pub-id pub-id-type="pmid">12401499</pub-id></mixed-citation></ref><ref id="B40"><label>40.</label><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Kabsch</surname><given-names>W.</given-names></name></person-group> (<year>2010</year>)
<article-title>XDS</article-title>. <source>Acta Crystallogr. D Biol.
Crystallogr</source>. <volume>66</volume>,
<fpage>125</fpage>–<lpage>132</lpage><pub-id pub-id-type="pmid">20124692</pub-id></mixed-citation></ref><ref id="B41"><label>41.</label><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Evans</surname><given-names>P.</given-names></name></person-group> (<year>2006</year>) <article-title>Scaling and
assessment of data quality</article-title>. <source>Acta Crystallogr. D
Biol. Crystallogr</source>. <volume>62</volume>,
<fpage>72</fpage>–<lpage>82</lpage><pub-id pub-id-type="pmid">16369096</pub-id></mixed-citation></ref><ref id="B42"><label>42.</label><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Grosse-Kunstleve</surname><given-names>R. W.</given-names></name><name><surname>Adams</surname><given-names>P. D.</given-names></name></person-group> (<year>2003</year>) <article-title>Substructure
search procedures for macromolecular structures</article-title>.
<source>Acta Crystallogr. D Biol. Crystallogr</source>. <volume>59</volume>,
<fpage>1966</fpage>–<lpage>1973</lpage><pub-id pub-id-type="pmid">14573951</pub-id></mixed-citation></ref><ref id="B43"><label>43.</label><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Terwilliger</surname><given-names>T. C.</given-names></name></person-group> (<year>2000</year>) <article-title>Maximum-likelihood
density modification</article-title>. <source>Acta Crystallogr. D Biol.
Crystallogr</source>. <volume>56</volume>,
<fpage>965</fpage>–<lpage>972</lpage><pub-id pub-id-type="pmid">10944333</pub-id></mixed-citation></ref><ref id="B44"><label>44.</label><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Terwilliger</surname><given-names>T. C.</given-names></name><name><surname>Adams</surname><given-names>P. D.</given-names></name><name><surname>Read</surname><given-names>R. J.</given-names></name><name><surname>McCoy</surname><given-names>A. J.</given-names></name><name><surname>Moriarty</surname><given-names>N. W.</given-names></name><name><surname>Grosse-Kunstleve</surname><given-names>R. W.</given-names></name><name><surname>Afonine</surname><given-names>P. V.</given-names></name><name><surname>Zwart</surname><given-names>P. H.</given-names></name><name><surname>Hung</surname><given-names>L. W.</given-names></name></person-group> (<year>2009</year>) <article-title>Decision-making in
structure solution using Bayesian estimates of map quality: the PHENIX
AutoSol wizard</article-title>. <source>Acta Crystallogr. D Biol.
Crystallogr</source>. <volume>65</volume>,
<fpage>582</fpage>–<lpage>601</lpage><pub-id pub-id-type="pmid">19465773</pub-id></mixed-citation></ref><ref id="B45"><label>45.</label><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Emsley</surname><given-names>P.</given-names></name><name><surname>Lohkamp</surname><given-names>B.</given-names></name><name><surname>Scott</surname><given-names>W. G.</given-names></name><name><surname>Cowtan</surname><given-names>K.</given-names></name></person-group> (<year>2010</year>) <article-title>Features and
development of Coot</article-title>. <source>Acta Crystallogr. D Biol.
Crystallogr</source>. <volume>66</volume>,
<fpage>486</fpage>–<lpage>501</lpage><pub-id pub-id-type="pmid">20383002</pub-id></mixed-citation></ref><ref id="B46"><label>46.</label><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Afonine</surname><given-names>P. V.</given-names></name><name><surname>Grosse-Kunstleve</surname><given-names>R. W.</given-names></name><name><surname>Echols</surname><given-names>N.</given-names></name><name><surname>Headd</surname><given-names>J. J.</given-names></name><name><surname>Moriarty</surname><given-names>N. W.</given-names></name><name><surname>Mustyakimov</surname><given-names>M.</given-names></name><name><surname>Terwilliger</surname><given-names>T. C.</given-names></name><name><surname>Urzhumtsev</surname><given-names>A.</given-names></name><name><surname>Zwart</surname><given-names>P. H.</given-names></name><name><surname>Adams</surname><given-names>P. D.</given-names></name></person-group> (<year>2012</year>) <article-title>Towards automated
crystallographic structure refinement with phenix.refine</article-title>.
<source>Acta Crystallogr. D Biol. Crystallogr</source>. <volume>68</volume>,
<fpage>352</fpage>–<lpage>367</lpage><pub-id pub-id-type="pmid">22505256</pub-id></mixed-citation></ref><ref id="B47"><label>47.</label><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Graham</surname><given-names>F. L.</given-names></name><name><surname>van der Eb</surname><given-names>A. J.</given-names></name></person-group> (<year>1973</year>) <article-title>A new technique
for the assay of infectivity of human adenovirus 5 DNA</article-title>.
<source>Virology</source><volume>52</volume>, <fpage>456</fpage>–<lpage>467</lpage><pub-id pub-id-type="pmid">4705382</pub-id></mixed-citation></ref><ref id="B48"><label>48.</label><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Lin</surname><given-names>M. H.</given-names></name><name><surname>Chuang</surname><given-names>S. J.</given-names></name><name><surname>Chen</surname><given-names>C. C.</given-names></name><name><surname>Cheng</surname><given-names>S. C.</given-names></name><name><surname>Cheng</surname><given-names>K. W.</given-names></name><name><surname>Lin</surname><given-names>C. H.</given-names></name><name><surname>Sun</surname><given-names>C. Y.</given-names></name><name><surname>Chou</surname><given-names>C. Y.</given-names></name></person-group> (<year>2014</year>) <article-title>Structural and
functional characterization of MERS coronavirus papain-like
protease</article-title>. <source>J. Biomed. Sci</source>.
<volume>21</volume>, <fpage>54</fpage><pub-id pub-id-type="pmid">24898546</pub-id></mixed-citation></ref><ref id="B49"><label>49.</label><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Lei</surname><given-names>J.</given-names></name><name><surname>Mesters</surname><given-names>J. R.</given-names></name><name><surname>Drosten</surname><given-names>C.</given-names></name><name><surname>Anemüller</surname><given-names>S.</given-names></name><name><surname>Ma</surname><given-names>Q.</given-names></name><name><surname>Hilgenfeld</surname><given-names>R.</given-names></name></person-group> (<year>2014</year>) <article-title>Crystal structure
of the papain-like protease of MERS coronavirus reveals unusual, potentially
druggable active-site features</article-title>. <source>Antiviral
Res</source>. <volume>109</volume>,
<fpage>72</fpage>–<lpage>82</lpage><pub-id pub-id-type="pmid">24992731</pub-id></mixed-citation></ref><ref id="B50"><label>50.</label><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Báez-Santos</surname><given-names>Y. M.</given-names></name><name><surname>Mielech</surname><given-names>A. M.</given-names></name><name><surname>Deng</surname><given-names>X.</given-names></name><name><surname>Baker</surname><given-names>S.</given-names></name><name><surname>Mesecar</surname><given-names>A. D.</given-names></name></person-group> (<year>2014</year>) <article-title>Catalytic function
and substrate specificity of the PLpro domain of nsp3 from the Middle East
respiratory syndrome coronavirus (MERS-CoV)</article-title>. <source>J.
Virol</source>. <volume>88</volume>,
<fpage>12511</fpage>–<lpage>12527</lpage><pub-id pub-id-type="pmid">25142582</pub-id></mixed-citation></ref><ref id="B51"><label>51.</label><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Ratia</surname><given-names>K.</given-names></name><name><surname>Saikatendu</surname><given-names>K. S.</given-names></name><name><surname>Santarsiero</surname><given-names>B. D.</given-names></name><name><surname>Barretto</surname><given-names>N.</given-names></name><name><surname>Baker</surname><given-names>S. C.</given-names></name><name><surname>Stevens</surname><given-names>R. C.</given-names></name><name><surname>Mesecar</surname><given-names>A. D.</given-names></name></person-group> (<year>2006</year>) <article-title>Severe acute
respiratory syndrome coronavirus papain-like protease: structure of a viral
deubiquitinating enzyme</article-title>. <source>Proc. Natl. Acad. Sci.
U.S.A</source>. <volume>103</volume>,
<fpage>5717</fpage>–<lpage>5722</lpage><pub-id pub-id-type="pmid">16581910</pub-id></mixed-citation></ref><ref id="B52"><label>52.</label><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Faesen</surname><given-names>A. C.</given-names></name><name><surname>Luna-Vargas</surname><given-names>M. P.</given-names></name><name><surname>Sixma</surname><given-names>T. K.</given-names></name></person-group> (<year>2012</year>) <article-title>The role of UBL
domains in ubiquitin-specific proteases</article-title>. <source>Biochem.
Soc. Trans</source>. <volume>40</volume>,
<fpage>539</fpage>–<lpage>545</lpage><pub-id pub-id-type="pmid">22616864</pub-id></mixed-citation></ref><ref id="B53"><label>53.</label><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Rawlings</surname><given-names>N. D.</given-names></name><name><surname>Waller</surname><given-names>M.</given-names></name><name><surname>Barrett</surname><given-names>A. J.</given-names></name><name><surname>Bateman</surname><given-names>A.</given-names></name></person-group> (<year>2014</year>) <article-title>MEROPS: the
database of proteolytic enzymes, their substrates and
inhibitors</article-title>. <source>Nucleic Acids Res</source>.
<volume>42</volume>, <fpage>D503</fpage>–<lpage>D509</lpage><pub-id pub-id-type="pmid">24157837</pub-id></mixed-citation></ref><ref id="B54"><label>54.</label><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Krishna</surname><given-names>S. S.</given-names></name><name><surname>Majumdar</surname><given-names>I.</given-names></name><name><surname>Grishin</surname><given-names>N. V.</given-names></name></person-group> (<year>2003</year>) <article-title>Structural
classification of zinc fingers: survey and summary</article-title>.
<source>Nucleic Acids Res</source>. <volume>31</volume>,
<fpage>532</fpage>–<lpage>550</lpage><pub-id pub-id-type="pmid">12527760</pub-id></mixed-citation></ref><ref id="B55"><label>55.</label><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Wojdyla</surname><given-names>J. A.</given-names></name><name><surname>Manolaridis</surname><given-names>I.</given-names></name><name><surname>van Kasteren</surname><given-names>P. B.</given-names></name><name><surname>Kikkert</surname><given-names>M.</given-names></name><name><surname>Snijder</surname><given-names>E. J.</given-names></name><name><surname>Gorbalenya</surname><given-names>A. E.</given-names></name><name><surname>Tucker</surname><given-names>P. A.</given-names></name></person-group> (<year>2010</year>) <article-title>Papain-like
protease 1 from transmissible gastroenteritis virus: crystal structure and
enzymatic activity toward viral and cellular substrates</article-title>.
<source>J. Virol</source>. <volume>84</volume>,
<fpage>10063</fpage>–<lpage>10073</lpage><pub-id pub-id-type="pmid">20668092</pub-id></mixed-citation></ref><ref id="B56"><label>56.</label><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Renatus</surname><given-names>M.</given-names></name><name><surname>Parrado</surname><given-names>S. G.</given-names></name><name><surname>D'Arcy</surname><given-names>A.</given-names></name><name><surname>Eidhoff</surname><given-names>U.</given-names></name><name><surname>Gerhartz</surname><given-names>B.</given-names></name><name><surname>Hassiepen</surname><given-names>U.</given-names></name><name><surname>Pierrat</surname><given-names>B.</given-names></name><name><surname>Riedl</surname><given-names>R.</given-names></name><name><surname>Vinzenz</surname><given-names>D.</given-names></name><name><surname>Worpenberg</surname><given-names>S.</given-names></name><name><surname>Kroemer</surname><given-names>M.</given-names></name></person-group> (<year>2006</year>) <article-title>Structural basis
of ubiquitin recognition by the deubiquitinating protease
USP2</article-title>. <source>Structure</source><volume>14</volume>, <fpage>1293</fpage>–<lpage>1302</lpage><pub-id pub-id-type="pmid">16905103</pub-id></mixed-citation></ref><ref id="B57"><label>57.</label><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Ye</surname><given-names>Y.</given-names></name><name><surname>Akutsu</surname><given-names>M.</given-names></name><name><surname>Reyes-Turcu</surname><given-names>F.</given-names></name><name><surname>Enchev</surname><given-names>R. I.</given-names></name><name><surname>Wilkinson</surname><given-names>K. D.</given-names></name><name><surname>Komander</surname><given-names>D.</given-names></name></person-group> (<year>2011</year>) <article-title>Polyubiquitin
binding and cross-reactivity in the USP domain deubiquitinase
USP21</article-title>. <source>EMBO Rep</source>. <volume>12</volume>,
<fpage>350</fpage>–<lpage>357</lpage><pub-id pub-id-type="pmid">21399617</pub-id></mixed-citation></ref><ref id="B58"><label>58.</label><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Chou</surname><given-names>C. Y.</given-names></name><name><surname>Lai</surname><given-names>H. Y.</given-names></name><name><surname>Chen</surname><given-names>H. Y.</given-names></name><name><surname>Cheng</surname><given-names>S. C.</given-names></name><name><surname>Cheng</surname><given-names>K. W.</given-names></name><name><surname>Chou</surname><given-names>Y. W.</given-names></name></person-group> (<year>2014</year>) <article-title>Structural basis
for catalysis and ubiquitin recognition by the severe acute respiratory
syndrome coronavirus papain-like protease</article-title>. <source>Acta
Crystallogr. D Biol. Crystallogr</source>. <volume>70</volume>,
<fpage>572</fpage>–<lpage>581</lpage><pub-id pub-id-type="pmid">24531491</pub-id></mixed-citation></ref><ref id="B59"><label>59.</label><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Hu</surname><given-names>M.</given-names></name><name><surname>Li</surname><given-names>P.</given-names></name><name><surname>Song</surname><given-names>L.</given-names></name><name><surname>Jeffrey</surname><given-names>P. D.</given-names></name><name><surname>Chenova</surname><given-names>T. A.</given-names></name><name><surname>Wilkinson</surname><given-names>K. D.</given-names></name><name><surname>Cohen</surname><given-names>R. E.</given-names></name><name><surname>Shi</surname><given-names>Y.</given-names></name></person-group> (<year>2005</year>) <article-title>Structure and
mechanisms of the proteasome-associated deubiquitinating enzyme
USP14</article-title>. <source>EMBO J</source>. <volume>24</volume>,
<fpage>3747</fpage>–<lpage>3756</lpage><pub-id pub-id-type="pmid">16211010</pub-id></mixed-citation></ref><ref id="B60"><label>60.</label><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Bailey-Elkin</surname><given-names>B. A.</given-names></name><name><surname>van Kasteren</surname><given-names>P. B.</given-names></name><name><surname>Snijder</surname><given-names>E. J.</given-names></name><name><surname>Kikkert</surname><given-names>M.</given-names></name><name><surname>Mark</surname><given-names>B. L.</given-names></name></person-group> (<year>2014</year>) <article-title>Viral OTU
deubiquitinases: a structural and functional comparison</article-title>.
<source>PLoS Pathog</source>. <volume>10</volume>,
<fpage>e1003894</fpage><pub-id pub-id-type="pmid">24676359</pub-id></mixed-citation></ref><ref id="B61"><label>61.</label><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>van Kasteren</surname><given-names>P. B.</given-names></name><name><surname>Bailey-Elkin</surname><given-names>B. A.</given-names></name><name><surname>James</surname><given-names>T. W.</given-names></name><name><surname>Ninaber</surname><given-names>D. K.</given-names></name><name><surname>Beugeling</surname><given-names>C.</given-names></name><name><surname>Khajehpour</surname><given-names>M.</given-names></name><name><surname>Snijder</surname><given-names>E. J.</given-names></name><name><surname>Mark</surname><given-names>B. L.</given-names></name><name><surname>Kikkert</surname><given-names>M.</given-names></name></person-group> (<year>2013</year>) <article-title>Deubiquitinase
function of arterivirus papain-like protease 2 suppresses the innate immune
response in infected host cells</article-title>. <source>Proc. Natl. Acad.
Sci. U.S.A</source>. <volume>110</volume>,
<fpage>E838</fpage>–<lpage>E847</lpage><pub-id pub-id-type="pmid">23401522</pub-id></mixed-citation></ref><ref id="B62"><label>62.</label><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Ratia</surname><given-names>K.</given-names></name><name><surname>Kilianski</surname><given-names>A.</given-names></name><name><surname>Baez-Santos</surname><given-names>Y. M.</given-names></name><name><surname>Baker</surname><given-names>S. C.</given-names></name><name><surname>Mesecar</surname><given-names>A.</given-names></name></person-group> (<year>2014</year>) <article-title>Structural basis
for the ubiquitin-linkage specificity and deISGylating activity of SARS-CoV
papain-like protease</article-title>. <source>PLoS Pathog</source>.
<volume>10</volume>, <fpage>e1004113</fpage><pub-id pub-id-type="pmid">24854014</pub-id></mixed-citation></ref><ref id="B63"><label>63.</label><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Dikic</surname><given-names>I.</given-names></name><name><surname>Wakatsuki</surname><given-names>S.</given-names></name><name><surname>Walters</surname><given-names>K. J.</given-names></name></person-group> (<year>2009</year>) <article-title>Ubiquitin-binding
domains: from structures to functions</article-title>. <source>Nat. Rev.
Mol. Cell Biol</source>. <volume>10</volume>,
<fpage>659</fpage>–<lpage>671</lpage><pub-id pub-id-type="pmid">19773779</pub-id></mixed-citation></ref><ref id="B64"><label>64.</label><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Eletr</surname><given-names>Z. M.</given-names></name><name><surname>Wilkinson</surname><given-names>K. D.</given-names></name></person-group> (<year>2014</year>) <article-title>Regulation of
proteolysis by human deubiquitinating enzymes</article-title>.
<source>Biochim. Biophys. Acta</source><volume>1843</volume>, <fpage>114</fpage>–<lpage>128</lpage><pub-id pub-id-type="pmid">23845989</pub-id></mixed-citation></ref><ref id="B65"><label>65.</label><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Sun</surname><given-names>Z.</given-names></name><name><surname>Chen</surname><given-names>Z.</given-names></name><name><surname>Lawson</surname><given-names>S. R.</given-names></name><name><surname>Fang</surname><given-names>Y.</given-names></name></person-group> (<year>2010</year>) <article-title>The cysteine
protease domain of porcine reproductive and respiratory syndrome virus
nonstructural protein 2 possesses deubiquitinating and interferon antagonism
functions</article-title>. <source>J. Virol</source>. <volume>84</volume>,
<fpage>7832</fpage>–<lpage>7846</lpage><pub-id pub-id-type="pmid">20504922</pub-id></mixed-citation></ref><ref id="B66"><label>66.</label><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Zheng</surname><given-names>D.</given-names></name><name><surname>Chen</surname><given-names>G.</given-names></name><name><surname>Guo</surname><given-names>B.</given-names></name><name><surname>Cheng</surname><given-names>G.</given-names></name><name><surname>Tang</surname><given-names>H.</given-names></name></person-group> (<year>2008</year>) <article-title>PLP2, a potent
deubiquitinase from murine hepatitis virus, strongly inhibits cellular type
I interferon production</article-title>. <source>Cell Res</source>.
<volume>18</volume>, <fpage>1105</fpage>–<lpage>1113</lpage><pub-id pub-id-type="pmid">18957937</pub-id></mixed-citation></ref><ref id="B67"><label>67.</label><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Xing</surname><given-names>Y.</given-names></name><name><surname>Chen</surname><given-names>J.</given-names></name><name><surname>Tu</surname><given-names>J.</given-names></name><name><surname>Zhang</surname><given-names>B.</given-names></name><name><surname>Chen</surname><given-names>X.</given-names></name><name><surname>Shi</surname><given-names>H.</given-names></name><name><surname>Baker</surname><given-names>S. C.</given-names></name><name><surname>Feng</surname><given-names>L.</given-names></name><name><surname>Chen</surname><given-names>Z.</given-names></name></person-group> (<year>2013</year>) <article-title>The papain-like
protease of porcine epidemic diarrhea virus negatively regulates type I
interferon pathway by acting as a viral deubiquitinase</article-title>.
<source>J. Gen. Virol</source>. <volume>94</volume>,
<fpage>1554</fpage>–<lpage>1567</lpage><pub-id pub-id-type="pmid">23596270</pub-id></mixed-citation></ref><ref id="B68"><label>68.</label><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Randow</surname><given-names>F.</given-names></name><name><surname>Lehner</surname><given-names>P. J.</given-names></name></person-group> (<year>2009</year>) <article-title>Viral avoidance
and exploitation of the ubiquitin system</article-title>. <source>Nat. Cell
Biol</source>. <volume>11</volume>,
<fpage>527</fpage>–<lpage>534</lpage><pub-id pub-id-type="pmid">19404332</pub-id></mixed-citation></ref><ref id="B69"><label>69.</label><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Hadari</surname><given-names>T.</given-names></name><name><surname>Warms</surname><given-names>J. V.</given-names></name><name><surname>Rose</surname><given-names>I. A.</given-names></name><name><surname>Hershko</surname><given-names>A.</given-names></name></person-group> (<year>1992</year>) <article-title>A ubiquitin
C-terminal isopeptidase that acts on polyubiquitin chains: role in protein
degradation</article-title>. <source>J. Biol. Chem</source>.
<volume>267</volume>, <fpage>719</fpage>–<lpage>727</lpage><pub-id pub-id-type="pmid">1309773</pub-id></mixed-citation></ref><ref id="B70"><label>70.</label><mixed-citation publication-type="book"><person-group person-group-type="author"><name><surname>DeLano</surname><given-names>W. L.</given-names></name></person-group> (<year>2010</year>) <source>The PyMOL Molecular
Graphics System</source>, <comment>version 1.3r1</comment>,
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New York</publisher-loc></mixed-citation></ref></ref-list></back></pmc></record>Pour manipuler ce document sous Unix (Dilib)
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