Structural basis for catalysis and ubiquitin recognition by the severe acute respiratory syndrome coronavirus papain-like protease.
Identifieur interne : 001045 ( PubMed/Corpus ); précédent : 001044; suivant : 001046Structural basis for catalysis and ubiquitin recognition by the severe acute respiratory syndrome coronavirus papain-like protease.
Auteurs : Chi-Yuan Chou ; Hsing-Yi Lai ; Hung-Yi Chen ; Shu-Chun Cheng ; Kai-Wen Cheng ; Ya-Wen ChouSource :
- Acta crystallographica. Section D, Biological crystallography [ 1399-0047 ] ; 2014.
English descriptors
- KwdEn :
- Amino Acid Sequence, Binding Sites, Biocatalysis, Crystallography, X-Ray, Escherichia coli (genetics), Escherichia coli (metabolism), Hydrophobic and Hydrophilic Interactions, Kinetics, Models, Molecular, Molecular Sequence Data, Mutation, Papain (chemistry), Papain (genetics), Papain (metabolism), Protein Structure, Secondary, Protein Structure, Tertiary, Proteolysis, SARS Virus (chemistry), SARS Virus (enzymology), Sequence Alignment, Sequence Homology, Amino Acid, Substrate Specificity, Taurine (analogs & derivatives), Taurine (chemistry), Taurine (metabolism), Ubiquitin (chemistry), Ubiquitin (genetics), Ubiquitin (metabolism), Viral Proteins (chemistry), Viral Proteins (genetics), Viral Proteins (metabolism).
- MESH :
- chemical , analogs & derivatives : Taurine.
- chemical , chemistry : Papain, Taurine, Ubiquitin, Viral Proteins.
- chemistry : SARS Virus.
- enzymology : SARS Virus.
- genetics : Escherichia coli, Papain, Ubiquitin, Viral Proteins.
- metabolism : Escherichia coli, Papain, Taurine, Ubiquitin, Viral Proteins.
- Amino Acid Sequence, Binding Sites, Biocatalysis, Crystallography, X-Ray, Hydrophobic and Hydrophilic Interactions, Kinetics, Models, Molecular, Molecular Sequence Data, Mutation, Protein Structure, Secondary, Protein Structure, Tertiary, Proteolysis, Sequence Alignment, Sequence Homology, Amino Acid, Substrate Specificity.
Abstract
Papain-like protease (PLpro) is one of two cysteine proteases involved in the proteolytic processing of the polyproteins of Severe acute respiratory syndrome coronavirus (SARS-CoV). PLpro also shows significant in vitro deubiquitinating and de-ISGylating activities, although the detailed mechanism is still unclear. Here, the crystal structure of SARS-CoV PLpro C112S mutant in complex with ubiquitin (Ub) is reported at 1.4 Å resolution. The Ub core makes mostly hydrophilic interactions with PLpro, while the Leu-Arg-Gly-Gly C-terminus of Ub is located in the catalytic cleft of PLpro, mimicking the P4-P1 residues and providing the first atomic insights into its catalysis. One of the O atoms of the C-terminal Gly residue of Ub is located in the oxyanion hole consisting of the main-chain amides of residues 112 and 113. Mutations of residues in the PLpro-Ub interface lead to reduced catalytic activity, confirming their importance for Ub binding and/or catalysis. The structure also revealed an N-cyclohexyl-2-aminethanesulfonic acid molecule near the catalytic triad, and kinetic studies suggest that this binding site is also used by other PLpro inhibitors. Overall, the structure provides a foundation for understanding the molecular basis of coronaviral PLpro catalysis.
DOI: 10.1107/S1399004713031040
PubMed: 24531491
Links to Exploration step
pubmed:24531491Le document en format XML
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Section D, Biological crystallography</title><idno type="eISSN">1399-0047</idno><imprint><date when="2014" type="published">2014</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Amino Acid Sequence</term><term>Binding Sites</term><term>Biocatalysis</term><term>Crystallography, X-Ray</term><term>Escherichia coli (genetics)</term><term>Escherichia coli (metabolism)</term><term>Hydrophobic and Hydrophilic Interactions</term><term>Kinetics</term><term>Models, Molecular</term><term>Molecular Sequence Data</term><term>Mutation</term><term>Papain (chemistry)</term><term>Papain (genetics)</term><term>Papain (metabolism)</term><term>Protein Structure, Secondary</term><term>Protein Structure, Tertiary</term><term>Proteolysis</term><term>SARS Virus (chemistry)</term><term>SARS Virus (enzymology)</term><term>Sequence Alignment</term><term>Sequence Homology, Amino Acid</term><term>Substrate Specificity</term><term>Taurine (analogs & derivatives)</term><term>Taurine (chemistry)</term><term>Taurine (metabolism)</term><term>Ubiquitin (chemistry)</term><term>Ubiquitin (genetics)</term><term>Ubiquitin (metabolism)</term><term>Viral Proteins (chemistry)</term><term>Viral Proteins (genetics)</term><term>Viral Proteins (metabolism)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="analogs & derivatives" xml:lang="en"><term>Taurine</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>Papain</term><term>Taurine</term><term>Ubiquitin</term><term>Viral Proteins</term></keywords><keywords scheme="MESH" qualifier="chemistry" xml:lang="en"><term>SARS Virus</term></keywords><keywords scheme="MESH" qualifier="enzymology" xml:lang="en"><term>SARS Virus</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Escherichia coli</term><term>Papain</term><term>Ubiquitin</term><term>Viral Proteins</term></keywords><keywords scheme="MESH" qualifier="metabolism" xml:lang="en"><term>Escherichia coli</term><term>Papain</term><term>Taurine</term><term>Ubiquitin</term><term>Viral Proteins</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Amino Acid Sequence</term><term>Binding Sites</term><term>Biocatalysis</term><term>Crystallography, X-Ray</term><term>Hydrophobic and Hydrophilic Interactions</term><term>Kinetics</term><term>Models, Molecular</term><term>Molecular Sequence Data</term><term>Mutation</term><term>Protein Structure, Secondary</term><term>Protein Structure, Tertiary</term><term>Proteolysis</term><term>Sequence Alignment</term><term>Sequence Homology, Amino Acid</term><term>Substrate Specificity</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Papain-like protease (PLpro) is one of two cysteine proteases involved in the proteolytic processing of the polyproteins of Severe acute respiratory syndrome coronavirus (SARS-CoV). PLpro also shows significant in vitro deubiquitinating and de-ISGylating activities, although the detailed mechanism is still unclear. Here, the crystal structure of SARS-CoV PLpro C112S mutant in complex with ubiquitin (Ub) is reported at 1.4 Å resolution. The Ub core makes mostly hydrophilic interactions with PLpro, while the Leu-Arg-Gly-Gly C-terminus of Ub is located in the catalytic cleft of PLpro, mimicking the P4-P1 residues and providing the first atomic insights into its catalysis. One of the O atoms of the C-terminal Gly residue of Ub is located in the oxyanion hole consisting of the main-chain amides of residues 112 and 113. Mutations of residues in the PLpro-Ub interface lead to reduced catalytic activity, confirming their importance for Ub binding and/or catalysis. The structure also revealed an N-cyclohexyl-2-aminethanesulfonic acid molecule near the catalytic triad, and kinetic studies suggest that this binding site is also used by other PLpro inhibitors. Overall, the structure provides a foundation for understanding the molecular basis of coronaviral PLpro catalysis.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">24531491</PMID><DateCompleted><Year>2014</Year><Month>10</Month><Day>21</Day></DateCompleted><DateRevised><Year>2020</Year><Month>04</Month><Day>18</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1399-0047</ISSN><JournalIssue CitedMedium="Internet"><Volume>70</Volume><Issue>Pt 2</Issue><PubDate><Year>2014</Year><Month>Feb</Month></PubDate></JournalIssue><Title>Acta crystallographica. Section D, Biological crystallography</Title><ISOAbbreviation>Acta Crystallogr. D Biol. Crystallogr.</ISOAbbreviation></Journal><ArticleTitle>Structural basis for catalysis and ubiquitin recognition by the severe acute respiratory syndrome coronavirus papain-like protease.</ArticleTitle><Pagination><MedlinePgn>572-81</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1107/S1399004713031040</ELocationID><Abstract><AbstractText>Papain-like protease (PLpro) is one of two cysteine proteases involved in the proteolytic processing of the polyproteins of Severe acute respiratory syndrome coronavirus (SARS-CoV). PLpro also shows significant in vitro deubiquitinating and de-ISGylating activities, although the detailed mechanism is still unclear. Here, the crystal structure of SARS-CoV PLpro C112S mutant in complex with ubiquitin (Ub) is reported at 1.4 Å resolution. The Ub core makes mostly hydrophilic interactions with PLpro, while the Leu-Arg-Gly-Gly C-terminus of Ub is located in the catalytic cleft of PLpro, mimicking the P4-P1 residues and providing the first atomic insights into its catalysis. One of the O atoms of the C-terminal Gly residue of Ub is located in the oxyanion hole consisting of the main-chain amides of residues 112 and 113. Mutations of residues in the PLpro-Ub interface lead to reduced catalytic activity, confirming their importance for Ub binding and/or catalysis. The structure also revealed an N-cyclohexyl-2-aminethanesulfonic acid molecule near the catalytic triad, and kinetic studies suggest that this binding site is also used by other PLpro inhibitors. Overall, the structure provides a foundation for understanding the molecular basis of coronaviral PLpro catalysis.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Chou</LastName><ForeName>Chi-Yuan</ForeName><Initials>CY</Initials><AffiliationInfo><Affiliation>Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Tapei 112, Taiwan.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Lai</LastName><ForeName>Hsing-Yi</ForeName><Initials>HY</Initials><AffiliationInfo><Affiliation>Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Tapei 112, Taiwan.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Chen</LastName><ForeName>Hung-Yi</ForeName><Initials>HY</Initials><AffiliationInfo><Affiliation>Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Tapei 112, Taiwan.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Cheng</LastName><ForeName>Shu-Chun</ForeName><Initials>SC</Initials><AffiliationInfo><Affiliation>Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Tapei 112, Taiwan.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Cheng</LastName><ForeName>Kai-Wen</ForeName><Initials>KW</Initials><AffiliationInfo><Affiliation>Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Tapei 112, Taiwan.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Chou</LastName><ForeName>Ya-Wen</ForeName><Initials>YW</Initials><AffiliationInfo><Affiliation>Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Tapei 112, Taiwan.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><DataBankList CompleteYN="Y"><DataBank><DataBankName>PDB</DataBankName><AccessionNumberList><AccessionNumber>4M0W</AccessionNumber></AccessionNumberList></DataBank></DataBankList><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2014</Year><Month>01</Month><Day>31</Day></ArticleDate></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>Acta Crystallogr D Biol Crystallogr</MedlineTA><NlmUniqueID>9305878</NlmUniqueID><ISSNLinking>0907-4449</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D025801">Ubiquitin</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D014764">Viral Proteins</NameOfSubstance></Chemical><Chemical><RegistryNumber>103-47-9</RegistryNumber><NameOfSubstance UI="C050927">2-(N-cyclohexylamino)ethanesulfonic acid</NameOfSubstance></Chemical><Chemical><RegistryNumber>1EQV5MLY3D</RegistryNumber><NameOfSubstance UI="D013654">Taurine</NameOfSubstance></Chemical><Chemical><RegistryNumber>EC 3.4.22.2</RegistryNumber><NameOfSubstance UI="D010206">Papain</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D000595" MajorTopicYN="N">Amino Acid Sequence</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D001665" MajorTopicYN="N">Binding Sites</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D055162" MajorTopicYN="N">Biocatalysis</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D018360" MajorTopicYN="N">Crystallography, X-Ray</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D004926" MajorTopicYN="N">Escherichia coli</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName><QualifierName 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Secondary</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D017434" MajorTopicYN="N">Protein Structure, Tertiary</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D059748" MajorTopicYN="N">Proteolysis</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D045473" MajorTopicYN="N">SARS Virus</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="Y">chemistry</QualifierName><QualifierName UI="Q000201" MajorTopicYN="N">enzymology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D016415" MajorTopicYN="N">Sequence Alignment</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D017386" MajorTopicYN="N">Sequence Homology, Amino Acid</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D013379" MajorTopicYN="N">Substrate Specificity</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D013654" MajorTopicYN="N">Taurine</DescriptorName><QualifierName UI="Q000031" MajorTopicYN="N">analogs & derivatives</QualifierName><QualifierName UI="Q000737" MajorTopicYN="N">chemistry</QualifierName><QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D025801" MajorTopicYN="N">Ubiquitin</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="Y">chemistry</QualifierName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName><QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D014764" MajorTopicYN="N">Viral Proteins</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="Y">chemistry</QualifierName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName><QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName></MeshHeading></MeshHeadingList><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">SARS-CoV</Keyword><Keyword MajorTopicYN="N">papain-like protease</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2013</Year><Month>08</Month><Day>23</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2013</Year><Month>11</Month><Day>12</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2014</Year><Month>2</Month><Day>18</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2014</Year><Month>2</Month><Day>18</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2014</Year><Month>10</Month><Day>22</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">24531491</ArticleId><ArticleId IdType="pii">S1399004713031040</ArticleId><ArticleId IdType="doi">10.1107/S1399004713031040</ArticleId><ArticleId IdType="pmc">PMC7161584</ArticleId></ArticleIdList></PubmedData></pubmed></record>Pour manipuler ce 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