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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">mRNA Cap-1 Methyltransferase in the SARS Genome</title>
<author><name sortKey="Von Grotthuss, Marcin" sort="Von Grotthuss, Marcin" uniqKey="Von Grotthuss M" first="Marcin" last="Von Grotthuss">Marcin Von Grotthuss</name>
</author>
<author><name sortKey="Wyrwicz, Lucjan S" sort="Wyrwicz, Lucjan S" uniqKey="Wyrwicz L" first="Lucjan S" last="Wyrwicz">Lucjan S. Wyrwicz</name>
</author>
<author><name sortKey="Rychlewski, Leszek" sort="Rychlewski, Leszek" uniqKey="Rychlewski L" first="Leszek" last="Rychlewski">Leszek Rychlewski</name>
</author>
</titleStmt>
<publicationStmt><idno type="wicri:source">PMC</idno>
<idno type="pmid">12809601</idno>
<idno type="pmc">7126025</idno>
<idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7126025</idno>
<idno type="RBID">PMC:7126025</idno>
<idno type="doi">10.1016/S0092-8674(03)00424-0</idno>
<date when="2003">2003</date>
<idno type="wicri:Area/Pmc/Corpus">000A71</idno>
<idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">000A71</idno>
</publicationStmt>
<sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">mRNA Cap-1 Methyltransferase in the SARS Genome</title>
<author><name sortKey="Von Grotthuss, Marcin" sort="Von Grotthuss, Marcin" uniqKey="Von Grotthuss M" first="Marcin" last="Von Grotthuss">Marcin Von Grotthuss</name>
</author>
<author><name sortKey="Wyrwicz, Lucjan S" sort="Wyrwicz, Lucjan S" uniqKey="Wyrwicz L" first="Lucjan S" last="Wyrwicz">Lucjan S. Wyrwicz</name>
</author>
<author><name sortKey="Rychlewski, Leszek" sort="Rychlewski, Leszek" uniqKey="Rychlewski L" first="Leszek" last="Rychlewski">Leszek Rychlewski</name>
</author>
</analytic>
<series><title level="j">Cell</title>
<idno type="ISSN">0092-8674</idno>
<idno type="eISSN">1097-4172</idno>
<imprint><date when="2003">2003</date>
</imprint>
</series>
</biblStruct>
</sourceDesc>
</fileDesc>
<profileDesc><textClass></textClass>
</profileDesc>
</teiHeader>
<front><div type="abstract" xml:lang="en"><p>The 3D jury system has predicted the methyltransferase fold for the nsp13 protein of the SARS coronavirus. Based on the conservation of a characteristic tetrad of residues, the mRNA cap-1 methyltransferase function has been assigned to this protein, which has potential implications for antiviral therapy.</p>
</div>
</front>
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</author>
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</author>
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</author>
</analytic>
</biblStruct>
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</analytic>
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<biblStruct><analytic><author><name sortKey="De Clercq, E" uniqKey="De Clercq E">E. De Clercq</name>
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</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Feder, M" uniqKey="Feder M">M. Feder</name>
</author>
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</author>
<author><name sortKey="Wyrwicz, L S" uniqKey="Wyrwicz L">L.S. Wyrwicz</name>
</author>
<author><name sortKey="Bujnicki, J M" uniqKey="Bujnicki J">J.M. Bujnicki</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Ginalski, K" uniqKey="Ginalski K">K. Ginalski</name>
</author>
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</author>
<author><name sortKey="Rychlewski, L" uniqKey="Rychlewski L">L. Rychlewski</name>
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</analytic>
</biblStruct>
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</author>
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</biblStruct>
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</analytic>
</biblStruct>
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<biblStruct><analytic><author><name sortKey="Reinisch, K M" uniqKey="Reinisch K">K.M. Reinisch</name>
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<biblStruct><analytic><author><name sortKey="Vlot, A C" uniqKey="Vlot A">A.C. Vlot</name>
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</listBibl>
</div1>
</back>
</TEI>
<pmc article-type="letter"><pmc-dir>properties open_access</pmc-dir>
<front><journal-meta><journal-id journal-id-type="nlm-ta">Cell</journal-id>
<journal-id journal-id-type="iso-abbrev">Cell</journal-id>
<journal-title-group><journal-title>Cell</journal-title>
</journal-title-group>
<issn pub-type="ppub">0092-8674</issn>
<issn pub-type="epub">1097-4172</issn>
<publisher><publisher-name>Cell Press.</publisher-name>
</publisher>
</journal-meta>
<article-meta><article-id pub-id-type="pmid">12809601</article-id>
<article-id pub-id-type="pmc">7126025</article-id>
<article-id pub-id-type="publisher-id">S0092-8674(03)00424-0</article-id>
<article-id pub-id-type="doi">10.1016/S0092-8674(03)00424-0</article-id>
<article-categories><subj-group subj-group-type="heading"><subject>Article</subject>
</subj-group>
</article-categories>
<title-group><article-title>mRNA Cap-1 Methyltransferase in the SARS Genome</article-title>
</title-group>
<contrib-group><contrib contrib-type="author"><name><surname>von Grotthuss</surname>
<given-names>Marcin</given-names>
</name>
</contrib>
<contrib contrib-type="author"><name><surname>Wyrwicz</surname>
<given-names>Lucjan S</given-names>
</name>
</contrib>
<contrib contrib-type="author"><name><surname>Rychlewski</surname>
<given-names>Leszek</given-names>
</name>
<email>leszek@bioinfo.pl</email>
<xref rid="COR1" ref-type="corresp">*</xref>
</contrib>
</contrib-group>
<aff>BioInfoBank Institute, Limanowskiego 24A, 60-744 Poznań, Poland</aff>
<author-notes><corresp id="COR1"><label>*</label>
Correspondence: Leszek Rychlewski, +48-61-8653520 (phone), +48-61-8643350 (fax) <email>leszek@bioinfo.pl</email>
</corresp>
</author-notes>
<pub-date pub-type="pmc-release"><day>15</day>
<month>4</month>
<year>2004</year>
</pub-date>
<pmc-comment> PMC Release delay is 0 months and 0 days and was based on .</pmc-comment>
<pub-date pub-type="ppub"><day>13</day>
<month>6</month>
<year>2003</year>
</pub-date>
<pub-date pub-type="epub"><day>15</day>
<month>4</month>
<year>2004</year>
</pub-date>
<volume>113</volume>
<issue>6</issue>
<fpage>701</fpage>
<lpage>702</lpage>
<permissions><copyright-statement>Copyright © 2003 Cell Press. All rights reserved.</copyright-statement>
<copyright-year>2003</copyright-year>
<copyright-holder>Cell Press</copyright-holder>
<license><license-p>Since January 2020 Elsevier has created a COVID-19 resource centre with free information in English and Mandarin on the novel coronavirus COVID-19. The COVID-19 resource centre is hosted on Elsevier Connect, the company's public news and information website. Elsevier hereby grants permission to make all its COVID-19-related research that is available on the COVID-19 resource centre - including this research content - immediately available in PubMed Central and other publicly funded repositories, such as the WHO COVID database with rights for unrestricted research re-use and analyses in any form or by any means with acknowledgement of the original source. These permissions are granted for free by Elsevier for as long as the COVID-19 resource centre remains active.</license-p>
</license>
</permissions>
<abstract><p>The 3D jury system has predicted the methyltransferase fold for the nsp13 protein of the SARS coronavirus. Based on the conservation of a characteristic tetrad of residues, the mRNA cap-1 methyltransferase function has been assigned to this protein, which has potential implications for antiviral therapy.</p>
</abstract>
</article-meta>
</front>
<body><sec><title>Main Text</title>
<p>The latest outbreak of the <italic>s</italic>
evere <italic>a</italic>
cute <italic>r</italic>
espiratory <italic>s</italic>
yndrome (SARS) epidemic has led to thousands of potentially lethally infected patients and hundreds of deaths. These numbers are likely to rise, and the spreading disease is already causing major medical and economical concerns. Meanwhile, the SARS coronavirus identified as the pathogen responsible for the disaster has been isolated, and its genome sequenced <xref rid="BIB9" ref-type="bibr">Marra et al. 2003</xref>
, <xref rid="BIB11" ref-type="bibr">Rota et al. 2003</xref>
.</p>
<p>We have applied the 3D jury meta predictor <xref rid="BIB6" ref-type="bibr">(Ginalski et al., 2003)</xref>
to annotate the structure and function of proteins encoded by the viral positive-strand ssRNA. Novel fold recognition methods utilize the global network of independent structure prediction servers. Detection of patterns of structural similarity between diverse models is used to consistently select the correct fold from a set of borderline predictions. Such methods made a dramatic impact on the last <italic>c</italic>
ritical <italic>a</italic>
ssessment of protein <italic>s</italic>
tructure <italic>p</italic>
rediction (CASP-5 experiment) conducted in the summer of 2002. One of the most interesting findings obtained during the SARS genome annotation process is a surprisingly reliable (3D jury score >100) assignment of the methyltransferase fold to the nsp13 (GI:30133975) domain located in the C-terminal part of the almost 7000 amino acid large pp1ab viral polyprotein <xref rid="FIG1" ref-type="fig">(Figure 1)</xref>
. Standard sequence comparison tools such as PSI-BLAST or RPS-BLAST applied using the conserved domain database <xref rid="BIB8" ref-type="bibr">(Marchler-Bauer et al., 2003)</xref>
failed to assign any function to this domain. The domain belongs to the ancient family of AdoMet-dependent ribose 2′-O-methyltransferases, which has been adapted by numerous viruses before the three domains of life evolved form the <italic>l</italic>
ast <italic>u</italic>
niversal <italic>c</italic>
ommon <italic>a</italic>
ncestor (LUCA) <xref rid="BIB5" ref-type="bibr">(Feder et al., 2003)</xref>
. The enzymatic role of the protein was confirmed by the presence of the conserved tetrad of residues K-D-K-E essential for mRNA cap-1 (mGpppNm) formation.<fig id="FIG1"><label>Figure 1</label>
<caption><p>3D Model of the nsp13 Domain of the SARS Coronavirus pp1ab Polyprotein</p>
<p>This model is based on the reassigned <xref rid="BIB3" ref-type="bibr">(Bujnicki and Rychlewski, 2001)</xref>
cap-1 methyltransferase of the reovirus λ2 protein (1ej6 <xref rid="BIB10" ref-type="bibr">[Reinisch et al., 2000]</xref>
). While other templates (1eiz or 1ej0) obtained marginally higher 3D jury scores, the selected template had the lowest number of insertions and deletions. Side chains of the conserved tetrad of residues (K-D-K-E) essential for cap-1 methylation and the docked AdoMet cofactor are shown. Four blocks of aligned motifs containing the conserved, function-specific residues are shown in upper right corner.</p>
</caption>
<graphic xlink:href="gr1_lrg"></graphic>
</fig>
</p>
<p>The mRNA cap methylation is found indispensable for efficient replication of many viruses <xref rid="BIB1" ref-type="bibr">Bach et al. 1995</xref>
, <xref rid="BIB13" ref-type="bibr">Woyciniuk et al. 1995</xref>
, <xref rid="BIB12" ref-type="bibr">Vlot et al. 2002</xref>
and represents an active area for drug development. Nevertheless, direct inhibitors of the nsp13 enzyme may fail to suppress viral replication, as the cap-1 formation seems to be less critical than the preceding cap-0 (mGpppN) formation <xref rid="BIB7" ref-type="bibr">Latner et al. 2002</xref>
, <xref rid="BIB14" ref-type="bibr">Wu and Guarino 2003</xref>
. The existence of the cap-1-forming enzyme in the genome would suggest that the virus also requires the AdoMet-dependent cap-0 methyltransferase. Both functions can be inhibited by carbocyclic analogs of adenosine, such as Neplanocin A or 3-deazaneplanocin A, which interfere with the AdoMet-AdoHcy metabolism of the host cell <xref rid="BIB4" ref-type="bibr">De Clercq 1998</xref>
, <xref rid="BIB2" ref-type="bibr">Bray et al. 2002</xref>
. Those compounds could complement other therapeutic strategies aimed at blocking enzymatic functions such as the RNA-dependent RNA polymerase, the protease, or the helicase encoded by the SARS virus.</p>
</sec>
</body>
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