{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,29]],"date-time":"2026-09-29T23:35:56Z","timestamp":1790724956683,"version":"4.1.0"},"reference-count":44,"publisher":"Oxford University Press (OUP)","issue":"22","license":[{"start":{"date-parts":[[2021,11,29]],"date-time":"2021-11-29T00:00:00Z","timestamp":1638144000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100000265","name":"Medical Research Council","doi-asserted-by":"publisher","award":["MR\/R009945\/1"],"award-info":[{"award-number":["MR\/R009945\/1"]}],"id":[{"id":"10.13039\/501100000265","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100010269","name":"Wellcome","doi-asserted-by":"publisher","award":["200835\/Z\/16\/Z"],"award-info":[{"award-number":["200835\/Z\/16\/Z"]}],"id":[{"id":"10.13039\/100010269","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100014013","name":"UKRI","doi-asserted-by":"publisher","award":["MR\/W005611\/1"],"award-info":[{"award-number":["MR\/W005611\/1"]}],"id":[{"id":"10.13039\/100014013","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000769","name":"University of Oxford","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000769","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,12,16]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>SARS-CoV-2 is a positive-sense RNA virus responsible for the Coronavirus Disease 2019 (COVID-19) pandemic, which continues to cause significant morbidity, mortality and economic strain. SARS-CoV-2 can cause severe respiratory disease and death in humans, highlighting the need for effective antiviral therapies. The RNA synthesis machinery of SARS-CoV-2 is an ideal drug target and consists of non-structural protein 12 (nsp12), which is directly responsible for RNA synthesis, and numerous co-factors involved in RNA proofreading and 5\u2032 capping of viral RNAs. The formation of the 5\u2032 7-methylguanosine (m7G) cap structure is known to require a guanylyltransferase (GTase) as well as a 5\u2032 triphosphatase and methyltransferases; however, the mechanism of SARS-CoV-2 RNA capping remains poorly understood. Here we find that SARS-CoV-2 nsp12 is involved in viral RNA capping as a GTase, carrying out the addition of a GTP nucleotide to the 5\u2032 end of viral RNA via a 5\u2032 to 5\u2032 triphosphate linkage. We further show that the nsp12 NiRAN (nidovirus RdRp-associated nucleotidyltransferase) domain performs this reaction, and can be inhibited by remdesivir triphosphate, the active form of the antiviral drug remdesivir. These findings improve understanding of coronavirus RNA synthesis and highlight a new target for novel or repurposed antiviral drugs against SARS-CoV-2.<\/jats:p>","DOI":"10.1093\/nar\/gkab1160","type":"journal-article","created":{"date-parts":[[2021,11,8]],"date-time":"2021-11-08T15:14:06Z","timestamp":1636384446000},"page":"13019-13030","source":"Crossref","is-referenced-by-count":49,"title":["The SARS-CoV-2 RNA polymerase is a viral RNA capping enzyme"],"prefix":"10.1093","volume":"49","author":[{"given":"Alexander P","family":"Walker","sequence":"first","affiliation":[{"name":"Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Haitian","family":"Fan","sequence":"additional","affiliation":[{"name":"Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jeremy R","family":"Keown","sequence":"additional","affiliation":[{"name":"Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michael L","family":"Knight","sequence":"additional","affiliation":[{"name":"Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jonathan\u00a0M","family":"Grimes","sequence":"additional","affiliation":[{"name":"Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK"},{"name":"Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot OX11 0DE, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ervin","family":"Fodor","sequence":"additional","affiliation":[{"name":"Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2021,11,29]]},"reference":[{"key":"2021121718035303400_B1","doi-asserted-by":"crossref","first-page":"536","DOI":"10.1038\/s41564-020-0695-z","article-title":"The species Severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2","volume":"5","author":"Gorbalenya","year":"2020","journal-title":"Nat. Microbiol."},{"key":"2021121718035303400_B2","doi-asserted-by":"crossref","first-page":"325","DOI":"10.1016\/j.chom.2020.02.001","article-title":"Genome composition and divergence of the novel coronavirus (2019-nCoV) originating in China","volume":"27","author":"Wu","year":"2020","journal-title":"Cell Host Microbe"},{"key":"2021121718035303400_B3","doi-asserted-by":"crossref","first-page":"17","DOI":"10.1016\/j.virusres.2006.01.017","article-title":"Nidovirales: evolving the largest RNA virus genome","volume":"117","author":"Gorbalenya","year":"2006","journal-title":"Virus Res."},{"key":"2021121718035303400_B4","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1016\/bs.aivir.2016.08.008","article-title":"The nonstructural directing coronavirus RNA synthesis and processing","volume":"96","author":"Snijder","year":"2016","journal-title":"Adv. Virus Res."},{"key":"2021121718035303400_B5","doi-asserted-by":"crossref","first-page":"155","DOI":"10.1038\/s41579-020-00468-6","article-title":"Coronavirus biology and replication: implications for SARS-CoV-2","volume":"19","author":"V\u2019kovski","year":"2021","journal-title":"Nat. Rev. Microbiol."},{"key":"2021121718035303400_B6","doi-asserted-by":"crossref","first-page":"6571","DOI":"10.1093\/emboj\/cdf635","article-title":"Discontinuous and non-discontinuous subgenomic RNA transcription in a nidovirus","volume":"21","author":"Van\u00a0Vliet","year":"2002","journal-title":"EMBO J."},{"key":"2021121718035303400_B7","doi-asserted-by":"crossref","first-page":"69","DOI":"10.1007\/978-1-4757-0456-3_5","article-title":"Genome structure of mouse hepatitis virus: comparative analysis by oligonucleotide mapping","volume":"142","author":"Lai","year":"1981","journal-title":"Adv. Exp. Med. Biol."},{"key":"2021121718035303400_B8","doi-asserted-by":"crossref","first-page":"661","DOI":"10.1128\/jvi.38.2.661-670.1981","article-title":"Comparative analysis of RNA genomes of mouse hepatitis viruses","volume":"38","author":"Lai","year":"1981","journal-title":"J. Virol."},{"key":"2021121718035303400_B9","doi-asserted-by":"crossref","first-page":"5619","DOI":"10.1128\/JVI.78.11.5619-5632.2004","article-title":"Multiple enzymatic activities associated with severe acute respiratory syndrome coronavirus helicase","volume":"78","author":"Ivanov","year":"2004","journal-title":"J. Virol."},{"key":"2021121718035303400_B10","doi-asserted-by":"crossref","first-page":"3484","DOI":"10.1073\/pnas.0808790106","article-title":"Functional screen reveals SARS coronavirus nonstructural protein nsp14 as a novel cap N7 methyltransferase","volume":"106","author":"Chen","year":"2009","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"key":"2021121718035303400_B11","doi-asserted-by":"crossref","first-page":"991","DOI":"10.1016\/S0022-2836(03)00865-9","article-title":"Unique and conserved features of genome and proteome of SARS-coronavirus, an early split-off from the coronavirus group 2 lineage","volume":"331","author":"Snijder","year":"2003","journal-title":"J. Mol. Biol."},{"key":"2021121718035303400_B12","doi-asserted-by":"crossref","first-page":"8071","DOI":"10.1128\/JVI.00407-08","article-title":"Coronavirus nonstructural protein 16 is a Cap-0 binding enzyme possessing (nucleoside-2\u2032O)-methyltransferase activity","volume":"82","author":"Decroly","year":"2008","journal-title":"J. Virol."},{"key":"2021121718035303400_B13","doi-asserted-by":"crossref","first-page":"184","DOI":"10.1016\/j.cell.2020.11.016","article-title":"Cryo-EM structure of an extended SARS-CoV-2 replication and transcription complex reveals an intermediate state in cap synthesis","volume":"184","author":"Yan","year":"2021","journal-title":"Cell"},{"key":"2021121718035303400_B14","doi-asserted-by":"crossref","first-page":"1499","DOI":"10.1126\/science.abc1560","article-title":"Structural basis for inhibition of the RNA-dependent RNA polymerase from SARS-CoV-2 by remdesivir","volume":"368","author":"Yin","year":"2020","journal-title":"Science"},{"key":"2021121718035303400_B15","doi-asserted-by":"crossref","first-page":"4682","DOI":"10.1038\/s41467-020-18463-z","article-title":"Rapid incorporation of Favipiravir by the fast and permissive viral RNA polymerase complex results in SARS-CoV-2 lethal mutagenesis","volume":"11","author":"Shannon","year":"2020","journal-title":"Nat. Commun."},{"key":"2021121718035303400_B16","doi-asserted-by":"crossref","first-page":"4690","DOI":"10.1021\/acs.jproteome.0c00392","article-title":"Nucleotide analogues as inhibitors of SARS-CoV-2 polymerase, a key drug target for COVID-19","volume":"19","author":"Chien","year":"2020","journal-title":"J. Proteome Res."},{"key":"2021121718035303400_B17","doi-asserted-by":"crossref","first-page":"8416","DOI":"10.1093\/nar\/gkv838","article-title":"Discovery of an essential nucleotidylating activity associated with a newly delineated conserved domain in the RNA polymerase-containing protein of all nidoviruses","volume":"43","author":"Lehmann","year":"2015","journal-title":"Nucleic Acids Res."},{"key":"2021121718035303400_B18","doi-asserted-by":"crossref","first-page":"e2022310118","DOI":"10.1073\/pnas.2022310118","article-title":"Coronavirus replication-transcription complex: Vital and selective NMPylation of a conserved site in nsp9 by the NiRAN-RdRp subunit","volume":"118","author":"Slanina","year":"2021","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"key":"2021121718035303400_B19","doi-asserted-by":"crossref","DOI":"10.1101\/2021.03.23.436564","article-title":"Protein-primed RNA synthesis in SARS-CoVs and structural basis for inhibition by AT-527","author":"Shannon","year":"2021"},{"key":"2021121718035303400_B20","doi-asserted-by":"crossref","first-page":"8822","DOI":"10.1093\/nar\/gkab677","article-title":"NMPylation and de-NMPylation of SARS-CoV-2 nsp9 by the NiRAN domain","volume":"49","author":"Wang","year":"2021","journal-title":"Nucleic Acids Res."},{"key":"2021121718035303400_B21","doi-asserted-by":"crossref","first-page":"E3900","DOI":"10.1073\/pnas.1323705111","article-title":"One severe acute respiratory syndrome coronavirus protein complex integrates processive RNA polymerase and exonuclease activities","volume":"111","author":"Subissi","year":"2014","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"key":"2021121718035303400_B22","doi-asserted-by":"crossref","first-page":"39578","DOI":"10.1074\/jbc.C300328200","article-title":"The severe acute respiratory syndrome (SARS) coronavirus NTPase\/helicase belongs to a distinct class of 5\u2032 to 3\u2032 viral helicases","volume":"278","author":"Tanner","year":"2003","journal-title":"J. Biol. Chem."},{"key":"2021121718035303400_B23","doi-asserted-by":"crossref","first-page":"1560","DOI":"10.1016\/j.cell.2020.07.033","article-title":"Structural basis for helicase-polymerase coupling in the SARS-CoV-2 replication-transcription complex","volume":"182","author":"Chen","year":"2020","journal-title":"Cell"},{"key":"2021121718035303400_B24","doi-asserted-by":"crossref","first-page":"5108","DOI":"10.1073\/pnas.0508200103","article-title":"Discovery of an RNA virus 3\u2032\u21925\u2032 exoribonuclease that is critically involved in coronavirus RNA synthesis","volume":"103","author":"Minskaia","year":"2006","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"key":"2021121718035303400_B25","doi-asserted-by":"crossref","first-page":"3474","DOI":"10.1016\/j.cell.2021.05.033","article-title":"Coupling of N7-methyltransferase and 3\u2032-5\u2032 exoribonuclease with SARS-CoV-2 polymerase reveals mechanisms for capping and proofreading","volume":"184","author":"Yan","year":"2021","journal-title":"Cell"},{"key":"2021121718035303400_B26","doi-asserted-by":"crossref","first-page":"49","DOI":"10.1016\/j.tibs.2011.10.005","article-title":"MultiBac: expanding the research toolbox for multiprotein complexes","volume":"37","author":"Bieniossek","year":"2012","journal-title":"Trends Biochem. Sci."},{"key":"2021121718035303400_B27","doi-asserted-by":"crossref","first-page":"E4238","DOI":"10.1073\/pnas.1315068110","article-title":"Isolation and characterization of the positive-sense replicative intermediate of a negative-strand RNA virus","volume":"110","author":"York","year":"2013","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"key":"2021121718035303400_B28","doi-asserted-by":"crossref","first-page":"914","DOI":"10.1016\/j.cell.2020.04.011","article-title":"The architecture of SARS-CoV-2 transcriptome","volume":"181","author":"Kim","year":"2020","journal-title":"Cell"},{"key":"2021121718035303400_B29","doi-asserted-by":"crossref","first-page":"51","DOI":"10.1038\/nrmicro2675","article-title":"Conventional and unconventional mechanisms for capping viral mRNA","volume":"10","author":"Decroly","year":"2012","journal-title":"Nat. Rev. Microbiol."},{"key":"2021121718035303400_B30","doi-asserted-by":"crossref","first-page":"11960","DOI":"10.1016\/S0021-9258(19)38494-7","article-title":"Catalytic activity of vaccinia mRNA capping enzyme subunits coexpressed in Escherichia coli","volume":"265","author":"Shuman","year":"1990","journal-title":"J. Biol. Chem."},{"key":"2021121718035303400_B31","doi-asserted-by":"crossref","first-page":"355","DOI":"10.1038\/nature06475","article-title":"The bacterial enzyme RppH triggers messenger RNA degradation by 5\u2032 pyrophosphate removal","volume":"451","author":"Deana","year":"2008","journal-title":"Nature"},{"key":"2021121718035303400_B32","doi-asserted-by":"crossref","first-page":"269","DOI":"10.1038\/s41422-020-0282-0","article-title":"Remdesivir and chloroquine effectively inhibit the recently emerged novel coronavirus (2019-nCoV) in vitro","volume":"30","author":"Wang","year":"2020","journal-title":"Cell Res."},{"key":"2021121718035303400_B33","doi-asserted-by":"crossref","first-page":"279","DOI":"10.1038\/s41467-020-20542-0","article-title":"Mechanism of SARS-CoV-2 polymerase stalling by remdesivir","volume":"12","author":"Kokic","year":"2021","journal-title":"Nat. Commun."},{"key":"2021121718035303400_B34","doi-asserted-by":"crossref","first-page":"6785","DOI":"10.1074\/jbc.RA120.013679","article-title":"Remdesivir is a direct-acting antiviral that inhibits RNA-dependent RNA polymerase from severe acute respiratory syndrome coronavirus 2 with high potency","volume":"295","author":"Gordon","year":"2020","journal-title":"J. Biol. Chem."},{"key":"2021121718035303400_B35","doi-asserted-by":"crossref","first-page":"16156","DOI":"10.1074\/jbc.AC120.015720","article-title":"Template-dependent inhibition of coronavirus RNA-dependent RNA polymerase by remdesivir reveals a second mechanism of action","volume":"295","author":"Tchesnokov","year":"2020","journal-title":"J. Biol. Chem."},{"key":"2021121718035303400_B36","doi-asserted-by":"crossref","first-page":"1548","DOI":"10.1016\/j.molcel.2021.01.035","article-title":"Remdesivir is a delayed translocation inhibitor of SARS-CoV-2 replication","volume":"81","author":"Bravo","year":"2021","journal-title":"Mol. Cell"},{"key":"2021121718035303400_B37","doi-asserted-by":"crossref","first-page":"1737","DOI":"10.1093\/nar\/gkr893","article-title":"The SARS-coronavirus nsp7+nsp8 complex is a unique multimeric RNA polymerase capable of both de novo initiation and primer extension","volume":"40","author":"Te\u00a0Velthuis","year":"2012","journal-title":"Nucleic Acids Res."},{"key":"2021121718035303400_B38","doi-asserted-by":"crossref","first-page":"2095","DOI":"10.1007\/s00705-012-1404-x","article-title":"Biochemical characterization of a recombinant SARS coronavirus nsp12 RNA-dependent RNA polymerase capable of copying viral RNA templates","volume":"157","author":"Ahn","year":"2012","journal-title":"Arch. Virol."},{"key":"2021121718035303400_B39","doi-asserted-by":"crossref","first-page":"4933","DOI":"10.1038\/sj.emboj.7601368","article-title":"A second, non-canonical RNA-dependent RNA polymerase in SARS coronavirus","volume":"25","author":"Imbert","year":"2006","journal-title":"EMBO J."},{"key":"2021121718035303400_B40","doi-asserted-by":"crossref","first-page":"9436","DOI":"10.1073\/pnas.1508686112","article-title":"Structural basis and functional analysis of the SARS coronavirus nsp14-nsp10 complex","volume":"112","author":"Ma","year":"2015","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"key":"2021121718035303400_B41","doi-asserted-by":"crossref","first-page":"e1002059","DOI":"10.1371\/journal.ppat.1002059","article-title":"Crystal structure and functional analysis of the SARS-coronavirus RNA cap 2\u2032-o-methyltransferase nsp10\/nsp16 complex","volume":"7","author":"Decroly","year":"2011","journal-title":"PLoS Pathog."},{"key":"2021121718035303400_B42","doi-asserted-by":"crossref","first-page":"e1002294","DOI":"10.1371\/journal.ppat.1002294","article-title":"Biochemical and structural insights into the mechanisms of sars coronavirus RNA ribose 2\u2032-O-methylation by nsp16\/nsp10 protein complex","volume":"7","author":"Chen","year":"2011","journal-title":"PLoS Pathog."},{"key":"2021121718035303400_B43","doi-asserted-by":"crossref","first-page":"566","DOI":"10.1038\/nri.2016.78","article-title":"Discriminating self from non-self in nucleic acid sensing","volume":"16","author":"Schlee","year":"2016","journal-title":"Nat. Rev. Immunol."},{"key":"2021121718035303400_B44","doi-asserted-by":"crossref","first-page":"11588","DOI":"10.1016\/S0021-9258(19)70330-5","article-title":"Purification and characterization of a GTP-pyrophosphate exchange activity from vaccinia virions","volume":"255","author":"Shuman","year":"1980","journal-title":"J. Biol. Chem."}],"container-title":["Nucleic Acids Research"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/nar\/article-pdf\/49\/22\/13019\/41811217\/gkab1160.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/nar\/article-pdf\/49\/22\/13019\/41811217\/gkab1160.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,12,17]],"date-time":"2021-12-17T14:34:05Z","timestamp":1639751645000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/nar\/article\/49\/22\/13019\/6445966"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2021,11,29]]},"references-count":44,"journal-issue":{"issue":"22","published-online":{"date-parts":[[2021,11,29]]},"published-print":{"date-parts":[[2021,12,16]]}},"URL":"https:\/\/doi.org\/10.1093\/nar\/gkab1160","relation":{},"ISSN":["0305-1048","1362-4962"],"issn-type":[{"value":"0305-1048","type":"print"},{"value":"1362-4962","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2021,12,16]]},"published":{"date-parts":[[2021,11,29]]}}}