Efficient RNA capping by the SARS-CoV-2 methyltransferase requires metal ions and a unique four-residue insert. Uniquely coronavirus Virally encoded 2′- O -methyltransferases catalyze the last step in the capping of viral RNAs, which protects the RNAs from degradation and prevents them from triggering host defenses. Minasov et al. report structures of the SARS-CoV-2 methyltransferase, a heterodimeric complex of the enzyme nsp16 and its coactivator nsp10, in complex with a short, capped RNA (instead of the RNA cap analogs used to generate previous structures), the methyl donor SAM, and divalent metal cations. The metal ions and a four-residue insert of nsp16 were important for precisely aligning the RNA substrate in the active site for efficient catalysis. This insert is present in coronavirus but not in mammalian methyltransferases, suggesting this site as a potential target for the design of coronavirus-specific methyltransferase inhibitors. Capping of viral messenger RNAs is essential for efficient translation, for virus replication, and for preventing detection by the host cell innate response system. The SARS-CoV-2 genome encodes the 2′- O -methyltransferase nsp16, which, when bound to the coactivator nsp10, uses S -adenosylmethionine (SAM) as a donor to transfer a methyl group to the first ribonucleotide of the mRNA in the final step of viral mRNA capping. Here, we provide biochemical and structural evidence that this reaction requires divalent cations, preferably Mn 2+ , and a coronavirus-specific four-residue insert. We determined the x-ray structures of the SARS-CoV-2 2′- O -methyltransferase (the nsp16-nsp10 heterodimer) in complex with its reaction substrates, products, and divalent metal cations. These structural snapshots revealed that metal ions and the insert stabilize interactions between the capped RNA and nsp16, resulting in the precise alignment of the ribonucleotides in the active site. Comparison of available structures of 2′- O -methyltransferases with capped RNAs from different organisms revealed that the four-residue insert unique to coronavirus nsp16 alters the backbone conformation of the capped RNA in the binding groove, thereby promoting catalysis. This insert is highly conserved across coronaviruses, and its absence in mammalian methyltransferases makes this region a promising site for structure-guided drug design of selective coronavirus inhibitors.
【초록키워드】 Structure, Coronaviruses, coronavirus, drug design, translation, inhibitors, RNAs, RNA, Viral, SARS-CoV-2 genome, mRNA, methyltransferase, nsp10, virus replication, Degradation, efficient, Donor, binding, Interaction, structures, host cell, host defenses, active site, innate response, Messenger RNA, methyl group, biochemical, viral RNAs, enzyme, complex, transfer, Final, organism, ribonucleotide, substrates, selective, backbone, ENCODE, adenosylmethionine, capping, catalysis, insert, metal ions, ribonucleotides, mammalian, triggering, Host, Alter, Prevent, structural evidence, PROTECT, X-ray structure, resulting, conserved, generate, absence, unique, SAM, aligning, coactivator, heterodimeric, metal ion, the SARS-CoV-2, 【제목키워드】 SARS-CoV-2, transfer, substrate, Coordinate,