Abstract
The SARS-CoV-2 nsp16/nsp10 enzyme complex modifies the 2'-OH of the first transcribed nucleotide of the viral mRNA by covalently attaching a methyl group to it. The 2'-O methylation of the first nucleotide converts the status of mRNA cap from Cap-0 to Cap-1, and thus, helps the virus evade immune surveillance in host cells. Here, we report two structures of nsp16/nsp10 representing pre- and post-release states of the RNA product (Cap-1). We observe overall widening of the enzyme upon product formation, and an inward twisting motion in the substrate binding region upon product release. These conformational changes reset the enzyme for the next round of catalysis. The structures also identify a unique binding mode and the importance of a divalent metal ion for 2'-O methylation. We also describe underlying structural basis for the perturbed enzymatic activity of a clinical variant of SARS-CoV-2, and a previous SARS-CoV outbreak strain.
Publication types
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Research Support, N.I.H., Extramural
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Research Support, Non-U.S. Gov't
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Research Support, U.S. Gov't, Non-P.H.S.
MeSH terms
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Amino Acid Sequence
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Binding Sites
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Biocatalysis
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Cloning, Molecular
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Crystallography, X-Ray
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Escherichia coli / genetics
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Escherichia coli / metabolism
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Gene Expression Regulation, Viral
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Humans
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Magnesium / chemistry*
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Magnesium / metabolism
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Methylation
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Methyltransferases
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Models, Molecular
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Protein Binding
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Protein Conformation, alpha-Helical
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Protein Conformation, beta-Strand
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Protein Interaction Domains and Motifs
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RNA Caps / chemistry
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RNA Caps / genetics
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RNA Caps / metabolism*
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RNA, Viral / chemistry
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RNA, Viral / genetics
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RNA, Viral / metabolism*
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Recombinant Proteins / chemistry
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Recombinant Proteins / genetics
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Recombinant Proteins / metabolism
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S-Adenosylmethionine / chemistry
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S-Adenosylmethionine / metabolism
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SARS-CoV-2 / enzymology
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SARS-CoV-2 / genetics*
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SARS-CoV-2 / ultrastructure
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Sequence Alignment
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Sequence Homology, Amino Acid
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Substrate Specificity
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Viral Nonstructural Proteins / chemistry
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Viral Nonstructural Proteins / genetics
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Viral Nonstructural Proteins / metabolism*
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Viral Regulatory and Accessory Proteins / chemistry
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Viral Regulatory and Accessory Proteins / genetics
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Viral Regulatory and Accessory Proteins / metabolism*
Substances
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NSP10 protein, SARS-CoV-2
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NSP16 protein, SARS-CoV-2
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RNA Caps
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RNA, Viral
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Recombinant Proteins
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Viral Nonstructural Proteins
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Viral Regulatory and Accessory Proteins
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S-Adenosylmethionine
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Methyltransferases
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Magnesium