A metal ion orients mRNA to ensure accurate 2’-O ribosyl methylation of the first nucleotide of the SARS-CoV-2 genome

Viswanathan, Thiruselvam; Misra, Anurag; Chan, Siu-Hong; Qi, Shan; Dai, Nan; Arya, Shailee; Martinez-Sobrido, Luis; Gupta, Yogesh K.

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 the host cell. 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.