Structural basis of RNA cap modification by SARS-CoV-2

Thiruselvam Viswanathan,Siu-Hong Chan,Luis Martinez-Sobrido,Fatai Oladunni,Shan Qi,Dmytro Kovalskyy,Shailee Arya,Yogesh K Gupta,Jun-Gyu Park,Nan Dai,Anurag Misra,Robert A Hromas

doi:10.1038/s41467-020-17496-8

Abstract

The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), the causative agent of COVID-19 illness, has caused millions of infections worldwide. In SARS coronaviruses, the non-structural protein 16 (nsp16), in conjunction with nsp10, methylates the 5′-end of virally encoded mRNAs to mimic cellular mRNAs, thus protecting the virus from host innate immune restriction. We report here the high-resolution structure of a ternary complex of SARS-CoV-2 nsp16 and nsp10 in the presence of cognate RNA substrate analogue and methyl donor, S-adenosyl methionine (SAM). The nsp16/nsp10 heterodimer is captured in the act of 2′-O methylation of the ribose sugar of the first nucleotide of SARS-CoV-2 mRNA. We observe large conformational changes associated with substrate binding as the enzyme transitions from a binary to a ternary state. This induced fit model provides mechanistic insights into the 2′-O methylation of the viral mRNA cap. We also discover a distant (25 Å) ligand-binding site unique to SARS-CoV-2, which can alternatively be targeted, in addition to RNA cap and SAM pockets, for antiviral development.

Highlights

The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), the causative agent of COVID-19 illness, has caused millions of infections worldwide
Nsp[16] forms an obligatory complex with nsp[10] to efficiently convert client mRNA species from the Cap-0 to the Cap-1 form, by methylating the ribose 2′-O of the first nucleotide of the nascent mRNA using SAM (S-adenosyl methionine) as the methyl donor[4,8]. While both Cap-0 and Cap-1 forms promote the recruitment of the host translation factor eIF4E, the Cap-0 form favors the binding of interferon-induced proteins with tetratricopeptide repeats 1 (IFIT1) to viral RNAs9
Our work provides a solid framework from which therapeutic modalities may be designed by targeting different ligand-binding sites of nsp[16], including RNA cap and SAM

Summary

Introduction

The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), the causative agent of COVID-19 illness, has caused millions of infections worldwide. Nsp16/nsp[10] in complex with the methyl donor (SAM) and its target, RNA cap me7GopppA1. We determined the ternary structure of nsp16/nsp[10] by molecular replacement using the SARS-CoV-1/SAM binary complex (PDB ID 3R24)[8] structure as a template (Supplementary Table 1).

Results

Conclusion