TY - JOUR
T1 - Structural basis of RNA cap modification by SARS-CoV-2
AU - Viswanathan, Thiruselvam
AU - Arya, Shailee
AU - Chan, Siu Hong
AU - Qi, Shan
AU - Dai, Nan
AU - Misra, Anurag
AU - Park, Jun Gyu
AU - Oladunni, Fatai
AU - Kovalskyy, Dmytro
AU - Hromas, Robert A.
AU - Martinez-Sobrido, Luis
AU - Gupta, Yogesh K.
N1 - Funding Information:
We are grateful to beamline scientists at NECAT-24ID, APS, Chicago for providing synchrotron beamtime and facilitating data collection. This work is based on research conducted at the Northeastern Collaborative Access Team beamlines (NIH grant P30GM124165, and U.S. Department of Energy Contract DE-AC02-06CH11357). We thank Drs. Bruce Nicholson and Patrick Sung for critically reading the manuscript. This work was supported by funding from the Max and Minnie Tomerlin Voelcker Foundation, San Antonio Area Foundation, a Pilot award from the UT Health San Antonio (UTHSA), and laboratory startup funds from the Greehey Children’s Cancer Research Institute of UTHSA to Y.K.G. R. A.H. is supported by NIH CA205224. T.V. is supported by a Research Training Award (RP170345) from the Cancer Prevention Research Institute of Texas (CPRIT). We also thank the X-ray core of UTHSA. Y.K.G. is also supported by a high impact/high risk award from the CPRIT (RP190534), and a Rising STARs award from the UT System.
Publisher Copyright:
© 2020, The Author(s).
PY - 2020/12/1
Y1 - 2020/12/1
N2 - 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.
AB - 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.
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U2 - 10.1038/s41467-020-17496-8
DO - 10.1038/s41467-020-17496-8
M3 - Article
C2 - 32709886
AN - SCOPUS:85088534595
SN - 2041-1723
VL - 11
JO - Nature Communications
JF - Nature Communications
IS - 1
M1 - 3718
ER -