Crystallographic structure of wild-type SARS-CoV-2 main protease acyl-enzyme intermediate with physiological C-terminal autoprocessing site

Lee, Jaeyong; Worrall, Liam J.; Vuckovic, Marija; Rosell, Federico I.; Gentile, Francesco; Ton, Anh-Tien; Caveney, Nathanael A.; Ban, Fuqiang; Cherkasov, Artem; Paetzel, Mark; Strynadka, Natalie J.

doi:10.1038/s41467-020-19662-4

Title: Crystallographic structure of wild-type SARS-CoV-2 main protease acyl-enzyme intermediate with physiological C-terminal autoprocessing site

Journal Article · Wed Nov 18 00:00:00 EST 2020 · Nature Communications

DOI:https://doi.org/10.1038/s41467-020-19662-4· OSTI ID:1729690

Lee, Jaeyong ^[1]; Worrall, Liam J. ^[2]; Vuckovic, Marija ^[2]; Rosell, Federico I. ^[2]; Gentile, Francesco ^[2];

^[2];

^[2]; Ban, Fuqiang ^[2];

^[2];

^[3];

^[2]

Univ. of British Columbia, Vancouver, BC (Canada); Simon Fraser Univ., Burnaby, BC (Canada)
Univ. of British Columbia, Vancouver, BC (Canada)
Simon Fraser Univ., Burnaby, BC (Canada)

AbstractSevere Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), the pathogen that causes the disease COVID-19, produces replicase polyproteins 1a and 1ab that contain, respectively, 11 or 16 nonstructural proteins (nsp). Nsp5 is the main protease (Mpro) responsible for cleavage at eleven positions along these polyproteins, including at its own N- and C-terminal boundaries, representing essential processing events for subsequent viral assembly and maturation. We have determined X-ray crystallographic structures of this cysteine protease in its wild-type free active site state at 1.8 Å resolution, in its acyl-enzyme intermediate state with the native C-terminal autocleavage sequence at 1.95 Å resolution and in its product bound state at 2.0 Å resolution by employing an active site mutation (C145A). We characterize the stereochemical features of the acyl-enzyme intermediate including critical hydrogen bonding distances underlying catalysis in the Cys/His dyad and oxyanion hole. We also identify a highly ordered water molecule in a position compatible for a role as the deacylating nucleophile in the catalytic mechanism and characterize the binding groove conformational changes and dimerization interface that occur upon formation of the acyl-enzyme. Collectively, these crystallographic snapshots provide valuable mechanistic and structural insights for future antiviral therapeutic development including revised molecular docking strategies based on Mpro inhibition.

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Research Organization:: Argonne National Lab. (ANL), Argonne, IL (United States). Advanced Photon Source (APS)

Sponsoring Organization:: National Institutes of Health (NIH); USDOE

OSTI ID:: 1729690

Journal Information:: Nature Communications, Vol. 11, Issue 1; ISSN 2041-1723

Publisher:: Nature Publishing GroupCopyright Statement

Country of Publication:: United States

Language:: ENGLISH

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