tetano
Editor, Senior Moderator
Nat Commun
. 2020 Nov 18;11(1):5877.
doi: 10.1038/s41467-020-19662-4.
Crystallographic structure of wild-type SARS-CoV-2 main protease acyl-enzyme intermediate with physiological C-terminal autoprocessing site
Jaeyong Lee[SUP] 1 2 [/SUP], Liam J Worrall[SUP] 1 [/SUP], Marija Vuckovic[SUP] 1 [/SUP], Federico I Rosell[SUP] 1 [/SUP], Francesco Gentile[SUP] 3 [/SUP], Anh-Tien Ton[SUP] 3 [/SUP], Nathanael A Caveney[SUP] 1 [/SUP], Fuqiang Ban[SUP] 3 [/SUP], Artem Cherkasov[SUP] 3 [/SUP], Mark Paetzel[SUP] 4 [/SUP], Natalie C J Strynadka[SUP] 5 [/SUP]
Affiliations
Abstract
Severe 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 (M[SUP]pro[/SUP]) 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 ? resolution, in its acyl-enzyme intermediate state with the native C-terminal autocleavage sequence at 1.95 ? resolution and in its product bound state at 2.0 ? 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 M[SUP]pro[/SUP] inhibition.
. 2020 Nov 18;11(1):5877.
doi: 10.1038/s41467-020-19662-4.
Crystallographic structure of wild-type SARS-CoV-2 main protease acyl-enzyme intermediate with physiological C-terminal autoprocessing site
Jaeyong Lee[SUP] 1 2 [/SUP], Liam J Worrall[SUP] 1 [/SUP], Marija Vuckovic[SUP] 1 [/SUP], Federico I Rosell[SUP] 1 [/SUP], Francesco Gentile[SUP] 3 [/SUP], Anh-Tien Ton[SUP] 3 [/SUP], Nathanael A Caveney[SUP] 1 [/SUP], Fuqiang Ban[SUP] 3 [/SUP], Artem Cherkasov[SUP] 3 [/SUP], Mark Paetzel[SUP] 4 [/SUP], Natalie C J Strynadka[SUP] 5 [/SUP]
Affiliations
- PMID: 33208735
- DOI: 10.1038/s41467-020-19662-4
Abstract
Severe 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 (M[SUP]pro[/SUP]) 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 ? resolution, in its acyl-enzyme intermediate state with the native C-terminal autocleavage sequence at 1.95 ? resolution and in its product bound state at 2.0 ? 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 M[SUP]pro[/SUP] inhibition.