7JOY

Product structure of SARS-CoV-2 Mpro C145A mutant in complex with its C-terminal autoprocessing sequence.

7JOY の概要

• エントリーDOI: 10.2210/pdb7joy/pdb
• 関連するPDBエントリー: 7JOX
• 分子名称: 3C-like proteinase (2 entities in total)
• 機能のキーワード: protease, sars-cov-2, viral protein
• 由来する生物種: Severe acute respiratory syndrome coronavirus 2 (2019-nCoV)
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 67586.96

構造登録者

Lee, J.,Worrall, L.J.,Paetzel, M.,Strynadka, N.C.J. (登録日: 2020-08-07, 公開日: 2020-10-07, 最終更新日: 2023-10-18)

主引用文献

Lee, J.,Worrall, L.J.,Vuckovic, M.,Rosell, F.I.,Gentile, F.,Ton, A.T.,Caveney, N.A.,Ban, F.,Cherkasov, A.,Paetzel, M.,Strynadka, N.C.J.
Crystallographic structure of wild-type SARS-CoV-2 main protease acyl-enzyme intermediate with physiological C-terminal autoprocessing site.
Nat Commun, 11:5877-5877, 2020

PubMed 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) 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 M inhibition.

PubMed: 33208735
DOI: 10.1038/s41467-020-19662-4

実験手法

X-RAY DIFFRACTION (2 Å)