7Z2K

Crystal structure of SARS-CoV-2 Main Protease in orthorhombic space group p212121

Summary for 7Z2K

• Entry DOI: 10.2210/pdb7z2k/pdb
• Descriptor: 3C-like proteinase nsp5, CHLORIDE ION, DIMETHYL SULFOXIDE, ... (5 entities in total)
• Functional Keywords: main protease, mpro, cystein protease, drug development, drug target, peptide-like inhibitor, sars-cov-2, covid-19, hydrolase
• Biological source: Severe acute respiratory syndrome coronavirus 2
• Total number of polymer chains: 2
• Total formula weight: 68058.45

Authors

Reinke, P.Y.A.,Falke, S.,Lieske, J.,Ewert, W.,Loboda, J.,Rahmani Mashhour, A.,Hauser, M.,Karnicar, K.,Usenik, A.,Lindic, N.,Lach, M.,Boehler, H.,Beck, T.,Cox, R.,Chapman, H.N.,Hinrichs, W.,Turk, D.,Guenther, S.,Meents, A. (deposition date: 2022-02-28, release date: 2023-03-22, Last modification date: 2024-07-31)

Primary citation

Reinke, P.Y.A.,Schubert, R.,Oberthur, D.,Galchenkova, M.,Rahmani Mashhour, A.,Gunther, S.,Chretien, A.,Round, A.,Seychell, B.C.,Norton-Baker, B.,Kim, C.,Schmidt, C.,Koua, F.H.M.,Tolstikova, A.,Ewert, W.,Pena Murillo, G.E.,Mills, G.,Kirkwood, H.,Brognaro, H.,Han, H.,Koliyadu, J.,Schulz, J.,Bielecki, J.,Lieske, J.,Maracke, J.,Knoska, J.,Lorenzen, K.,Brings, L.,Sikorski, M.,Kloos, M.,Vakili, M.,Vagovic, P.,Middendorf, P.,de Wijn, R.,Bean, R.,Letrun, R.,Han, S.,Falke, S.,Geng, T.,Sato, T.,Srinivasan, V.,Kim, Y.,Yefanov, O.M.,Gelisio, L.,Beck, T.,Dore, A.S.,Mancuso, A.P.,Betzel, C.,Bajt, S.,Redecke, L.,Chapman, H.N.,Meents, A.,Turk, D.,Hinrichs, W.,Lane, T.J.
SARS-CoV-2 M pro responds to oxidation by forming disulfide and NOS/SONOS bonds.
Nat Commun, 15:3827-3827, 2024

PubMed Abstract: The main protease (M) of SARS-CoV-2 is critical for viral function and a key drug target. M is only active when reduced; turnover ceases upon oxidation but is restored by re-reduction. This suggests the system has evolved to survive periods in an oxidative environment, but the mechanism of this protection has not been confirmed. Here, we report a crystal structure of oxidized M showing a disulfide bond between the active site cysteine, C145, and a distal cysteine, C117. Previous work proposed this disulfide provides the mechanism of protection from irreversible oxidation. M forms an obligate homodimer, and the C117-C145 structure shows disruption of interactions bridging the dimer interface, implying a correlation between oxidation and dimerization. We confirm dimer stability is weakened in solution upon oxidation. Finally, we observe the protein's crystallization behavior is linked to its redox state. Oxidized M spontaneously forms a distinct, more loosely packed lattice. Seeding with crystals of this lattice yields a structure with an oxidation pattern incorporating one cysteine-lysine-cysteine (SONOS) and two lysine-cysteine (NOS) bridges. These structures further our understanding of the oxidative regulation of M and the crystallization conditions necessary to study this structurally.

PubMed: 38714735
DOI: 10.1038/s41467-024-48109-3

Experimental method

X-RAY DIFFRACTION (1.65 Å)