10DV
Room Temperature X-Ray Structure of SARS CoV-2 Main Protease Intermediate Precursor with Ensitrelvir (ESV)
Summary for 10DV
| Entry DOI | 10.2210/pdb10dv/pdb |
| Descriptor | Replicase polyprotein 1ab,Immunoglobulin G-binding protein G, 6-[(6-chloranyl-2-methyl-indazol-5-yl)amino]-3-[(1-methyl-1,2,4-triazol-3-yl)methyl]-1-[[2,4,5-tris(fluoranyl)phenyl]methyl]-1,3,5-triazine-2,4-dione (3 entities in total) |
| Functional Keywords | sars cov-2 main protease, enzyme-inhibitor complex, hydrolase, hydrolase-hydrolase inhibitor complex, hydrolase/hydrolase inhibitor |
| Biological source | Homo sapiens (human) More |
| Total number of polymer chains | 2 |
| Total formula weight | 83729.08 |
| Authors | |
| Primary citation | Aniana, A.,Nashed, N.T.,Ghirlando, R.,Bhandari, D.,Kovalevsky, A.,Louis, J.M. Cleavage at the nsp5-nsp6 site of SARS-CoV-2 main protease intermediate precursor is faster from a monomer than a dimer form. J.Biol.Chem., 302:111395-111395, 2026 Cited by PubMed Abstract: Our previous studies of severe acute respiratory syndrome coronavirus 2 main protease (MPro) precursor monomer indicate that the initial N-terminal nonstructural protein (nsp)4/nsp5 cleavage occurs intramolecularly, with a small fraction of the active site loop equilibrium being in the active state. To understand the influence of dimer formation of MPro upon N-terminal cleavage on the subsequent C-terminal nsp5/nsp6 intermolecular cleavage kinetics, the stepwise processing of a monomeric, inactive precursor containing the native terminal cleavage sites of MPro (MBP-MPro-GB1-6H, 86.2 kDa) by mature WT MPro (MPro) was investigated. Differential scanning fluorimetry and analytical ultracentrifugation measurements of various MPro constructs suggest that the C145A mutation decreases the dimer dissociation constant (K) by ∼26-fold, relative to WT C145 and H41A. The monomeric precursor's nsp4-nsp5 site appears to saturate MPro's active sites and cleave faster, followed by a slower first-order cleavage at the C-terminal site. No detectable product resulting from the C-terminal cleavage is observed until most of the N-terminal cleavage is complete. The initial intermediate product (termed MPro) is a homodimer with an estimated K of <0.05 μM. In contrast, the first-order kinetics observed for the cleavage of the monomeric form of the intermediate product is at least 300 times faster than that of the dimer form. Room-temperature X-ray structure of the MPro-ensitrelvir complex is like that of the MPro-ensitrelvir complex and reveals a dynamic C-terminal region including MPro residues 302 to 306. These results are interpreted from the point of view of a mechanism in which nsp5-nsp6 cleavage may occur from a monomeric intermediate, and dimer formation restricts this cleavage. PubMed: 41866037DOI: 10.1016/j.jbc.2026.111395 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (2.05 Å) |
Structure validation
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