9CV5 image
Deposition Date 2024-07-28
Release Date 2025-07-02
Last Version Date 2025-07-02
Entry Detail
PDB ID:
9CV5
Keywords:
Title:
Crystal structure of the metallo-beta-lactamase VIM-31 with L-captopril
Biological Source:
Source Organism:
Method Details:
Experimental Method:
Resolution:
1.40 Å
R-Value Free:
0.18
R-Value Work:
0.15
R-Value Observed:
0.16
Space Group:
I 2 2 2
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Metallo-beta-lactamase type 2
Gene (Uniprot):blaVIM-31
Chain IDs:A
Chain Length:243
Number of Molecules:1
Biological Source:Enterobacter cloacae
Primary Citation
Mutation of an active site-adjacent residue in VIM indirectly dictates interactions with and blunts inhibition by D-captopril.
J.Inorg.Biochem. 271 112975 112975 (2025)
PMID: 40513263 DOI: 10.1016/j.jinorgbio.2025.112975

Abstact

Activity assays and X-ray crystallographic studies were undertaken to elucidate the inhibitory mechanism of captopril stereoisomers on Verona integron-encoded metallo-β-lactamases, specifically VIM-20, VIM-31, and VIM-15. All three VIM-2-like variants (VIM-20, VIM-31, and VIM-15) and VIM-2 expressed in Escherichia coli exhibited catalytic activity with comparable steady-state kinetic parameters. Among the tested thiol drugs (L- and D-captopril, D,L-thiorphan, and 2,3-dimercaprol), IC50 analyses indicated that D-captopril and 2,3-dimercaprol were more potent inhibitors against the VIM enzymes examined in this study. Notably, the IC50 value of D-captopril against VIM-31 was an exception, closely resembling that of L-captopril. To elucidate this exceptional inhibitory potency of D-captopril and its binding mode in the active site of VIM-31, high-resolution crystal structures of VIM-20, VIM-31, and VIM-15 in complex with both L- and D-captopril are reported. These findings will help evaluate whether the identified potent inhibitor D-captopril could be further developed as a pan inhibitor targeting the VIM-family enzymes.

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Primary Citation of related structures