7DTM image
Entry Detail
PDB ID:
7DTM
Keywords:
Title:
Crystal structure of metallo-beta-lactamase IMP-1 in complex with citrate.
Biological Source:
Source Organism:
PDB Version:
Deposition Date:
2021-01-06
Release Date:
2021-08-04
Method Details:
Experimental Method:
Resolution:
2.00 Å
R-Value Free:
0.24
R-Value Work:
0.21
R-Value Observed:
0.21
Space Group:
P 1
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:Metallo-beta-lactamase type 2
Chain IDs:A, B, C, D
Chain Length:228
Number of Molecules:4
Biological Source:Serratia marcescens
Primary Citation
Crystal Structures of Metallo-beta-Lactamase (IMP-1) and Its D120E Mutant in Complexes with Citrate and the Inhibitory Effect of the Benzyl Group in Citrate Monobenzyl Ester.
J.Med.Chem. 64 10019 10026 (2021)
PMID: 34242022 DOI: 10.1021/acs.jmedchem.1c00308

Abstact

The emergence and rapid spread of carbapenem-resistant pathogens producing metallo-β-lactamases such as IMP-1 and NDM-1 have been of great concern in the global clinical setting. The X-ray crystal structures of IMP-1 from Serratia marcescens and its single mutant, D120E, in complexes with citrate were determined at resolutions of 2.00 and 1.85 Å, respectively. Two crystal structures indicate that a single mutation at position 120 caused a structural change around Zn1, where the geometry changes from a tetrahedron in the native IMP-1 to a square pyramid in D120E. Based on these two complex structures, the authors synthesized citrate monobenzyl ester 1 to evaluate the structural requirement for the inhibitory activity against IMP-1 and compared the inhibitory activities with nonsubstituted citrate. The introduction of a benzyl group into citrate enhanced the inhibitory activity in comparison to citrate (IC50 > 5 mM).

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