7XHW

Crystal structure of metallo-beta-lactamase IMP-1

Summary for 7XHW

• Entry DOI: 10.2210/pdb7xhw/pdb
• Descriptor: Beta-lactamase, ZINC ION (3 entities in total)
• Functional Keywords: metallo-b-lactamase, carbapenemase, zinc protein, hydrolase, antimicrobial protein
• Biological source: Escherichia coli
• Total number of polymer chains: 4
• Total formula weight: 109143.86

Authors

Yamamoto, K.,Tanaka, H.,Kurisu, G.,Nakano, R.,Yano, H.,Sakai, H. (deposition date: 2022-04-11, release date: 2023-02-15, Last modification date: 2023-11-29)

Primary citation

Yamamoto, K.,Tanaka, H.,Kurisu, G.,Nakano, R.,Yano, H.,Sakai, H.
Structural insights into the substrate specificity of IMP-6 and IMP-1 metallo-beta-lactamases.
J.Biochem., 173:21-30, 2022

PubMed Abstract: IMP-type metallo-β-lactamases confer resistance to carbapenems and a broad spectrum of β-lactam antibiotics. IMP-6 and IMP-1 differ by only a point mutation: Ser262 in IMP-1 and Gly262 in IMP-6. The kcat/Km values of IMP-1 for imipenem and meropenem are nearly identical; however, for IMP-6, the kcat/Km for meropenem is 7-fold that for imipenem. In clinical practice, this may result in an ineffective therapeutic regimen and, consequently, in treatment failure. Here, we report the crystal structures of IMP-6 and IMP-1 with the same space group and similar cell constants at resolutions of 1.70 and 1.94 Å, respectively. The overall structures of IMP-6 and IMP-1 are similar. However, the loop region (residues 60-66), which participates in substrate binding, is more flexible in IMP-6 than in IMP-1. This difference in flexibility determines the substrate specificity of IMP-type metallo-β-lactamases for imipenem and meropenem. The amino acid at position 262 alters the mobility of His263; this affects the flexibility of the loop via a hydrogen bond with Pro68, which plays the role of a hinge in IMP-type metallo-β-lactamases. The substitution of Pro68 with a glycine elicited an increase in the Km of IMP-6 for imipenem, whereas the affinity for meropenem remained unchanged.

PubMed: 36174533
DOI: 10.1093/jb/mvac080

Experimental method

X-RAY DIFFRACTION (1.94 Å)