Structural insights into the substrate specificity of IMP-6 and IMP-1 metallo-β-lactamases

• Published in: Journal of biochemistry (Tokyo) Vol. 173; no. 1; pp. 21 - 30
• Main Authors: Yamamoto, Keizo, Tanaka, Hideaki, Kurisu, Genji, Nakano, Ryuichi, Yano, Hisakazu, Sakai, Hiromi
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 01.01.2023
• Subjects: Anti-Bacterial Agents - pharmacology; beta-Lactamases - chemistry; beta-Lactamases - genetics; beta-Lactamases - metabolism; Carbapenems - pharmacology; Imipenem - pharmacology; Meropenem; Microbial Sensitivity Tests; Regular Paper; Substrate Specificity; X-ray crystallography; carbapenemase; loop flexibility; metallo-β-lactamase; substrate specificity
• ISSN: 0021-924X; 1756-2651
• DOI: 10.1093/jb/mvac080

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.