5EV6

Crystal structure of the native, di-zinc metallo-beta-lactamase IMP-1

Summary for 5EV6

• Entry DOI: 10.2210/pdb5ev6/pdb
• Descriptor: Beta-lactamase IMP-1, ZINC ION, 1,2-ETHANEDIOL, ... (5 entities in total)
• Functional Keywords: inhibitor, carbapenemase, antibiotic resistance, hydrolase
• Biological source: Serratia marcescens
• Cellular location: Periplasm : P52699
• Total number of polymer chains: 4
• Total formula weight: 101909.83

Authors

Spencer, J.,Hinchliffe, P. (deposition date: 2015-11-19, release date: 2016-06-01, Last modification date: 2024-01-10)

Primary citation

Hinchliffe, P.,Gonzalez, M.M.,Mojica, M.F.,Gonzalez, J.M.,Castillo, V.,Saiz, C.,Kosmopoulou, M.,Tooke, C.L.,Llarrull, L.I.,Mahler, G.,Bonomo, R.A.,Vila, A.J.,Spencer, J.
Cross-class metallo-beta-lactamase inhibition by bisthiazolidines reveals multiple binding modes.
Proc.Natl.Acad.Sci.USA, 113:E3745-E3754, 2016

PubMed Abstract: Metallo-β-lactamases (MBLs) hydrolyze almost all β-lactam antibiotics and are unaffected by clinically available β-lactamase inhibitors (βLIs). Active-site architecture divides MBLs into three classes (B1, B2, and B3), complicating development of βLIs effective against all enzymes. Bisthiazolidines (BTZs) are carboxylate-containing, bicyclic compounds, considered as penicillin analogs with an additional free thiol. Here, we show both l- and d-BTZ enantiomers are micromolar competitive βLIs of all MBL classes in vitro, with Kis of 6-15 µM or 36-84 µM for subclass B1 MBLs (IMP-1 and BcII, respectively), and 10-12 µM for the B3 enzyme L1. Against the B2 MBL Sfh-I, the l-BTZ enantiomers exhibit 100-fold lower Kis (0.26-0.36 µM) than d-BTZs (26-29 µM). Importantly, cell-based time-kill assays show BTZs restore β-lactam susceptibility of Escherichia coli-producing MBLs (IMP-1, Sfh-1, BcII, and GOB-18) and, significantly, an extensively drug-resistant Stenotrophomonas maltophilia clinical isolate expressing L1. BTZs therefore inhibit the full range of MBLs and potentiate β-lactam activity against producer pathogens. X-ray crystal structures reveal insights into diverse BTZ binding modes, varying with orientation of the carboxylate and thiol moieties. BTZs bind the di-zinc centers of B1 (IMP-1; BcII) and B3 (L1) MBLs via the free thiol, but orient differently depending upon stereochemistry. In contrast, the l-BTZ carboxylate dominates interactions with the monozinc B2 MBL Sfh-I, with the thiol uninvolved. d-BTZ complexes most closely resemble β-lactam binding to B1 MBLs, but feature an unprecedented disruption of the D120-zinc interaction. Cross-class MBL inhibition therefore arises from the unexpected versatility of BTZ binding.

PubMed: 27303030
DOI: 10.1073/pnas.1601368113

Experimental method

X-RAY DIFFRACTION (1.984 Å)