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Crystal structures of VIM-1 complexes explain active site heterogeneity in VIM-class metallo-β-lactamases

DOI: 10.1111/febs.14695 DOI Help

Authors: Ramya Salimraj (University of Bristol) , Philip Hinchliffe (University of Bristol) , Magda Kosmopoulou (University of Bristol) , Jonathan M. Tyrrell (Cardiff University) , Jurgen Brem (University of Oxford) , Sander S. Van Berkel (University of Oxford) , Anil Verma (Oxford Protein Production Facility UK, The Research Complex at Harwell) , Raymond J. Owens (Oxford Protein Production Facility UK, The Research Complex at Harwell) , Michael A. Mcdonough (University of Oxford) , Timothy R. Walsh (Cardiff University) , Christopher J. Schofield (University of Oxford) , James Spencer (University of Bristol)
Co-authored by industrial partner: No

Type: Journal Paper
Journal: The Febs Journal

State: Published (Approved)
Published: November 2018
Diamond Proposal Number(s): 313

Abstract: Metallo‐β‐Lactamases (MBLs) protect bacteria from almost all β‐lactam antibiotics. VIM enzymes are among the most clinically important MBLs, with VIM‐1 increasing in carbapenem‐resistant Enterobacteriaceae (Escherichia coli, Klebsiella pneumoniae) that are amongst the hardest bacterial pathogens to treat. VIM enzymes display sequence variation at residues (224 and 228) that in related MBLs are conserved and participate in substrate binding. How they accommodate this variability, while retaining catalytic efficiency against a broad substrate range, has remained unclear. Here we present crystal structures of VIM‐1 and its complexes with a substrate‐mimicking thioenolate inhibitor, ML302F, that restores meropenem activity against a range of VIM‐1 producing clinical strains, and the hydrolysed product of the carbapenem meropenem. Comparison of these two structures identifies a water‐mediated hydrogen bond, between the carboxylate group of substrate/inhibitor and the backbone carbonyl of the active site zinc ligand Cys221, that is common to both complexes. Structural comparisons show that the responsible Cys221‐bound water is observed in all known VIM structures, participates in carboxylate binding with other inhibitor classes, and thus effectively replicates the role of the conserved Lys224 in analogous complexes with other MBLs. These results provide a mechanism for substrate binding that permits the variation at positions 224 and 228 that is a hallmark of VIM MBLs.

Journal Keywords: antibiotic resistance; X‐ray crystallography; hydrolase; metalloenzyme; zinc; metallo‐β‐lactamase; VIM‐1; carbapenem

Subject Areas: Biology and Bio-materials


Instruments: I02-Macromolecular Crystallography , I04-Macromolecular Crystallography , I24-Microfocus Macromolecular Crystallography