The three-dimensional structure of VIM-31--a metallo-β-lactamase from Enterobacter cloacae in its native and oxidized form

FEBS J. 2015 Jun;282(12):2352-60. doi: 10.1111/febs.13283. Epub 2015 Apr 13.

Abstract

The metallo-β-lactamase VIM-31 differs from VIM-2 by only two Tyr224His and His252Arg substitutions. Located close to the active site, the Tyr224His substitution is also present in VIM-1, VIM-4, VIM-7 and VIM-12. The VIM-31 variant was reported in 2012 from Enterobacter cloacae and kinetically characterized. It exhibits globally lower catalytic efficiencies than VIM-2. In the present study, we report the three-dimensional structures of VIM-31 in its native (reduced) and oxidized forms. The so-called 'flapping-loop' (loop 1) and loop 3 of VIM-31 were not positioned as in VIM-2 but instead were closer to the active site as in VIM-4, resulting in a narrower active site in VIM-31. Also, the presence of His224 in VIM-31 disrupts hydrogen-bonding networks close to the active site. Moreover, a third zinc-binding site, which also exists in VIM-2 structures, could be identified as a structural explanation for the decreased activity of VIM-MBLs at high zinc concentrations.

Keywords: Enterobacter cloacae; active site; antibiotic resistance; crystallographic structures; metallo-β-lactamase.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Substitution
  • Bacterial Proteins / chemistry*
  • Bacterial Proteins / metabolism
  • Binding Sites
  • Catalytic Domain
  • Enterobacter cloacae / enzymology*
  • Hydrogen Bonding
  • Isoenzymes / chemistry
  • Isoenzymes / genetics
  • Isoenzymes / metabolism
  • Kinetics
  • Metalloproteins / chemistry*
  • Metalloproteins / genetics
  • Metalloproteins / metabolism
  • Oxidation-Reduction
  • Protein Conformation
  • Protein Structure, Secondary
  • Recombinant Proteins / chemistry
  • Recombinant Proteins / metabolism
  • Zinc / metabolism
  • beta-Lactamases / chemistry*
  • beta-Lactamases / genetics
  • beta-Lactamases / metabolism

Substances

  • Bacterial Proteins
  • Isoenzymes
  • Metalloproteins
  • Recombinant Proteins
  • beta-Lactamases
  • metallo-beta-lactamase VIM-4, Enterobacter cloacae
  • Zinc

Associated data

  • PDB/4FR7
  • PDB/4FSB