4FR7

Crystal structure of the metallo-beta-lactamase VIM-31 in its reduced form at 1.61 A

Summary for 4FR7

• Entry DOI: 10.2210/pdb4fr7/pdb
• Related: 4FSB
• Descriptor: Metallo-beta-lactamase VIM-31, ZINC ION, ACETATE ION, ... (5 entities in total)
• Functional Keywords: metallo-beta-lactamase superfamily, beta-lactam hydrolyzing enzyme, zinc binding, hydrolase
• Biological source: Enterobacter cloacae
• Total number of polymer chains: 1
• Total formula weight: 25542.73

Authors

Herzog, K.,Hoffmann, K.M. (deposition date: 2012-06-26, release date: 2013-06-26, Last modification date: 2023-12-06)

Primary citation

Kupper, M.B.,Herzog, K.,Bennink, S.,Schlomer, P.,Bogaerts, P.,Glupczynski, Y.,Fischer, R.,Bebrone, C.,Hoffmann, K.M.
The three-dimensional structure of VIM-31 - a metallo-beta-lactamase from Enterobacter cloacae in its native and oxidized form.
Febs J., 282:2352-2360, 2015

PubMed 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.

PubMed: 25825035
DOI: 10.1111/febs.13283

Experimental method

X-RAY DIFFRACTION (1.61 Å)