Protonation state of Asp120 in the binuclear active site of the metallo-beta-lactamase from Bacteroides fragilis

Inorg Chem. 2003 Jul 14;42(14):4245-7. doi: 10.1021/ic026059j.

Abstract

The determination of the protonation state of enzyme active sites may be crucial for the investigation of their mechanism of action. In the bizinc beta-lactamase family of enzymes, no consensus has been reached on the protonation state of a fully conserved amino acid present in the active site, Asp120. To address this issue, we carry out here density functional theory (DFT) calculations on large models (based on Bacteroides fragilis X-ray structure) which include the metal coordination polyhedron and groups interacting with it. Our calculations suggest that Asp120 is ionized. The relevance of this finding for site-directed mutagenesis experiments on the 120 position and on the mechanism of action is discussed.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Aspartic Acid / chemistry*
  • Bacteroides fragilis / enzymology*
  • Binding Sites
  • Catalysis
  • Computational Biology
  • Models, Molecular
  • Molecular Conformation
  • Mutagenesis, Site-Directed
  • Protons
  • beta-Lactamases / chemistry*
  • beta-Lactamases / genetics

Substances

  • Protons
  • Aspartic Acid
  • beta-Lactamases