Catalytic mechanism of class B2 metallo-beta-lactamase

J Biol Chem. 2006 Mar 31;281(13):8740-7. doi: 10.1074/jbc.M512517200. Epub 2006 Jan 19.

Abstract

The initial nucleophilic substitution step of biapenem hydrolysis catalyzed by a subclass B2 metallo-beta-lactamase (CphA from Aeromonas hydrophila) is investigated using hybrid quantum mechanical/molecular mechanical methods and density functional theory. We focused on a recently proposed catalytic mechanism that involves a non-metal-binding water nucleophile in the active site of the monozinc CphA. Both theoretical models identified a single transition state featuring nearly concomitant nucleophilic addition and elimination steps, and the activation free energy from the potential of mean force calculations was estimated to be approximately 14 kcal/mol. The theoretical results also identified the general base for activating the water nucleophile to be the metal-binding Asp-120 rather than His-118, as suggested earlier. The protonation of Asp-120 leads to cleavage of the O(delta2)-Zn coordination bond, whereas the negatively charged nitrogen leaving group resulting from the ring opening replaces Asp-120 as the fourth ligand of the sole zinc ion. The electrophilic catalysis by the metal ion provides sufficient stabilization for the leaving group to avoid a tetrahedral intermediate. The theoretical studies provided detailed insights into the catalytic strategy of this unique metallo-beta-lactamase.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Aeromonas hydrophila / enzymology
  • Aspartic Acid / chemistry
  • Bacterial Proteins / chemistry
  • Bacterial Proteins / classification*
  • Bacterial Proteins / metabolism*
  • Binding Sites
  • Carbapenems / metabolism
  • Catalysis
  • Hydrolysis
  • Ligands
  • Models, Chemical
  • Models, Molecular
  • Models, Theoretical
  • Protein Binding
  • Protein Conformation
  • Protons
  • Quantum Theory
  • Thermodynamics
  • Thienamycins / metabolism
  • Water / chemistry
  • Zinc / chemistry
  • beta-Lactamases / chemistry
  • beta-Lactamases / classification*
  • beta-Lactamases / metabolism*

Substances

  • Bacterial Proteins
  • Carbapenems
  • Ligands
  • Protons
  • Thienamycins
  • Water
  • Aspartic Acid
  • beta-Lactamases
  • Zinc
  • biapenem