Structural and functional analysis of a novel haloalkane dehalogenase with two halide-binding sites

Acta Crystallogr D Biol Crystallogr. 2014 Jul;70(Pt 7):1884-97. doi: 10.1107/S1399004714009018. Epub 2014 Jun 29.


The crystal structure of the novel haloalkane dehalogenase DbeA from Bradyrhizobium elkanii USDA94 revealed the presence of two chloride ions buried in the protein interior. The first halide-binding site is involved in substrate binding and is present in all structurally characterized haloalkane dehalogenases. The second halide-binding site is unique to DbeA. To elucidate the role of the second halide-binding site in enzyme functionality, a two-point mutant lacking this site was constructed and characterized. These substitutions resulted in a shift in the substrate-specificity class and were accompanied by a decrease in enzyme activity, stability and the elimination of substrate inhibition. The changes in enzyme catalytic activity were attributed to deceleration of the rate-limiting hydrolytic step mediated by the lower basicity of the catalytic histidine.

Keywords: catalytic activity; enzyme stability; halide-binding site; haloalkane dehalogenase; substrate specificity.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Binding Sites
  • Crystallization
  • Halogens / metabolism*
  • Hydrolases / chemistry
  • Hydrolases / metabolism*
  • Kinetics
  • Principal Component Analysis


  • Halogens
  • Hydrolases
  • haloalkane dehalogenase

Associated data

  • PDB/4K2A