4K2A

Crystal structure of haloalkane dehalogenase DbeA from Bradyrhizobium elkani USDA94

Summary for 4K2A

• Entry DOI: 10.2210/pdb4k2a/pdb
• Related: 1cij 1cv2 2bn6 2qvb 3a2m
• Descriptor: Haloalkane dehalogenase, CHLORIDE ION, ACETATE ION, ... (4 entities in total)
• Functional Keywords: structural genomics, enzyme function initiative, structure 2 function project, s2f, two domain organization, dimer catalytic pentad, hydrolase, halogen binding
• Biological source: Bradyrhizobium elkanii
• Total number of polymer chains: 4
• Total formula weight: 131345.78

Authors

Prudnikova, T.,Chaloupkova, R.,Rezacova, P.,Mozga, T.,Koudelakova, T.,Sato, Y.,Kuty, M.,Nagata, Y.,Damborsky, J.,Kuta Smatanova, I.,Structure 2 Function Project (S2F) (deposition date: 2013-04-08, release date: 2014-06-25, Last modification date: 2024-02-28)

Primary citation

Chaloupkova, R.,Prudnikova, T.,Rezacova, P.,Prokop, Z.,Koudelakova, T.,Daniel, L.,Brezovsky, J.,Ikeda-Ohtsubo, W.,Sato, Y.,Kuty, M.,Nagata, Y.,Kuta Smatanova, I.,Damborsky, J.
Structural and functional analysis of a novel haloalkane dehalogenase with two halide-binding sites.
Acta Crystallogr.,Sect.D, 70:1884-1897, 2014

PubMed Abstract: 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.

PubMed: 25004965
DOI: 10.1107/S1399004714009018

Experimental method

X-RAY DIFFRACTION (2.2 Å)