Binding modes of DL-2-haloacid dehalogenase revealed by crystallography, modeling and isotope effects studies

• Published in: Archives of biochemistry and biophysics Vol. 540; no. 1-2; pp. 26 - 32
• Main Authors: Siwek, Agata, Omi, Rie, Hirotsu, Ken, Jitsumori, Keiji, Esaki, Nobuyoshi, Kurihara, Tatsuo, Paneth, Piotr
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 01.12.2013
• Subjects: active sites; Binding isotope effect; Catalytic Domain; chlorine; Chlorine isotope effect; crystallography; Crystallography, X-Ray; dechlorination; Dehalogenation; DL-DEX; enantiomers; Enzyme Inhibitors - metabolism; Enzyme Inhibitors - pharmacology; enzymes; Hydrolases - antagonists & inhibitors; Hydrolases - chemistry; Hydrolases - genetics; Hydrolases - metabolism; isotope fractionation; Isotopes; Mechanism; Molecular Docking Simulation; Mutagenesis, Site-Directed; Mutation; Propionates - metabolism; Propionates - pharmacology; Protein Binding; Stereoisomerism; Chlorine isotope effect; Dehalogenation; DL-DEX; Mechanism; Binding isotope effect
• ISSN: 0003-9861; 1096-0384
• DOI: 10.1016/j.abb.2013.09.012

[Display omitted] •Crystal structure of DL-DEX with inhibitor has been solved.•Two sites, binding and reactive, have been identified.•Significant participation of binding isotope effects in the overall chlorine kinetic isotope effects have been concluded. Several pathways of biotic dechlorination can be found in enzymes, each characterized by different chlorine isotopic fractionation, which can thus serve as a signature of a particular mechanism. Unlike other dehalogenases, DL-2-haloacid dehalogenase, DL-DEX, converts both enantiomers of the substrate. Chlorine isotope effects for this enzyme are larger than in the case of other dehalogenases. Recently, the 3D structure of this enzyme became available and enabled us to model these isotope effects and seek their origin. We show that the elevated values of the chlorine kinetic isotope effects originate in part in the processes of binding and migration within the enzyme active site that precede the dehalogenation step.