title: Insights into the stereospecificity of the d-specific dehalogenase fromRhizobiumsp. RC1 toward d- and l-2-chloropropionate.
abstract: Halogenated compounds are recalcitrant environmental pollutants prevalent in agricultural fields, waste waters and industrial by-products, but they can be degraded by dehalogenase-containing microbes. Notably, 2-haloalkanoic acid dehalogenases are employed to resolve optically active chloropropionates, as exemplified by the d-specific dehalogenase fromRhizobiumsp. RCI (DehD), which acts on d-2-chloropropionate but not on its l-enantiomer. The catalytic residues of this dehalogenase responsible for its affinity toward d-2-chloropropionate have not been experimentally determined, although its three-dimensional crystal structure has been solved. For this study, we performedin silicodocking and molecular dynamic simulations of complexes formed by this dehalogenase and d- or l-2-chloropropionate. Arg134 of the enzyme plays the key role in the stereospecific binding and Arg16 is in a position that would allow it to activate a water molecule for hydrolytic attack on the d-2-chloropropionate chiral carbon for release of the halide ion to yield l-2-hydroxypropionate. We propose that within the DehD active site, the NH group of Arg134 can form a hydrogen bond with the carboxylate of d-2-chloropropionate with a strength of ∼4 kcal/mol that may act as an acid-base catalyst, whereas, when l-2-chloropropionate is present, this bond cannot be formed. The significance of the present work is vital for rational design of this dehalogenase in order to confirm the involvement of Arg16 and Arg134 residues implicated in hydrolysis and binding of d-2-chloropropionate in the active site of d-specific dehalogenase fromRhizobiumsp. RC1.
authors.affiliation: Faculty of Biosciences and Medical Engineering (FBME), Universiti Teknologi Malaysia , Johor Bahru , Johor , Malaysia.
authors.forename: Ismaila Yada
authors.initials: IY
authors.lastname: Sudi
authors.affiliation: Faculty of Science, International Islamic University Malaysia , Kuantan , Pahang , Malaysia.
authors.forename: Azzmer Azzar Abdul
authors.initials: AA
authors.lastname: Hamid
authors.affiliation: Faculty of Biosciences and Medical Engineering (FBME), Universiti Teknologi Malaysia , Johor Bahru , Johor , Malaysia.
authors.forename: Mohd Shahir
authors.initials: MS
authors.lastname: Shamsir
authors.affiliation: Faculty of Biosciences and Medical Engineering (FBME), Universiti Teknologi Malaysia , Johor Bahru , Johor , Malaysia.
authors.forename: Haryati
authors.initials: H
authors.lastname: Jamaluddin
authors.affiliation: Faculty of Science, Universiti Teknologi Malaysia , Johor Bahru , Johor , Malaysia.
authors.forename: Roswanira Abdul
authors.initials: RA
authors.lastname: Wahab
authors.affiliation: Faculty of Biosciences and Medical Engineering (FBME), Universiti Teknologi Malaysia , Johor Bahru , Johor , Malaysia.
authors.forename: Fahrul
authors.initials: F
authors.lastname: Huyop
keywords: binding energy; d-2-chloropropionate; d-specific dehalogenase; dehalogenase; hydrogen-bond length; interacting residue; stereospecificity