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Insights into the stereospecificity of the d-specific dehalogenase from Rhizobium sp. RC1 toward D-and L-2-chloropropionate

Sudi, Ismaila Yada and Abdul Hamid, Azzmer Azzar and Shamsir, Mohd Shahir and Jamaluddin, Haryati and Abdul Wahab, Roswanira and Huyop, Fahrul (2014) Insights into the stereospecificity of the d-specific dehalogenase from Rhizobium sp. RC1 toward D-and L-2-chloropropionate. Biotechnology & Biotechnological Equipment, 28 (4). pp. 608-615. ISSN 1310-2818

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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 from Rhizobium sp. 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 performed in silico docking 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 from Rhizobium sp. RC1.

Item Type: Article (Journal)
Additional Information: 7089/39624
Uncontrolled Keywords: binding energy, D-specific dehalogenase, D-2 chloropropionate, dehalogenase, interacting residue, hydrogen-bond length, stereospecificity
Subjects: T Technology > TP Chemical technology > TP248.13 Biotechnology
Kulliyyahs/Centres/Divisions/Institutes (Can select more than one option. Press CONTROL button): Kulliyyah of Science > Department of Biotechnology
Depositing User: Br Azzmer Azzar Abdul Hamid
Date Deposited: 15 Dec 2014 09:31
Last Modified: 20 Sep 2017 09:53
URI: http://irep.iium.edu.my/id/eprint/39624

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