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

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 chloropropionat...

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Main Authors:	Sudi, Ismaila Yada, Abdul Hamid, Azzmer Azzar, Shamsir, Mohd Shahir, Jamaluddin, Haryati, Abdul Wahab, Roswanira, Huyop, Fahrul
Format:	Article
Language:	English English
Published:	Taylor and Francis 2014
Subjects:	TP248.13 Biotechnology
Online Access:	http://irep.iium.edu.my/39624/ http://irep.iium.edu.my/39624/ http://irep.iium.edu.my/39624/ http://irep.iium.edu.my/39624/4/insights_into_the.pdf http://irep.iium.edu.my/39624/7/39624_Insights%20into%20the%20stereospecificity.SCOPUSpdf.pdf

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recordtype	eprints
spelling	iium-396242017-09-20T01:53:02Z http://irep.iium.edu.my/39624/ Insights into the stereospecificity of the d-specific dehalogenase from Rhizobium sp. RC1 toward D-and L-2-chloropropionate Sudi, Ismaila Yada Abdul Hamid, Azzmer Azzar Shamsir, Mohd Shahir Jamaluddin, Haryati Abdul Wahab, Roswanira Huyop, Fahrul TP248.13 Biotechnology 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. Taylor and Francis 2014-11-14 Article PeerReviewed application/pdf en http://irep.iium.edu.my/39624/4/insights_into_the.pdf application/pdf en http://irep.iium.edu.my/39624/7/39624_Insights%20into%20the%20stereospecificity.SCOPUSpdf.pdf 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 http://www.tandfonline.com/doi/abs/10.1080/13102818.2014.937907#.VI45lvmSxqU 10.1080/13102818.2014.937907
repository_type	Digital Repository
institution_category	Local University
institution	International Islamic University Malaysia
building	IIUM Repository
collection	Online Access
language	English English
topic	TP248.13 Biotechnology
spellingShingle	TP248.13 Biotechnology Sudi, Ismaila Yada Abdul Hamid, Azzmer Azzar Shamsir, Mohd Shahir Jamaluddin, Haryati Abdul Wahab, Roswanira Huyop, Fahrul Insights into the stereospecificity of the d-specific dehalogenase from Rhizobium sp. RC1 toward D-and L-2-chloropropionate
description	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.
format	Article
author	Sudi, Ismaila Yada Abdul Hamid, Azzmer Azzar Shamsir, Mohd Shahir Jamaluddin, Haryati Abdul Wahab, Roswanira Huyop, Fahrul
author_facet	Sudi, Ismaila Yada Abdul Hamid, Azzmer Azzar Shamsir, Mohd Shahir Jamaluddin, Haryati Abdul Wahab, Roswanira Huyop, Fahrul
author_sort	Sudi, Ismaila Yada
title	Insights into the stereospecificity of the d-specific dehalogenase from Rhizobium sp. RC1 toward D-and L-2-chloropropionate
title_short	Insights into the stereospecificity of the d-specific dehalogenase from Rhizobium sp. RC1 toward D-and L-2-chloropropionate
title_full	Insights into the stereospecificity of the d-specific dehalogenase from Rhizobium sp. RC1 toward D-and L-2-chloropropionate
title_fullStr	Insights into the stereospecificity of the d-specific dehalogenase from Rhizobium sp. RC1 toward D-and L-2-chloropropionate
title_full_unstemmed	Insights into the stereospecificity of the d-specific dehalogenase from Rhizobium sp. RC1 toward D-and L-2-chloropropionate
title_sort	insights into the stereospecificity of the d-specific dehalogenase from rhizobium sp. rc1 toward d-and l-2-chloropropionate
publisher	Taylor and Francis
publishDate	2014
url	http://irep.iium.edu.my/39624/ http://irep.iium.edu.my/39624/ http://irep.iium.edu.my/39624/ http://irep.iium.edu.my/39624/4/insights_into_the.pdf http://irep.iium.edu.my/39624/7/39624_Insights%20into%20the%20stereospecificity.SCOPUSpdf.pdf
first_indexed	2023-09-18T20:56:57Z
last_indexed	2023-09-18T20:56:57Z
_version_	1777410367501107200

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

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