Molecular modelling and functional studies of the non-stereospecific α-haloalkanoic acid dehalogenase (DehE) from Rhizobium sp. RC1 and its association with 3-chloropropionic acid (β-chlorinated aliphatic acid)

Many environmental pollutions are caused by the abundance of xenobiotic compounds in nature. For instance, halogenated compounds released from chemical industries were proven to be toxic and recalcitrant in the environment. However, haloalkanoic acid dehalogenases can catalyse the removal of halides...

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Main Authors:	Abdul Hamid, Azzmer Azzar, Wong, Ee Lin, Joyce-Tan, Kwee Hong, Shamsir, Mohd Shahir, Tengku Abdul Hamid, Tengku Haziyamin, Huyop, Fahrul Zaman
Format:	Article
Language:	English
Published:	Diagnosis Press 2013
Subjects:	Q Science (General) QD Chemistry TD172 Environmental pollution
Online Access:	http://irep.iium.edu.my/30093/ http://irep.iium.edu.my/30093/ http://irep.iium.edu.my/30093/ http://irep.iium.edu.my/30093/1/molecular_modelling_and_functional_studies_of_the_non_stereospecific.pdf

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spelling	iium-300932014-08-05T01:24:16Z http://irep.iium.edu.my/30093/ Molecular modelling and functional studies of the non-stereospecific α-haloalkanoic acid dehalogenase (DehE) from Rhizobium sp. RC1 and its association with 3-chloropropionic acid (β-chlorinated aliphatic acid) Abdul Hamid, Azzmer Azzar Wong, Ee Lin Joyce-Tan, Kwee Hong Shamsir, Mohd Shahir Tengku Abdul Hamid, Tengku Haziyamin Huyop, Fahrul Zaman Q Science (General) QD Chemistry TD172 Environmental pollution Many environmental pollutions are caused by the abundance of xenobiotic compounds in nature. For instance, halogenated compounds released from chemical industries were proven to be toxic and recalcitrant in the environment. However, haloalkanoic acid dehalogenases can catalyse the removal of halides from organic haloacids and thus have gained interest for bioremediation and synthesis of industrial chemicals. This study presents the first structural model and the key residues of the non-stereospecific haloalkanoic acid dehalogenase, DehE, from Rhizobium sp. RC1. The enzyme was built using a homology modelling technique; the structure of DehI from Pseudomonas putida PP3 was used as a template, because of its homology to DehE. The structure of DehE consists of only α-helices. Twelve conserved residues that line the active site were identified: Trp34, Ala36, Phe37, Asn114, Tyr117 Ala187, Ser188, Asp189, Tyr265, Phe268, Ile269, and Ile272. These residues are consistent with the residues found in the active site of DehI and D,L-DEX 113 from Pseudomonas sp. 113. Asp189 activates the water molecule as a nucleophile to attack the substrate chiral centre, which would result in an inversion of configuration of either D- or L-substrates. Both D- and L-substrates bind to and interact with the enzyme by hydrogen bonding with three residues, Trp34, Phe37, and Ser188. In addition, a putative tunnel was also identified that would provide a channel for the substrate to access the binding site. Based on computational analysis, DehE was proven to have the substrate affinity towards 3-chloropropionic acid (3CP)/β-chlorinated aliphatic acid, however, its dehalogenation process is far from clear. This DehE structural information will allow for rational design of non-stereospecific haloalkanoic acid dehalogenases in the future. Diagnosis Press 2013 Article PeerReviewed application/pdf en http://irep.iium.edu.my/30093/1/molecular_modelling_and_functional_studies_of_the_non_stereospecific.pdf Abdul Hamid, Azzmer Azzar and Wong, Ee Lin and Joyce-Tan, Kwee Hong and Shamsir, Mohd Shahir and Tengku Abdul Hamid, Tengku Haziyamin and Huyop, Fahrul Zaman (2013) Molecular modelling and functional studies of the non-stereospecific α-haloalkanoic acid dehalogenase (DehE) from Rhizobium sp. RC1 and its association with 3-chloropropionic acid (β-chlorinated aliphatic acid). Biotechnology & Biotechnological Equipment, 27 (2). pp. 3725-3736. ISSN 1310-2818 http://dx.doi.org/10.5504/bbeq.2012.0142 10.5504/bbeq.2012.0142
repository_type	Digital Repository
institution_category	Local University
institution	International Islamic University Malaysia
building	IIUM Repository
collection	Online Access
language	English
topic	Q Science (General) QD Chemistry TD172 Environmental pollution
spellingShingle	Q Science (General) QD Chemistry TD172 Environmental pollution Abdul Hamid, Azzmer Azzar Wong, Ee Lin Joyce-Tan, Kwee Hong Shamsir, Mohd Shahir Tengku Abdul Hamid, Tengku Haziyamin Huyop, Fahrul Zaman Molecular modelling and functional studies of the non-stereospecific α-haloalkanoic acid dehalogenase (DehE) from Rhizobium sp. RC1 and its association with 3-chloropropionic acid (β-chlorinated aliphatic acid)
description	Many environmental pollutions are caused by the abundance of xenobiotic compounds in nature. For instance, halogenated compounds released from chemical industries were proven to be toxic and recalcitrant in the environment. However, haloalkanoic acid dehalogenases can catalyse the removal of halides from organic haloacids and thus have gained interest for bioremediation and synthesis of industrial chemicals. This study presents the first structural model and the key residues of the non-stereospecific haloalkanoic acid dehalogenase, DehE, from Rhizobium sp. RC1. The enzyme was built using a homology modelling technique; the structure of DehI from Pseudomonas putida PP3 was used as a template, because of its homology to DehE. The structure of DehE consists of only α-helices. Twelve conserved residues that line the active site were identified: Trp34, Ala36, Phe37, Asn114, Tyr117 Ala187, Ser188, Asp189, Tyr265, Phe268, Ile269, and Ile272. These residues are consistent with the residues found in the active site of DehI and D,L-DEX 113 from Pseudomonas sp. 113. Asp189 activates the water molecule as a nucleophile to attack the substrate chiral centre, which would result in an inversion of configuration of either D- or L-substrates. Both D- and L-substrates bind to and interact with the enzyme by hydrogen bonding with three residues, Trp34, Phe37, and Ser188. In addition, a putative tunnel was also identified that would provide a channel for the substrate to access the binding site. Based on computational analysis, DehE was proven to have the substrate affinity towards 3-chloropropionic acid (3CP)/β-chlorinated aliphatic acid, however, its dehalogenation process is far from clear. This DehE structural information will allow for rational design of non-stereospecific haloalkanoic acid dehalogenases in the future.
format	Article
author	Abdul Hamid, Azzmer Azzar Wong, Ee Lin Joyce-Tan, Kwee Hong Shamsir, Mohd Shahir Tengku Abdul Hamid, Tengku Haziyamin Huyop, Fahrul Zaman
author_facet	Abdul Hamid, Azzmer Azzar Wong, Ee Lin Joyce-Tan, Kwee Hong Shamsir, Mohd Shahir Tengku Abdul Hamid, Tengku Haziyamin Huyop, Fahrul Zaman
author_sort	Abdul Hamid, Azzmer Azzar
title	Molecular modelling and functional studies of the non-stereospecific α-haloalkanoic acid dehalogenase (DehE) from Rhizobium sp. RC1 and its association with 3-chloropropionic acid (β-chlorinated aliphatic acid)
title_short	Molecular modelling and functional studies of the non-stereospecific α-haloalkanoic acid dehalogenase (DehE) from Rhizobium sp. RC1 and its association with 3-chloropropionic acid (β-chlorinated aliphatic acid)
title_full	Molecular modelling and functional studies of the non-stereospecific α-haloalkanoic acid dehalogenase (DehE) from Rhizobium sp. RC1 and its association with 3-chloropropionic acid (β-chlorinated aliphatic acid)
title_fullStr	Molecular modelling and functional studies of the non-stereospecific α-haloalkanoic acid dehalogenase (DehE) from Rhizobium sp. RC1 and its association with 3-chloropropionic acid (β-chlorinated aliphatic acid)
title_full_unstemmed	Molecular modelling and functional studies of the non-stereospecific α-haloalkanoic acid dehalogenase (DehE) from Rhizobium sp. RC1 and its association with 3-chloropropionic acid (β-chlorinated aliphatic acid)
title_sort	molecular modelling and functional studies of the non-stereospecific α-haloalkanoic acid dehalogenase (dehe) from rhizobium sp. rc1 and its association with 3-chloropropionic acid (β-chlorinated aliphatic acid)
publisher	Diagnosis Press
publishDate	2013
url	http://irep.iium.edu.my/30093/ http://irep.iium.edu.my/30093/ http://irep.iium.edu.my/30093/ http://irep.iium.edu.my/30093/1/molecular_modelling_and_functional_studies_of_the_non_stereospecific.pdf
first_indexed	2023-09-18T20:44:11Z
last_indexed	2023-09-18T20:44:11Z
_version_	1777409564482732032

Molecular modelling and functional studies of the non-stereospecific α-haloalkanoic acid dehalogenase (DehE) from Rhizobium sp. RC1 and its association with 3-chloropropionic acid (β-chlorinated aliphatic acid)

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