In silico molecular analysis of novel L-specific dehalogenase from Rhizobium sp. RC1

Aims: This study presents the first structural model and proposed the identity of four important key amino acid residues,Asp13, Arg51, Ser131 and Asp207 for the stereospecific haloalkanoic acid dehalogenase from Rhizobium sp. RC1. Methodology and results: The enzyme was built using a homology model...

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Main Authors:	Hanif Harisna, Azza, Edbeib, Mohamed Faraj, Adamu, Aliyu, Abdul Hamid, Azzmer Azzar, Abdul Wahab, Roswanira, Widodo, Nashi, Huyop, Fahrul Zaman
Format:	Article
Language:	English English
Published:	Malaysian Society for Microbiology 2017
Subjects:	Q Science (General) QR Microbiology
Online Access:	http://irep.iium.edu.my/59639/ http://irep.iium.edu.my/59639/ http://irep.iium.edu.my/59639/9/59639-In%20silico%20molecular%20analysis%20of%20novel%20L-specific.pdf http://irep.iium.edu.my/59639/8/59639-In%20silico%20molecular%20analysis%20of%20novel%20L_SCOPUS.pdf

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spelling	iium-596392017-11-27T08:10:28Z http://irep.iium.edu.my/59639/ In silico molecular analysis of novel L-specific dehalogenase from Rhizobium sp. RC1 Hanif Harisna, Azza Edbeib, Mohamed Faraj Adamu, Aliyu Abdul Hamid, Azzmer Azzar Abdul Wahab, Roswanira Widodo, Nashi Huyop, Fahrul Zaman Q Science (General) QR Microbiology Aims: This study presents the first structural model and proposed the identity of four important key amino acid residues,Asp13, Arg51, Ser131 and Asp207 for the stereospecific haloalkanoic acid dehalogenase from Rhizobium sp. RC1. Methodology and results: The enzyme was built using a homology modeling technique; the structure of crystallized LDEX YL from Pseudomonas sp. strain YL as a template. Model validation was performed using PROCHECK to generate the Ramachandran plot. The results showed 80.4% of its residues were located in the most favoured regions suggested that the model is acceptable. Molecular dynamics simulation of the model protein was performed in water for 10 nanoseconds in which Na+ was added to neutralize the negative charge and achieved energy minimization. The energy value and RMSD fluctuation of Cα backbone of the model were computed and confirmed the stability of the model protein. Conclusion, significance and impact of study: In silico or computationally based function prediction is important to complement with future empirical approaches. L-haloacid dehalogenase (DehL), previously isolated from Rhizobium sp. RC1 was known to degrade halogenated environmental pollutants. However, its structure and functions are still unknown. This structural information of DehL provides insights for future work in the rational design of stereospecific haloalkanoic acid dehalogenases Malaysian Society for Microbiology 2017-03 Article PeerReviewed application/pdf en http://irep.iium.edu.my/59639/9/59639-In%20silico%20molecular%20analysis%20of%20novel%20L-specific.pdf application/pdf en http://irep.iium.edu.my/59639/8/59639-In%20silico%20molecular%20analysis%20of%20novel%20L_SCOPUS.pdf Hanif Harisna, Azza and Edbeib, Mohamed Faraj and Adamu, Aliyu and Abdul Hamid, Azzmer Azzar and Abdul Wahab, Roswanira and Widodo, Nashi and Huyop, Fahrul Zaman (2017) In silico molecular analysis of novel L-specific dehalogenase from Rhizobium sp. RC1. Malaysian Journal of Microbiology, 13 (1). pp. 50-60. ISSN 1823-8262 E-ISSN 2231-7538 http://mjm.usm.my/uploads/issues/882/8.%20In%20silico%20molecular%20analysis%20of%20novel%20L-specific%20dehalogenase%20from%20Rhizobium%20sp.%20RC1.pdfhttp://mjm.usm.my/uploads/issues/882/8.%20In%20silico%20molecular%20analysis%20of%20novel%20L-specific%20dehalogenase%20from%20Rhizobium%20sp.%20RC1.pdf
repository_type	Digital Repository
institution_category	Local University
institution	International Islamic University Malaysia
building	IIUM Repository
collection	Online Access
language	English English
topic	Q Science (General) QR Microbiology
spellingShingle	Q Science (General) QR Microbiology Hanif Harisna, Azza Edbeib, Mohamed Faraj Adamu, Aliyu Abdul Hamid, Azzmer Azzar Abdul Wahab, Roswanira Widodo, Nashi Huyop, Fahrul Zaman In silico molecular analysis of novel L-specific dehalogenase from Rhizobium sp. RC1
description	Aims: This study presents the first structural model and proposed the identity of four important key amino acid residues,Asp13, Arg51, Ser131 and Asp207 for the stereospecific haloalkanoic acid dehalogenase from Rhizobium sp. RC1. Methodology and results: The enzyme was built using a homology modeling technique; the structure of crystallized LDEX YL from Pseudomonas sp. strain YL as a template. Model validation was performed using PROCHECK to generate the Ramachandran plot. The results showed 80.4% of its residues were located in the most favoured regions suggested that the model is acceptable. Molecular dynamics simulation of the model protein was performed in water for 10 nanoseconds in which Na+ was added to neutralize the negative charge and achieved energy minimization. The energy value and RMSD fluctuation of Cα backbone of the model were computed and confirmed the stability of the model protein. Conclusion, significance and impact of study: In silico or computationally based function prediction is important to complement with future empirical approaches. L-haloacid dehalogenase (DehL), previously isolated from Rhizobium sp. RC1 was known to degrade halogenated environmental pollutants. However, its structure and functions are still unknown. This structural information of DehL provides insights for future work in the rational design of stereospecific haloalkanoic acid dehalogenases
format	Article
author	Hanif Harisna, Azza Edbeib, Mohamed Faraj Adamu, Aliyu Abdul Hamid, Azzmer Azzar Abdul Wahab, Roswanira Widodo, Nashi Huyop, Fahrul Zaman
author_facet	Hanif Harisna, Azza Edbeib, Mohamed Faraj Adamu, Aliyu Abdul Hamid, Azzmer Azzar Abdul Wahab, Roswanira Widodo, Nashi Huyop, Fahrul Zaman
author_sort	Hanif Harisna, Azza
title	In silico molecular analysis of novel L-specific dehalogenase from Rhizobium sp. RC1
title_short	In silico molecular analysis of novel L-specific dehalogenase from Rhizobium sp. RC1
title_full	In silico molecular analysis of novel L-specific dehalogenase from Rhizobium sp. RC1
title_fullStr	In silico molecular analysis of novel L-specific dehalogenase from Rhizobium sp. RC1
title_full_unstemmed	In silico molecular analysis of novel L-specific dehalogenase from Rhizobium sp. RC1
title_sort	in silico molecular analysis of novel l-specific dehalogenase from rhizobium sp. rc1
publisher	Malaysian Society for Microbiology
publishDate	2017
url	http://irep.iium.edu.my/59639/ http://irep.iium.edu.my/59639/ http://irep.iium.edu.my/59639/9/59639-In%20silico%20molecular%20analysis%20of%20novel%20L-specific.pdf http://irep.iium.edu.my/59639/8/59639-In%20silico%20molecular%20analysis%20of%20novel%20L_SCOPUS.pdf
first_indexed	2023-09-18T21:24:30Z
last_indexed	2023-09-18T21:24:30Z
_version_	1777412101151653888

In silico molecular analysis of novel L-specific dehalogenase from Rhizobium sp. RC1

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