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: Harisna, A. H., Edbeib, M. F., Adamu, A., Hamid, A. A. A., Wahab, R. A ., Widodo, Widodo, Huyop, F.
Format: Article
Language:English
Published: Universiti Sains Malaysia 2017
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Online Access:http://eprints.utm.my/id/eprint/76824/1/RoswaniraAbdulWahab2017_InSilicoMolecularAnalysisofNovelL.pdf
http://eprints.utm.my/id/eprint/76824/
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spelling my.utm.768242018-04-30T14:10:41Z http://eprints.utm.my/id/eprint/76824/ In silico molecular analysis of novel L-specific dehalogenase from Rhizobium sp. RC1 Harisna, A. H. Edbeib, M. F. Adamu, A. Hamid, A. A. A. Wahab, R. A . Widodo, Widodo Huyop, F. TP Chemical technology 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 Ca 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. Universiti Sains Malaysia 2017 Article PeerReviewed application/pdf en http://eprints.utm.my/id/eprint/76824/1/RoswaniraAbdulWahab2017_InSilicoMolecularAnalysisofNovelL.pdf Harisna, A. H. and Edbeib, M. F. and Adamu, A. and Hamid, A. A. A. and Wahab, R. A . and Widodo, Widodo and Huyop, F. (2017) In silico molecular analysis of novel L-specific dehalogenase from Rhizobium sp. RC1. Malaysian Journal of Microbiology, 13 (1). pp. 50-60. ISSN 2231-7538 https://www.scopus.com/inward/record.uri?eid=2-s2.0-85016927418&partnerID=40&md5=b7a2e4eda80fe0a59b76a5826dd86717
institution Universiti Teknologi Malaysia
building UTM Library
collection Institutional Repository
continent Asia
country Malaysia
content_provider Universiti Teknologi Malaysia
content_source UTM Institutional Repository
url_provider http://eprints.utm.my/
language English
topic TP Chemical technology
spellingShingle TP Chemical technology
Harisna, A. H.
Edbeib, M. F.
Adamu, A.
Hamid, A. A. A.
Wahab, R. A .
Widodo, Widodo
Huyop, F.
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 Ca 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 Harisna, A. H.
Edbeib, M. F.
Adamu, A.
Hamid, A. A. A.
Wahab, R. A .
Widodo, Widodo
Huyop, F.
author_facet Harisna, A. H.
Edbeib, M. F.
Adamu, A.
Hamid, A. A. A.
Wahab, R. A .
Widodo, Widodo
Huyop, F.
author_sort Harisna, A. H.
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 Universiti Sains Malaysia
publishDate 2017
url http://eprints.utm.my/id/eprint/76824/1/RoswaniraAbdulWahab2017_InSilicoMolecularAnalysisofNovelL.pdf
http://eprints.utm.my/id/eprint/76824/
https://www.scopus.com/inward/record.uri?eid=2-s2.0-85016927418&partnerID=40&md5=b7a2e4eda80fe0a59b76a5826dd86717
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score 13.211869