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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Universiti Sains Malaysia
2017
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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 |
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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 |
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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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1643657419301060608 |
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13.211869 |