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Structure prediction and analysis of MxaF from obligate, facultative and restricted facultative methylobacterium

Methylobacteria are ubiquitous in the biosphere which are capable of growing on C1 compounds such as formate, formaldehyde, methanol and methylamine as well as on a wide range of multi-carbon growth substrates such as C2, C3 and C4 compounds due to the methylotrophic enzymes methanol dehydrogenase (...

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Autores principales: Singh, Raghvendra Pratap, Singh, Ram Nageena, Srivastava, Manish K, Srivastava, Alok Kumar, Kumar, Sudheer, Dubey, Ramesh Chandra, Sharma, Arun Kumar
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Biomedical Informatics 2012
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3524886/
https://www.ncbi.nlm.nih.gov/pubmed/23275704
http://dx.doi.org/10.6026/97320630081042
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author Singh, Raghvendra Pratap
Singh, Ram Nageena
Srivastava, Manish K
Srivastava, Alok Kumar
Kumar, Sudheer
Dubey, Ramesh Chandra
Sharma, Arun Kumar
author_facet Singh, Raghvendra Pratap
Singh, Ram Nageena
Srivastava, Manish K
Srivastava, Alok Kumar
Kumar, Sudheer
Dubey, Ramesh Chandra
Sharma, Arun Kumar
author_sort Singh, Raghvendra Pratap
collection PubMed
description Methylobacteria are ubiquitous in the biosphere which are capable of growing on C1 compounds such as formate, formaldehyde, methanol and methylamine as well as on a wide range of multi-carbon growth substrates such as C2, C3 and C4 compounds due to the methylotrophic enzymes methanol dehydrogenase (MDH). MDH is performing these functions with the help of a key protein mxaF. Unfortunately, detailed structural analysis and homology modeling of mxaF is remains undefined. Hence, the objective of this research is the characterization and three dimensional modeling of mxaF protein from three different methylotrophs by using I-TASSER server. The predicted model were further optimize and validate by Profile 3D, Errat, Verifiy3-D and PROCHECK server. Predicted and best evaluated models have been successfully deposited to PMDB database with PMDB ID PM0077505, PM0077506 and PM0077507. Active site identification revealed 11, 13 and 14 putative functional site residues in respected models. It may play a major role during protein-protein, and protein-cofactor interactions. This study can provide us an ab-initio and detail information to understand the structure, mechanism of action and regulation of mxaF protein.
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spelling pubmed-35248862012-12-28 Structure prediction and analysis of MxaF from obligate, facultative and restricted facultative methylobacterium Singh, Raghvendra Pratap Singh, Ram Nageena Srivastava, Manish K Srivastava, Alok Kumar Kumar, Sudheer Dubey, Ramesh Chandra Sharma, Arun Kumar Bioinformation Hypothesis Methylobacteria are ubiquitous in the biosphere which are capable of growing on C1 compounds such as formate, formaldehyde, methanol and methylamine as well as on a wide range of multi-carbon growth substrates such as C2, C3 and C4 compounds due to the methylotrophic enzymes methanol dehydrogenase (MDH). MDH is performing these functions with the help of a key protein mxaF. Unfortunately, detailed structural analysis and homology modeling of mxaF is remains undefined. Hence, the objective of this research is the characterization and three dimensional modeling of mxaF protein from three different methylotrophs by using I-TASSER server. The predicted model were further optimize and validate by Profile 3D, Errat, Verifiy3-D and PROCHECK server. Predicted and best evaluated models have been successfully deposited to PMDB database with PMDB ID PM0077505, PM0077506 and PM0077507. Active site identification revealed 11, 13 and 14 putative functional site residues in respected models. It may play a major role during protein-protein, and protein-cofactor interactions. This study can provide us an ab-initio and detail information to understand the structure, mechanism of action and regulation of mxaF protein. Biomedical Informatics 2012-10-31 /pmc/articles/PMC3524886/ /pubmed/23275704 http://dx.doi.org/10.6026/97320630081042 Text en © 2012 Biomedical Informatics This is an open-access article, which permits unrestricted use, distribution, and reproduction in any medium, for non-commercial purposes, provided the original author and source are credited.
spellingShingle Hypothesis
Singh, Raghvendra Pratap
Singh, Ram Nageena
Srivastava, Manish K
Srivastava, Alok Kumar
Kumar, Sudheer
Dubey, Ramesh Chandra
Sharma, Arun Kumar
Structure prediction and analysis of MxaF from obligate, facultative and restricted facultative methylobacterium
title Structure prediction and analysis of MxaF from obligate, facultative and restricted facultative methylobacterium
title_full Structure prediction and analysis of MxaF from obligate, facultative and restricted facultative methylobacterium
title_fullStr Structure prediction and analysis of MxaF from obligate, facultative and restricted facultative methylobacterium
title_full_unstemmed Structure prediction and analysis of MxaF from obligate, facultative and restricted facultative methylobacterium
title_short Structure prediction and analysis of MxaF from obligate, facultative and restricted facultative methylobacterium
title_sort structure prediction and analysis of mxaf from obligate, facultative and restricted facultative methylobacterium
topic Hypothesis
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3524886/
https://www.ncbi.nlm.nih.gov/pubmed/23275704
http://dx.doi.org/10.6026/97320630081042
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