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Characterization of a hypothetical protein YVRE from Bacillus subtilis indicates its key role as glucono-lactonase in pentose phosphate pathway and glucose metabolism
Hypothetical proteins are functionally uncharacterized proteins with assigned function using sequence annotation tools. Almost half of the coding regions of several genomes are hypothetical proteins. Therefore, it is of our interest to characterize a hypothetical protein YVRE from the model system B...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Biomedical Informatics
2017
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5767921/ https://www.ncbi.nlm.nih.gov/pubmed/29379263 http://dx.doi.org/10.6026/97320630013430 |
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author | Reshma, S.V. Sathyanarayanan, Nitish Nagendra, H.G. |
author_facet | Reshma, S.V. Sathyanarayanan, Nitish Nagendra, H.G. |
author_sort | Reshma, S.V. |
collection | PubMed |
description | Hypothetical proteins are functionally uncharacterized proteins with assigned function using sequence annotation tools. Almost half of the coding regions of several genomes are hypothetical proteins. Therefore, it is of our interest to characterize a hypothetical protein YVRE from the model system Bacillus subtilis using known data. YVRE is assigned the function as a glucono-lactonase using prediction and phylogenetic analysis. A molecular dynamics simulated homology model of YVRE (with calcium) using human senescence marker protein 30 /SMP30 (PDB ID: 3G4E) as template is reported for functional inference. It is observed that the protein possesses bivalent metal binding domain. Molecular docking studies with the substrate glucono-δ-lactone show YVRE binding with the substrate. This data was further validated using cloning and sub-cloning in pUC57 and pET22b+ respectively, followed by expression and purification using nickel affinity chromatography. The activity of YVRE using the substrate glucono-δ-lactone was calculated. The results show the function of YVRE as a gluconolactonase, with higher preference to zinc than calcium or magnesium. Thus, YVRE is shown to play key role in three metabolic pathways namely, pentose phosphate pathway, ascorbate and aldarate metabolism, and caprolactam degradation. |
format | Online Article Text |
id | pubmed-5767921 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2017 |
publisher | Biomedical Informatics |
record_format | MEDLINE/PubMed |
spelling | pubmed-57679212018-01-29 Characterization of a hypothetical protein YVRE from Bacillus subtilis indicates its key role as glucono-lactonase in pentose phosphate pathway and glucose metabolism Reshma, S.V. Sathyanarayanan, Nitish Nagendra, H.G. Bioinformation Hypothesis Hypothetical proteins are functionally uncharacterized proteins with assigned function using sequence annotation tools. Almost half of the coding regions of several genomes are hypothetical proteins. Therefore, it is of our interest to characterize a hypothetical protein YVRE from the model system Bacillus subtilis using known data. YVRE is assigned the function as a glucono-lactonase using prediction and phylogenetic analysis. A molecular dynamics simulated homology model of YVRE (with calcium) using human senescence marker protein 30 /SMP30 (PDB ID: 3G4E) as template is reported for functional inference. It is observed that the protein possesses bivalent metal binding domain. Molecular docking studies with the substrate glucono-δ-lactone show YVRE binding with the substrate. This data was further validated using cloning and sub-cloning in pUC57 and pET22b+ respectively, followed by expression and purification using nickel affinity chromatography. The activity of YVRE using the substrate glucono-δ-lactone was calculated. The results show the function of YVRE as a gluconolactonase, with higher preference to zinc than calcium or magnesium. Thus, YVRE is shown to play key role in three metabolic pathways namely, pentose phosphate pathway, ascorbate and aldarate metabolism, and caprolactam degradation. Biomedical Informatics 2017-12-31 /pmc/articles/PMC5767921/ /pubmed/29379263 http://dx.doi.org/10.6026/97320630013430 Text en © 2017 Biomedical Informatics http://creativecommons.org/licenses/by/3.0/ This is an Open Access article which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. This is distributed under the terms of the Creative Commons Attribution License. |
spellingShingle | Hypothesis Reshma, S.V. Sathyanarayanan, Nitish Nagendra, H.G. Characterization of a hypothetical protein YVRE from Bacillus subtilis indicates its key role as glucono-lactonase in pentose phosphate pathway and glucose metabolism |
title | Characterization of a hypothetical protein YVRE from Bacillus subtilis indicates its key role as glucono-lactonase in pentose phosphate pathway and glucose metabolism |
title_full | Characterization of a hypothetical protein YVRE from Bacillus subtilis indicates its key role as glucono-lactonase in pentose phosphate pathway and glucose metabolism |
title_fullStr | Characterization of a hypothetical protein YVRE from Bacillus subtilis indicates its key role as glucono-lactonase in pentose phosphate pathway and glucose metabolism |
title_full_unstemmed | Characterization of a hypothetical protein YVRE from Bacillus subtilis indicates its key role as glucono-lactonase in pentose phosphate pathway and glucose metabolism |
title_short | Characterization of a hypothetical protein YVRE from Bacillus subtilis indicates its key role as glucono-lactonase in pentose phosphate pathway and glucose metabolism |
title_sort | characterization of a hypothetical protein yvre from bacillus subtilis indicates its key role as glucono-lactonase in pentose phosphate pathway and glucose metabolism |
topic | Hypothesis |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5767921/ https://www.ncbi.nlm.nih.gov/pubmed/29379263 http://dx.doi.org/10.6026/97320630013430 |
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