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Modeling and phylogenetic analysis of cytosolic ascorbate peroxidase (OsAPX1) from rice reveal signature motifs that may play a role in stress tolerance

Ascorbate peroxidase (APX) is a crucial, haeme-containing enzyme of the ascorbate glutathione cycle that detoxifies reactive oxygen species in plants by catalyzing the conversion of hydrogen peroxide to water using ascorbate as a specific electron donor. Different APX isoforms are present in discret...

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Autores principales: Pandey, Saurabh, Negi, Yogesh Kumar, Chinreddy, Subramanyam, Sathelly, Krishnamurthy, Arora, Sandeep, Kaul, Tanushri
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Biomedical Informatics 2014
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3974237/
https://www.ncbi.nlm.nih.gov/pubmed/24748750
http://dx.doi.org/10.6026/97320630010119
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author Pandey, Saurabh
Negi, Yogesh Kumar
Chinreddy, Subramanyam
Sathelly, Krishnamurthy
Arora, Sandeep
Kaul, Tanushri
author_facet Pandey, Saurabh
Negi, Yogesh Kumar
Chinreddy, Subramanyam
Sathelly, Krishnamurthy
Arora, Sandeep
Kaul, Tanushri
author_sort Pandey, Saurabh
collection PubMed
description Ascorbate peroxidase (APX) is a crucial, haeme-containing enzyme of the ascorbate glutathione cycle that detoxifies reactive oxygen species in plants by catalyzing the conversion of hydrogen peroxide to water using ascorbate as a specific electron donor. Different APX isoforms are present in discrete subcellular compartments in rice and their expression is stress regulated. We revealed the homology model of OsAPX1 protein using the crystal structure of soybean GmAPX1 (PDB ID: 2XIF) as template by Modeller 9.12. The resultant OsAPX1 model structure was refined by PROCHECK, ProSA, Verify3D and RMSD that indicated the model structure is reliable with 83 % amino acid sequence identity with template, RMSD (1.4 Å), Verify3D (86.06 %), Zscores (-8.44) and Ramachandran plot analysis showed that conformations for 94.6% of amino acid residues are within the most favoured regions. Investigation revealed two conserved signatures for haeme ligand binding and peroxidase activity in the alpha helical region that may play a significant role during stress.
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spelling pubmed-39742372014-04-18 Modeling and phylogenetic analysis of cytosolic ascorbate peroxidase (OsAPX1) from rice reveal signature motifs that may play a role in stress tolerance Pandey, Saurabh Negi, Yogesh Kumar Chinreddy, Subramanyam Sathelly, Krishnamurthy Arora, Sandeep Kaul, Tanushri Bioinformation Hypothesis Ascorbate peroxidase (APX) is a crucial, haeme-containing enzyme of the ascorbate glutathione cycle that detoxifies reactive oxygen species in plants by catalyzing the conversion of hydrogen peroxide to water using ascorbate as a specific electron donor. Different APX isoforms are present in discrete subcellular compartments in rice and their expression is stress regulated. We revealed the homology model of OsAPX1 protein using the crystal structure of soybean GmAPX1 (PDB ID: 2XIF) as template by Modeller 9.12. The resultant OsAPX1 model structure was refined by PROCHECK, ProSA, Verify3D and RMSD that indicated the model structure is reliable with 83 % amino acid sequence identity with template, RMSD (1.4 Å), Verify3D (86.06 %), Zscores (-8.44) and Ramachandran plot analysis showed that conformations for 94.6% of amino acid residues are within the most favoured regions. Investigation revealed two conserved signatures for haeme ligand binding and peroxidase activity in the alpha helical region that may play a significant role during stress. Biomedical Informatics 2014-03-19 /pmc/articles/PMC3974237/ /pubmed/24748750 http://dx.doi.org/10.6026/97320630010119 Text en © 2014 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
Pandey, Saurabh
Negi, Yogesh Kumar
Chinreddy, Subramanyam
Sathelly, Krishnamurthy
Arora, Sandeep
Kaul, Tanushri
Modeling and phylogenetic analysis of cytosolic ascorbate peroxidase (OsAPX1) from rice reveal signature motifs that may play a role in stress tolerance
title Modeling and phylogenetic analysis of cytosolic ascorbate peroxidase (OsAPX1) from rice reveal signature motifs that may play a role in stress tolerance
title_full Modeling and phylogenetic analysis of cytosolic ascorbate peroxidase (OsAPX1) from rice reveal signature motifs that may play a role in stress tolerance
title_fullStr Modeling and phylogenetic analysis of cytosolic ascorbate peroxidase (OsAPX1) from rice reveal signature motifs that may play a role in stress tolerance
title_full_unstemmed Modeling and phylogenetic analysis of cytosolic ascorbate peroxidase (OsAPX1) from rice reveal signature motifs that may play a role in stress tolerance
title_short Modeling and phylogenetic analysis of cytosolic ascorbate peroxidase (OsAPX1) from rice reveal signature motifs that may play a role in stress tolerance
title_sort modeling and phylogenetic analysis of cytosolic ascorbate peroxidase (osapx1) from rice reveal signature motifs that may play a role in stress tolerance
topic Hypothesis
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3974237/
https://www.ncbi.nlm.nih.gov/pubmed/24748750
http://dx.doi.org/10.6026/97320630010119
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