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Title

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

Authors

Saurabh Pandey1, 2, Yogesh Kumar Negi3, Subramanyam Chinreddy1, Krishnamurthy Sathelly1, Sandeep Arora4 & Tanushri Kaul1*

 

Affiliation

1Plant Molecular Biology Laboratory, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi-110067, India; 2Uttarakhand Technical University, Dehradun 248007, India; 3Department of Basic Sciences, College of Forestry & Hill Agriculture, Uttarakhand University of Horticulture & Forestry, Ranichauri 249199, India; 4Department of Molecular Biology and Genetic Engineering, College of Basic Science and Humanities, Govind VallabhPant Agriculture University and Technology, Pantnagar, Uttarakahand-263145, India

 

 

Email

tanushrikaul@gmail.com; *Corresponding author

 

Article Type

Hypothesis

 

Date

Received January 26, 2014; Accepted January 31, 2014; Published March 19, 2014

 

Abstract

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 ), 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 

 

Keywords

Haeme ligand, homology modeling, ascorbate peroxidase, Oryza sativa.

 

Citation

Pandey et al. Bioinformation 10(3): 119-123 (2014)
 

Edited by

P Kangueane

 

ISSN

0973-2063

 

Publisher

Biomedical Informatics

 

License

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.