title: Modeling and phylogenetic analysis of cytosolic ascorbate peroxidase (OsAPX1) from rice reveal signature motifs that may play a role in stress tolerance.
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 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.
authors.affiliation: Plant Molecular Biology Laboratory, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi-110067, India ; Uttarakhand Technical University, Dehradun - 248007, India.
authors.forename: Saurabh
authors.initials: S
authors.lastname: Pandey
authors.affiliation: Department of Basic Sciences, College of Forestry & Hill Agriculture, Uttarakhand University of Horticulture & Forestry, Ranichauri 249199, India.
authors.forename: Yogesh Kumar
authors.initials: YK
authors.lastname: Negi
authors.affiliation: Plant Molecular Biology Laboratory, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi-110067, India.
authors.forename: Subramanyam
authors.initials: S
authors.lastname: Chinreddy
authors.affiliation: Plant Molecular Biology Laboratory, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi-110067, India.
authors.forename: Krishnamurthy
authors.initials: K
authors.lastname: Sathelly
authors.affiliation: Department of Molecular Biology and Genetic Engineering, College of Basic Science and Humanities, Govind VallabhPant Agriculture University and Technology, Pantnagar, Uttarakahand-263145, India.
authors.forename: Sandeep
authors.initials: S
authors.lastname: Arora
authors.affiliation: Plant Molecular Biology Laboratory, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi-110067, India.
authors.forename: Tanushri
authors.initials: T
authors.lastname: Kaul
keywords: Haeme ligand; Oryza sativa; ascorbate peroxidase; homology modeling
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