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Genomics Proteomics Bioinformatics. 2009 Dec;7(4):185-93. doi: 10.1016/S1672-0229(08)60048-0.

In silico characterization and homology modeling of thylakoid-bound ascorbate peroxidase from a drought tolerant wheat cultivar.

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1
National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, New Delhi 110012, India.

Abstract

Ascorbate peroxidase, a haem protein (EC 1.11.1.11), efficiently scavenges hydrogen peroxide (H(2)O(2)) in cytosol and chloroplasts of plants. In this study, a full-length coding sequence of thylakoid-bound ascorbate peroxidase cDNA (TatAPX) was cloned from a drought tolerant wheat cultivar C306. Homology modeling of the TatAPX protein was performed by using the template crystal structure of chloroplastic ascorbate peroxidase from tobacco plant (PDB: 1IYN). The model structure was further refined by molecular mechanics and dynamic methods using various tools such as PROCHECK, ProSA and Verify3D. The predicted model was then tested for docking with H(2)O(2), the substrate for TatAPX enzyme. The results revealed that Arg233 and Glu255 in the predicted active site of the enzyme are two important amino acid residues responsible for strong hydrogen bonding affinity with H(2)O(2), which might play an important role in scavenging of H(2)O(2) from the plant system.

PMID:
20172491
PMCID:
PMC5054410
DOI:
10.1016/S1672-0229(08)60048-0
[Indexed for MEDLINE]
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