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Comparative Study
. 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

A Katiyar  1 , S K Lenka, K Lakshmi, V Chinnusamy, K C Bansal
Affiliations
Comparative Study

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

A Katiyar et al. Genomics Proteomics Bioinformatics. 2009 Dec.

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.

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Figures

Figure 1
Figure 1
Phylogenetic tree showing sequence similarity of wheat ascorbate peroxidase cDNA (TatAPX) with other relatives.
Figure 2
Figure 2
The final 3D structure of TatAPX-4 model protein. The structure was obtained by Modeller 9v5 and verified using PROCHECK, Verify3D and ProSA servers (Ribbon shape model visualized in chimera).
Figure 3
Figure 3
Ramachandran plot calculation on 3D model of TatAPX-4. The plot calculations were done by PROCHECK program and the plot reveals that 100% of all residues of TatAPX-4 were found in the most favored regions according to Ramachandran plot analysis.
Figure 4
Figure 4
Superimposition of template protein 1IYN (represented in white color) and refined model TatAPX-4 (represented in magenta color).
Figure 5
Figure 5
A. Molecular interaction between TatAPX-4 model protein and the substrate hydrogen peroxide (H2O2). B. Binding of the H2O2 substrate with the residues in the active site of TatAPX-4 using Sybyl 8.0 software suite.
See this image and copyright information in PMC

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