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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.

Pandey S, Negi YK, Chinreddy S, Sathelly K, Arora S, Kaul T - Bioinformation (2014)

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

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.

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.

No MeSH data available.


Related in: MedlinePlus

Validation of OsAPX1 structure model by ProSAIItools. The Z-score values of A) OsAPX1 (Target) and B)GmAPX1 (Template) proteins determined by NMR(represented in dark blue) and X-ray (represented in light blue).The two black dots represent Z-score value of template andtarget.
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Figure 3: Validation of OsAPX1 structure model by ProSAIItools. The Z-score values of A) OsAPX1 (Target) and B)GmAPX1 (Template) proteins determined by NMR(represented in dark blue) and X-ray (represented in light blue).The two black dots represent Z-score value of template andtarget.

Mentions: ProSA-Web analysis of the model revealed a Z-score value oftarget protein. The Z-score indicates overall model quality andmeasures the deviation of the total energy of the structure withrespect to an energy distribution derived from randomconformations. In order to facilitate interpretation of the Z scoreof the specified protein, its particular value was displayedin a plot that contains the Z scores of all experimentallydetermined protein chains in OsAPX1 PDB. Groups ofstructures from different sources (X-ray, NMR) aredistinguished by different colours (NMR in dark blue and X rayin light blue). This plot can be used to check whether the Zscoreof the protein in question is within the range of scorestypically found for proteins of similar size belonging to one ofthese groups. It can be seen in (Figure 3A) that Z-score value (-8.04) of the target model of cytosolic OsAPX1 is located withinthe space of proteins determined by X ray crystallography andNMR. This value was extremely close to the value of templateGmAPX (-8.6), which suggested that the obtained model wasreliable and very close to experimentally determined structures(Figure 3B). Verify3D showed 86.06% of the residues had ascore greater than 0.2 that corresponded to the quality of theOsAPX1 model that was reliable and acceptable. The degree ofstructural similarity was measured by RSMD performedbetween equivalent atom pairs. RSMD analysis of the OsAPX1model was measured from its template (2XIF) from soybeanusing MOE software. The Cα RMSD and backbone RSMDdeviation for the OsAPX1 model and the GmAPX template(2XIF) crystal structure were 1.06 Å, and 1.04 Å, respectivelyand over all RMSD was 1.57 Å (Figure 4). Thus, the OsAPX1model generated by Modeller 9.12 was confirmed to be reliableand accurate.


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

Pandey S, Negi YK, Chinreddy S, Sathelly K, Arora S, Kaul T - Bioinformation (2014)

Validation of OsAPX1 structure model by ProSAIItools. The Z-score values of A) OsAPX1 (Target) and B)GmAPX1 (Template) proteins determined by NMR(represented in dark blue) and X-ray (represented in light blue).The two black dots represent Z-score value of template andtarget.
© Copyright Policy - open-access
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3974237&req=5

Figure 3: Validation of OsAPX1 structure model by ProSAIItools. The Z-score values of A) OsAPX1 (Target) and B)GmAPX1 (Template) proteins determined by NMR(represented in dark blue) and X-ray (represented in light blue).The two black dots represent Z-score value of template andtarget.
Mentions: ProSA-Web analysis of the model revealed a Z-score value oftarget protein. The Z-score indicates overall model quality andmeasures the deviation of the total energy of the structure withrespect to an energy distribution derived from randomconformations. In order to facilitate interpretation of the Z scoreof the specified protein, its particular value was displayedin a plot that contains the Z scores of all experimentallydetermined protein chains in OsAPX1 PDB. Groups ofstructures from different sources (X-ray, NMR) aredistinguished by different colours (NMR in dark blue and X rayin light blue). This plot can be used to check whether the Zscoreof the protein in question is within the range of scorestypically found for proteins of similar size belonging to one ofthese groups. It can be seen in (Figure 3A) that Z-score value (-8.04) of the target model of cytosolic OsAPX1 is located withinthe space of proteins determined by X ray crystallography andNMR. This value was extremely close to the value of templateGmAPX (-8.6), which suggested that the obtained model wasreliable and very close to experimentally determined structures(Figure 3B). Verify3D showed 86.06% of the residues had ascore greater than 0.2 that corresponded to the quality of theOsAPX1 model that was reliable and acceptable. The degree ofstructural similarity was measured by RSMD performedbetween equivalent atom pairs. RSMD analysis of the OsAPX1model was measured from its template (2XIF) from soybeanusing MOE software. The Cα RMSD and backbone RSMDdeviation for the OsAPX1 model and the GmAPX template(2XIF) crystal structure were 1.06 Å, and 1.04 Å, respectivelyand over all RMSD was 1.57 Å (Figure 4). Thus, the OsAPX1model generated by Modeller 9.12 was confirmed to be reliableand accurate.

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

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.

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.

No MeSH data available.


Related in: MedlinePlus