In silico modeling and hydrogen peroxide binding study of rice catalase.
Homology modeling of the catalase, CatC cloned and sequenced from rice (Oryza sativa L., cv Ratna an Indica cultivar) has been performed based on the crystal structure of the catalase CatF (PDB code 1m7s) by using the software MODELLER. With the aid of molecular mechanics and molecular dynamics methods, the final model is obtained and is further assessed by PROCHECK and VERIFY - 3D graph, which show that the final refined model is reliable. With this model, a flexible docking study with the hydrogen peroxide, the substrate for catalase, is performed and the results indicate that Arg310, Asp343 and Arg346 in catalase are three important determinant residues in binding as they have strong hydrogen bonding contacts with the substrate. These hydrogen-bonding interactions play an important role for the stability of the complex. Our results may be helpful for further experimental investigations.
Sekhar
Pagadala Nataraj
PN
Department of Genetics, Osmania University, Hyderabad - 500 007, India.
Kishor
Polavarapu B Kavi
PB
Reddy
Lakkireddy Ananda
LA
Mondal
Prosenjit
P
Dash
Ardhendu K
AK
Kar
Manoranjan
M
Mohanty
Satya
S
Sabat
Surendra C
SC
D000595:Amino Acid Sequence; D001120:Arginine / Q000737:chemistry; D001224:Aspartic Acid / Q000737:chemistry; D001483:Base Sequence; D001665:Binding Sites; D002374:Catalase / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D020134:Catalytic Domain; D003001:Cloning, Molecular; D003198:Computer Simulation; D018744:DNA, Plant / Q000235:genetics; D017343:Genes, Plant; D006861:Hydrogen Peroxide / Q000378:metabolism; D008958:Models, Molecular; D008969:Molecular Sequence Data; D012275:Oryza / Q000201:enzymology* / Q000235:genetics; D011487:Protein Conformation; D016415:Sequence Alignment; D012984:Software
D018744:DNA, Plant; D001224:Aspartic Acid; D001120:Arginine; D006861:Hydrogen Peroxide; D002374:Catalase