Bioinformatic approach: Cu, Zn superoxide dismutase of Dinoccus radiodurans

Bioinformatic Analysis of Cu, Zn superoxide dismutase protein of Dinococcus radiodurans strain R1 was performed. The protein's net positive charge is due to arginine and lysine and is alkaline with Ip >7 (9.8) and hydrophobicity is 53.5%. Proscan server identified five functional sites on it like Myristylation site, three phosphorylation sites and an N-glycosylation site. The secondary structure showed βturns predominant along with disulphide bonds and is confirmed by SOPMA. A further study showed that in contain three domains as Cu, Zn SOD binding, six bladed propeller, TOIB like and SMP-30/Gluconolaconase/LRE like. The sequence of the domains was analyzed for various parameters like extinction coefficient, half life, instability index, aliphatic index and grand average hydropathy (GRAVY).The sequence was then used to generate tertiary structure which suggest that the Cu, Zn SOD binding site belongs to oxidoreductase fold and metal binding family, the TOIB like site designated as peptidoglycan associated lipoprotein and SMP-30 domain assigned as hydrolyzing enzyme. The 3D-structures were evaluated by Rampage, ProQ and Combinatorial Extension (CE) and visualized by Rasmol.