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Online Journal of Bioinformatics©
Volume 22 (1):1-11, 2021.
In silico 3D model of copper and zinc superoxide dismutase from Deinococcus radiodurans.
Ashokan KV1 and Pillai MM2
1Department(s) of Biological Science,† PVP College, Kavathe Mahankal, Sangli, Mharashtrea, 2Biotechnology, KIITís Engineering College, Gokulshirgoan, Kolhapur, India.
Ashokan KV, Pillai MM., In silico 3D model of copper and zinc superoxide dismutase from Deinococcus radiodurans. Onl J Bioinform., 22 (1):1-11, 2021. We report in Silico copper and zinc superoxide dismutase R1 strain protein 3D structure model from Deinococcus† radiodurans. Primary sequence positive charge was due to arginine and lysine with pH 9.8 and hydrophobicity 53.5%. Functional characterization by PROSCAN identified 1 myristic, 3 phosphoryl and 1 N-glycosylating amino acid functional sites. Secondary structure predicted by JPRED revealed β-turns with disulphide bonds confirmed by SOPMA server. INTERPROSCAN revealed integral copper and zinc superoxide dismutase six bladed propeller, TOIB like and SMP-30/Gluconolaconase/LRE binding domains. These domain sequences were analyzed by EXPASY for extinction coefficient, half-life, instability and aliphatic indices and grand average hydropathy (GRAVY). This sequence generated a tertiary structure by HHPRED showing that copper and zinc SOD binding had a oxidoreductase fold with metal binding peptidoglycan associated lipoprotein and SMP-30 domain hydrolyzing enzyme which protects against aging stress. The 3D-structure of the domains were confirmed by Rampage. ProQ and Combinatorial Extension (CE) servers were visualized by Rasmol.
Key words: Cu, Zn superoxide dismutase, Deinococcus† rdaiodurans, Radiation resistance, TOIB protein and SMP-30 protein and 3Dstructure.