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OJBTM
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,
KIIT’s Engineering College, Gokulshirgoan, Kolhapur,
India.
ABSTRACT
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.
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