Comparative analysis and modeling of superoxide dismutases (SODs) in Brachypodium distachyon L.
Superoxide dismutase (SOD, EC 1.15.1.1) is an enzyme catalyzing the dismutation of superoxide radical to hydrogen peroxide and dioxygen. To date, four types of SODs--Cu/ZnSOD, MnSOD, FeSOD, and NiSOD--have been identified. In this study, SOD proteins of Brachypodium distachyon (L.) Beauv. were screened by utilization of bioinformatics approaches. According to our results, Mn/FeSODs and Cu/ZnSODs of B. distachyon were found to be in basic and acidic character, respectively. Domain analyzes of SOD proteins revealed that iron/manganese SOD and copper/zinc SOD were within studied SOD proteins. Based on the seconder structure analyzes, Mn/FeSODs and Cu/ZnSODs of B. distachyon were found as having similar sheets, turns and coils. Although helical structures were noticed in the types of Mn/FeSODs, no the type of Cu/ZnSODs were identified having helical structures. The predicted binding sites of Fe/MnSODs and Cu/ZnSODs were confirmed for having His-His-Asp-His and His-His-His-Asp-Ser residues with different positions, respectively. The 3D structure analyzes of SODs revealed that some structural divergences were observed in patterns of SODs domains. Based on phylogenetic analysis, Mn/FeSODs were found to have similarities whereas Cu/ZnSODs were clustered independently in phylogenetic tree.
Department of Crop and Animal Production, Cilimli Vocational School, Duzce University, 81750, Cilimli, Duzce, Turkey, ertugrulfiliz@gmail.com.
Ertugrul
E
Filiz
Ibrahim
I
Koc
Ibrahim Ilker
II
Ozyigit
D000595:Amino Acid Sequence; D001665:Binding Sites; D058431:Brachypodium / Q000201:enzymology*; D019295:Computational Biology; D017124:Conserved Sequence; D008958:Models, Molecular; D008969:Molecular Sequence Data; D010802:Phylogeny; D017434:Protein Structure, Tertiary; D017421:Sequence Analysis; D013482:Superoxide Dismutase / Q000737:chemistry* / Q000378:metabolism*
D013482:Superoxide Dismutase