SHORT COMMUNICATION In silico analyses of superoxide dismutases (SODs) of rice (Oryza sativa L.) Budheswar Dehury & Kishore Sarma & Ranjan Sarmah & Jagajjit Sahu & Smita Sahoo & Mousumi Sahu & Priyabrata Sen & Mahendra Kumar Modi & Gauri Dutta Sharma & Manabendra Dutta Choudhury & Madhumita Barooah Received: 21 February 2012 / Accepted: 22 June 2012 # Society for Plant Biochemistry and Biotechnology 2012 Abstract Superoxide dismutases (SODs), members of the metalloenzymes family are most effective intracellu- lar enzymatic antioxidant in aerobic organisms. These enzymes provide the first line of defense in plants against the toxic effects of elevated levels of reactive oxygen species (ROS) generated during various environ- mental stresses. The availability of high-throughput computational tools has provided better opportunities to characterize the protein features and determine their function. In the present study an attempt was made to gain an insight into the structure and evolution of sub- units of SODs (Cu-Zn, Mn and Fe SODs) of rice. The 3-Dimensional structures of SODs were modeled based on available X-ray crystal structures and further validat- ed. The primary sequence, secondary and tertiary struc- ture analysis revealed Mn and Fe SOD to be structurally homologous while Cu-Zn SOD is un-related to either of them. Comparative structural study also revealed former two were dominated by α-helices followed by β-strands in contrast; Cu-Zn SOD dominated by β-strands. Molecular phylogeny indicated a common evolutionary origin of Mn and Fe SOD while Cu-Zn SOD may have evolved separately. Keywords Superoxide dismutase . Reactive oxygen species . Comparative modeling . Phylogeny Abbreviations ROS Reactive oxygen species SOD Superoxide dismutase RMSD Root mean square deviation The recent change in global climate has threatened rice (Oryza stiva L.) production from various stresses includ- ing exposure to elevated levels of reactive oxygen spe- cies (ROS) limiting the crop productivity world wide. Superoxide dismutases (SOD, EC 1.15.1.1) are ubiqui- tous enzymes, which are widely distributed among ox- ygen consuming organisms, aerotolerant anaerobes and some obligate anaerobes (Fridovich 1986 ). These enzymes act as the first line of defence against oxygen free radical mediated injury. All SODs irrespective of source are multimeric mettaloproteins that scavenge the superoxide radicals into hydrogen peroxide and molec- ular oxygen and prevents almost all green living cells against oxidative stress generated under aerobic condi- tions (Sigaud-Kutner et al. 2002). Based on the metal co-factor used by the enzyme, SODs are broadly cate- gorised in to three distinct groups viz, Iron SOD (Fe B. Dehury : K. Sarma : R. Sarmah : J. Sahu : S. Sahoo : M. Sahu : P. Sen : M. K. Modi : M. Barooah (*) Agri-Bioinformatics Promotion Programme, Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat 785013 Assam, India e-mail: m17barooah@yahoo.co.in B. Dehury : G. D. Sharma : M. D. Choudhury Department of Life Science & Bioinformatics, Assam University, Silchar 788011 Assam, India J. Plant Biochem. Biotechnol. DOI 10.1007/s13562-012-0121-6