Abstract
One of the major classes of antioxidant enzymes, which protect the cellular and subcellular components against harmful reactive oxygen species (ROS), is superoxide dismutase (SOD). SODs play pivotal role in scavenging highly reactive free oxygen radicals and protecting cells from toxic effects. In Oryza sativa three types of SODs are available based on their metal content viz. Cu-Zn SOD, Mn SOD and Fe SOD. In the present study attempts were made to critically assess the structure and phylogenetic relationship among Oryza sativa SODs. The sequence similarity search using local BLAST shows that Mn SODs and Fe SODs have greater degree of similarity compared with that of Cu-Zn SODs. The multiple alignment reveals that seven amino acids were found to be totally conserved. The secondary structure shows that Mn SODs and Fe SODs have similar helixes, sheets, turns and coils compared with that of Cu-Zn SODs. The comparative analysis also displayed greater resemblance in primary, secondary and tertiary structures of Fe SODs and Mn SODs. Comparison between the structure and sequence analysis reveals that Mn SOD and Fe SOD are found to be closely related whereas Cu-Zn SOD evolves independently.
Highlights
Protein sequence comparison is the most powerful tool in characterizing protein sequences because of the enormous amount of information kept in the protein domain throughout the evolutionary process
In Oryza sativa three types of superoxide dismutase (SOD) are available based on their metal content viz. Cu-Zn SOD, Mn SOD and Fe SOD
Comparison between the structure and sequence analysis reveals that Mn SOD and Fe SOD are found to be closely related whereas Cu-Zn SOD evolves independently
Summary
Protein sequence comparison is the most powerful tool in characterizing protein sequences because of the enormous amount of information kept in the protein domain throughout the evolutionary process. Sequence comparison is most effective in homologous protein, which always shares the common active sites or binding domains. Rice has several advantages as a model plant It has a relatively small genome (~430 Mb) that has been almost completely sequenced [6]. SODs are metalloenzymes in aerobic organisms that play a crucial role in protecting organisms against ROS in rice [8]). The present investigation is an attempt to analyze the sequence of Oryza sativa SODs by using computational tools and techniques in order to understand the biological functions and evolutionary relationships among the Oryza sativa SODs. By understanding the sequence, structure and function relationships between SODs in future new proteins having all possible characters of SODs can be designed to produce cultivars tolerant to reactive oxygen
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