Kaiser Jamil1, M Sabeena2
1Bhagwan Mahavir Medical Research Centre, Mahavir Marg, Hyderabad – 500 004, A.P.; School of Life Sciences (SLS), Jawaharlal Nehru Institute of Advanced Studies, (JNIAS), Secunderabad-500 003, India.
2Research Associate, Centre for Biotechnology and Bioinformatics- (CBB), Jawaharlal Nehru Institute of Advanced Studies, (JNIAS), Secunderabad-500 003, A.P, India.
ABSTRACT
In this study we determined the functional diversity of the Enolase enzyme superfamily. The mechanistically diverse Enolase superfamily is encoded by the genome of Escherichia coli K-12. Some structures of the uncharacterized family in the barrel domain provide a versatile scaffold for the catalytic residues of both single- and multidomain proteins. Clustering of such superfamilies with a complete set of residues are likely to be of functional importance. Hence a Tree-based approach was used to define the functionally specific families that are useful under the proposed superfamily classification. The following protocols were used: obtaining gene sequences from UniProt KB, determining the alignment among the sequences by Multiple Sequence Alignment and ClustalW algorithm for the selecting closely related sequences. ConSurf server was used for evolutionary conservation analysis of the proteins of known structures in the PDB based on the obtained sequence alignment from major groups such as archaea and bacteria with respect to E.coli. The SCI-PHY server was used for subfamily determination and classification and ExPASy tools and Swiss PDB Viewer for pattern matching and domain recognition and visualization softwares such as Rasmol for residue recognition and functional elucidation. The study identified five group of subfamilies and the functional amino acid residues which predicted the various functions in major groups like archaea and bacteria. We conclude that Bioinformatics based sequence analysis can significantly improve the identification and assignment of function of new members of the mechanistically-diverse protein superfamilies. Read More …
