Bioinformatics Center School of Biotechnology, Madurai Kamaraj University, Madurai 625 021 India
The crystal structure of restriction endonucleases EcoRI and BamHI have shown these two enzymes to possess striking 3D structural resemblence, ie these have a similar overall fold and similar active sites, although these do not possess appreciable sequence homology. Based on the 3D structures of these endonucleases we have analysed sequences of endonucleases and were able to identify conserved motifs.These motifs are distributed throughout the sequence comprise of hydrophobic as well as charged residues and are not detectable by standard sequence alignment programs. The details of the alignment, the nature of the motifs and the evolutionary implications of this will be presented and discussed.