Three-Dimensional Modeling and Analysis of the Peptidoglycan Connecting Peptide Bridge Synthesizing D-Alanine D-Alanine Ligase (Ddl) of Enterococcus Faecalis

D-alanine: D-alanine ligase (DDL) is a vital enzyme in the bacterial cell wall biosynthesis. It is involved in the synthesis of D-alanine dipeptide which crosslinks the peptidoglycan for integrity. In this study, the 3Dimensional structure of theDDL of Enterococcus faecalis (E.faecalis) was determined through Homology Modeling, on the basis of crystal structure coordinates of DDL of Staphylococcus aureus (PDB ID=2I80). Using a variety of programs the structure was then refined and analyzed for its active sites, ligand binding pockets, topology, conserved residues, and evolutionary relationship. The predicted model was then subjected to docking with norleucinephosphonate. It is concluded that structure of DDL-E.faecalis was quite similar to the DDL-S.aureus except the ω-loop, involved in substrate recognition/ binding, is present in the target molecule but missing in the template.