title: Structural bioinformatics of Neisseria meningitidis LD-carboxypeptidase: implications for substrate binding and specificity.
abstract: Neisseria meningitidis, a gram negative bacterium, is the leading cause of bacterial meningitis and severe sepsis. Neisseria meningitidis genome contains 2,160 predicted coding regions including 1,000 hypothetical genes. Re-annotation of N. meningitidis hypothetical proteins identified nine putative peptidases. Among them, the NMB1620 protein was annotated as LD-carboxypeptidase involved in peptidoglycan recycling. Structural bioinformatics studies of NMB1620 protein using homology modeling and ligand docking were carried out. Structural comparison of substrate binding site of LD-carboxypeptidase was performed based on binding of tetrapeptide substrate 'L-alanyl-D-glutamyl-meso-diaminopimelyl-D-alanine'. Inspection of different subsite-forming residues showed changeability in the S1 subsite across different bacterial species. This variability was predicted to provide a structural basis to S1-subsite for accommodating different amino acid residues at P1 position of the tetrapeptide substrate 'L-alanyl-D-glutamyl-meso-diaminopimelyl-D-alanine'.
authors: H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan.
authors: Yasmeen
authors: Y
authors: Rashid
authors: M
authors: M
authors: Kamran Azim
mesh_terms: D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D001665:Binding Sites; D002268:Carboxypeptidases / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D019295:Computational Biology; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009345:Neisseria meningitidis / Q000737:chemistry / Q000201:enzymology* / Q000235:genetics; D011485:Protein Binding; D017433:Protein Structure, Secondary; D016415:Sequence Alignment; D013379:Substrate Specificity
chemical_list: D001426:Bacterial Proteins; D002268:Carboxypeptidases; C021505:LD-carboxypeptidase