Structural Bioinformatics of <Emphasis Type="Italic">Neisseria meningitidis</Emphasis> LD-Carboxypeptidase: Implications for Substrate Binding and Specificity |
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Authors: | Yasmeen?Rashid Email author" target="_blank">M?Kamran AzimEmail author |
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Institution: | (1) H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270, Pakistan; |
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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’. |
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