The Protein Journal

, Volume 30, Issue 8, pp 558–565

Structural Bioinformatics of Neisseria meningitidis LD-Carboxypeptidase: Implications for Substrate Binding and Specificity

Article

DOI: 10.1007/s10930-011-9364-7

Cite this article as:
Rashid, Y. & Kamran Azim, M. Protein J (2011) 30: 558. doi:10.1007/s10930-011-9364-7

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’.

Keywords

Neisseria meningitidisLD-carboxypeptidaseHomology modelingMolecular dockingHypothetical protein

Abbreviations

AE-mesoDAP-A

l-alanyl-d-glutamyl-meso-diaminopimelyl-d-alanine

CMR

Comprehensive microbial resource

DUF

Domain of unknown function

GlcNAc

N-acetyl glucoseamine

GOLD

Genetic optimization of ligand docking

LdcA

LD-carboxypeptidase

MurNAc

N-acetyl muramic acid

Nm

Neisseria meningitidis

NMB

Neisseria meningitidis serogroup B

Pa

Psedumonas aeruginosa

PDB

Protein data bank

PSIBLAST

Position specific iterated Basic local alignment search tool

UDP-MurNAc

Uridine diphosphate-N-acetyl muramic acid

Copyright information

© Springer Science+Business Media, LLC 2011

Authors and Affiliations

  1. 1.H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological SciencesUniversity of KarachiKarachiPakistan