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    Table of contents
    1. 1. Protein Summary
    2. 2. Ligand Summary
    3. 3. References

    Title Structural Basis of Murein Peptide Specificity of a gamma-D-Glutamyl-L-Diamino Acid Endopeptidase. Structure 17 303-313 2009
    Site JCSG
    PDB Id 2fg0 Target Id 359701
    Related PDB Ids 2evr 
    Molecular Characteristics
    Source Nostoc punctiforme pcc 73102
    Alias Ids TPS1429,53686717, PF00877, 291250 Molecular Weight 25920.58 Da.
    Residues 234 Isoelectric Point 4.71
    Sequence mvrlseaevqnpklgeyqcladlnlfdspectrlatqsasgrhlwvtsnhqnlavevylceddypgwls lsdfdslqpatvpyqaatfseseikkllaeviaftqkamqqsnyylwggtvgpnydcsglmqaafasvg iwlprdayqqegftqpitiaelvagdlvffgtsqkathvglyladgyyihssgkdqgrdgigidilseq gdavslsyyqqlrgagrvfksyepqrr
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 2
    Resolution (Å) 1.79 Rfree 0.172
    Matthews' coefficent 3.43 Rfactor 0.154
    Waters 428 Solvent Content 63.86

    Ligand Information


    Google Scholar output for 2fg0
    1. Decision-making in structure solution using Bayesian estimates of map quality: the PHENIX AutoSol wizard
    TC Terwilliger, PD Adams, RJ Read - Section D: Biological , 2009 - scripts.iucr.org
    2. Structural Basis of Murein Peptide Specificity of a [gamma]-D-Glutamyl-L-Diamino Acid Endopeptidase
    Q Xu, S Sudek, D McMullan, MD Miller, B Geierstanger - Structure, 2009 - Elsevier
    3. Structure of the-D-glutamyl-L-diamino acid endopeptidase YkfC from Bacillus cereus in complex with L-Ala--D-Glu: insights into substrate recognition by NlpC/P60
    Q Xu, P Abdubek, T Astakhova, HL Axelrod - Section F: Structural , 2010 - scripts.iucr.org

    Protein Summary

     The gene Npun_R0659 from Nostoc punctiforme encodes the protein YP_001864356, a gamma-D-Glutamyl-L-Diamino acid endopeptidase  EC:  The 2fg0 structure contains two domains: the N-terminal domain is a bacterial SH3-like domain (SH3b), and the C-terminal domain is a ubiquitous cell-wall-associated NlpC/P60 (or CHAP) cysteine peptidase domain PF00877 [Ref].  The SH3-like domain reveals SH3-like barrel fold type SCOP50036, while the NlpC/P60 domain belongs to the cysteine proteinases fold type SCOP54000

     The same structure has been solved at 1.6A resolution (see: 2EVR).  The crystal structure of homologous NlpC/P60 domain from Anabaena variabilis has been previously solved 2HBW3h41 is a third NlpC/P60 structure related to the previous ones with a Dali Z-scr=21. The active site of the enzyme is located near the interface between the SH3b and NlpC/P60 domains.  The enzymes from this family contain conserved cysteine and histidine residues and hydrolyze γ-glutamyl-containing substrates. These cysteine residues have been shown to be essential for activity of several of these amidases and their thiol groups apparently function as the nucleophiles in the catalytic mechanisms of all enzymes containing the CHAP domain.  Several phage-encoded peptidoglycan hydrolases have been found to share a conserved CHAP domain with a variety of bacterial autolysins [Ref].  Because of substrate specificity in a species dependent manner, these enzyme are considered as promising antibacterial agents [Ref].

    Ligand Summary





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