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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 2evr Target Id 359701
    Related PDB Ids 2fg0 
    Molecular Characteristics
    Source Nostoc punctiforme pcc 73102
    Alias Ids TPS1921,53686717, 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 1
    Resolution (Å) 1.60 Rfree 0.176
    Matthews' coefficent 3.19 Rfactor 0.159
    Waters 300 Solvent Content 61.16

    Ligand Information


    Google Scholar output for 2evr
    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. Solution NMR Structure of the NlpC/P60 Domain of Lipoprotein Spr from Escherichia coli: Structural Evidence for a Novel Cysteine Peptidase Catalytic Triad
    JM Aramini, P Rossi, YJ Huang, L Zhao, M Jiang - Biochemistry, 2008 - ACS Publications
    3. 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
    4. Peptidoglycan remodeling in Mycobacterium tuberculosis-comparison of structures and catalytic activities of RipA and RipB
    D Bth, G Schneider, R Schnell - Journal of Molecular Biology, 2011 - Elsevier
    5. Structural elucidation of the Cys_His_Glu_Asn proteolytic relay in the secreted CHAP domain enzyme from the human pathogen Staphylococcus saprophyticus
    P Rossi, JM Aramini, R Xiao, CX Chen - Proteins: Structure, , 2009 - Wiley Online Library
    6. Structural insights into the Pseudomonas aeruginosa type VI virulence effector Tse1 bacteriolysis and self-protection mechanisms
    J Ding, W Wang, H Feng, Y Zhang, DC Wang - Journal of Biological , 2012 - ASBMB

    Protein Summary

    Gene Npun_R0659 from Nostoc punctiforme encodes the protein YP_001864356, a cell associated hydrolase from the NlpC/P60 family (PF00877). It is a first structural representative of a very large (over 1000 homologs) family of bacterial proteins that are associated with pathogenesis (invasins, invasion associated proteins) and in the protease database MEROPS is classified as a peptidase C40. Distant homology to several other families of bacterial and eukaryotic proteins (Bacteriophage peptidoglycan hydrolase, DUF1175, DUF1287, DUF1105) can be identified by profile-profile methods.

    The first of the two domains is one of the first examples of a bacterial version of a SH3 domain. Based on domain organization we can speculate that the SH3-like domain binds and orient the substrate (Peptidylglycan?). The second, catalytic domain, defines a new alpha/beta fold that shares remote structural similarity with prostaphopain B cysteine protease (PDB 1x9y).

    The closest structural similarity identified with Dali is with the NlpC proteins 2hbw (Zscr=38), and 3h41 (Zscr=21); followed by the lipoproteins 2jyx and 2k1g (Zscr=15).

    A second structural model was solved at 1.79 A resolution and is available as a PDB entry 2fg0 [Ref].

    Ligand Summary





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