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2evr

    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
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    Related PDB Ids 2fg0 
    Molecular Characteristics
    Source
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    Alias Ids
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    TPS1921,53686717, PF00877, 291250
    Molecular Weight
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    Da.
    Residues
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    Isoelectric Point
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    Sequence
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      BLAST   FFAS

    Structure Determination
    Method XRAY
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    Chains 1
    Resolution (Å)
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    Rfree
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    Matthews' coefficent 3.19 Rfactor 0.159
    Waters
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    Solvent Content 61.16

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    Ligand Information
    Ligands
    Metals

    Jmol

     
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    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
     

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    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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