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The Open Protein Structure Annotation Network
PDB Keyword
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2hbw

    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 2hbw Target Id 360689
    Molecular Characteristics
    Source Anabaena variabilis atcc 29413
    Alias Ids TPS1450,YP_323898.1, PF00877, 90727 Molecular Weight 25313.22 Da.
    Residues 234 Isoelectric Point 5.33
    Sequence mlsnlessiqspksgeyqclaalnlydspectslatqaavgrhlqvtsnqqgaavevclceddypgwls lgdlgllkpatvlyqaksfseseikkllpgaiaftqkamqqsnyylwggtvgpnydcsglmqaafvsvg iwlprdayqqeaftqaitidelapgdlvffgtpvkathvglylgdgcyihssgkaqgrdgigidilseq gdvvsrsyyqqlrgagrvvksykpqrh
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 1.05 Rfree 0.149
    Matthews' coefficent 2.43 Rfactor 0.125
    Waters 363 Solvent Content 49.28

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 2hbw
    1. 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
     
    2. Folds and activities of peptidoglycan amidases
    M Firczuk, M Bochtler - FEMS microbiology reviews, 2007 - Wiley Online Library
     
    3. 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
     
    4. 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
     
    5. 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
     
    6. 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
     
    7. 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
     
    8. Crystal structure of type VI effector Tse1 from Pseudomonas aeruginosa
    H Zhang, ZQ Gao, XD Su, YH Dong - FEBS letters, 2012 - Elsevier
     
    9. Structural insight into functioning of Pseudomonas aeruginosa peptidoglycan-hydolase Tse1 and its immunity protein Tsi1
    S Guijun, L Xiuhua, L Defen, Z Junbing, L Ning - Biochemical , 2012 - biochemj.org
     

    Protein Summary

    Gene Ava_3396 from Anabaena variabilis atcc 29413 encodes the YP_323898 protein whose C-terminal region sequence shows homology to the NlpC/P60 family (PF00877). Analysis of its genome context indicates a possible functional link (score 0.8) with its neighboring gene, Ava_3397, a glycosyl transferase.

    Pre-SCOP classifies 2hbw N-terminal domain (13-86) in the prokaryotic SH3-related domain superfamily; and the C-terminal domain (114-232) in the cysteine proteinase superfamily, NlpC/P60 family. DALI top hits are with cell wall associated hydrolases 2evr and 2fg0 (Z=38), the NlpC/P60 protein 3h41 (Z=21), and the lipoprotein 2jyx (Z=15).


    2hbw coordinates correspond to the crystal structure of a putative D-g-glutamyl-L-diamino acid endopeptidase (EC 3.4.22.-). It is the first representative of a large class of cell wall related cysteine proteases which have not been previously characterized structurally. These enzymes contain an N-terminal bacterial SH3b domain and a C-terminal NlpC/P60 cysteine protease domain. The NlpC/P60 domain is a primitive cysteine protease which contains a Cys126/His176/His188 triad and a conserved catalytic core similar to papain-like proteases. The active site is located near the interface between the SH3b domain and the NlpC/P60 domain. Analysis of the active site suggests that these proteins are highly specific D-g-glutamyl-diaminopimelate DL-endopeptidases. Instead of functioning as a targeting domain, the SH3b domain helps to define substrate specificity such that only stem peptides with a free N-terminal L-alanine can bind the active site. The structures provide new insights into the functions of SH3b domain and the catalytic domain and how substrate specificity is achieved for this class of cysteine proteases containing an NlpC/P60 domain.

    Ligand Summary



    References

    Reviews

    References

     

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