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

    Title Structure of Bacillus Subtilis YXEP Protein, a Dinuclear Metal Binding Peptidase from M20 Family. To be Published
    Site MCSG
    PDB Id 1ysj Target Id APC1829
    Molecular Characteristics
    Source Bacillus subtilis
    Alias Ids TPS4567,P54955, 1423 Molecular Weight 41594.08 Da.
    Residues 380 Isoelectric Point 5.44
    Sequence madkafhtrlinmrrdlhehpelsfqevettkkirrwleeeqieildvpqlktaviaeikgredgpvia iradidalpiqeqtnlpfaskvdgtmhacghdfhtasiigtamllnqrraelkgtvrfifqpaeeiaag arkvleagvlngvsaifgmhnkpdlpvgtigvkegplmasvdrfeivikgkgghasipnnsidpiaaag qiisglqsvvsrnisslqnavvsitrvqagtswnvipdqaemegtvrtfqkearqavpehmrrvaegia agygaqaefkwfpylpsvqndgtflnaaseaaarlgyqtvhaeqspggedfalyqekipgffvwmgtng teewhhpaftldeealtvasqyfaelavivletik
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 2
    Resolution (Å) 2.40 Rfree 0.24709
    Matthews' coefficent 2.00 Rfactor 0.18173
    Waters 317 Solvent Content 38.90

    Ligand Information
    Metals NI (NICKEL) x 4


    Google Scholar output for 1ysj
    1. Prediction of transition metal_binding sites from apo protein structures
    M Babor, S Gerzon, B Raveh - Proteins: Structure, , 2008 - Wiley Online Library
    2. An iterative knowledge_based scoring function for proteinprotein recognition
    SY Huang, X Zou - Proteins: Structure, Function, and , 2008 - Wiley Online Library
    3. X_ray structure of ILL2, an auxin_conjugate amidohydrolase from Arabidopsis thaliana
    E Bitto, CA Bingman, L Bittova - Proteins: Structure, , 2009 - Wiley Online Library
    4. Auxin amidohydrolases from Brassica rapa cleave the alanine conjugate of indolepropionic acid as a preferable substrate: a biochemical and modeling approach
    B Savi_, S Tomi_, V Magnus, K Gruden - Plant and cell , 2009 - Jpn Soc Plant Physiol
    5. The LabelHash algorithm for substructure matching
    M Moll, DH Bryant, LE Kavraki - BMC bioinformatics, 2010 - biomedcentral.com
    6. Characterization of thermostable aminoacylase from hyperthermophilic archaeon Pyrococcus horikoshii
    K Tanimoto, N Higashi, M Nishioka, K Ishikawa - FEBS , 2008 - Wiley Online Library
    7. Probing the Acyl-Binding Pocket of Aminoacylase-1
    HA Lindner, A Alary, M Wilke, T Sulea - Biochemistry, 2008 - ACS Publications
    8. Mutational and structural analysis of LN-carbamoylase: new insights into a peptidase M20/M25/M40 family member.
    S Martnez-Rodrguez, A Garca-Pino - Journal of , 2012 - Am Soc Microbiol

    Protein Summary

    This protein is homologous to metallopeptidases in family M20 subfamily D.  Unusually, the YxeP protein has two nickel ions bound in its active site; where known, all peptidases in family M20 bind two zinc ions.  Unusually, cysteine is one of the metal ligands.  In all metallopeptidases so far discovered, cysteine has only been seen to bind zinc ions that perform a structural role not a catalytic one.  Recently, the crystal structure of the HmrA protein from Staphylococcus aureus was solved (Botelho et al., J. Biol. Chem (2011) in press; PubMed 21622555; PDB 3RAM).  This protein is also a member of subfamily M20D, and binds two zinc ions using the same ligands as found in the YxeP structure, including the cysteine.  Intriguingly, the HmrA protein was shown to have peptidase activity, being able to cleave several quenched fluorescent substrates as well as albumin and casein.  Peptidase family M20 had been thought to contain only exopeptidases (aminopeptidase and carboxypeptidases), but clearly the HmrA protein is an endopeptidase.  It is very ususual, especially amongst metallopeptidases, for one family to contain both exo- and endopeptidases.   

    Ligand Summary




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