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The Open Protein Structure Annotation Network
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1vjv

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

    Title Crystal structure of Ubiquitin carboxyl-terminal hydrolase 6 (yfr010w) from Saccharomyces cerevisiae at 1.74 A resolution. To be published
    Site JCSG
    PDB Id 1vjv Target Id 355004
    Molecular Characteristics
    Source Saccharomyces cerevisiae
    Alias Ids TPS1345,YFR010W Molecular Weight 57107.88 Da.
    Residues 499 Isoelectric Point 6.71
    Sequence msgetfefnirhsgkvypitlstdatsadlkskaeeltqvpsarqkymvkgglsgeesikiyplikpgs tvmllgtpdanliskpakknnfiedlapeqqvqqfaqlpvgfknmgntcylnatlqalyrvndlrdmil nynpsqgvsnsgaqdeeihkqiviemkrcfenlqnksfksvlpivllntlrkcypqfaerdsqggfykq qdaeelftqlfhsmsivfgdkfsedfriqfkttikdtandnditvkenesdsklqchisgttnfmrngl leglnekiekrsdltgansiysvekkisrlpkfltvqyvrffwkrstnkkskilrkvvfpfqldvadml tpeyaaekvkvrdelrkvekeknekereikrrkfdpsssenvmtpreqyetqvalnesekdqwleeykk hfppnlekgenpscvynligvithqgansesghyqafirdeldenkwykfnddkvsvvekekieslagg gesdsalilmykgfgl
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 1.74 Rfree 0.20892
    Matthews' coefficent 2.14 Rfactor 0.17917
    Waters 241 Solvent Content 42.44

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 1vjv
    1. Exploiting heterogeneous sequence properties improves prediction of protein disorder
    Z Obradovic, K Peng, S Vucetic - Proteins: Structure, , 2005 - Wiley Online Library
     
    2. The Buccaneer software for automated model building. 1. Tracing protein chains
    K Cowtan - Acta Crystallographica Section D: Biological , 2006 - scripts.iucr.org
     
    3. Severe acute respiratory syndrome coronavirus papain-like protease: structure of a viral deubiquitinating enzyme
    K Ratia, KS Saikatendu - Proceedings of the , 2006 - National Acad Sciences
     
    4. The structure of the CYLD USP domain explains its specificity for Lys63-linked polyubiquitin and reveals a B box module
    D Komander, CJ Lord, H Scheel, S Swift, K Hofmann - Molecular cell, 2008 - Elsevier
     
    5. Prediction of enzyme function based on 3D templates of evolutionarily important amino acids
    D Kristensen, RM Ward, A Lisewski, S Erdin - BMC , 2008 - biomedcentral.com
     
    6. Domain definition and target classification for CASP6
    M Tress, CH Tai, G Wang, I Ezkurdia - PROTEINS: , 2005 - Wiley Online Library
     
    7. Fast and accurate algorithms for protein side-chain packing
    J Xu, B Berger - Journal of the ACM (JACM), 2006 - dl.acm.org
     
    8. Dissection of USP catalytic domains reveals five common insertion points
    Y Ye, H Scheel, K Hofmann, D Komander - Mol. BioSyst., 2009 - xlink.rsc.org
     
    9. Prediction of protein domain boundaries from statistics of appearance of amino acid residues
    OV Galzitskaya, NV Dovidchenko, MY Lobanov - Molecular Biology, 2006 - Springer
     
    10. Protein structure prediction based on the sliced lattice model
    CC Wang, CB Yang, HY Ann - 2008 Conference on , 2005 - etd.lib.nsysu.edu.tw
     
    11. Prediction of Protein Backbone Based on the Sliced Lattice Model
    CC Wang, CB Yang, HY Ann, HY Chang - 2008 - csie.npu.edu.tw
     
    12. A bacterial effector targets the TRAF6-NF_B pathway to modulate the acute inflammatory response to bacterial invasion of epithelial cells
    T Sanada, M Kim, H Mimuro, H Ashida, M Ogawa - , 2012 - landesbioscience.com
     
    13. Deubiquitination of Lys63-Linkage by a CYLD UBP
    Y Shi - Structure, 2008 - Elsevier
     
    14. Protein loop prediction by fragment assembly
    Z Liu - Masters Abstracts International, 2007 - el.trc.gov.om
     
    15. Structure, function, and inhibition of the papain-like protease from SARS coronavirus
    K Ratia - 2008 - books.google.com
     

    Protein Summary

    UBP6 from Saccharomyces cerevisiae is a cysteine peptidase (EC:3.1.2.15) and contains two domains - an N-terminal ubiquitin (Ub) domain and a C-terminal catalytic domain. The crystal structure corresponds to the catalytic domain of UBP6 which belongs to the C.19.079 family of MEROPS database.  The cysteine peptidase deubiquitinating enzyme (DUBs) family can be further subdivided into four subfamilies namely the Ub-specific protease (USP), Ub C-terminal hydrolase (UCH), Otubain protease (OTU) and Machado-Joseph disease protease (MJD). UBP6 belongs to the USP subfamily which is the largest and most diverse among the DUBs. The catalytic triad of this cysteine peptidase is comprised of residues C118, H447 and N465. N113 is also in the vicinity of the active site. In addition the UBP6 protein has a degraded zinc ribbon motif (unlikely to bind zinc in UBP6) inserted between structural elements of the peptidase core. The presence of the zinc ribbon was predicted by Krishna and Grishin (2004) based on the structure of the human protein HAUSP {ref Cell cycle 2004}. The structure of the homologous USP8 contains an intact zinc-binding ribbon. Crystallographic packing indicates UBP6 to be a monomer.

    Ligand Summary



    References

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