The Open Protein Structure Annotation Network
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    Table of contents
    1. 1. Protein Summary
    2. 2. Ligand Summary
    3. 3. References

    Title Crystal structure of 3-isopropylmalate dehydrogenase (TM0556) from Thermotoga maritima at 1.90 A resolution. To be published
    Site JCSG
    PDB Id 1vlc Target Id 282429
    Molecular Characteristics
    Source Thermotoga maritima msb8
    Alias Ids TPS1213,TM0556, 89993, 289533 Molecular Weight 39188.19 Da.
    Residues 354 Isoelectric Point 5.44
    Sequence mkiavlpgdgigpevvrealkvlevvekktgktfekvfghiggdaidrfgeplpeetkkicleadaifl gsvggpkwddlppekrpeiggllalrkmlnlyanirpikvyrslvhvsplkekvigsgvdlvtvrelsy gvyygqprgldeekgfdtmiydrktveriartafeiaknrrkkvtsvdkanvlyssmlwrkvvnevare ypdvelthiyvdnaamqlilkpsqfdvilttnmfgdilsdesaalpgslgllpsasfgdknlyepaggs apdiagknianpiaqilslammlehsfgmveearkieravelvieegyrtrdiaedpekavstsqmgdl ickkleeiw
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 1.90 Rfree 0.21822
    Matthews' coefficent 2.84 Rfactor 0.18779
    Waters 106 Solvent Content 56.62

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    Ligand Information


    Google Scholar output for 1vlc
    1. The Buccaneer software for automated model building. 1. Tracing protein chains
    K Cowtan - Acta Crystallographica Section D: Biological , 2006 - scripts.iucr.org
    2. His-tag impact on structure
    M Carson, DH Johnson, H McDonald - Section D: Biological , 2007 - scripts.iucr.org
    3. Evaluating the usefulness of protein structure models for molecular replacement
    A Giorgetti, D Raimondo, AE Miele - Bioinformatics, 2005 - Oxford Univ Press
    4. Domain definition and target classification for CASP6
    M Tress, CH Tai, G Wang, I Ezkurdia - PROTEINS: , 2005 - Wiley Online Library
    5. Fast and accurate algorithms for protein side-chain packing
    J Xu, B Berger - Journal of the ACM (JACM), 2006 - dl.acm.org
    6. Pervasive cryptic epistasis in molecular evolution
    M Lunzer, GB Golding, AM Dean - PLoS genetics, 2010 - dx.plos.org
    7. Rates of unfolding, rather than refolding, determine thermal stabilities of thermophilic, mesophilic, and psychrotrophic 3-isopropylmalate dehydrogenases
    Grczer, A Varga, I Hajd, B Melnik, A Szilgyi - Biochemistry, 2007 - ACS Publications
    8. Comparison of composer and ORCHESTRAR
    MA Dolan, M Keil, DS Baker - Proteins: Structure, Function, and , 2008 - Wiley Online Library
    9. Stochastic pairwise alignments and scoring methods for comparative protein structure modeling
    AC Marko, K Stafford, T Wymore - Journal of chemical information , 2007 - ACS Publications
    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. Comparison of common homology modeling algorithms: application of user-defined alignments.
    MA Dolan, JW Noah, D Hurt - Methods in molecular biology (Clifton, NJ), 2012 - Springer
    12. Automatic procedure for using models of proteins in molecular replacement
    D Raimondo, A Giorgetti, S Bosi - PROTEINS: Structure, , 2007 - Wiley Online Library
    13. Prediction of Protein Backbone Based on the Sliced Lattice Model
    CC Wang, CB Yang, HY Ann, HY Chang - 2008 - csie.npu.edu.tw
    14. Protein loop prediction by fragment assembly
    Z Liu - Masters Abstracts International, 2007 - el.trc.gov.om
    15. On the Origin and Evolution of Thermophily: Reconstruction of Functional Precambrian Enzymes from Ancestors of Bacillus
    JK Hobbs, C Shepherd, DJ Saul, NJ Demetras - Molecular biology and , 2012 - SMBE
    16. Structure determination, thermal stability and catalytic mechanism of hyperthermostable isocitrate dehydrogenases
    M Karlstrm - year: 2006, 2006 - diss.kib.ki.se

    Protein Summary

    The TM0556 gene of Thermotoga maritima encodes a 3-isopropylmalate dehydrogenase (PF00180, COG0473, EC, an enzyme implicated in the biosynthesis of valine, isoleucine and leucine. The TM0556 structure adopts an isocitrate/isopropylmalate-like fold and shows strong structural similarity (main-chain rmsd 1.3 Å over 340-350 residues with 55-57% sequence identity) with homologs from another hyperthermophile, Thermus thermophilus (PDB id: 1hex) and Salmonella typhimurium (PDB id: 1cnz). For more details on the structure and function, see Hurley 1994 and Wallon 1997.


    Ligand Summary





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