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The Open Protein Structure Annotation Network
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1vkw

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

    Title Crystal structure of Putative Nitroreductase (TM1586) from Thermotoga maritima at 2.00 A resolution. To be published
    Site JCSG
    PDB Id 1vkw Target Id 359768
    Molecular Characteristics
    Source Thermotoga maritima msb8
    Alias Ids TPS1432,TM1586, 3.40.109.10, 429689 Molecular Weight 24065.62 Da.
    Residues 206 Isoelectric Point 7.70
    Sequence mnifeaienrhsvrdflerkmpervkddienllvkfitkkldwkinlssfpsyiyakaekhfdelveyg fqgeqivlfltaqgfgtcwmarsphpdvpyiivfgyprtrnftrkrrpitsflendleelppeivkive mtilapsalnrqpwkikytggelcisserpvdlgialshayltareifkrepviqkrgedtyclilnp
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 2.00 Rfree 0.24281
    Matthews' coefficent 2.20 Rfactor 0.21022
    Waters 95 Solvent Content 43.58

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 1vkw
    1. Comparative modeling for protein structure prediction
    K Ginalski - Current opinion in structural biology, 2006 - Elsevier
     
    2. The Buccaneer software for automated model building. 1. Tracing protein chains
    K Cowtan - Acta Crystallographica Section D: Biological , 2006 - scripts.iucr.org
     
    3. Generalized protein structure prediction based on combination of fold_recognition with de novo folding and evaluation of models
    A Koli_ski, JM Bujnicki - Proteins: Structure, Function, and , 2005 - Wiley Online Library
     
    4. Physics-based protein-structure prediction using a hierarchical protocol based on the UNRES force field: Assessment in two blind tests
    S O_dziej, C Czaplewski, A Liwo - Proceedings of the , 2005 - National Acad Sciences
     
    5. Comparative modeling in CASP6 using consensus approach to template selection, sequence_structure alignment, and structure assessment
    _ Venclovas, M Margelevi_ius - Proteins: Structure, Function, , 2005 - Wiley Online Library
     
    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. Protein structure prediction using a variety of profile libraries and 3D verification
    K Tomii, T Hirokawa, C Motono - : Structure, Function, and , 2005 - Wiley Online Library
     
    9. Protein structure prediction in CASP6 using CHIMERA and FAMS
    M Takeda_Shitaka, G Terashi, D Takaya - PROTEINS: , 2005 - Wiley Online Library
     
    10. Efficient protein tertiary structure retrievals and classifications using content based comparison algorithms
    PH Chi - 2007 - mospace.umsystem.edu
     
    11. Crystal Structure of a Minimal Nitroreductase, ydjA, from Escherichia coli K12 with and without FMN Cofactor
    JW Choi, J Lee, K Nishi, YS Kim, CH Jung - Journal of molecular , 2008 - Elsevier
     
    12. Prediction of protein domain boundaries from statistics of appearance of amino acid residues
    OV Galzitskaya, NV Dovidchenko, MY Lobanov - Molecular Biology, 2006 - Springer
     
    13. Protein structure prediction based on the sliced lattice model
    CC Wang, CB Yang, HY Ann - 2008 Conference on , 2005 - etd.lib.nsysu.edu.tw
     
    14. Coulomb energies of protein-protein complexes with monopole-free charge distributions
    M Das, G Basu - Journal of Molecular Graphics and Modelling, 2009 - Elsevier
     
    15. Prediction of Protein Backbone Based on the Sliced Lattice Model
    CC Wang, CB Yang, HY Ann, HY Chang - 2008 - csie.npu.edu.tw
     
    16. Protein loop prediction by fragment assembly
    Z Liu - Masters Abstracts International, 2007 - el.trc.gov.om
     
    17. Protein Structure Prediction Using a Profile-Profile Comparison Method: FORTE
    _____ - ____, 2006 - J-STAGE
     
    18. Cysteine 38 Holds the Key to NF-_B Activation
    ND Perkins - Molecular Cell, 2012 - Elsevier
     
    19. Crystal Structure of a Minimal Nitroreductase
    CH Jung, JS Kim - J. Mol. Biol, 2008 - ws.ajou.ac.kr
     

    Protein Summary

    Gene TM1586 from Thermotoga maritima encodes the protein NP_229386 that shows a weak hit with the PFAM nitroreductase family (PF00881). Analysis of its genomic neighbourhood detects the presence (score 0.87) of a putative glycerate kinase (TM1585).

    SCOP classifies 1vkw in the alpha+beta class, FMN-dependent nitroreductase-like superfamily, putative nitroreductase TM1586 family. Using 1vkw as query, Dali top hits are with nitroreductase-like proteins such as: PDB:3ge6 (Z-scr=12), PDB:1nec (Z-scr=12), PDB:1oon (Z-scr=12), PDB:1icv (Z-scr=11), and PDB:1zch (Z-scr=10).

    1vkw contains an internal duplication of the minimal FMN-dependent nitroreductase-like fold, mimicking a usual dimeric arrangement of a standard NADH oxidase/flavin reductases, but only one of the units has conserved active site residues.

    1vkw was the first structure solved representative of a large (>1000 proteins) sub-family of PF00881. The second, B. subtilis YcnD (PDB:1zch) was solved a year later (Morokutti, A.,  Lyskowski, A.,  Sollner, S.,  Pointner, E.,  Fitzpatrick, T.B.,  Kratky, C.,  Gruber, K.,  Macheroux, P.   (2005) Structure and Function of YcnD from Bacillus subtilis, a Flavin-Containing Oxidoreductase.   Biochemistry   44: 13724-13733  )

    Ligand Summary



    References

    Reviews

    References

     

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