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The Open Protein Structure Annotation Network
PDB Keyword
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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
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    Molecular Characteristics
    Source
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    Alias Ids
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    TPS1432,TM1586, 3.40.109.10, 429689
    Molecular Weight
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    Da.
    Residues
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    Isoelectric Point
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    Sequence
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      BLAST   FFAS

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

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    Ligand Information
    Ligands
    Metals

    Jmol

     
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    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
     

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    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:

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    (Z-scr=12),
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    (Z-scr=12),
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    (Z-scr=12),
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    (Z-scr=11), and
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    (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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