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 a putative modulator of DNA gyrase (pmbA) from Thermotoga maritima at 1.95 A resolution reveals a new fold. Proteins 61 444-448 2005
    Site JCSG
    PDB Id 1vl4 Target Id 282597
    Molecular Characteristics
    Source Thermotoga maritima msb8
    Alias Ids TPS1229,TM0727, 282661, 90026 Molecular Weight 48303.93 Da.
    Residues 435 Isoelectric Point 5.13
    Sequence mtfeefkdrlfalakkngvevqisfletrefslrlangdldqytdagkfnveikvlkdgktgtfrtqvl enpekcfeealsnlqvkdseekeyffeggkeyremetyvgrfeklsvkekmdmakkahesaakdervvm vptvmykdmvikkiitntlgldvesqmdggflfamaiardanprsgswyelartpedlnpeeigkraae eaisligsktipsgkypvlmrntalldlmemfipmisaenvqknlsplkgklgeqvgnpavsikdlpyh pkglsstpfddegvpttekfvlengvlktflhnlktarkegveptgngfvggirpvnlmlmpgeksfee llkemdrgvvitevegmhagansisgefslfakgywvengeiahgveditisgnfldllrkivlvgndv kvsqhtiapsvlvevldvagk
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 2
    Resolution (Å) 1.95 Rfree 0.22099
    Matthews' coefficent 2.59 Rfactor 0.17389
    Waters 493 Solvent Content 52.46

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    Ligand Information


    Google Scholar output for 1vl4
    1. The Buccaneer software for automated model building. 1. Tracing protein chains
    K Cowtan - Acta Crystallographica Section D: Biological , 2006 - scripts.iucr.org
    2. Assessment of CASP6 predictions for new and nearly new fold targets
    JJ Vincent, CH Tai - PROTEINS: Structure, , 2005 - Wiley Online Library
    3. Microbial biochemistry, physiology, and biotechnology of hyperthermophilic Thermotoga species
    SB Conners, EF Mongodin, MR Johnson - FEMS microbiology , 2006 - Wiley Online Library
    4. An iterative knowledge_based scoring function for proteinprotein recognition
    SY Huang, X Zou - Proteins: Structure, Function, and , 2008 - Wiley Online Library
    5. Domain definition and target classification for CASP6
    M Tress, CH Tai, G Wang, I Ezkurdia - PROTEINS: , 2005 - Wiley Online Library
    6. The prediction of protein function at CASP6
    S Soro, A Tramontano - Proteins: Structure, Function, and , 2005 - Wiley Online Library
    7. Structural characteristics of novel protein folds
    N Fernandez-Fuentes, JM Dybas, A Fiser - PLoS computational biology, 2010 - dx.plos.org
    8. Evaluation of the structural quality of modeled proteins by using globularity criteria
    S Costantini, AM Facchiano - BMC structural biology, 2007 - biomedcentral.com
    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. Crystal structure of a putative modulator of DNA gyrase (pmbA) from Thermotoga maritima at 1.95 resolution reveals a new fold
    C Rife, R Schwarzenbacher - Proteins: Structure, , 2005 - Wiley Online Library
    12. Re-Annotation of Two Hyperthermophilic Archaea Pyrococcus abyssi GE5 and Pyrococcus furiosus DSM 3638
    J Gao, J Wang - Current microbiology, 2012 - Springer
    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. Carbohydrate utilization pathway analysis in the hyperthermophile Thermotoga maritima
    SB Conners - 2006 - repository.lib.ncsu.edu

    Protein Summary

    Gene TM0727 from Thermotoga maritima encodes the NP_228536  protein, a putative modulator of DNA gyrase PmbA (PF01523)(PubMed:16104019). TM0727 is similar to proteins from COG0312 (predicted Zn-dependent proteases and their inactivated homologs). Its genomic neighbour shows the presence of TM0726 (TldD) with similar sequence.  PmbA and TldD regulate DNA gyrase function and are involved in protein maturation (PubMed:12029038, 8604133, and 2082149).

    SCOP classifies 1vl4 in the alpha+beta class, putative modulator of DNA gyrase PmbA/TldD (super)family. TM0727 is homologous to another JCSG solved structure from Bacteroides thetaiotaomicron https://www.topsan.org/WikiHome/Public/356879 (PDB ID: 1vpb), with high structural similarity (2.52 A RMSD for 418 Ca aligned positions) and moderate sequence identity (25% seq id), and a Dali Z-score of 38. The most conserved residues Asp286, Glu288, and Gly289 are located in a small cleft facing a big gap that separates the two chains in the TM0727 dimer.

    Ligand Summary





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