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The Open Protein Structure Annotation Network
PDB Keyword
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1vpb

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

    Title Crystal structure of Putative modulator of DNA gyrase (bt3649) from Bacteroides thetaiotaomicron vpi-5482 at 1.75 A resolution. To be Published
    Site JCSG
    PDB Id 1vpb Target Id
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    Molecular Characteristics
    Source
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    Alias Ids
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    TPS1369,BT3649, 289762
    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 2.80 Rfactor 0.17822
    Waters
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    Solvent Content 55.65

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    Ligand Information
    Ligands
    Metals

    Jmol

     
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    Google Scholar output for 1vpb
    1. The Buccaneer software for automated model building. 1. Tracing protein chains
    K Cowtan - Acta Crystallographica Section D: Biological , 2006 - scripts.iucr.org
     
    2. Protein structure prediction based on the sliced lattice model
    CC Wang, CB Yang, HY Ann - 2008 Conference on , 2005 - etd.lib.nsysu.edu.tw
     
    3. Prediction of Protein Backbone Based on the Sliced Lattice Model
    CC Wang, CB Yang, HY Ann, HY Chang - 2008 - csie.npu.edu.tw
     

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    Protein Summary

    The structure of Bacteroides thetaiotaomicron descr protein bt3649 contains two domains, both with (different) alpha + beta folds (however SCOP classifies the whole structure as a single domain). The first domain has an internal duplication of an alpha-beta(3)-alpha motif, with betas from both domains forming one beta sheet with 321456 order. The second domain contains a (n=5, S=10) beta barrel.

    This is a second protein from the PmbA_TldD family, the first, also solved by JCSG (1vl4) was described in [Ref]. PmbA_TldD family is a large (>600 homologs) of bacterial and archeal proteins.

    It has been suggested that proteins from this family are peptidases, classified by MEROPS as family U62 (clan U-). The peptidases associated with clan U- have an unknown catalytic mechanism. The type example is microcin-processing peptidase 1 from Escherichia coli, which is the product of the gene PmbA. It has been suggests that the pmbA gene product acts to inhibit the interaction between the letD protein and the A subunit of DNA gyrase. The letA (ccdA) and letD (ccdB) genes of the F plasmid, located just outside the sequence essential for F-plasmid replication, contribute to stable maintenance of the plasmid in E. coli cells. The letD gene product acts to inhibit partitioning of chromosomal DNA and cell division by inhibiting DNA gyrase activity, whereas the letA gene product acts to reverse the inhibitory activity of the letD gene product PUBMED:8604133.

    Ligand Summary



    References

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