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2ook

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

    Title Open and closed conformations of two SpoIIAA-like proteins (YP_749275.1 and YP_001095227.1) provide insights into membrane association and ligand binding. Acta Crystallogr.,Sect.F 66 1245-1253 2010
    Site JCSG
    PDB Id 2ook Target Id 372476
    Molecular Characteristics
    Source Shewanella frigidimarina ncimb 400
    Alias Ids TPS1611,YP_749275.1, BIG_470, BIG_496, 103450 Molecular Weight 14501.86 Da.
    Residues 126 Isoelectric Point 4.89
    Sequence mdmkkhglsiginriesvffvtlkaigtlthedylvitpmlegalsqvdqpkvslfldateldgwdlra awddlklglkhksefervailgnkdwqewaakigswfiageikyfededdalkwlry
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 2
    Resolution (Å) 1.80 Rfree 0.233
    Matthews' coefficent 2.16 Rfactor 0.183
    Waters 224 Solvent Content 42.97

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 2ook
    1. Decision-making in structure solution using Bayesian estimates of map quality: the PHENIX AutoSol wizard
    TC Terwilliger, PD Adams, RJ Read - Section D: Biological , 2009 - scripts.iucr.org
     
    2. TOPSAN: use of a collaborative environment for annotating, analyzing and disseminating data on JCSG and PSI structures
    SS Krishna, D Weekes, C Bakolitsa - Section F: Structural , 2010 - scripts.iucr.org
     
    3. Structural classification of proteins and structural genomics: new insights into protein folding and evolution
    A Andreeva, AG Murzin - Acta Crystallographica Section F: Structural , 2010 - scripts.iucr.org
     
    4. Open and closed conformations of two SpoIIAA-like proteins (YP_749275. 1 and YP_001095227. 1) provide insights into membrane association and ligand binding
    A Kumar, A Lomize, KK Jin, D Carlton - Section F: Structural , 2009 - scripts.iucr.org
     
    5. The Contribution of Surface Residues to Membrane Binding and Ligand Transfer by the _-Tocopherol Transfer Protein (_-TTP)
    WX Zhang, V Thakur, A Lomize, I Pogozheva - Journal of molecular , 2011 - Elsevier
     
    6. New variants of known folds: do they bring new biology?
    EV Koonin - Acta Crystallographica Section F: Structural Biology , 2010 - scripts.iucr.org
     


    Protein Summary

    Gene Sfri_0576 from S. frigidimarina encodes a protein of unknown function (YP_749275, Q087X8_SHEFN). Its amino acid sequence belongs to PSRP-3_Ycf65 (PF04839) family of proteins that associate with the 30S ribosomal subunit of cyanobacteria and plant plastids where they are thought to mediate protein-protein interactions.

     

    The structure is an alpha+beta fold with distant structural similarity to proteins with a SpoIIaa- like fold, for instance to the Anti-sigma factor antagonist SpoIIaa from T. maritima (PDB 1vc1, TM1442) with 97 equivalent positions with an RMSD of 3.15 A without twists in the FATCAT alignment. Two other homologous proteins were determined by the JCSG (3BL4 and 2Q3L). Both 2OOK and 2Q3L are apparent orthologs of possible universal stress protein SO3682 from Shewanella oneidensis MR-1. Despite a very high sequence identity (54%), the two structures reveal large-scale differences in the subunit conformations and distinct dimerization modes (for details, see the 2Q3L page). The 3BL4 structure is a segment-swapped dimer of a more distant homolog of 2Q3L and 2OOK. The common core of the three structures comprises the mixed five-stranded sheet and the C-terminal helix.

    Ligand Summary



    References

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