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2q3l

    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 2q3l Target Id
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    Molecular Characteristics
    Source
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    Alias Ids
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    TPS1604,YP_001095227.1, BIG_496, BIG_470
    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 2
    Resolution (Å)
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    Rfree
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    Matthews' coefficent 2.63 Rfactor 0.181
    Waters
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    Solvent Content 53.29

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    Ligand Information
    Ligands
    Metals

    Jmol

     
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    Google Scholar output for 2q3l
    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. Ligands in PSI structures
    A Kumar, HJ Chiu, HL Axelrod, A Morse - Section F: Structural , 2010 - scripts.iucr.org
     
    5. 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
     
    6. 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
     
    7. New variants of known folds: do they bring new biology?
    EV Koonin - Acta Crystallographica Section F: Structural Biology , 2010 - scripts.iucr.org
     

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    Protein Summary

    Gene SFRI0576 from Shewanella sp. pv-4 encodes the YP_001095227 sequence of a protein of unknown function from the DUF3478 group (PF11964).

    2q3l 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,without twists in the FATCAT alignment. Three dimensional structures of two other homologous proteins were determined by the JCSG (3BL4 and 2OOK with a Dali Zscr=12).

    Both 2OOK and 2Q3L are apparent orthologs of SO3682 from Shewanella oneidensis MR-1 that may be a universal stress protein ([Ref]). Despite a very high sequence identity (54%), the two structures reveal large-scale differences in the subunit conformations and distinct dimerization modes ([Ref]).

    2q3l_2ook_aln.png


    Side-by-side comparison of subunit conformations of 2Q3L (left) and 2OOK (right). Shown in stick are selected sequentially equivalent non-polar residues (highlighted in the above alignment), which are exposed on the 2Q3L surface, but are buried in the 2OOK core.

    2q3l_2ook_sbs.png

    The 2Q3L crystal packing suggests two possible dimerization modes; both are distinct from the 2OOK mode. In the dimeric interface as in the PDB entry (above), there is a substantial contribution of the N-terminal Gly 0, which is a cloning artifact, absent in the natural sequence. The alternative dimer is shown below.

            


    2q3l_alternative_dimer.png

    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

    1. Gao H. et al. (2006) J. Bacteriol. 188:4560-4569. PMID: 16740962

    2. Murzin A.G. (2008) Science 320:1725-1726. PMID: 18583598

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    Files (4)

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    2q3l_2ook_aln.png
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    86.73 kB01:32, 9 Jul 2008krishnaActions
     2q3l_2ook_fatcataln.pse
    PyMOL session of FATCAT structural alignment of 2ook and 2q3l. Equivalent hydrophobic residues from both structures are shown in ball-and-stick. These evolutionarily conserved residues are packed very differently in the two structures.
    612.98 kB01:53, 11 Jul 2008krishnaActions
    2q3l_2ook_sbs.png
    No description
    89.02 kB01:32, 9 Jul 2008krishnaActions
    2q3l_alternative_dimer.png
    No description
    83.8 kB01:32, 9 Jul 2008krishnaActions
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