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3lur

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

    Title Crystal structure of Putative bacterial transcription regulation protein (NP_372959.1) from Staphylococcus aureus MU50 at 1.81 A resolution. To be published
    Site JCSG
    PDB Id 3lur Target Id 399559
    Molecular Characteristics
    Source Staphylococcus aureus subsp. aureus mu50
    Alias Ids TPS30598,NP_372959.1, _0046.001003_, 323503 Molecular Weight 17660.20 Da.
    Residues 157 Isoelectric Point 4.98
    Sequence meyqlqqlasltlvgiketyengrqaqqhiagfwqrcyqegviadlqlknngdlagilglcipeldgkm symiavtgdnsadiakydvitlasskymvfeaqgavpkavqqkmeevhhyihqyqantvksapffelyq dgdttsekyiteiwmpvkg
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 3
    Resolution (Å) 1.81 Rfree 0.218
    Matthews' coefficent 2.07 Rfactor 0.176
    Waters 322 Solvent Content 40.65

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3lur
    1. Predicting protein structures with a multiplayer online game
    S Cooper, F Khatib, A Treuille, J Barbero, J Lee - Nature, 2010 - nature.com
     
    2. Crystal Structure of an Integron Gene Cassette-Associated Protein from Vibrio cholerae Identifies a Cationic Drug-Binding Module
    CN Deshpande, SJ Harrop, Y Boucher, KA Hassan - PloS one, 2011 - dx.plos.org
     

    Protein Summary

    Gene SAV2435 from encodes the NP_372959 protein that has been determined to a resolution of 1.81 Angstroms using three-wavelength Se-MAD. The target belongs to AraC_E_bind (PF06445) Pfam A family that includes the effector binding domains of bacterial transcription regulators. This group of transcription factors regulates gene expression for proteins involved in antibiotic resistance, oxidative damage, heavy metal resistance, and inhibition of DNA gyrase.

    monomer_view1.pngmonomer_view2.png

     

    Shown above are two ribbon representations of the 3lur structure color-coded along the amino acid sequence from blue at the N-terminus to red at the C-terminus. The orientation of the second image was obtained from the first by rotating 90 degrees counter-clockwise about a horizontal axis in the plane of the images.

     

    Shown below is a ribbon representation of the structure of the 3lur monomer. A 2-fold pseudo-symmetry axis related many structural elements in the N and C-terminal halves of the monomer. The N-terminal half (residues 1-76) is shown in blue and the C-terminal half (residues 87-155) is shown in red. An helix-loop region between the N and C-terminal halves is shown in yellow. The pseudo two-fold is perpendicular to the plane of the image.

    pseudosymmetry.png

     

    A DALI search reveals that 3lur has similarity to the following structures

    PDB ID
    DALI Z-Score
    rmsd (Ang)
    aligned residues
    number of residues
    % Sequence ID
    Description
    3gk6 14.9 2.7 138 153 19 Integron cassette potein VCH_CASS2 from Vibrio cholerae.
    1jyh 13.9 3.3 141 155 11 E. coli Sbm C protein (AKS Gyrase Inhibitory Protein Gyr1, AKA YeeB
    1d5y 13.8 2.5 138 288 17 E. coli ROB transcription factor in complex with DNA
     3e0h  12.3  3.5  140  153  14  Uncharacterized protein from Chlorobium tepidum NESG target CtR107
     2kcu  11.1  3.2  135  166  12 Solution NMR structure of Uncharacterized protein from Chlorobium tepidum NESG target CtR107
     3d6y  10.3  3.2  127  277  10  R275E mutant of BMRR bound to DNA and berberine
     3b49  9.4  3.5  132  204  9  Uncharacterized conserved protein from Listeria innocua
     2gov  8.9  4.4  134  184  8  SOUL/HBP Family of Heme-binding proteins P22HBP

     

    MI15962B_to_3d6y.png

     

    Shown to the left is a comparison of the structures of 3lur (green) and PDB ID 3d6y (orange), the BmrR multidrug binding transcription factor from Bacillus subtilus. A drug molecule berberine (magenta) and single-stranded DNA (yellow) are bound to the crystal structure of BmrR. A molecule of PEG bound to the crystal structure of 3lur is shown in blue. The position of the drug molecule in BmrR is similar to that of PEG in 3lur. 

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     A PEG molecule from the crystallization was observed in the crystal structure. Shown below is a surface representation of the 3lur structure (grey). A ribbons representation of the structure is superimposed and color coded with the N-terminus in blue and the C-terminus in red. The bound PEG molecule is shown by sticks.

     

    PEG.png

    References

    Romanowski, M.J.; Ginbey, S.A. and Burley, S.K. (2002) "Crystal Structure of the Escherichia coli SbmC Protein that Protects Cells From the DNA Replication Inhibitor Microcin B17" Proteins: Structure, Function, and Genetics" 47: 403-407.

     

    Newberry, K.J, Huffman, J.L., Miller, M.C., Vazquez-Laslop, N., Neyfakh, A.A., and Brennan, R.G. (2008) "Structures of BmrR-Drug Complexes Reveal a Rigid Multidrup Binding Pocket and Transcription Activation through Tyrosine Explusion" J. Biol. Chem. Vol 283 No. 39, pp. 26795-26804.

     

    Kwon, H.J., Bennik, M.H.J., Demple, B., and Ellenberger, T. (2000) "Crystal Structure of the Escherichia coli Rob Transcription Factor in Complex with DNA" Nature Structural Biology Vol. 7 Number 5 p. 424.

     

    Dias, J.S>, Macedo, A.L., Ferreira, G.C., Peterson, F.C., Volkman, B.F., and Goodfellow, B.J. "The First Structure from the SOUL/HBP Family of Heme-binding Proteins, Murine P22HBP. (2006) J. Biol. Chem. Vol 281, Number 42, pp. 31553-31561


    Ligand Summary

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