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3pnx

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

    Title Crystal structure of a putative sulfurtransferase dsrE (Swol_2425) from Syntrophomonas wolfei str. Goettingen at 1.92 A resolution. To be published
    Site JCSG
    PDB Id 3pnx Target Id 381737
    Molecular Characteristics
    Source Syntrophomonas wolfei subsp. wolfei
    Alias Ids TPS26515,YP_755085.1, BIG_508, 86905 Molecular Weight 18150.31 Da.
    Residues 159 Isoelectric Point 5.01
    Sequence menkkmnlllfsgdydkalasliianaaremeievtifcafwgllllrdpekasqedkslyeqafsslt preaeelplskmnlggigkkmllemmkeekapklsdllsgarkkevkfyacqlsveimgfkkeelfpev qimdvkeylknalesdlqlfi
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 6
    Resolution (Å) 1.92 Rfree 0.2152
    Matthews' coefficent 2.18 Rfactor 0.1896
    Waters 189 Solvent Content 43.63

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3pnx
    1. Assessment of protein structure refinement in CASP9
    JL MacCallum, A Prez, MJ Schnieders - Proteins: Structure, , 2011 - Wiley Online Library
     
    2. Blind prediction of quaternary structures of homo-oligomeric proteins from amino acid sequences based on templates
    M Morita, M Kakuta, K Shimizu, S Nakamura - 2012 - hoajonline.com
     
    3. Protein Physics by Advanced Computational Techniques: Conformational Sampling and Folded State Discrimination
    PC Tejada - 2011 - sissa.it
     
    4. PackHelix: A tool for helix_sheet packing during protein structure prediction
    C Hu, P Koehl, N Max - Proteins: Structure, Function, and , 2011 - Wiley Online Library
     

    Protein Summary

    Pfam Update:  On building this, the first match found was to DrsE (PF02635), a family with many other structures. I will try and get this protein into the family.

    The x-ray crystal structure of target id 381737 was determined by Se-MAD at a resolution of 1.97 Angstroms, The amino acid sequence of this target show similarity to those belonging to the DrsE/DrsF (PF02635) Pfam Family. These proteins are annotated as being involved in intracellular sulfur reduction.

    monomer.png

    Shown above is a ribbons representation of the crystal structure of target ID 381737 color coded with the N-terminal in blue and the C-terminal end of the polypeptide chain in red. The structure suggests that this target can most likely be classified into the DsrEFH-like SCOP fold. A DALI search show that target ID 381737 shows structural similarity to the following PDB entries.

     

    PDB ID
    DALI Z-Score
    rmsd overlap (Angstroms)
    aligned residues
    total residues
    %sequence ID
    Description
    2qs7 16.6 2.2 129 138 27 Protein of Unknown Function (NP_342590.1) from Sulfolobus solfataricus
    1jx7 13.0 2.6 111 117 18  ychN protein from E. coli.
    1l1s 12.6 1.9 106 111 13  Unknown Function MTH1491 from Methanobacterium thermoautophicum
    2hyb 11.9 2.6 110 130 15 Putative sulfurtransferase DsrEFH
    2pd2 11.5 2.1 101 108 15 Conserved hypothetical protein from Sulfolobus tokodaii strain 7
    2d1p 11.3 3.0 112 130 11  Heterohexameric TusBCD protein, which are crucial for tRNA modification
    2fb6 10.5 2.2 105 116 12 Conserved protein of unknown function BT1422 from Bacteroides thetaiotamicron

    Shown below are the some of the  DALI hits superimposed on the structure of target ID 381737

     

     

    2qs7_to_PU9842C.png

    PDB ID 2qs7 (red)
    DALI Z Score=16.6
    rmsd overlap=2.2 Å
    alignment 129/138 residues
    Sequence id=27%
    JCSG Protein of Unknown Function

     

     

     

     

     

     

     

     

     

     

     

    1jx7_to_PU9842C.pngPDB ID 1jx7 (cyan)
    DALI Z Score=13.0
    rmsd overlap=2.6 Å
    alignment 111/117 residues
    Sequence id=18%
    ychN protein from E. coli
    Kim Lab BCSG J. Stru. Func. Genomics vol 2 (2002) pp. 53-66

     

     

     

     

     

     

     

     

     

     

     

     

    1lis_to_PU9842C.pngPDB ID 1l1s (magenta)
    DALI Z Score=12.6
    rmsd overlap=1.9 Å
    alignment 106/111 residues
    Sequence id=13%
    Unkown Function MTH1491 from Methanobacterium thermautochipum
    Arrowsmith et al. Prot. Sci. vol  11 (2002) pp. 1409-1414

     

     

     

     

     

     

     

     

     

     

     

     

    2d1p_to_PU9842C.pngPDB ID 2d1p
    DALI Z Score=11.3
    rmsd overlap=3.0 Å
    alignment 112/130 residues
    Sequence id=11%
    Heterohexameric TusBCD protein, crucial for tRNA modification  
    Numata et al. J. Structure vol 14(2) (2002) pp. 357-66

     

     

     

     

     

     

     

     

     

     

     

     

     

     

    Analytical size exclusion chromatography and crystal packing indicate that a trimer is a significant oligomerization state. Shown below is a ribbons representation with the individual polypeptide chains shown in different colors.

     

    trimer.png

     

    OCS.bmp

    The crystal structure of target ID indicates that Cys 120 in target ID 381737. Shown on the left is the covalently-modifed Cys 120.  Electron density, contoured at 1 sigma and shown in purple, suggests that Cys 120 is oxidized to cysteinesulfonic acid. This covalent modification was observed on all six subunits in the asymmetric unit. More analysis is necessary to assess the functional implications of this modification for annotation of this target as being involved sulfate oxidation/reduction. The figure shown immediately below shows a positioning of the modified Cys 120 residue on the monomer. This modified Cys 120 is positioned on the surface of each monomer within a putative active site and does not face the interface of the hexamer.

     

     

     

     

     

     

    OCS.png

    Ligand Summary

    Reviews

    References

     

    No references found.

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