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The Open Protein Structure Annotation Network
PDB Keyword
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3hdu

    Title Crystal structure of putative thioesterase (YP_461911.1) from SYNTROPHUS ACIDITROPHICUS SB at 2.50 A resolution. To be published
    Site JCSG
    PDB Id 3hdu Target Id 379820
    Molecular Characteristics
    Source Syntrophus aciditrophicus sb
    Alias Ids TPS7220,YP_461911.1, 289638 Molecular Weight 17474.55 Da.
    Residues 156 Isoelectric Point 5.92
    Sequence mpnfskneevlfsavneifeekipfnkiiglkvrfispeqvklsfemrdelignairrmlyggvissai dmtaglaafmgfqekmsgkpmeeklamigrlstmslhveylrpglgrefvctgynvrtgnkvavirtel mndqdeliavgsvsyilv
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 3
    Resolution (Å) 2.50 Rfree 0.257
    Matthews' coefficent 2.27 Rfactor 0.237
    Waters Solvent Content 45.88

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3hdu
    1. Geometric similarities of protein-protein interfaces at atomic resolution are only observed within homologous families: An exhaustive structural classification study
    AR Kinjo, H Nakamura - Journal of molecular biology, 2010 - Elsevier
     

    Protein Summary

    The SYN_01977 (YP_461911.1) gene from Syntrophicus acidophilus sb encodes a protein that does not have any functional annotation yet. It belongs to PFAM PF03061 which  is a family of thioesterases.

     

    The monomer structure is a beta-barrel with a very long helix running through its center. Two views of the monomer are shown below.

    FN9768A_mon1.png            FN9768A_mon2.png

    There are three monomers in the crystallographic asu and they assemble as a trimer of dimers, as shown below.

    FN9768A_hexamer.png

     

     

    There are a few structural homologs of this protein.

    Top ten DALI Structural Homologs
    N PDB Z-score RMSD LALI NRES %ID TITLE
    1 3e8p 20.0 2.4 149 153 31 UNCHARACTERIZED PROTEIN
    2 3e1e 16.6 2.2 129 137 20 THIOESTERASE FAMILY PROTEIN
    3 3e29 16.5 2.5 130 135 20 UNCHARACTERIZED PROTEIN Q7WE92_BORBR
    4 2qwz 15.7 2.6 128 137 13 PHENYLACETIC ACID DEGRADATION-RELATED PROTEIN
    5 1zki 15.6 2.1 122 126 20 HYPOTHETICAL PROTEIN PA5202
    6 3f1t 15.5 2.9 132 136 16 UNCHARACTERIZED PROTEIN Q9I3C8_PSEAE
    7 2b6e 15.2 2.4 127 137 11 HYPOTHETICAL UPF0152 PROTEIN HI1161
    8 1sbk 15.2 2.3 127 138 9 HYPOTHETICAL PROTEIN YDII
    9 2fs2 15.1 2.5 128 138 16 PHENYLACETIC ACID DEGRADATION PROTEIN PAAI
    10 1sc0 15.1 2.5 127 137 11 HYPOTHETICAL PROTEIN HI1161
    SSM Structural Homologs
    N PDB Q-score RMSD TITLE
    1 3e8p 0.6026 1.894 THE PROTEIN Q8E9M7 FROM SHEWANELLA ONEIDENSIS RELATED TO THIOESTERASE SUPERFAMILY. NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET SOR246.
    2 3e29 0.5315 1.776 X-RAY STRUCTURE OF THE PROTEIN Q7WE92_BORBR FROM THIOESTERASE SUPERFAMILY. NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET BOR214A.

     

    A superposition of these two structure on this target reveals a high degree of structural similarity, shown below.

    FN9768A_3e29_3e8p.pngYP_461911.1 (green), 3e29 (cyan), 3e8p (magenta)
     

     

    This protein is predicted to be have a thioesterase function.

    Literature references
    1. Benning MM, Wesenberg G, Liu R, Taylor KL, Dunaway-Mariano D, Holden HM; , J Biol Chem 1998;273:33572-33579.: The three-dimensional structure of 4-hydroxybenzoyl-CoA thioesterase from Pseudomonas sp. Strain CBS-3. PUBMED:9837940

    2. Leesong M, Henderson BS, Gillig JR, Schwab JM, Smith JL; , Structure 1996;4:253-264.: Structure of a dehydratase-isomerase from the bacterial pathway for biosynthesis of unsaturated fatty acids: two catalytic activities in one active site. PUBMED:8805534

    Ligand Summary

    Reviews

    References

     

    No references found.

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