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The Open Protein Structure Annotation Network
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3gf6

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

    Title Crystal structure of bacterial lipoprotein of unknown function (NP_810146.1) from BACTEROIDES THETAIOTAOMICRON VPI-5482 at 1.69 A resolution. To be Published
    Site JCSG
    PDB Id 3gf6 Target Id 392967
    Molecular Characteristics
    Source Bacteroides thetaiotaomicron vpi-5482
    Alias Ids TPS20265,NP_810146.1, 324894 Molecular Weight 25538.34 Da.
    Residues 223 Isoelectric Point 4.49
    Sequence dndaiyypvgdvdierggpalevgeedvlvarsfneedyvldtiaqypndptlgkltfmidlknqqkdq nvadfngvgkskltmslgykdgnypsesqvpiytsqdvtakyavklrlkgellvsgdewmidyvyaqla slfqpyppanfpevfmckggmklgtfdsfrrtctfditydrsdlsfsqlyfnlfinlagqkrenrvrlr idkesyfelyeqseem
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 2
    Resolution (Å) 1.69 Rfree 0.211
    Matthews' coefficent 2.18 Rfactor 0.161
    Waters 677 Solvent Content 43.62

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3gf6
    1. S-nitrosylation of Drp1 links excessive mitochondrial fission to neuronal injury in neurodegeneration
    T Nakamura, P Cieplak, DH Cho, A Godzik, SA Lipton - Mitochondrion, 2010 - Elsevier
     

    Protein Summary

     B. thetaiotamicron gene BT_1233 (protein ID: NP_810146) encodes a secreted all-beta protein which likely functions as a monomer. BT_1233 is a member of a novel, small protein family specific to Bacteroides, with twelve homologs in fully sequenced genomes and two in metagenomics samples. This family have been since added to PFAM and would appear in PFAM release 25 as PF12956 (DUF3845).

    3gf6 has a beta sandwich fold with weak, but statistically significant similarity to a TNF-like jelly roll fold. FATCAT alignment to 1rj7 (EDA, Ectodysplasin) has an RMSD of 3.15A over 140 residues, with 4% sequence identity. DALI hits 1rj7 with a weak Z score of 8.0. The similarity is especially strong in one of the two beta sheets. Possible functional consequences of this similarity needs to be investigated further as TNF-like proteins have never been reported from bacteria before.

    Predictions from LipPred (cleavage residue: 19) and LipoP (CleavII 18-19 12.0006 # LCLTG|CVRDN Pos+2=V) servers strongly indicates that BT1233 is a bacterial lipoprotein and it is not secreted to the environment.

     

    Figure 1. monomer structure of 3gf6

    GS13247A.png

     

    Figure 2: Structural alignment of Ectodysplasin A (PDB 1rj7; colored red) with 3gf6 (colored blue).

    BT1233.pngBT1233_1rj7_alignDALI.png1rj7A.png

    Ligand Summary

    Reviews

    References

     

    No references found.

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    Files (5)

    FileSizeDateAttached by 
     1rj7A.png
    crystal structure of EDA-A1 (PDB: 1rj7 chain A). EDA-A1 belongs to the TNF-like fold of SCOP
    67.64 kB20:15, 19 Feb 2009krishnaActions
     BT1233.png
    crystal structure of a bacterial protein, BT_1233 that adopts a TNF-like fold.
    97.29 kB20:15, 19 Feb 2009krishnaActions
     BT1233_1rj7_alignDALI.png
    Structural alignment of EDA-A1 (PDB 1rj7; TNF-like fold of SCOP) and BT_1233. The structures were aligned by the DALI webserver with a Z-score of 7.9. The RMSD for the alignment is 3.3 A over 126 residues with a sequence identity of 6 %.
    131.53 kB20:15, 19 Feb 2009krishnaActions
     GS13247A.png
    392967 monomer
    799.85 kB20:16, 2 Feb 2009qxuActions
     tnf-like.pse
    PyMOL session file for FATCAT alignment of 1rj7 and BT1233
    883.27 kB20:29, 19 Feb 2009krishnaActions
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