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The Open Protein Structure Annotation Network
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3kdw

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

    Title Crystal structure of Putative sugar binding protein (YP_001300177.1) from Bacteroides vulgatus ATCC 8482 at 1.70 A resolution. To be published
    Site JCSG
    PDB Id 3kdw Target Id 393277
    Molecular Characteristics
    Source Bacteroides vulgatus atcc 8482
    Alias Ids TPS27817,YP_001300177.1, 324139 Molecular Weight 22950.07 Da.
    Residues 202 Isoelectric Point 8.98
    Sequence avdldregrdpayvesivkrsqkivdkleltdtvaarevttiianryfklndiyetrdakvklaketlt gdakqeavkaaeaekdaalyrthfafpadlslyldakqidavkdgmtygvvmvtykatvdmiptlkeee kaqimawlvearefamdaensnkkhaafgkykgrinnylskrgydlvkerkawyerikarggki
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 1.70 Rfree 0.191
    Matthews' coefficent 2.79 Rfactor 0.152
    Waters 253 Solvent Content 55.87

    Ligand Information
    Ligands
    Metals

    Jmol

     

    Protein Summary

    Protein BVU_2916 (JCSG target ID 393277, JCSG target accession code GS13982A, GenBank accession code YP_001300177.1) is a 222-residue long protein from Bacteroides vulgatus, an anaerobic, gram-negative bacterium that is a prevalent member of the human intestinal flora.  The protein belongs to family DUF3826 in Pfam, members of which are putative sugar-binding proteins.

    The structure of of an N-terminally truncated version of BVU_2916 (residues 21-222) was solved by Se-MAD to a resolution of 1.7 Angstroms and reveals an all-alpha fold in which two helical bundles are perpendicular to each other (Figure 1).

    Figure 1.  Structure of BVU_2916 gradiently colored from the N- (blue) to the C-terminus (red).

    GS13982A-monomer-gradient.png

    The functional oligomeric state of this protein is unclear.  While the structure was solved with one molecule per asymmetric unit, PISA analysis indicates that a dimer would be stable in solution (Figure 2).

    Figure 2.  Orthogonal views of BVU_2916 as a dimer.

    GS13982A-dimer-1.png  GS13982A-dimer-2.png

    Protein Homologs:

    Both FFAS and DALI (Table 1) searches reveal that a very closely related protein, both in terms of sequences (78% seq id) and structure (Figure 3), is 3g6i, a JCSG structure which has been annotated as an outer membrane protein that is part of a carbohydrate binding complex from the closely related gut bacteria Bacteriodes thetaiotaomicron (TOPSAN).

    Table 1.  Structural neighbors of BVU_2916 as assessed by Dali.

    N PDB Z-score RMSD LALI NRES %ID TITLE
    1 3g6i 27.5 0.7 199 200 78 PUTATIVE OUTER MEMBRANE PROTEIN, PART OF (TOPSAN)
    2 2cwe 8.2 4.5 96 191 16 HYPOTHETICAL TRANSCRIPTION REGULATOR PROTEIN,
    3 1uly 7.6 4.9 96 190 16 HYPOTHETICAL PROTEIN PH1932
    4 1wqf 7.3 3.9 80 183 10 RIBOSOME RECYCLING FACTOR
    5 2fic 7.1 4.4 93 191 14 BRIDGING INTEGRATOR 1
    6 2j68 6.8 16.2 114 680 8 BACTERIAL DYNAMIN-LIKE PROTEIN
    7 1x03 6.8 4.1 88 210 10 SH3-CONTAINING GRB2-LIKE PROTEIN 2
    8 2d4c 6.7 4.0 90 231 12 SH3-CONTAINING GRB2-LIKE PROTEIN 2
    9 1is1 6.7 2.7 75 185 15 RIBOSOME RECYCLING FACTOR
    10 1ek8 6.6 2.5 75 185 13 RIBOSOME RECYCLING FACTOR

     

    Figure 3.  Superposition of BVU_2916 (yellow) with homolog 3g6i (blue) reveals nearly identical structures.

    GS13982A-3g6i-superpose.png

    Electrostatic Potential Surface Map:

    While the electrostatic potential surface of BVU_2916 reveals that there are large positively charged regions as in homolog 3g6i, these areas are also interspersed with some negatively charged regions, unlike in 3g6i (see 3g6i TOPSAN page for the electrostatic potential surface map of 3g6i).

    GS13982A-emap.png

     

    Genome Context:

    Genome context analysis with STRING reveals that the following proteins, listed in order from highest to lowest score, may be functional partners of BVU_2916:

    • BVU_2915:  Polysaccharide lyase family 1, candidate pectate lyase
    • BVU_2917:  Polysaccharide lyase family 1
    • BVU_2918:  Putative uncharacterized protein
    • BVU_2914:  Putative outer membrane protein, probably involved in nutrient binding
    • BVU_2913:  Putative outer membrane protein, probably involved in nutrient binding

     

    The evidence suggests that BVU_2916, like its homolog 3g6i, may be involved in carbohydrate binding/metabolism.

    Ligand Summary

    Reviews

    References

     

    No references found.

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