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The Open Protein Structure Annotation Network
PDB Keyword
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3u22

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

    Title Crystal structure of a putative HmuY_like heme binding protein (BVU_2192) from Bacteroides vulgatus ATCC 8482 at 2.12 A resolution. To be published
    Site JCSG
    PDB Id 3u22 Target Id 393117
    Molecular Characteristics
    Source Bacteroides vulgatus atcc 8482
    Alias Ids TPS66195,YP_001299475.1, 324146 Molecular Weight 22626.04 Da.
    Residues 201 Isoelectric Point 4.43
    Sequence acdgilegiydspaasdsnelgfirtdpsthsgtiyidatdyrrwtfidfhtqkvdsvnvtdseqkepe ewdiavhrydvktnagavletgftgfsalrnadampegayvedvwttakiaidmsgmmdgnivymesyy neelskwlnvdksnmpptytlsnkvymvklkdgtyaavrltnymnasgvkgfmtidyiypfel
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 2
    Resolution (Å) 2.12 Rfree 0.1724
    Matthews' coefficent Rfactor 0.1647
    Waters 276 Solvent Content

    Ligand Information
    Ligands
    Metals

    Jmol

     

    Protein Summary

    The protein BVU_2192 (YP_001299475.1) is a distant homolog of the heme binding protein HmuY from Porphyromonas Gingivalis Heme-binding protein (pdb code 3h8t). These are only two solved proteins from a large family of uncharacterized proteins, not yet defned in PFAM. The structure of 3h8t is was described as new all-beta fold mimicking a right hand. It is not classifed in SCOP yet.

     

    The structure of the monomer is shown below.

     

    GS13310B.png

     

    The structure binds an unknown ligand (UNL, shown in magents spheres) betwen two monomers of the protein.

    GS13310B_unl.png

     

    An unbiased electron density surrounding the ligand is shown below.

    GS13310B_unl_density.png

     

    The oligomeric organization of the protein may be a tetramer.

    GS13310B_tetramer.png

     

    Structure similarity search supports the homology between BVU_2192 (YP_001299475.1) the Porphyromonas Gingivalis Heme-binding protein (pdb code 3h8t) with Z-score of 20 and rmsd of 2.6 over 160 residues. A superposition to this protein is shown below.

    GS13310B_3h8t.png

    3h8t (cyan), BVU_2192 (YP_001299475.1). The UNL  (rd spheres) in YP_001299475.1 binds in teh same location as HEME binds in 3h8t.

    Ligand Summary

    Reviews

    References

     

    No references found.

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