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3d33

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

    Title Crystal structure of Domain of Unknown Function with an Immunoglobulin-like Beta-sandwich Fold (YP_001297618.1) from Bacteroides vulgatus ATCC 8482 at 1.70 A resolution. To be published
    Site JCSG
    PDB Id 3d33 Target Id
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    Molecular Characteristics
    Source
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    Alias Ids
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    TPS1784,YP_001297618.1, 88197
    Molecular Weight
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    Da.
    Residues
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    Isoelectric Point
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    Sequence
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      BLAST   FFAS

    Structure Determination
    Method XRAY
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    Chains 2
    Resolution (Å)
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    Rfree
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    Matthews' coefficent 2.42 Rfactor 0.174
    Waters
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    Solvent Content 49.11

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    Ligand Information
    Ligands
    Metals

    Jmol

     
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    Google Scholar output for 3d33
    1. Structure of a membrane-attack complex/perforin (MACPF) family protein from the human gut symbiont Bacteroides thetaiotaomicron
    Q Xu, P Abdubek, T Astakhova, HL Axelrod - Section F: Structural , 2010 - scripts.iucr.org
     
    2. Towards structure-based protein drug design
    C Zhang, L Lai - Biochemical Society Transactions, 2011 - www-06.all-portland.net
     

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    Protein Summary

    Gene BVU_0276 from Bacteroides vulgatus atcc 8482 encodes the YP_001297618 protein, the first representative with solved structure of the DUF3244 family (PF11589) of ~100 proteins present only in Bacteoides and in the human gut metagenome. DUF3244 family belongs to the Pfam clan of hydroxyisourate hydrolases (HIUase)/transthyretins (TTR). The function of this protein is unknown, and the homologs show extreme sequence divergence with almost no conserved positions across the entire family. The BVU_0276 protein contains a signal peptide with a predicted cleavage site between 28-29. As a result, the crystalized structure (3d33) contains only the 28-134 region of the protein.

    The 3d33 structure belongs to the SCOP immunoglobulin-like beta-sandwich fold and structurally is most similar  to fibronectin (e.g. 1ten rmsd 2.0 for 73 aligned Ca atoms; Dali Z-score=7). DALI top hits are with the glycoside hydrolase family-2 3gm8 (Z=8), tenascin 1qr4 (Z=7), and a fibronectin type III module 1fna (Z=7). A weaker hit is observed with the zebra fish HIUase 2h1x (Z=4.3; 16% seq.id.).

    FFAS shows significant (-12.3) similarity between YP_001297618 and a family of copper resistance proteins CopC (PF04234). This is an unusual, methionine-rich family of copper binding proteins with an immunoglobulin-like fold, represented by the E. coli protein 1ix2 (Dali Z=6). CopC binds copper, but only the apo structure was solved and the molecular details of copper binding are uknown; therefore it is not possible to comment on the conservation of the copper binding site between YP_001297618 and CopC. 3d33 is structurally similar to 1ix2, but the similarity appears to be more distant than that of 3d33 with 1ten (fibronectin).



     

    Ligand Summary



    References

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