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3s9j

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

    Title Crystal structure of a Member of DUF4221 family (BVU_1028) from Bacteroides vulgatus ATCC 8482 at 1.75 A resolution. To be published
    Site JCSG
    PDB Id 3s9j Target Id
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    Molecular Characteristics
    Source
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    Alias Ids
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    TPS63561,YP_001298343.1, 88151
    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 1
    Resolution (Å)
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    Rfree
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    Matthews' coefficent 3.31 Rfactor 0.1423
    Waters
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    Solvent Content 62.88

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    Ligand Information
    Ligands
    Metals

    Jmol

     
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    Google Scholar output for 3s9j

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    Protein Summary

    This is a protein of unknown function BVU_1028 from B. vulgatus with a signal peptide. It could be a secreted protein.

    Pfam update: This target has been assigned to the Pfam family DUF4221, PF13970, which have all bacterial members. There are two highly conserved residues, a Cys near the start and a Asp in the middle, so it should be explored whether it could be an enzyme.

    The Cys is the most likely the fatty acid binding site for the lipoprotein after cleavage of the signal peptide and the Asp is probably part of the repeat portion.

    FFAS shows similarities to some hydrolases and dehydrogenases with < 10% sequence identity.

    The structure is that of a 6-bladed beta propeller, similar to that of WD40/YVTN repeat-like domains. Proteins with similar structures have been solved at the JCSG, for example, as seen in the TOPSAN page for the recently solved target 390003. Proteins with WD repeats are involved in a wide variety of functions including enzyme function and scaffolding for forming protein-protein complexes and have been reviewed in several papers (PMID: 10322433, PMID: 8090199, PMID: 21468892).

     

    Fig1.png

    A search for other proteins with similar structures using SSM (EBI) results in top hits with other beta-propeller proteins like the brain tumor NHL domain (PDB id 1q7f), with 7% seq id, 3.2 A rmsd and Q-score 0.27.

    Ligand Summary

    Reviews

    References

     

    No references found.

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    299.04 kB21:39, 9 May 2011debanuActions
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