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The Open Protein Structure Annotation Network
PDB Keyword
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3uc2

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

    Title Crystal structure of a hypothetical protein with immunoglobulin-like fold (PA0388) from Pseudomonas aeruginosa PAO1 at 2.09 A resolution. To be published
    Site JCSG
    PDB Id 3uc2 Target Id
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    Molecular Characteristics
    Source
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    Alias Ids
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    TPS47455,NP_249079.1, 324518
    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 2.38 Rfactor 0.2110
    Waters
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    Solvent Content 48.27

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    Ligand Information
    Ligands
    Metals

    Jmol

     
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    Google Scholar output for 3uc2

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    Protein Summary

    PA0388 is a founding member of a new protein family of over 100 proteins, all of them with unknown functions. This family has been just added to PFAM as DUF4426 (PF14467). Members of this family are found mostly in g-proteobacteria, especially in Vibrio. Strangely enough, there seems to be one eukaryotic homolog in Nematostella vectensis (NEMVEDRAFT_v1g226006), where the PA0388-like domain is fused with a domain homogous to the Methionine biosynthesis protein MetW (see below). In several Pseudomonas species, but also in Vibrio vulnificus and Azotobacter vinelandii PA0388 homologs are  genomic neighbors of Nucleoside 5-triphosphatase RdgB (dHAPTP, dITP, XTP-specific) (EC 3.6.1.15) and Methionine biosynthesis protein MetW. On the other hand, in most Vibrio species it appears as a part of a conserved operon involved in possible response to stress.

     

    A search for other proteins of similar structure (using EBI SSM/PDBeFOLD) shows significant hits (Q-scores ~0.4, r.m.s.d ~2.4A) to the E. coli FetP (PDB id 3nrp, involved in iron uptake, 6% sequence id), a membrane lipoprotein (PDB id 2o6d, 15% sequence id), a beta-1,3-xylanase (PDB id 2cov, 15% sequence id), and a DUF3244 family protein that is a JCSG structure (PDB id 3d33, TOPSAN page here, 8% sequence id).

     

    The protein has a beta-sandwhich structure and a signal peptide that was deleted prior to cloning. It needs to be checked if this signal peptide has a lipoprotein/Sp11 cleavage signature/site.

    Fig1.png

     

    The ig-like beta barrel structure of PA0388 is most similar to eukaryotic dimerizing ig-like structures, here for instance is the structural alignment of PA0388 (green) with yeast GAE domain (red, PDB:3mnm)

    pymol.png

    Ligand Summary

    Reviews

    References

     

    No references found.

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    Files (2)

    FileSizeDateAttached by 
     Fig1.png
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    230.94 kB22:06, 17 Aug 2011debanuActions
     pymol.png
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    104.73 kB19:28, 21 Aug 2011adamActions
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