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3npd

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

    Title Crystal structure of a putative quorum sensing-regulated protein (PA3611) from the Pseudomonas-specific DUF4146 family. Proteins 82 1086-1092 2014
    Site JCSG
    PDB Id 3npd Target Id 416819
    Molecular Characteristics
    Source Pseudomonas aeruginosa pao1
    Alias Ids TPS33848,NP_252301.1, 327508 Molecular Weight 12952.81 Da.
    Residues 117 Isoelectric Point 8.65
    Sequence aslkdfelskmlekvakessvgtprainedildqgytvegnqlinhlsvrashaermrsnpdsvrsqlg dsvcsntgyrqllargailtysfteyktnqpvaterfdagscriqgkk
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 1.60 Rfree 0.2046
    Matthews' coefficent 1.95 Rfactor 0.1602
    Waters 130 Solvent Content 36.80

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3npd
    1. ASTRO_FOLD 2.0: An enhanced framework for protein structure prediction
    A Subramani, Y Wei, CA Floudas - AIChE Journal, 2011 - Wiley Online Library
     
    2. Blind prediction of quaternary structures of homo-oligomeric proteins from amino acid sequences based on templates
    M Morita, M Kakuta, K Shimizu, S Nakamura - 2012 - hoajonline.com
     

    Protein Summary

     

    This target is annotated as a protein of unknown function from Pseudomonas aeruginosa PA01.

     

    A search for other proteins of similar sequence (BLAST search in UniProt database or PSI-BLAST search of NR database) shows that there are ~20 other similar proteins but they are found only in different pseudomonas species. These are thus pseudomonas-specific secreted proteins.

     

    This has been built into a small Pseudomonas-specific famiy called DUF4146, PF13652.

     

    The protein is present as a monomer in the crystal structure and crystal packing analysis suggests that it is a monomer in solution as well. There are some sulfate, CAPS and ethylene glycol molecules from the crystallization and cryoprotectant solutions bound to the protein:

    Fig1.png

     

     

     

    FFAS does not indicate significant hits to other proteins.

     

    A DALI search of other proteins of similar structures results in a Z-score of > 4.0 with Saframycin MX1 Synthetase B, with sequence identity ~11% and rmsd ~3.5A (PDB ids 3lnv and 3kxw). There are lower hits with many other proteins.

     

    A SSM search results in top weak (Q-scores < 0.20) hits to a ribosome binding factor A (PDB id 2dyj), putative zinc transporter CZRB (PDB id 3byp), cation diffusion family protein (PDB id 2zzt), etc. with rmsd ~3.0A and sequence identities from ~5-15%.

     

    A FATCAT search gives top hits to proteins with RbfA ribosome binding factor protein and some prokaryotic KH domain proteins.

     

    Overall, this appears to be a unique protein and structure with some overall fold similarities to other proteins.

     

    According to Uniprot and BLAST search, this protein has the locus name PA3611, UniProt id Q9HY15_PSEAE. A search in the STRING database for function associations indicates that this target may have some association with PA3612 (uncharacterized protein, confidence ~0.8) and Polyamine transport protein PotD (lower confidence ~0.5).

     

    An earlier biochemical analysis indicates that this target may be a QS-regulated (Quorum Sensing regulated) protein but the actual function is not known [Ref].

     

    A close homolog (84% seq id) of PA3611 was among 8 genes specifically expressed during Pseudomonas putida colonization of a plant-pathogenic fungus, Phytophthora parasitica [Ref] - this was found using a PubServer (beta) analysis of DUF families in PFAM (paper in preparation).

     

    A short manuscript is in preparation describing this crystal structure.

    Ligand Summary

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    References

     

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