The Open Protein Structure Annotation Network
PDB Keyword


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

    Title Crystal structure of Phenylacetic acid degradation-related protein (YP_298971.1) from Ralstonia eutropha JMP134 at 2.20 A resolution. To be published
    Site JCSG
    PDB Id 2pim Target Id 370429
    Molecular Characteristics
    Source Ralstonia eutropha jmp134
    Alias Ids TPS1565,YP_298971.1, 92550 Molecular Weight 14643.93 Da.
    Residues 140 Isoelectric Point 5.37
    Sequence msqdnyfsrmlrgeapvpavagtlggviravdleagslesdyvatdaflnpvgqvqggmlgamlddvta mlvtatledgascstlnlnlsflrpaqagllrgrarlerrgrnvcnvvgelsqdgklvatatatcmvar ra
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 2.20 Rfree 0.222
    Matthews' coefficent 2.79 Rfactor 0.182
    Waters 55 Solvent Content 55.96

    Ligand Information


    Google Scholar output for 2pim
    1. Analysis of proteins with the'hot dog'fold: Prediction of function and identification of catalytic residues of hypothetical proteins
    LS Pidugu, K Maity, K Ramaswamy - BMC structural , 2009 - biomedcentral.com

    Protein Summary

    Gene Reut_B4779 from Ralstonia eutropha jmp134 encodes the YP_298971 protein that belongs to the 4HBT thioesterase group (PF03061). This protein has a high sequence homology to phenylacetic acid degradation proteins from many other organisms and it contains the PaaI thioesterase domain according to the Conserved Domain Database.

    According to pre-SCOP, 2pim protein fold is that of the "Hot-Dog" Thioesterase fold, thioesterase/thyil ester dehydrase isomerase superfamily, PaaI/YdiI-like family. There is a six-stranded beta sheet wrapped around a helix. The N-terminal helix shows conformational variability in the different structures. However, there is no structural coverage of proteins that are close in sequence. There is structural coverage of two PaaI's with low sequence homology (~25%) from E. coli and T. thermophilus. 2pim is structurally similar to E. coli PaaI (phenylacetic acid degradation protein, 1PSU.pdb) with rmsd ~1.7A for ~83% Ca  atoms with ~24% seq id and a Dali Z-scr=19; and to T. thermophilus PaaI (1WN3.pdb) with rmsd ~1.3A for ~80% Ca atoms with ~25% seq id and a Dali Zscr=18. It is also similar to the Arthrobacter 4-HBA-CoA thioesterase (1Q4T.pdb; Z=17).

    The reaction center in the E. coli PaaI is comprised of residues N46, H52, G53, D61 and T62.
    By a structure-based sequence alignment, most of these residues are identical in this
    target including N50(purple), G57(blue), and D65(red). The other 2 are substituted as
    His->Gln56 (brown) and Thr->Asp66 (cyan). The 2 key catalytic residues which function as a nucleophile/
    general base and engage in hydrogen bond formation are strictly conserved as D65(red) and
    G57(Blue) respectively. The ligand 4-hydroxyphenacyl-CoA from the 4-Hydroxybenzoyl-CoA
    thioesterase structure (1Q4T.pdb) has been modeled at the putative active site formed by the dimer.

    This target is from the organism Ralstonia eutropha JMP134 which has a possible important application in bioremediation since it is able to degrade a large number of choloroaromatic compounds and related chemical pollutants.  It is also a model system for studying microbial production of polyhydroxyalkanoates and chemolithoautotrophic metabolism. In fact, Ralstonia eutropha H16 is already used for the bioproduction of the biodegradable polymer Biopol (www.metabolix.com, MA, USA). It has the potential of being developed in a future hydrogen based biotechnology for the production of diverse, commercially valuable compounds such as metabolites and polymers.
    This phenylacetic acid degradation protein from R. eutropha JMP134 has 62% sequence id to that from R. eutropha H16. Exact substrates for these proteins are not known.

    Ligand Summary





    No references found.

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