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The Open Protein Structure Annotation Network
PDB Keyword
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3bbj

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

    Title Crystal structure of putative thioesterase II (YP_290423.1) from Thermobifida fusca YX at 2.45 A resolution. To be published
    Site JCSG
    PDB Id 3bbj Target Id 371241
    Molecular Characteristics
    Source Thermobifida fusca yx
    Alias Ids TPS1577,YP_290423.1, 285339 Molecular Weight 29733.94 Da.
    Residues 271 Isoelectric Point 5.75
    Sequence mvpmtrfdsatevvrvgenryaveldpgyligtamnggylmtvlqrsalaesdhlhavsssyhfhrpas sgpaeietrvlkrgrtvttvqttlfqegrtiltgtlatatldphaepryaapqpaippqhqcrrvdprq shlpddgflarvdvdfspdsyaalarertvttpelcgyvdlsardggsakdplaflplavdalppivsl lvdwswaptveltwhlraipepgplafrstcalvsdgwfdenvdlwdargrlvaqsrqlarvgr
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 2
    Resolution (Å) 2.16 Rfree 0.243
    Matthews' coefficent 2.36 Rfactor 0.181
    Waters 164 Solvent Content 47.85

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3bbj
    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

    The gene Tfu_2367 from Thermobifida fusca YX encodes for a protein structure homologous to thioesterase II from E. coli (1c8u). Each monomer contains two thioesterase "hot-dog" units (SCOP) related by duplication.  Similar to 1c8u, the first domain is made of residues 0-116 (red), the 2nd domain contains residues 117-271 (green).


    The dimer (shown below) is formed through beta sheets of two monomers.


    Despite limited sequence homology, this core of this protein (red) is very similar to 1c8u (green, RMSD 1.6 for 218 ~81% aligned CA, 15% seq id) .


    The active site location can be inferred from sequence and structure comparisons. In this case, the sequence conservation pattern is very clear, besides the conservation on the dimer-dimer interface, most of the conserved residues are located along strand 213-217. This include residues: G37, G38, D199, P200, P202, W213, A214, P215. This is also the active site of 1c8u, it is interesting that it appears that amino acid of two active sites aren't very conserved except for a few residues D199, T216, Q265. It will not be surprising if these are catalytic residues. As a result, this protein is likely to function as thioesterase II as well.

    One interesting of the dimer is that there are two conformations for 213-317 (as well as C-terminus). In B chain, the active site pocket is open, while in A chain the active site is close. In the figure below 213-217 is colored red,  199/216/265 are colored  orange.  It is  apparent that in closed conformation, the catalytic residues can not be ready accessible. It is plausible that this segment function as a door to open/close and trap ligand.
    open conformationclosed conformation


     

    Ligand Summary



    References

    Reviews

    References

     

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