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 putative thioesterase (YP_613385.1) from Silicibacter sp. TM1040 at 2.15 A resolution. To be published
    Site JCSG
    PDB Id 2qwz Target Id 376409
    Molecular Characteristics
    Source Silicibacter sp. tm1040
    Alias Ids TPS1677,YP_613385.1, 93130 Molecular Weight 15249.80 Da.
    Residues 140 Isoelectric Point 5.68
    Sequence melvfdkdglsayleevfpqiqgefsidalakgeitmrlnvqerhlrpggtvsgpsmfaladvsvyalv lahlgrealavttnasldfmrkpesgrdllgqarllklgrtlavgdillfsegmeapvarstmtysipp kr
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 2.15 Rfree 0.252
    Matthews' coefficent 2.43 Rfactor 0.200
    Waters 172 Solvent Content 49.33

    Ligand Information


    Google Scholar output for 2qwz
    1. Decision-making in structure solution using Bayesian estimates of map quality: the PHENIX AutoSol wizard
    TC Terwilliger, PD Adams, RJ Read - Section D: Biological , 2009 - scripts.iucr.org
    2. 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
    3. Geometric similarities of protein-protein interfaces at atomic resolution are only observed within homologous families: An exhaustive structural classification study
    AR Kinjo, H Nakamura - Journal of molecular biology, 2010 - Elsevier

    Protein Summary

    The TM1040_1390 gene from Silicibacter sp. TM1040 (also known as Ruegeria sp. TM1040) encodes the YP_613385 protein from the thioesterase superfamily (PF03061, cl00509). On the NCBI site, it is annotated as phenylacetic acid degradation-related protein. The 4 chains of the 2qwz structure show several acetate molecules bound in different locations.

    Pre-SCOP classifies 2qwz in the alpha+beta class, thioesterase/thiol ester dehydrase isomerase superfamily, PaaI/YdiI-like family. A search for structural similarity using DALI returns as top hits the HI1161 protein 1o0i (Z=18), the YDII protein 1vi8 (Z=17), and the thioesterase family protein 3e1e (Z=16). Additional information related to this Pfam family is found for the JCSG determined structures 2pim (Z=15), 2gf6 (Z=8), 1vpm (Z=10), 2gvh (Z=11), 3ck1 (Z=8). Other structurally highly similar proteins from PSI efforts include 3e1e, 3f1t (Z=18), and 2fs2 (Z=16).

    The protein structures contained in this family share a hot dog-like fold which is characteristic of thioesterases [Ref]. Most of these structures are catalytically active with one exception, FapR, a PaaI-like protein involved in transcriptional regulation. 

    Ligand Summary





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