The Open Protein Structure Annotation Network
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    Table of contents
    1. 1. Protein Summary
    2. 2. Ligand Summary
    3. 3. References

    Title Crystal structure of putative thioesterase (YP_496845.1) from Novosphingobium aromaticivorans DSM 12444 at 1.70 A resolution. To be published
    Site JCSG
    PDB Id 3cjy Target Id 371292
    Molecular Characteristics
    Source Novosphingobium aromaticivorans dsm 12444
    Alias Ids TPS1579,YP_496845.1, 103433 Molecular Weight 26783.94 Da.
    Residues 258 Isoelectric Point 5.18
    Sequence mteafpalvrqddaryaitvgpdlavgppghaylfggasmalaldvaaetvgrpvvqgslqfvsftplg svldltvevlqsgrtlaqarvagtvdgrlvfhsgislgmregfsarqwalappvpqpdncppcttlpaq ddnarylegievreaggpevpsgrtrlwlrrkdgapldaaslamfadflpialgratgcsgggnsldns lritgaaapgwclcdmiipssasgfaqgqvtlwdqsgrllatgaqslllkg
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 1.70 Rfree 0.203
    Matthews' coefficent 2.32 Rfactor 0.173
    Waters 196 Solvent Content 47.00

    Ligand Information


    Google Scholar output for 3cjy

    Protein Summary

    The crystal structure of this protein shows that the protein has a 12-stranded beta sheet wrapped around 2 alpha-helices resembling the uncommon "Double Hot Dog fold". The presence of 2 thioesterase_II repeats is confirmed by a search against the Conserved Domain Database.
        It is similar in structure to the E. coli thioesterase II which shares ~45% sequence identity with the human protein that interacts with the product of the HIV-1 Nef gene (see Ref 2 below).

        There is 1 molecule in the asu. Analysis of crystal packing suggests that the protein may be dimeric in solution. SEC results are not available yet. There is also no Pfam annotation yet.

        One round of PSI-BLAST produces hits with hypothetical proteins and acyl-CoA thioesterase II from many different organisms but there are no structures available for any of the proteins with more than ~26% sequence identity to this protein.
        The top 2 SSM hits for structurally similar proteins are 3BBJ (~88% match of secondary structure elements over the whole protein length, ~19% sequence identity, Ref 1) and 1C8U (~72% match of secondary structure elements over the whole protein length, ~22% sequence identity).

    The structural superposition with the 1C8U (cyan) is shown below:

        The 2 structures are quite similar except for the loop/helix region between residue 133-148 and 153-161 in this protein which shows a different conformation in 1C8U. The loop between residues 20-34 in this protein is longer than the counterpart in 1C8U and the N-terminal helix is missing in the structure of this protein which can be seen in 1C8U.

        The catalytic site in the 1C8U (verified by site directed mutagenesis is D204, Q278 and T228, which activate a nucleophilic water molecule, Ref 2). These are almost identically conserved in this protein as D185, Q252 and S203. 
    This putative active site is highlighted below.

    Ligand Summary





    No references found.

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