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The Open Protein Structure Annotation Network
PDB Keyword
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3fgy

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

    Title Crystal structure of NTF2-like protein of unknown function. (YP_554211.1) from BURKHOLDERIA XENOVORANS LB400 at 1.59 A resolution. To be published
    Site JCSG
    PDB Id 3fgy Target Id
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    Molecular Characteristics
    Source
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    Alias Ids
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    TPS24385,YP_554211.1, 3.10.450.50
    Molecular Weight
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    Da.
    Residues
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    Isoelectric Point
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    Sequence
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      BLAST   FFAS

    Structure Determination
    Method XRAY
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    Chains 2
    Resolution (Å)
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    Rfree
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    Matthews' coefficent 2.31 Rfactor 0.183
    Waters
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    Solvent Content 46.64

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    Ligand Information
    Ligands
    Metals

    Jmol

     
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    Google Scholar output for 3fgy
    1. Ligands in PSI structures
    A Kumar, HJ Chiu, HL Axelrod, A Morse - Section F: Structural , 2010 - scripts.iucr.org
     

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    Protein Summary

    Gene Bxe_B1094 from Burkholderia xenovorans lb400 encodes the YP_554211 protein belonging to the NTF2-like SCOP superfamily. Using 3fgy as query, DALI top hits are with other NTF2-like proteins 3ebt, 3ec9, 3g8z (Z-scr=17), polyketide cyclases 3i0y, 3f7x, 3f8h (Z-scr=15) and with ketosteroid isomerase-like proteins 3d9r, 1nww, 1nu3 (Z-scr=14).

    3fgy structure presents two protomers in the asymmetric unit of the unit cell in the crystal. Crystal packing analysis using the PISA server (EBI) suggests that this dimer should be the significant oligomeric form in solution. An unidentified ligand (UNL, green spheres) has been modeled at what should be the putative active for this protein based on comparison with other proteins of similar structure.

    Fig1.png

    The modeling of the UNL (yellow spheres) in the initial (unmodeled) Fo-Fc map (green) and 2Fo-Fc map (blue) is shown below:

    unl-omit.jpg

    Superimposition of 3fgy (pink) with that of the top FFAS hit (PDB id 1NU3 in cyan, limonene-1,2-epoxide hydrolase from Rhodococcus erythropolis with bound ligand VPR, 2-Propylpentanamide as cyan spheres, < 20% sequence identity) and with another recently determined JCSG structure,  3f7x , a putative polyketide cyclase from Pseudomonas putida kt2440 with a bound UNL (green), shows the basis for the annotation of this region in 3fgy as the putative active site:

    Fig2.png

    A structure-based sequence alignment (using the program CE) between 3fgy and 1NU3.pdb (Ref 1), shows that only the Tyr53 in 1NU3 (Ref 1), known to be functionally important, is conserved in 3fgy as a Trp. Other important amino acids in the 1NU3 are underlined:

     

    USR1:A 4/4   TQENVQIVKDFFAAXGRGDKKGLLAVSAEDIEWIIPGEWPLAGTHRGHAALAALLQKASE
    1NU3:M 21/22 STPDEKIVLEFXDALTSNDAAKLIEYFAEDTXYQNXP----LPPAYGRDAVEQTLAGLFT


    USR1
    :A 64/64 XVEISYPEPPEFVAQGERVLVVGFATGRVKSTNRTFEDDWVFAITVRKSKVTSIREYIDT
    1NU3:M 77/78 VXSIDAVETFHIGSSNGLVYTERVDVLRALPTGKSYNLSILGVFQLTEGKITGWRDYFDL


    USR1:A 124/124 LALAR-ATNFNA
    1NU3:M 137/138 REFEEAVDLPLR

     

    This suggests that although this is the likely active site of 3fgy, it is probably involved in a different function or has a different substrate specificity.

     

    References:

    1. Arand M, Hallberg BM, Zou J, Bergfors T, Oesch F, van der Werf MJ, de Bont JA, Jones TA, Mowbray SL. 

    Structure of Rhodococcus erythropolis limonene-1,2-epoxide hydrolase reveals a novel active site.
    EMBO J. 2003 Jun 2;22(11):2583-92.

    Ligand Summary

    Unidentified ligand (UNL) modeled at the putative active site

    Reviews

    References

     

    No references found.

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