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The Open Protein Structure Annotation Network
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3ejv

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

    Title Crystal structure of protein of unknown function with a cystatin-like fold (YP_498036.1) from NOVOSPHINGOBIUM AROMATICIVORANS DSM 12444 at 1.40 A resolution. To be published
    Site JCSG
    PDB Id 3ejv Target Id 391050
    Molecular Characteristics
    Source Novosphingobium aromaticivorans dsm 12444
    Alias Ids TPS18319,YP_498036.1, 3.10.450.50, 85626 Molecular Weight 17413.05 Da.
    Residues 160 Isoelectric Point 5.50
    Sequence mtmadetiilnvlgqytrahdrrdpdamaalfapeatieivdavggasrsisrlegrdairvavrqmma phgyrawsqnvvnapiiviegdhavldaqfmvfsilaaevpdggwptgtfgaqgrivpieagqyrltlr tvadgwvisamriehrlpmafg
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 1.40 Rfree 0.161
    Matthews' coefficent 2.08 Rfactor 0.142
    Waters 178 Solvent Content 40.85

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3ejv
    1. Ligands in PSI structures
    A Kumar, HJ Chiu, HL Axelrod, A Morse - Section F: Structural , 2010 - scripts.iucr.org
     
    2. Dimensionality reduction in computational demarcation of protein tertiary structures
    RR Joshi, PR Panigrahi, RN Patil - Journal of Molecular Modeling, 2011 - Springer
     

    Protein Summary

    Gene Saro_2766 from Novosphingobium aromaticivorans dsm 12444 encodes the YP_498036 protein annotated as a protein of unknown function with a cystatin-like fold. It has not been annotated in Pfam A but shows a hit with Pfam B PB000019 (exp 1.7e-80). There are no hits with proteins in the Conserved Domain Database. One round of PSI-BLAST shows only 2 significant hits: with hypothetical protein Caul_2397 from Caulobacter sp. K31 (48% identity, exp=1e-32) and with hypothetical protein nfa48050 from Nocardia farcinica IFM10152 (26% id, exp=9e-04). Two rounds of PSI-BLAST reveal hits with other conserved hypothetical proteins from different organisms but also show similarities to ethyl tert-butyl ether degradation protein EthD (19% id, exp=2e-07) and aromatic ring hydroxylating dioxygenase beta subunit (EC: 1.14.12.-, 20% id, exp 3e-07).

    SCOP classifies 3ejv in the alpha+beta class, cystatin-like fold, NTF2-like superfamily, BaiE/LinA-like family. FFAS shows numerous other PDB structures with significant sequence similarity. DALI top hits (Z=17) are with cystatin-like proteins PDB:2rgq, PDB:2chc, PDB:3b8l.


    3ejv crystal structure shows one protein molecule in the asymmetric unit cell. An unknown ligand (UNL, cyan) resembling benzoic acid (BEZ) was found and modeled in a region surrounded by the residues Tyr16, Tyr133, Phe99, His 20, His153 on one side (in green) and Ile38, Ile40, Leu54, Met68 and Ile151 on the other (in yellow), together forming a hydrophobic cavity.

    Fig1_monomer_wtihUNLsurround.png

    Based on the above sequence information, it is possible that the observed ligand may be functionally relevant.

    The fit of the ligand (red) in the electron density calculated from density modified experimental phases is shown below:

    UNL_BEZ_dmmap.png

    Crystal packing analysis suggests that the preferred oligomeric form of 3ejv in solution is a trimer:

    Fig2_trimer.png

    A search for structurally similar proteins using SSM (EBI) returns hits with two  unique PDB ids (of Q-score > 0.5): 2rgq (Domain of unknown function with cystatin-like fold, Z-score 7.9, rmsd 1.34A over 119 aa, TOPSAN entry) and  1gy7 (Nuclear transport factor NTF2 S. cerevisiae, Z-score 6.4, rmsd 1.69A over 113 aa, Ref1).

    A structural superimposition of 3ejv (magenta) with 2rgq (red) and 1gy7 (grey) shows that the core structure is conserved but the three prominent loops in 3ejv are much larger:

    comparison.png

    References:

    1) Bayliss R, Leung SW, Baker RP, Quimby BB, Corbett AH, Stewart M. Structural basis for the interaction between NTF2 and nucleoporin FxFG repeats. EMBO J. 2002 Jun 17;21(12):2843-53.

    Ligand Summary

    UNL has been modeled.

    It resembles and is likely to be benzoic acid (BEZ) or a benzoate. 

    Reviews

    References

     

    No references found.

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