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The Open Protein Structure Annotation Network
PDB Keyword
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3ez0

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

    Title Crystal structure of protein of unknown function with ferritin-like fold (YP_832262.1) from Arthrobacter sp. FB24 at 2.33 A resolution. To be published
    Site JCSG
    PDB Id 3ez0 Target Id 376073
    Molecular Characteristics
    Source Arthrobacter sp. fb24
    Alias Ids TPS6900,YP_832262.1, 383099 Molecular Weight 24907.67 Da.
    Residues 224 Isoelectric Point 5.44
    Sequence mstspadtarynrfvadlfgmmaygelsaferfsadarysptlhdravlgriavvefrhyelvsarlea mgidaedamlpfqaavdyfhsrtrpadwyeslmkayvidtvsadfyraisryvdagtrdvieqiqasde ttevlrerlrsaladdprlasrlalwgrrllgealtqaqrvsyehaflgsliggedsaaakelvsglia glaekhskrmtqlgltg
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 4
    Resolution (Å) 2.33 Rfree 0.262
    Matthews' coefficent 2.11 Rfactor 0.210
    Waters 173 Solvent Content 41.67

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3ez0
    1. Ligands in PSI structures
    A Kumar, HJ Chiu, HL Axelrod, A Morse - Section F: Structural , 2010 - scripts.iucr.org
     
    2. Structural insights into the metal binding properties of hypothetical protein MJ0754 from Methanococcus jannaschii
    EH Lee, HS Kim, HY Kim, YH Jeon - Proteins: Structure, , 2011 - Wiley Online Library
     

    Protein Summary

    Gene Arth_2783 from Arthrobacter sp. fb24 encodes the YP_832262 amino acid sequence that folds into an all alpha protein. BLAST sequence homoly search indicates that YP_832262 belongs tot he ferritin-like superfamily. Genome context analysis indicates a functional link by co-ocurrence (score 0.76) with gene Arth_0249, encoding an HhH-GPD family protein (YP_829750).

    SCOP classifies 3ez0 in the all-alpha class, ferritin-like superfamily. DALI identified many similar structures, including 2inn, 1t0q, 1xvb, 1mhy, 1xu3, etc. Most similar structures are components for mono-oxygenases (Z-scr=19-17; phenol, methane, hydrocarbon oxidizing). The active site of 3ez0 differs from that of 2inn mono-oxygenase, but several residues seems to overlap spatially (E26, H59). These corresponding residues in 2inn are involved in metal binding, while in 3ez0 they appear to interact with a phosphate like moiety (the negative charges may not favor an actual phosphoryl group here). This suggests that 3ez0 is a member of Ferritin-fold; however, it is not clear whether it can also bind metals. The possible substrates are likely lipid related molecules.

    3ez0 likely biomolecule is a dimer. The dimer interface is not very extensive, but consists of favorable hydrophobic interactions (Figure 1). A large hydrophobic cavity  is observed in the center of the protein. The opening of the cavity to the solvent is small (Figure 2). One unknown ligand (UNL) was observed to occupy this cavity.  The UNL resembles glycerol-3-phosphate (G3P) attached to a lipid chain, thus is similar to 1-acyl-glycerone 3-phosphate. There may be a second weaker entity in the cavity resembling PEG. The cavity is likely the active site since the active sites of its structurally similar proteins are located in similar places. 

     

     

    Figure 1. Puatative dimer of 3ez0 (UNL=red sticks)

    FL10716A-dimer.png

    Figure 2. Surface representation of a 3ez0 monomer (red is UNL in spheres)

    FL10716A-surf.png

    Ligand Summary

    An UNL ligand resembling 1-acyl-glycerone 3-phosphate is model, the source of the UNL is unknown.

    Reviews

    References

     

    No references found.

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    Files (2)

    FileSizeDateAttached by 
     FL10716A-dimer.png
    putative dimer of 376073
    96.12 kB21:18, 19 Sep 2008qxuActions
     FL10716A-surf.png
    surface representation of 376073 monomer
    99.02 kB21:34, 19 Sep 2008qxuActions
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