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2ifx

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

    Title Crystal structure of hypothetical protein (YP_295714.1) from Ralstonia Eutropha JMP134 at 2.00 A resolution. To be published
    Site JCSG
    PDB Id 2ifx Target Id
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    Molecular Characteristics
    Source
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    Alias Ids
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    TPS1495,YP_295714.1, 3.30.70.900, 430151
    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 1
    Resolution (Å)
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    Rfree
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    Matthews' coefficent 2.59 Rfactor 0.171
    Waters
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    Solvent Content 52.19

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    Ligand Information
    Ligands
    Metals

    Jmol

     
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    Google Scholar output for 2ifx
    1. Crystal structure and catalytic mechanism of 4-methylmuconolactone methylisomerase
    M Marn, DW Heinz, DH Pieper, BU Klink - Journal of Biological Chemistry, 2009 - ASBMB
     

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    Protein Summary

    The YP_295714 from R. eutropha JMP134 is an outlier of the EthD (for Ethyl tert-butyl ether degradation) protein family (PF07110). This family is a member of the SCOP superfamily of dimeric alpha+beta barrel [54909]. 1ifx is classified as a 4-methylmuconolactone ([(2S)-2-methyl-5-oxo-2,5-dihydrofuran-2-yl]acetic acid) methylisomerase. A BLAST search identifies other isomerases and hypothetical proteins as its closest homologs and classifies it in the MmlI family. The protein is a homodimer.

    Structure of YP_295714 belongs to the ferredoxin-like fold. With top DALI hits to PDB:2fb0 (Z-score 8.1; RMSD 2.6; 10% sequence identity for 82 superimposed residues), and JCSG structure PDB:2ftr (Z-score 7.6; RMSD 2.3; 18% sequence identity for 85 superimposed residues), and to ActVA-Orf6 monooxygenase (PDB:1lq9; Z-score 7.4; RMSD 2.7; 8% sequence identity for for 83 superimposed residues).

    Analysis of the crystallographic packing of YP_295714 using the PQS server {Henrick, 1998 #73} indicates that a dimer(non-crystallographic) is the biologically relevant form. The dimer is structurally similar to 4-methylmuconolactone methylisomerase from Pseudomonas reinekei, which was solved in complex with MES buffer, 4-methylmuconolactone and 3-methylmuconolactone (pdb codes 3hds, 3hf5 and 3hfk), and is 70% identical to 1ifx. JCSG also solved the structure of a more distant (no homology detected) but structurally similar EthD family dimer from Bacillus halodurans, 2ftr, with an unknown ligand, and other structures referenced in that entry.

    Ligand Summary



    References

    Reviews

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