The Open Protein Structure Annotation Network
PDB Keyword


    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 366988
    Molecular Characteristics
    Source Ralstonia eutropha jmp134
    Alias Ids TPS1495,YP_295714.1,, 430151 Molecular Weight 12873.00 Da.
    Residues 113 Isoelectric Point 5.60
    Sequence mirllyllvkpagmsdetfraeclrhyemshdvpglhkyevrlvaeqptdthvpffdighvdaigecwf kddaayatymasdirkawfehgktfigqlkpfrtapvagdepas
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 2.00 Rfree 0.202
    Matthews' coefficent 2.59 Rfactor 0.171
    Waters 125 Solvent Content 52.19

    Ligand Information


    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

    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





    No references found.

    Files (0)

    You must login to post a comment.
    All content on this site is licensed under a Creative Commons Attribution 3.0 License
    Powered by MindTouch