3HFK

Crystal structure of 4-methylmuconolactone methylisomerase (H52A) in complex with 4-methylmuconolactone


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.185 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure and catalytic mechanism of 4-methylmuconolactone methylisomerase

Marin, M.Heinz, D.W.Pieper, D.H.Klink, B.U.

(2009) J.Biol.Chem. 284: 32709-32716

  • DOI: 10.1074/jbc.M109.024604
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • When methyl-substituted aromatic compounds are degraded via ortho (intradiol)-cleavage of 4-methylcatechol, the dead-end metabolite 4-methylmuconolactone (4-ML) is formed. Degradation of 4-ML has only been described in few bacterial species, includin ...

    When methyl-substituted aromatic compounds are degraded via ortho (intradiol)-cleavage of 4-methylcatechol, the dead-end metabolite 4-methylmuconolactone (4-ML) is formed. Degradation of 4-ML has only been described in few bacterial species, including Pseudomonas reinekei MT1. The isomerization of 4-ML to 3-methylmuconolactone (3-ML) is the first step required for the mineralization of 4-ML and is catalyzed by an enzyme termed 4-methylmuconolactone methylisomerase (MLMI). We identified the gene encoding MLMI in P. reinekei MT1 and solved the crystal structures of MLMI in complex with 3-ML at 1.4-A resolution, with 4-ML at 1.9-A resolution and with a MES buffer molecule at 1.45-A resolution. MLMI exhibits a ferredoxin-like fold and assembles as a tight functional homodimeric complex. We were able to assign the active site clefts of MLMI from P. reinekei MT1 and of the homologous MLMI from Cupriavidus necator JMP134, which has previously been crystallized in a structural genomics project. Kinetic and structural analysis of wild-type MLMI and variants created by site-directed mutagenesis indicate Tyr-39 and His-26 to be the most probable catalytic residues. The previously proposed involvement of Cys-67 in covalent catalysis can now be excluded. Residue His-52 was found to be important for substrate affinity, with only marginal effect on catalytic activity. Based on these results, a novel catalytic mechanism for the isomerization of 4-ML to 3-ML by MLMI, involving a bislactonic intermediate, is proposed. This broadens the knowledge about the diverse group of proteins exhibiting a ferredoxin-like fold.


    Organizational Affiliation

    Department of Microbial Pathogenesis, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, 38124 Braunschweig, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
4-methylmuconolactone methylisomerase
A, B, C, D
116Pseudomonas reinekeiMutation(s): 1 
Gene Names: mmlI
Find proteins for C5MR76 (Pseudomonas reinekei)
Go to UniProtKB:  C5MR76
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
4ML
Query on 4ML

Download SDF File 
Download CCD File 
A, B, C, D
[(2S)-2-methyl-5-oxo-2,5-dihydrofuran-2-yl]acetic acid
4-methylmuconolactone
C7 H8 O4
FIKLRROSHXQNFN-SSDOTTSWSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.185 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 82.170α = 90.00
b = 84.360β = 90.00
c = 150.470γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata scaling
PDB_EXTRACTdata extraction
REFMACrefinement
DNAdata collection
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-09-29
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2014-01-22
    Type: Database references