3EN1

Crystal structure of Toluene 2,3-Dioxygenase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.185 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structures of the multicomponent Rieske non-heme iron toluene 2,3-dioxygenase enzyme system

Friemann, R.Lee, K.Brown, E.N.Gibson, D.T.Eklund, H.Ramaswamy, S.

(2009) Acta Crystallogr.,Sect.D 65: 24-33

  • DOI: 10.1107/S0907444908036524
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Bacterial Rieske non-heme iron oxygenases catalyze the initial hydroxylation of aromatic hydrocarbon substrates. The structures of all three components of one such system, the toluene 2,3-dioxygenase system, have now been determined. This system cons ...

    Bacterial Rieske non-heme iron oxygenases catalyze the initial hydroxylation of aromatic hydrocarbon substrates. The structures of all three components of one such system, the toluene 2,3-dioxygenase system, have now been determined. This system consists of a reductase, a ferredoxin and a terminal dioxygenase. The dioxygenase, which was cocrystallized with toluene, is a heterohexamer containing a catalytic and a structural subunit. The catalytic subunit contains a Rieske [2Fe-2S] cluster and mononuclear iron at the active site. This iron is not strongly bound and is easily removed during enzyme purification. The structures of the enzyme with and without mononuclear iron demonstrate that part of the structure is flexible in the absence of iron. The orientation of the toluene substrate in the active site is consistent with the regiospecificity of oxygen incorporation seen in the product formed. The ferredoxin is Rieske type and contains a [2Fe-2S] cluster close to the protein surface. The reductase belongs to the glutathione reductase family of flavoenzymes and consists of three domains: an FAD-binding domain, an NADH-binding domain and a C-terminal domain. A model for electron transfer from NADH via FAD in the reductase and the ferredoxin to the terminal active-site mononuclear iron of the dioxygenase is proposed.


    Related Citations: 
    • Purification, crystallization and preliminary X-ray diffraction studies of the three components of the toluene 2,3-dioxygenase enzyme system
      Lee, K.,Friemann, R.,Parales, J.V.,Gibson, D.T.,Ramaswamy, S.
      (2005) Acta Crystallogr.,Sect.F 61: 669


    Organizational Affiliation

    Department of Molecular Biology, Swedish University of Agricultural Sciences, Box 590, 75124 Uppsala, Sweden.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Benzene 1,2-dioxygenase subunit alpha
A
450Pseudomonas putida (strain ATCC 700007 / DSM 6899 / BCRC 17059 / F1)Mutation(s): 0 
Gene Names: bnzA (todC1)
EC: 1.14.12.3
Find proteins for A5W4F2 (Pseudomonas putida (strain ATCC 700007 / DSM 6899 / BCRC 17059 / F1))
Go to UniProtKB:  A5W4F2
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Benzene 1,2-dioxygenase subunit beta
B
187Pseudomonas putida (strain ATCC 700007 / DSM 6899 / BCRC 17059 / F1)Mutation(s): 0 
Gene Names: bnzB (todC2)
EC: 1.14.12.3
Find proteins for A5W4F1 (Pseudomonas putida (strain ATCC 700007 / DSM 6899 / BCRC 17059 / F1))
Go to UniProtKB:  A5W4F1
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MBN
Query on MBN

Download SDF File 
Download CCD File 
A
TOLUENE
C7 H8
YXFVVABEGXRONW-UHFFFAOYSA-N
 Ligand Interaction
FES
Query on FES

Download SDF File 
Download CCD File 
A
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
FE2
Query on FE2

Download SDF File 
Download CCD File 
A, B
FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
 Ligand Interaction
PE3
Query on PE3

Download SDF File 
Download CCD File 
A
3,6,9,12,15,18,21,24,27,30,33,36,39-TRIDECAOXAHENTETRACONTANE-1,41-DIOL
POLYETHYLENE GLYCOL
C28 H58 O15
ILLKMACMBHTSHP-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.185 
  • Space Group: P 43 3 2
Unit Cell:
Length (Å)Angle (°)
a = 234.531α = 90.00
b = 234.531β = 90.00
c = 234.531γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
ProDCdata collection
SCALAdata scaling
MOSFLMdata reduction
AMoREphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-03-17
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-10-25
    Type: Refinement description
  • Version 1.3: 2018-01-24
    Type: Database references