5TDS

Toluene bound in the resting active site of toluene 4-monooxygenase (T4moH)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.719 Å
  • R-Value Free: 0.173 
  • R-Value Work: 0.130 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

In-crystal reaction cycle of a toluene-bound diiron hydroxylase.

Acheson, J.F.Bailey, L.J.Brunold, T.C.Fox, B.G.

(2017) Nature 544: 191-195

  • DOI: 10.1038/nature21681
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Electrophilic aromatic substitution is one of the most important and recognizable classes of organic chemical transformation. Enzymes create the strong electrophiles that are needed for these highly energetic reactions by using O2, electrons, and met ...

    Electrophilic aromatic substitution is one of the most important and recognizable classes of organic chemical transformation. Enzymes create the strong electrophiles that are needed for these highly energetic reactions by using O2, electrons, and metals or other cofactors. Although the nature of the oxidants that carry out electrophilic aromatic substitution has been deduced from many approaches, it has been difficult to determine their structures. Here we show the structure of a diiron hydroxylase intermediate formed during a reaction with toluene. Density functional theory geometry optimizations of an active site model reveal that the intermediate is an arylperoxo Fe2+/Fe3+ species with delocalized aryl radical character. The structure suggests that a carboxylate ligand of the diiron centre may trigger homolytic cleavage of the O-O bond by transferring a proton from a metal-bound water. Our work provides the spatial and electronic constraints needed to propose a comprehensive mechanism for diiron enzyme arene hydroxylation that accounts for many prior experimental results.


    Organizational Affiliation

    Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Toluene-4-monooxygenase system protein A
A, D
493Pseudomonas mendocinaMutation(s): 0 
Gene Names: tmoA
EC: 1.14.13.236
Find proteins for Q00456 (Pseudomonas mendocina)
Go to UniProtKB:  Q00456
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Toluene-4-monooxygenase system protein E
B, E
327Pseudomonas mendocinaMutation(s): 0 
Gene Names: tmoE
EC: 1.14.13.236
Find proteins for Q00460 (Pseudomonas mendocina)
Go to UniProtKB:  Q00460
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Toluene-4-monooxygenase system protein B
C, F
84Pseudomonas mendocinaMutation(s): 0 
Gene Names: tmoB
EC: 1.14.13.236
Find proteins for Q00457 (Pseudomonas mendocina)
Go to UniProtKB:  Q00457
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MBN
Query on MBN

Download SDF File 
Download CCD File 
A, B, D
TOLUENE
C7 H8
YXFVVABEGXRONW-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download SDF File 
Download CCD File 
D
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B, C, D, E
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
FE
Query on FE

Download SDF File 
Download CCD File 
A, D
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.719 Å
  • R-Value Free: 0.173 
  • R-Value Work: 0.130 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 169.386α = 90.00
b = 176.906β = 90.00
c = 55.944γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
HKL-2000data scaling
PHENIXrefinement
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-03-22
    Type: Initial release
  • Version 1.1: 2017-04-12
    Type: Database references
  • Version 1.2: 2017-04-26
    Type: Database references
  • Version 1.3: 2017-09-27
    Type: Author supporting evidence