5TDS

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free: 0.173 
  • R-Value Work: 0.130 
  • R-Value Observed: 0.131 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.4 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: https://doi.org/10.1038/nature21681
  • Primary Citation of Related Structures:  
    5TDS, 5TDT, 5TDU, 5TDV

  • 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 O 2 , 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 Fe 2+ /Fe 3+ 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Toluene-4-monooxygenase system protein A
A, D
493Ectopseudomonas mendocinaMutation(s): 0 
Gene Names: tmoA
EC: 1.14.13 (PDB Primary Data), 1.14.13.236 (UniProt)
UniProt
Find proteins for Q00456 (Pseudomonas mendocina)
Explore Q00456 
Go to UniProtKB:  Q00456
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ00456
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Toluene-4-monooxygenase system protein E
B, E
327Ectopseudomonas mendocinaMutation(s): 0 
Gene Names: tmoE
EC: 1.14.13 (PDB Primary Data), 1.14.13.236 (UniProt)
UniProt
Find proteins for Q00460 (Pseudomonas mendocina)
Explore Q00460 
Go to UniProtKB:  Q00460
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ00460
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Toluene-4-monooxygenase system protein B
C, F
84Ectopseudomonas mendocinaMutation(s): 0 
Gene Names: tmoB
EC: 1.14.13 (PDB Primary Data), 1.14.13.236 (UniProt)
UniProt
Find proteins for Q00457 (Pseudomonas mendocina)
Explore Q00457 
Go to UniProtKB:  Q00457
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ00457
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MBN
Query on MBN

Download Ideal Coordinates CCD File 
AA [auth D]
J [auth A]
K [auth A]
L [auth A]
M [auth A]
AA [auth D],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
R [auth B],
W [auth D],
X [auth D],
Z [auth D]
TOLUENE
C7 H8
YXFVVABEGXRONW-UHFFFAOYSA-N
FE
Query on FE

Download Ideal Coordinates CCD File 
G [auth A],
H [auth A],
T [auth D],
U [auth D]
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
Y [auth D]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG
Query on MG

Download Ideal Coordinates CCD File 
BA [auth E]
CA [auth E]
I [auth A]
N [auth B]
O [auth B]
BA [auth E],
CA [auth E],
I [auth A],
N [auth B],
O [auth B],
P [auth B],
Q [auth B],
S [auth C],
V [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free: 0.173 
  • R-Value Work: 0.130 
  • R-Value Observed: 0.131 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 169.386α = 90
b = 176.906β = 90
c = 55.944γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-03-22
    Type: Initial release
  • Version 1.1: 2017-04-12
    Changes: Database references
  • Version 1.2: 2017-04-26
    Changes: Database references
  • Version 1.3: 2017-09-27
    Changes: Author supporting evidence
  • Version 1.4: 2023-10-04
    Changes: Data collection, Database references, Derived calculations, Refinement description