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 

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:  
    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 ...

    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)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Toluene-4-monooxygenase system protein AA, D493Pseudomonas 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
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Toluene-4-monooxygenase system protein EB, E327Pseudomonas 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
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Toluene-4-monooxygenase system protein BC, F84Pseudomonas 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
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / 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] , R [auth B] , W [auth D] , X [auth D] , 
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
 Ligand Interaction
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
 Ligand Interaction
CL
Query on CL

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

Download Ideal Coordinates CCD File 
BA [auth E] , CA [auth E] , I [auth A] , N [auth B] , O [auth B] , P [auth B] , Q [auth B] , S [auth C] , 
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
 Ligand Interaction
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

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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