5TDT

Oxygenated toluene intermediate in toluene 4-monooxygenase (T4moHD) after reaction in the crystal


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.82 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.153 
  • R-Value Observed: 0.153 

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: 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)
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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, F307Pseudomonas 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)
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Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Toluene-4-monooxygenase system protein BC, G84Pseudomonas 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)
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Toluene-4-monooxygenase system protein DE, H103Pseudomonas mendocinaMutation(s): 0 
Gene Names: tmoD
EC: 1.14.13
UniProt
Find proteins for Q00459 (Pseudomonas mendocina)
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Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.82 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.153 
  • R-Value Observed: 0.153 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.898α = 90
b = 116.253β = 90
c = 181.607γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United StatesMCB-0843239
Department of Energy (DOE, United States)United StatesW-31-109-ENG-38

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: 2017-09-20
    Changes: Author supporting evidence
  • Version 1.4: 2019-11-27
    Changes: Author supporting evidence