3RNF

Structure of the Toluene/o-Xylene Monooxygenase Hydroxylase T201S/V271A Double Mutant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.154 
  • R-Value Observed: 0.156 

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

Tracking a defined route for O2 migration in a dioxygen-activating diiron enzyme.

Song, W.J.Gucinski, G.Sazinsky, M.H.Lippard, S.J.

(2011) Proc Natl Acad Sci U S A 108: 14795-14800

  • DOI: https://doi.org/10.1073/pnas.1106514108
  • Primary Citation of Related Structures:  
    3RN9, 3RNA, 3RNB, 3RNC, 3RNE, 3RNF, 3RNG

  • PubMed Abstract: 

    For numerous enzymes reactive toward small gaseous compounds, growing evidence indicates that these substrates diffuse into active site pockets through defined pathways in the protein matrix. Toluene/o-xylene monooxygenase hydroxylase is a dioxygen-activating enzyme. Structural analysis suggests two possible pathways for dioxygen access through the α-subunit to the diiron center: a channel or a series of hydrophobic cavities. To distinguish which is utilized as the O(2) migration pathway, the dimensions of the cavities and the channel were independently varied by site-directed mutagenesis and confirmed by X-ray crystallography. The rate constants for dioxygen access to the diiron center were derived from the formation rates of a peroxodiiron(III) intermediate, generated upon treatment of the diiron(II) enzyme with O(2). This reaction depends on the concentration of dioxygen to the first order. Altering the dimensions of the cavities, but not the channel, changed the rate of dioxygen reactivity with the enzyme. These results strongly suggest that voids comprising the cavities in toluene/o-xylene monooxygenase hydroxylase are not artifacts of protein packing/folding, but rather programmed routes for dioxygen migration through the protein matrix. Because the cavities are not fully connected into the diiron active center in the enzyme resting state, conformational changes will be required to facilitate dioxygen access to the diiron center. We propose that such temporary opening and closing of the cavities may occur in all bacterial multicomponent monooxygenases to control O(2) consumption for efficient catalysis. Our findings suggest that other gas-utilizing enzymes may employ similar structural features to effect substrate passage through a protein matrix.


  • Organizational Affiliation

    Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Toluene o-xylene monooxygenase component498Pseudomonas sp. OX1Mutation(s): 3 
Gene Names: touA
EC: 1.14
UniProt
Find proteins for Q6IV66 (Pseudomonas sp. OX1)
Explore Q6IV66 
Go to UniProtKB:  Q6IV66
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6IV66
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Toluene o-xylene monooxygenase component330Pseudomonas sp. OX1Mutation(s): 0 
Gene Names: touE
EC: 1.14
UniProt
Find proteins for Q6IV62 (Pseudomonas sp. OX1)
Explore Q6IV62 
Go to UniProtKB:  Q6IV62
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6IV62
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Toluene o-xylene monooxygenase component86Pseudomonas sp. OX1Mutation(s): 0 
Gene Names: touB
EC: 1.14
UniProt
Find proteins for Q6IV65 (Pseudomonas sp. OX1)
Explore Q6IV65 
Go to UniProtKB:  Q6IV65
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6IV65
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.154 
  • R-Value Observed: 0.156 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 183.34α = 90
b = 183.34β = 90
c = 68.37γ = 120
Software Package:
Software NamePurpose
iMOSFLMdata reduction
MOLREPphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-08-17
    Type: Initial release
  • Version 1.1: 2011-09-07
    Changes: Database references
  • Version 1.2: 2011-09-21
    Changes: Database references
  • Version 1.3: 2017-08-23
    Changes: Data collection
  • Version 1.4: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description