3RNE

Structure of the Toluene/o-Xylene Monooxygenase Hydroxylase T201S/I276E Double Mutant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.185 

wwPDB Validation   3D Report Full Report


This is version 1.2 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: 10.1073/pnas.1106514108
  • Primary Citation of Related Structures:  
    3RNG, 3RNA, 3RNB, 3RNC, 3RNE, 3RNF, 3RN9

  • 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 ...

    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)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Toluene o-xylene monooxygenase componentA498Pseudomonas sp. OX1Mutation(s): 3 
Gene Names: touA
EC: 1.14
UniProt
Find proteins for Q6IV66 (Pseudomonas sp. OX1)
Explore Q6IV66 
Go to UniProtKB:  Q6IV66
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Toluene o-xylene monooxygenase componentB330Pseudomonas sp. OX1Mutation(s): 0 
Gene Names: touE
EC: 1.14
UniProt
Find proteins for Q6IV62 (Pseudomonas sp. OX1)
Explore Q6IV62 
Go to UniProtKB:  Q6IV62
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Toluene o-xylene monooxygenase componentC86Pseudomonas sp. OX1Mutation(s): 0 
Gene Names: touB
EC: 1.14
UniProt
Find proteins for Q6IV65 (Pseudomonas sp. OX1)
Explore Q6IV65 
Go to UniProtKB:  Q6IV65
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FE
Query on FE

Download Ideal Coordinates CCD File 
D [auth A], E [auth A]FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
OH
Query on OH

Download Ideal Coordinates CCD File 
F [auth A], G [auth A]HYDROXIDE ION
H O
XLYOFNOQVPJJNP-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.185 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 182.984α = 90
b = 182.984β = 90
c = 67.976γ = 120
Software Package:
Software NamePurpose
ADSCdata collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data 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