2YFJ

Crystal structure of Biphenyl dioxygenase variant RR41 with dibenzofuran

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.205 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

Retuning Rieske-Type Oxygenases to Expand Substrate Range.

Mohammadi, M., Viger, J., Kumar, P., Barriault, D., Bolin, J.T., Sylvestre, M.

(2011) J Biol Chem 286: 27612

  • DOI: 10.1074/jbc.M111.255174
  • Primary Citation of Related Structures:  
    2YFI, 2YFJ

  • PubMed Abstract: 

    • Rieske-type oxygenases are promising biocatalysts for the destruction of persistent pollutants or for the synthesis of fine chemicals. In this work, we explored pathways through which Rieske-type oxygenases evolve to expand their substrate range. BphAE(p4), a variant biphenyl dioxygenase generated from Burkholderia xenovorans LB400 BphAE(LB400) by the double substitution T335A/F336M, and BphAE(RR41), obtained by changing Asn(338), Ile(341), and Leu(409) of BphAE(p4) to Gln(338), Val(341), and Phe(409), metabolize dibenzofuran two and three times faster than BphAE(LB400), respectively ...

    Rieske-type oxygenases are promising biocatalysts for the destruction of persistent pollutants or for the synthesis of fine chemicals. In this work, we explored pathways through which Rieske-type oxygenases evolve to expand their substrate range. BphAE(p4), a variant biphenyl dioxygenase generated from Burkholderia xenovorans LB400 BphAE(LB400) by the double substitution T335A/F336M, and BphAE(RR41), obtained by changing Asn(338), Ile(341), and Leu(409) of BphAE(p4) to Gln(338), Val(341), and Phe(409), metabolize dibenzofuran two and three times faster than BphAE(LB400), respectively. Steady-state kinetic measurements of single- and multiple-substitution mutants of BphAE(LB400) showed that the single T335A and the double N338Q/L409F substitutions contribute significantly to enhanced catalytic activity toward dibenzofuran. Analysis of crystal structures showed that the T335A substitution relieves constraints on a segment lining the catalytic cavity, allowing a significant displacement in response to dibenzofuran binding. The combined N338Q/L409F substitutions alter substrate-induced conformational changes of protein groups involved in subunit assembly and in the chemical steps of the reaction. This suggests a responsive induced fit mechanism that retunes the alignment of protein atoms involved in the chemical steps of the reaction. These enzymes can thus expand their substrate range through mutations that alter the constraints or plasticity of the catalytic cavity to accommodate new substrates or that alter the induced fit mechanism required to achieve proper alignment of reaction-critical atoms or groups.

    Organizational Affiliation: 

    Institut National de la Recherche Scientifique-Institut Armand-Frappier, Laval, Quebec H7V 1B7, Canada.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
BIPHENYL DIOXYGENASE SUBUNIT ALPHA
A, C, E, G, I, K
A, C, E, G, I, K
459Paraburkholderia xenovorans LB400Mutation(s): 5 
Gene Names: bphA, Bxeno_C1131, Bxe_C1197
EC: 1.14.12.18
UniProt
Find proteins for P37333 (Paraburkholderia xenovorans (strain LB400))
Explore P37333 
Go to UniProtKB:  P37333
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP37333
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
BIPHENYL DIOXYGENASE SUBUNIT BETA
B, D, F, H, J, L
B, D, F, H, J, L
188Paraburkholderia xenovorans LB400Mutation(s): 0 
Gene Names: bphE, Bxeno_C1130, Bxe_C1196
EC: 1.14.12.18
UniProt
Find proteins for P37334 (Paraburkholderia xenovorans (strain LB400))
Explore P37334 
Go to UniProtKB:  P37334
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP37334
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FES
Query on FES
Download Ideal Coordinates CCD File 
M [auth A],
P [auth C],
S [auth E],
V [auth G],
X [auth I],
M [auth A],
P [auth C],
S [auth E],
V [auth G],
X [auth I],
Z [auth K]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N		 Ligand Interaction
1IT
Query on 1IT
Download Ideal Coordinates CCD File 
O [auth A],
R [auth C],
U [auth E]		DIBENZOFURAN
C12 H8 O
TXCDCPKCNAJMEE-UHFFFAOYSA-N		 Ligand Interaction
FE2
Query on FE2
Download Ideal Coordinates CCD File 
AA [auth K],
N [auth A],
Q [auth C],
T [auth E],
W [auth G],
AA [auth K],
N [auth A],
Q [auth C],
T [auth E],
W [auth G],
Y [auth I]
FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.205 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.979α = 90
b = 278.125β = 117.65
c = 92.956γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-06-08
    Type: Initial release
  • Version 1.1: 2011-08-10
    Changes: Database references, Version format compliance