2XRX

CRYSTAL STRUCTURE OF BIPHENYL DIOXYGENASE IN COMPLEX WITH BIPHENYL FROM BURKHOLDERIA XENOVORANS LB400


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.42 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.233 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural Insight Into the Expanded Pcb-Degrading Abilities of a Biphenyl Dioxygenase Obtained by Directed Evolution.

Kumar, P.Mohammadi, M.Viger, J.F.Barriault, D.Gomez-Gil, L.Eltis, L.D.Bolin, J.T.Sylvestre, M.

(2011) J.Mol.Biol. 405: 531

  • DOI: 10.1016/j.jmb.2010.11.009
  • Primary Citation of Related Structures:  2XR8, 2XSH, 2XSO

  • PubMed Abstract: 
  • The biphenyl dioxygenase of Burkholderia xenovorans LB400 is a multicomponent Rieske-type oxygenase that catalyzes the dihydroxylation of biphenyl and many polychlorinated biphenyls (PCBs). The structural bases for the substrate specificity of the en ...

    The biphenyl dioxygenase of Burkholderia xenovorans LB400 is a multicomponent Rieske-type oxygenase that catalyzes the dihydroxylation of biphenyl and many polychlorinated biphenyls (PCBs). The structural bases for the substrate specificity of the enzyme's oxygenase component (BphAE(LB400)) are largely unknown. BphAE(p4), a variant previously obtained through directed evolution, transforms several chlorobiphenyls, including 2,6-dichlorobiphenyl, more efficiently than BphAE(LB400), yet differs from the parent oxygenase at only two positions: T335A/F336M. Here, we compare the structures of BphAE(LB400) and BphAE(p4) and examine the biochemical properties of two BphAE(LB400) variants with single substitutions, T335A or F336M. Our data show that residue 336 contacts the biphenyl and influences the regiospecificity of the reaction, but does not enhance the enzyme's reactivity toward 2,6-dichlorobiphenyl. By contrast, residue 335 does not contact biphenyl but contributes significantly to expansion of the enzyme's substrate range. Crystal structures indicate that Thr335 imposes constraints through hydrogen bonds and nonbonded contacts to the segment from Val320 to Gln322. These contacts are lost when Thr is replaced by Ala, relieving intramolecular constraints and allowing for significant movement of this segment during binding of 2,6-dichlorobiphenyl, which increases the space available to accommodate the doubly ortho-chlorinated congener 2,6-dichlorobiphenyl. This study provides important insight about how Rieske-type oxygenases can expand substrate range through mutations that increase the plasticity and/or mobility of protein segments lining the catalytic cavity.


    Organizational Affiliation

    Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
BIPHENYL DIOXYGENASE SUBUNIT ALPHA
A, C, E, G, I, K, M, O, Q, S, U, W
459Burkholderia xenovorans (strain LB400)Gene Names: bphA
EC: 1.14.12.18
Find proteins for P37333 (Burkholderia xenovorans (strain LB400))
Go to UniProtKB:  P37333
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
BIPHENYL DIOXYGENASE SUBUNIT BETA
B, D, F, H, J, L, N, P, R, T, V, X
188Burkholderia xenovorans (strain LB400)Gene Names: bphE
EC: 1.14.12.18
Find proteins for P37334 (Burkholderia xenovorans (strain LB400))
Go to UniProtKB:  P37334
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FES
Query on FES

Download SDF File 
Download CCD File 
A, C, E, G, I, K, M, O, Q, S, U, W
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
BNL
Query on BNL

Download SDF File 
Download CCD File 
A, C, E, G, I, K, M, O, Q, S, U, W
BIPHENYL
C12 H10
ZUOUZKKEUPVFJK-UHFFFAOYSA-N
 Ligand Interaction
FE2
Query on FE2

Download SDF File 
Download CCD File 
A, C, E, G, I, K, M, O, Q, S, U, W
FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.42 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.233 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 132.824α = 102.65
b = 132.646β = 101.11
c = 130.423γ = 105.31
Software Package:
Software NamePurpose
SCALEPACKdata scaling
HKL-2000data reduction
REFMACrefinement
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2010-09-23 
  • Released Date: 2010-11-24 
  • Deposition Author(s): Kumar, P., Bolin, J.T.

Revision History 

  • Version 1.0: 2010-11-24
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance