2YFL

Crystal Structure of Biphenyl dioxygenase variant RR41 with 2-chloro dibenzofuran


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.215 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural Insights Into the Metabolism of 2-Chlorodibenzofuran by an Evolved Biphenyl Dioxygenase.

Kumar, P.Mohammadi, M.Dhindwal, S.Pham, T.T.Bolin, J.T.Sylvestre, M.

(2012) Biochem.Biophys.Res.Commun. 421: 757

  • DOI: 10.1016/j.bbrc.2012.04.078

  • PubMed Abstract: 
  • The biphenyl dioxygenase of Burkholderia xenovorans LB400 (BphAE(LB400)) is a Rieske-type oxygenase that catalyzes the stereospecific oxygenation of many heterocyclic aromatics including dibenzofuran. In a previous work, we evolved BphAE(LB400) and o ...

    The biphenyl dioxygenase of Burkholderia xenovorans LB400 (BphAE(LB400)) is a Rieske-type oxygenase that catalyzes the stereospecific oxygenation of many heterocyclic aromatics including dibenzofuran. In a previous work, we evolved BphAE(LB400) and obtained BphAE(RR41). This variant metabolizes dibenzofuran and 2-chlorodibenzofuran more efficiently than BphAE(LB400). However, the regiospecificity of BphAE(RR41) toward these substrates differs. Dibenzofuran is metabolized principally through a lateral dioxygenation whereas 2-chlorodibenzofuran is metabolized principally through an angular dioxygenation. In order to explain this difference, we examined the crystal structures of both substrate-bound forms of BphAE(RR41) obtained under anaerobic conditions. This structure analysis, in combination with biochemical data for a Ser283Gly mutant provided evidences that the substrate is compelled to move after oxygen-binding in BphAE(RR41):dibenzofuran. In BphAE(RR41):2-chlorodibenzofuran, the chlorine atom is close to the side chain of Ser283. This contact is missing in the BphAE(RR41):dibenzofuran, and strong enough in the BphAE(RR41):2-chlorodibenzofuran to help prevent substrate movement during the catalytic reaction.


    Organizational Affiliation

    Department of Biological Sciences and Center for Cancer Research, 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
459Paraburkholderia xenovorans (strain LB400)Mutation(s): 5 
Gene Names: bphA
EC: 1.14.12.18
Find proteins for P37333 (Paraburkholderia xenovorans (strain LB400))
Go to UniProtKB:  P37333
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
BIPHENYL DIOXYGENASE SUBUNIT BETA
B, D, F, H, J, L
188Paraburkholderia xenovorans (strain LB400)Mutation(s): 0 
Gene Names: bphE
EC: 1.14.12.18
Find proteins for P37334 (Paraburkholderia 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
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
FE2
Query on FE2

Download SDF File 
Download CCD File 
A, C, E, G, I, K
FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
 Ligand Interaction
DC4
Query on DC4

Download SDF File 
Download CCD File 
A, C
2-CHLORODIBENZOFURAN
C12 H7 Cl O
PRKTYWJFCODJOA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.215 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 86.556α = 90.00
b = 275.982β = 117.46
c = 92.057γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
MOLREPphasing
SCALEPACKdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2011-04-06 
  • Released Date: 2012-05-16 
  • Deposition Author(s): Kumar, P., Bolin, J.T.

Revision History 

  • Version 1.0: 2012-05-16
    Type: Initial release
  • Version 1.1: 2012-05-30
    Type: Other