1LKD

CRYSTAL STRUCTURE OF 2,3-DIHYDROXYBIPHENYL 1,2-DIOXYGENASE (DHBD) COMPLEXED WITH 2',6'-DICL DIHYDROXYBIPHENYL (DHB)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.203 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Identification and analysis of a bottleneck in PCB biodegradation

Dai, S.Vaillancourt, F.H.Maaroufi, H.Drouin, N.M.Neau, D.B.Snieckus, V.Bolin, J.T.Eltis, L.D.

(2002) Nat.Struct.Mol.Biol. 9: 934-939

  • DOI: 10.1038/nsb866
  • Primary Citation of Related Structures:  1LGT

  • PubMed Abstract: 
  • The microbial degradation of polychlorinated biphenyls (PCBs) provides the potential to destroy these widespread, toxic and persistent environmental pollutants. For example, the four-step upper bph pathway transforms some of the more than 100 differe ...

    The microbial degradation of polychlorinated biphenyls (PCBs) provides the potential to destroy these widespread, toxic and persistent environmental pollutants. For example, the four-step upper bph pathway transforms some of the more than 100 different PCBs found in commercial mixtures and is being engineered for more effective PCB degradation. In the critical third step of this pathway, 2,3-dihydroxybiphenyl (DHB) 1,2-dioxygenase (DHBD; EC 1.13.11.39) catalyzes aromatic ring cleavage. Here we demonstrate that ortho-chlorinated PCB metabolites strongly inhibit DHBD, promote its suicide inactivation and interfere with the degradation of other compounds. For example, k(cat)(app) for 2',6'-diCl DHB was reduced by a factor of approximately 7,000 relative to DHB, and it bound with sufficient affinity to competitively inhibit DHB cleavage at nanomolar concentrations. Crystal structures of two complexes of DHBD with ortho-chlorinated metabolites at 1.7 A resolution reveal an explanation for these phenomena, which have important implications for bioremediation strategies.


    Organizational Affiliation

    Markey Center for Structural Biology, Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907-1392, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
BIPHENYL-2,3-DIOL 1,2-DIOXYGENASE
A
297Burkholderia xenovorans (strain LB400)Gene Names: bphC
EC: 1.13.11.39
Find proteins for P47228 (Burkholderia xenovorans (strain LB400))
Go to UniProtKB:  P47228
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
P6G
Query on P6G

Download SDF File 
Download CCD File 
A
HEXAETHYLENE GLYCOL
POLYETHYLENE GLYCOL PEG400
C12 H26 O7
IIRDTKBZINWQAW-UHFFFAOYSA-N
 Ligand Interaction
FE2
Query on FE2

Download SDF File 
Download CCD File 
A
FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
 Ligand Interaction
BP6
Query on BP6

Download SDF File 
Download CCD File 
A
2',6'-DICHLORO-BIPHENYL-2,6-DIOL
C12 H8 Cl2 O2
MCZUCSAAGDCHHN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.203 
  • Space Group: I 4 2 2
Unit Cell:
Length (Å)Angle (°)
a = 122.640α = 90.00
b = 122.640β = 90.00
c = 107.232γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
CNSrefinement
SCALEPACKdata scaling
HKL-2000data collection
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2002-04-24 
  • Released Date: 2002-11-27 
  • Deposition Author(s): Dai, S., Bolin, J.T.

Revision History 

  • Version 1.0: 2002-11-27
    Type: Initial release
  • Version 1.1: 2008-04-28
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Source and taxonomy, Version format compliance