1KNF

Crystal Structure of 2,3-dihydroxybiphenyl 1,2-dioxygenase Complexed with 3-methyl Catechol under Anaerobic Condition


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.168 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Molecular basis for the stabilization and inhibition of 2, 3-dihydroxybiphenyl 1,2-dioxygenase by t-butanol.

Vaillancourt, F.H.Han, S.Fortin, P.D.Bolin, J.T.Eltis, L.D.

(1998) J.Biol.Chem. 273: 34887-34895

  • Primary Citation of Related Structures:  1KMY, 1KND

  • PubMed Abstract: 
  • The steady-state cleavage of catechols by 2,3-dihydroxybiphenyl 1, 2-dioxygenase (DHBD), the extradiol dioxygenase of the biphenyl biodegradation pathway, was investigated using a highly active, anaerobically purified preparation of enzyme. The kinet ...

    The steady-state cleavage of catechols by 2,3-dihydroxybiphenyl 1, 2-dioxygenase (DHBD), the extradiol dioxygenase of the biphenyl biodegradation pathway, was investigated using a highly active, anaerobically purified preparation of enzyme. The kinetic data obtained using 2,3-dihydroxybiphenyl (DHB) fit a compulsory order ternary complex mechanism in which substrate inhibition occurs. The Km for dioxygen was 1280 +/- 70 microM, which is at least 2 orders of magnitude higher than that reported for catechol 2,3-dioxygenases. Km and Kd for DHB were 22 +/- 2 and 8 +/- 1 microM, respectively. DHBD was subject to reversible substrate inhibition and mechanism-based inactivation. In air-saturated buffer, the partition ratios of catecholic substrates substituted at C-3 were inversely related to their apparent specificity constants. Small organic molecules that stabilized DHBD most effectively also inhibited the cleavage reaction most strongly. The steady-state kinetic data and crystallographic results suggest that the stabilization and inhibition are due to specific interactions between the organic molecule and the active site of the enzyme. t-Butanol stabilized the enzyme and inhibited the cleavage of DHB in a mixed fashion, consistent with the distinct binding sites occupied by t-butanol in the crystal structures of the substrate-free form of the enzyme and the enzyme-DHB complex. In contrast, crystal structures of complexes with catechol and 3-methylcatechol revealed relationships between the binding of these smaller substrates and t-butanol that are consistent with the observed competitive inhibition.


    Related Citations: 
    • Crystal Structure of the Biphenyl-cleaving Extradiol Dioxygenase from a PCB-degrading Pseudomonad.
      Han, S.,Eltis, L.D.,Timmis, K.N.,Muchmore, S.W.,Bolin, J.T.
      (1995) Science 270: 976
    • 2,3-Dihydroxybiphenyl 1,2-dioxygenase.
      Bolin, J.T.,Eltis, L.D.
      (2001) Handbook of Metalloproteins --: 632


    Organizational Affiliation

    Department of Biochemistry, Pavillon Marchand, Université Laval, Québec City, P.Q. G1K 7P4, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
2,3-DIHYDROXYBIPHENYL 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
FE2
Query on FE2

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

Download SDF File 
Download CCD File 
A
3-METHYLCATECHOL
3-METHYL-BENZENE-1,2-DIOL
C7 H8 O2
PGSWEKYNAOWQDF-UHFFFAOYSA-N
 Ligand Interaction
TBU
Query on TBU

Download SDF File 
Download CCD File 
A
TERTIARY-BUTYL ALCOHOL
2-METHYL-2-PROPANOL
C4 H10 O
DKGAVHZHDRPRBM-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.168 
  • Space Group: I 4 2 2
Unit Cell:
Length (Å)Angle (°)
a = 123.100α = 90.00
b = 123.100β = 90.00
c = 110.600γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
SCALEPACKdata scaling
DENZOdata reduction
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2001-12-18 
  • Released Date: 2002-03-27 
  • Deposition Author(s): Han, S., Bolin, J.T.

Revision History 

  • Version 1.0: 2002-03-27
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Source and taxonomy, Version format compliance