1KMY

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.198 

wwPDB Validation   3D Report Full Report


This is version 1.3 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

  • DOI: https://doi.org/10.1074/jbc.273.52.34887
  • Primary Citation of Related Structures:  
    1KMY, 1KND, 1KNF

  • 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 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.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
2,3-DIHYDROXYBIPHENYL 1,2-DIOXYGENASE297Paraburkholderia xenovorans LB400Mutation(s): 0 
Gene Names: bphCBxeno_C1125Bxe_C1191
EC: 1.13.11.39
UniProt
Find proteins for P47228 (Paraburkholderia xenovorans (strain LB400))
Explore P47228 
Go to UniProtKB:  P47228
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP47228
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BPY
Query on BPY

Download Ideal Coordinates CCD File 
C [auth A]BIPHENYL-2,3-DIOL
C12 H10 O2
YKOQAAJBYBTSBS-UHFFFAOYSA-N
TBU
Query on TBU

Download Ideal Coordinates CCD File 
D [auth A]TERTIARY-BUTYL ALCOHOL
C4 H10 O
DKGAVHZHDRPRBM-UHFFFAOYSA-N
FE2
Query on FE2

Download Ideal Coordinates CCD File 
B [auth A]FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
BPY PDBBind:  1KMY Kd: 8000 (nM) from 1 assay(s)
Binding MOAD:  1KMY Kd: 8000 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.198 
  • Space Group: I 4 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 123.3α = 90
b = 123.3β = 90
c = 110.9γ = 90
Software Package:
Software NamePurpose
AMoREphasing
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-02-20
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Source and taxonomy, Version format compliance
  • Version 1.3: 2023-08-16
    Changes: Data collection, Database references, Derived calculations, Refinement description