Crystal structure of 2,3-dihydroxybiphenyal dioxygenase (BphC) at 1.45 A resolution

Experimental Data Snapshot

  • Resolution: 1.45 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.162 

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Crystal Structures of the Reaction Intermediate and its Homologue of an Extradiol-cleaving Catecholic Dioxygenase

Sato, N.Uragami, Y.Nishizaki, T.Takahashi, Y.Sazaki, G.Sugimoto, K.Nonaka, T.Masai, E.Fukuda, M.Senda, T.

(2002) J Mol Biol 321: 621-636

  • DOI: https://doi.org/10.1016/s0022-2836(02)00673-3
  • Primary Citation of Related Structures:  
    1KW3, 1KW6, 1KW8, 1KW9, 1KWB, 1KWC

  • PubMed Abstract: 

    BphC derived from Pseudomonas sp. strain KKS102 is an extradiol-cleaving catecholic dioxygenase. This enzyme contains a non-heme iron atom and plays an important role in degrading biphenyl/polychlorinated biphenyls (PCBs) in the microbe. To elucidate detailed structures of BphC reaction intermediates, crystal structures of the substrate-free form, the BphC-substrate complex, and the BphC-substrate-NO (nitric oxide) complex were determined. These crystal structures revealed (1) the binding site of the O(2) molecule in the coordination sphere and (2) conformational changes of His194 during the catalytic reaction. On the basis of these findings, we propose a catalytic mechanism for the extradiol-cleaving catecholic dioxygenase in which His194 seems to play three distinct roles. At the early stage of the catalytic reaction, His194 appears to act as a catalytic base, which likely deprotonates the hydroxyl group of the substrate. At the next stage, the protonated His194 seems to stabilize a negative charge on the O2 molecule located in the hydrophobic O2-binding cavity. Finally, protonated His194 seems to function as a proton donor, whose existence has been proposed.

  • Organizational Affiliation

    Department of BioEngineering, Nagaoka University of Technology, Nagaoka, Niigata, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
2,3-Dihydroxybiphenyl dioxygenaseA [auth B]292Pseudomonas sp. KKS102Mutation(s): 0 
Find proteins for P17297 (Pseudomonas sp. (strain KKS102))
Explore P17297 
Go to UniProtKB:  P17297
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP17297
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.45 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.162 
  • Space Group: I 4 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 121.76α = 90
b = 121.76β = 90
c = 108.91γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
CCP4data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-01-28
    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: 2024-03-13
    Changes: Data collection, Database references, Derived calculations