1KW6

Crystal structure of 2,3-dihydroxybiphenyl dioxygenase (BphC) in complex with 2,3-dihydroxybiphenyl at 1.45 A resolution

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.171 
  • R-Value Work: 0.163 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 

Literature

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

  • Primary Citation of Related Structures:  

  • 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 ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
2,3-Dihydroxybiphenyl dioxygenase
B
292Pseudomonas sp. (strain KKS102)Mutation(s): 0 
Gene Names: bphC
EC: 1.13.11.39
Find proteins for P17297 (Pseudomonas sp. (strain KKS102))
Go to UniProtKB:  P17297
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BPY
Query on BPY
Download SDF File 
Download CCD File 
B
BIPHENYL-2,3-DIOL
C12 H10 O2
YKOQAAJBYBTSBS-UHFFFAOYSA-N
 Ligand Interaction
FE2
Query on FE2
Download SDF File 
Download CCD File 
B
FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
 Ligand Interaction
MPD
Query on MPD
Download SDF File 
Download CCD File 
B
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.171 
  • R-Value Work: 0.163 
  • Space Group: I 4 2 2
Unit Cell:
Length (Å)Angle (°)
a = 121.829α = 90.00
b = 121.829β = 90.00
c = 109.357γ = 90.00
Software Package:
Software NamePurpose
CCP4data scaling
MOSFLMdata reduction
AMoREphasing
SCALAdata scaling
REFMACrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-01-28
    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