PDBsum entry: 1kwb

Oxidoreductase

PDB id: 1kwb

Contents

Protein chain

288 a.a. *

Waters ×219

* Residue conservation analysis

PDB id:

1kwb

Name:

Oxidoreductase

Title:

Crystal structure of the his145ala mutant of 2,3-dihydroxybi dioxygenase (bphc)

Structure:

2,3-dihydroxybiphenyl dioxygenase. Chain: b. Synonym: bphc, biphenyl-2,3-diol 1,2-dioxygenase. Engineered: yes. Mutation: yes

Source:

Pseudomonas sp.. Organism_taxid: 307. Strain: kks102. Expressed in: escherichia coli. Expression_system_taxid: 562

Biol. unit:

Octamer (from PDB file)

Resolution:

2.00Å R-factor: 0.166 R-free: 0.175

Authors:

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

Key ref:

N.Sato et al. (2002). Crystal structures of the reaction intermediate and its homologue of an extradiol-cleaving catecholic dioxygenase. J Mol Biol, 321, 621-636. PubMed id: 12206778 DOI: 10.1016/S0022-2836(02)00673-3

Date:

29-Jan-02 Release date: 29-Jan-03

Protein chain

P17297  (BPHC_PSES1) -  Biphenyl-2,3-diol 1,2-dioxygenase

Seq: 293 a.a.

Struc: 288 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.1.13.11.39 - Biphenyl-2,3-diol 1,2-dioxygenase.
• Reaction: Biphenyl-2,3-diol + O₂ = 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate
• Cofactor: Manganese or iron

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 Gene Ontology (GO) functional annotation 

• Biological process: oxidation-reduction process (3 terms)
• Biochemical function: catalytic activity (6 terms)

reference

DOI no: 10.1016/S0022-2836(02)00673-3

J Mol Biol 321:621-636 (2002)

PubMed id: 12206778

Crystal structures of the reaction intermediate and its homologue of an extradiol-cleaving catecholic dioxygenase.

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

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.

Selected figure(s)

Figure 2.
Figure 2. Stereo view of the active-site structure of (a) the substrate-free form, (b) the ES(100) complex, and (c) the ES-NO complex. Hydrogen bonds are shown as red dotted lines. The NO molecule is shown in green. These Figures were prepared using the programs MOLSCRIPT[33] and Raster3D. [34]

Figure 8.
Figure 8. Proposed mechanism for extradiol ring cleavage of 2,3-DHBP by BphC. The ES-NO complex is presented in the center.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2002, 321, 621-636) copyright 2002.

Figures were selected by an automated process.