1KW6

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

1KW6 の概要

• エントリーDOI: 10.2210/pdb1kw6/pdb
• 関連するPDBエントリー: 1EIM 1KW3 1KW8 1KW9 1KWB 1KWC
• 分子名称: 2,3-Dihydroxybiphenyl dioxygenase, FE (II) ION, BIPHENYL-2,3-DIOL, ... (5 entities in total)
• 機能のキーワード: four time repetitions of the beta-alpha-beta-beta-beta motif, oxidoreductase
• 由来する生物種: Pseudomonas sp.
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 32629.94

構造登録者

Sato, N.,Uragami, Y.,Nishizaki, T.,Takahashi, Y.,Sazaki, G.,Sugimoto, K.,Nonaka, T.,Masai, E.,Fukuda, M.,Senda, T. (登録日: 2002-01-28, 公開日: 2003-01-28, 最終更新日: 2024-03-13)

主引用文献

Sato, N.,Uragami, Y.,Nishizaki, T.,Takahashi, Y.,Sazaki, G.,Sugimoto, K.,Nonaka, T.,Masai, E.,Fukuda, M.,Senda, T.
Crystal Structures of the Reaction Intermediate and its Homologue of an Extradiol-cleaving Catecholic Dioxygenase
J.Mol.Biol., 321:621-636, 2002

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.

PubMed: 12206778
DOI: 10.1016/S0022-2836(02)00673-3

実験手法

X-RAY DIFFRACTION (1.45 Å)