1KW9

Crystal structure of 2,3-dihydroxybiphenyl dioxygenase (BphC) in complex with 2,3-dihydroxybiphenyl at 2.0A resolution

Replaces:  1EIM

Summary for 1KW9

• Entry DOI: 10.2210/pdb1kw9/pdb
• Related: 1KW3 1KW6 1KW8 1KWB 1KWC
• Descriptor: 2,3-Dihydroxybiphenyl dioxygenase, FE (II) ION, BIPHENYL-2,3-DIOL, ... (4 entities in total)
• Functional Keywords: four time repetitions of the beta-alpha-beta-beta-beta motif, oxidoreductase
• Biological source: Pseudomonas sp.
• Total number of polymer chains: 1
• Total formula weight: 32393.60

Authors

Sato, N.,Uragami, Y.,Nishizaki, T.,Takahashi, Y.,Sazaki, G.,Sugimoto, K.,Nonaka, T.,Masai, E.,Fukuda, M.,Senda, T. (deposition date: 2002-01-29, release date: 2003-01-29, Last modification date: 2024-03-13)

Primary citation

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

Experimental method

X-RAY DIFFRACTION (1.95 Å)