101. Crystal Structures of the Reaction Intermediate and its Homologue of an Extradiol-cleaving Catecholic Dioxygenase
- Author
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Eiji Masai, Toshiya Senda, Gen Sazaki, T. Nishizaki, Yoshito Takahashi, N. Sato, Masao Fukuda, Takamasa Nonaka, Y. Uragami, and Keisuke Sugimoto
- Subjects
Models, Molecular ,Coordination sphere ,Protein Conformation ,Stereochemistry ,Catechols ,Protonation ,Reaction intermediate ,Crystallography, X-Ray ,Nitric Oxide ,Catalysis ,Nonheme Iron Proteins ,Dioxygenases ,chemistry.chemical_compound ,Structural Biology ,Oxidoreductase ,Dioxygenase ,Pseudomonas ,Anaerobiosis ,Binding site ,Molecular Biology ,chemistry.chemical_classification ,Biphenyl ,Binding Sites ,Estradiol ,Biphenyl Compounds ,Substrate (chemistry) ,Oxygen ,chemistry ,Mutation ,Oxygenases ,Protons ,Crystallization ,Hydrophobic and Hydrophilic Interactions - 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 O 2 molecule located in the hydrophobic O 2 -binding cavity. Finally, protonated His194 seems to function as a proton donor, whose existence has been proposed.
- Published
- 2002
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