Structural insight into the substrate- and dioxygen-binding manner in the catalytic cycle of rieske nonheme iron oxygenase system, carbazole 1,9a-dioxygenase.
BACKGROUND
Dihydroxylation of tandemly linked aromatic carbons in a cis-configuration, catalyzed by multicomponent oxygenase systems known as Rieske nonheme iron oxygenase systems (ROs), often constitute the initial step of aerobic degradation pathways for various aromatic compounds. Because such RO reactions inherently govern whether downstream degradation processes occur, novel oxygenation mechanisms involving oxygenase components of ROs (RO-Os) is of great interest. Despite substantial progress in structural and physicochemical analyses, no consensus exists on the chemical steps in the catalytic cycles of ROs. Thus, determining whether conformational changes at the active site of RO-O occur by substrate and/or oxygen binding is important. Carbazole 1,9a-dioxygenase (CARDO), a RO member consists of catalytic terminal oxygenase (CARDO-O), ferredoxin (CARDO-F), and ferredoxin reductase. We have succeeded in determining the crystal structures of oxidized CARDO-O, oxidized CARDO-F, and both oxidized and reduced forms of the CARDO-O: CARDO-F binary complex.


RESULTS
In the present study, we determined the crystal structures of the reduced carbazole (CAR)-bound, dioxygen-bound, and both CAR- and dioxygen-bound CARDO-O: CARDO-F binary complex structures at 1.95, 1.85, and 2.00 Å resolution. These structures revealed the conformational changes that occur in the catalytic cycle. Structural comparison between complex structures in each step of the catalytic mechanism provides several implications, such as the order of substrate and dioxygen bindings, the iron-dioxygen species likely being Fe(III)-(hydro)peroxo, and the creation of room for dioxygen binding and the promotion of dioxygen binding in desirable fashion by preceding substrate binding.


CONCLUSIONS
The RO catalytic mechanism is proposed as follows: When the Rieske cluster is reduced, substrate binding induces several conformational changes (e.g., movements of the nonheme iron and the ligand residue) that create room for oxygen binding. Dioxygen bound in a side-on fashion onto nonheme iron is activated by reduction to the peroxo state [Fe(III)-(hydro)peroxo]. This state may react directly with the bound substrate, or O-O bond cleavage may occur to generate Fe(V)-oxo-hydroxo species prior to the reaction. After producing a cis-dihydrodiol, the product is released by reducing the nonheme iron. This proposed scheme describes the catalytic cycle of ROs and provides important information for a better understanding of the mechanism.
Biotechnology Research Center, The University of Tokyo, Bunkyo-ku, Tokyo, Japan.
Yuji
Y
Ashikawa
Zui
Z
Fujimoto
Yusuke
Y
Usami
Kengo
K
Inoue
Haruko
H
Noguchi
Hisakazu
H
Yamane
Hideaki
H
Nojiri
D001419:Bacteria / Q000201:enzymology*; D001426:Bacterial Proteins / Q000737:chemistry* / Q000378:metabolism*; D055162:Biocatalysis; D002227:Carbazoles / Q000378:metabolism; D020134:Catalytic Domain; D018360:Crystallography, X-Ray; D049308:Dioxygenases / Q000737:chemistry* / Q000378:metabolism*; D014450:Electron Transport Complex III / Q000378:metabolism*; D005288:Ferredoxins / Q000737:chemistry / Q000378:metabolism; D006418:Heme / Q000378:metabolism*; D010100:Oxygen / Q000378:metabolism*; D011485:Protein Binding; D011487:Protein Conformation; D011522:Protons; D013056:Spectrophotometry, Ultraviolet; D013379:Substrate Specificity; D014867:Water
D001426:Bacterial Proteins; D002227:Carbazoles; D005288:Ferredoxins; D011522:Protons; C037989:Rieske iron-sulfur protein; D014867:Water; C041514:carbazole; D006418:Heme; D049308:Dioxygenases; C108434:carbazole 1,9a-dioxygenase; D014450:Electron Transport Complex III; D010100:Oxygen