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Logo of bmcsbBioMed Centralsearchsubmit a manuscriptregisterthis articleBMC Structural Biology
 
BMC Struct Biol. 2012; 12: 15.
Published online Jun 24, 2012. doi:  10.1186/1472-6807-12-15
PMCID: PMC3423008
Structural insight into the substrate- and dioxygen-binding manner in the catalytic cycle of rieske nonheme iron oxygenase system, carbazole 1,9a-dioxygenase
Yuji Ashikawa,1,5 Zui Fujimoto,2 Yusuke Usami,1 Kengo Inoue,3 Haruko Noguchi,1,4,6 Hisakazu Yamane,1 and Hideaki Nojiricorresponding author1,4
1Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
2Protein Research Unit, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan
3Interdisciplinary Research Organization, University of Miyazaki, 5200 Kihara, Kiyotake, Miyazaki, 889-1692, Japan
4Professional Programme for Agricultural Bioinformatics, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
5Education and Research Support Section, Technology Management Division, Administration and Technology Management Center for Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo, 169-8555, Japan
6Department of Applied Biology and Chemistry, Faculty of Applied Bio-Science, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo, 156-8502, Japan
corresponding authorCorresponding author.
Yuji Ashikawa: yashikawa/at/waseda.jp; Zui Fujimoto: zui/at/affrc.go.jp; Yusuke Usami: yusuke_usami/at/suntory.co.jp; Kengo Inoue: kinoue/at/cc.miyazaki-u.ac.jp; Haruko Noguchi: h3noguch/at/nodai.ac.jp; Hisakazu Yamane: ayamane/at/mail.ecc.u-tokyo.ac.jp; Hideaki Nojiri: anojiri/at/mail.ecc.u-tokyo.ac.jp
Received March 16, 2012; Accepted June 24, 2012.
Abstract
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.
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