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Structural insight into the substrate- and dioxygen-binding manner in the catalytic cycle of rieske nonheme iron oxygenase system, carbazole 1,9a-dioxygenase

Yuji Ashikawa15, Zui Fujimoto2, Yusuke Usami1, Kengo Inoue3, Haruko Noguchi146, Hisakazu Yamane1 and Hideaki Nojiri14*

Author Affiliations

1 Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan

2 Protein Research Unit, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan

3 Interdisciplinary Research Organization, University of Miyazaki, 5200 Kihara, Kiyotake, Miyazaki, 889-1692, Japan

4 Professional Programme for Agricultural Bioinformatics, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan

5 Education 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

6 Department of Applied Biology and Chemistry, Faculty of Applied Bio-Science, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo, 156-8502, Japan

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BMC Structural Biology 2012, 12:15  doi:10.1186/1472-6807-12-15

Published: 24 June 2012

Additional files

Additional file 1::

Title of data: Figure S1 Illustrations of the active site in complex structures. Description of data: All panels show the active site of chain C in complex structures. (A) Binding of CAR at the active site of Oxy: Fdred-CAR [(3) in Figure 1]. The omitted density map (Fo-Fc) is shown as a black wire mesh and contoured at 3.5 δ. Only the nonheme iron (sphere), waters liganded to the iron (small sphere), iron-coordinated residues (H183, H187, and D333; stick), and CAR (stick) are shown and colored magenta. (B) Binding of dioxygen to the nonheme iron in Oxy: FdO2 [(3’) in Figure 1]. Dioxygen molecule is shown as stick-and-ball and the presentation of other atoms is identical to that in panel (A), and their color coding is salmon. The black map is an Fo-Fc omit map (5 δ) of both dioxygen atoms. The green and red maps are Fo-Fc omit maps (5 δ) for the O1 atom and O2 atom, respectively, of the dioxygen molecule. (C) Binding of dioxygen molecule at the active site with the presence of CAR in Oxy: FdCAR-O2 [(4) in Figure 1]. Color coding is white. The Fo-Fc omit maps (2.5 δ) of CAR, both dioxygen atoms, the O1 atom, and the O2 atom are colored cyan, black, green, and red, respectively.

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