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J. Biol. Chem., Vol. 281, Issue 29, 20567-20576, July 21, 2006

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Three-dimensional Structure of AzoR from Escherichia coli

AN OXIDEREDUCTASE CONSERVED IN MICROORGANISMS^*

Kosuke Ito, Masayuki Nakanishi, Woo-Cheol Lee, Hiroshi Sasaki, Shuhei Zenno^¶, Kaoru Saigo^¶, Yukio Kitade, and Masaru Tanokura¹

From the Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan, the Department of Biomolecular Science, Faculty of Engineering, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan, and the ^¶Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan

The crystal structure of AzoR (azoreductase) has been determined in complex with FMN for two different crystal forms at 1.8 and 2.2Å resolution. AzoR is an oxidoreductase isolated from Escherichia coli as a protein responsible for the degradation of azo compounds. This enzyme is an FMN-dependent NADH-azoreductase and catalyzes the reductive cleavage of azo groups by a ping-pong mechanism. The structure suggests that AzoR acts in a homodimeric state forming the two identical catalytic sites to which both monomers contribute. The structure revealed that each monomer of AzoR has a flavodoxin-like structure, without the explicit overall amino acid sequence homology. Superposition of the structures from the two different crystal forms revealed the conformational change and suggested a mechanism for accommodating substrates of different size. Furthermore, comparison of the active site structure with that of NQO1 complexed with substrates provides clues to the possible substrate-binding mechanism of AzoR.

Received for publication, December 15, 2005 , and in revised form, April 5, 2006.

The atomic coordinates and structure factors (codes 1v4b and 2d5i) have been deposited in the Protein Data Bank, Research Collaboratory for Structural Bioinformatics, Rutgers University, New Brunswick, NJ (http://www.rcsb.org/).

^* This work was supported in part by the National Project on Protein Structural and Functional Analyses of the Ministry of Education, Culture, Sports, Science and Technology of Japan and by grants-in-aid for Scientific Research from the Ministry of Education, Culture, Sports, Science and Technology of Japan. The synchrotron-radiation experiments were performed at BL6A and BL18B in PF (Tsukuba, Japan) and BL41XU in SPring-8 (Harima, Japan) with the approval of the Photon Factory, KEK (Proposals 2000G307 and 2003G127), and the Japan Synchrotron Radiation Research Institute (Proposal 2002A0741-RL1-np), respectively. The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked "advertisement" in accordance with 18 U.S.C. Section 1734 solely to indicate this fact.

¹ To whom correspondence should be addressed. Tel.: 81-3-5841-5165; Fax: 81-3-5841-8023; E-mail: amtanok{at}mail.ecc.u-tokyo.ac.jp.

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