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J. Biol. Chem., Vol. 278, Issue 34, 32150-32156, August 22, 2003

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The Three-dimensional Structure of the Core Domain of Naf Y from Azotobacter vinelandii determined at 1.8-Å Resolution^*

David H. Dyer , Luis M. Rubio , James B. Thoden, Hazel M. Holden, Paul W. Ludden  and Ivan Rayment ¶

From the Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706

The Azotobacter vinelandii NafY protein (nitrogenase accessory factor Y) is able to bind either to the iron molybdenum cofactor (FeMo-co) or to apodinitrogenase and is believed to facilitate the transfer of FeMo-co into apodinitrogenase. The NafY protein has two domains: an N-terminal domain (residues Met¹–Leu⁹⁸) and a C-terminal domain (residues Glu⁹⁹–Ser²³²), referred here to as the "core domain." The core domain of NafY is shown here to be capable of binding the FeMo cofactor of nitrogenase but unable to bind to apodinitrogenase in the absence of the first domain. The three-dimensional molecular structure of the core domain of NafY has been solved to 1.8-Å resolution, revealing that the protein consists of a mixed five-stranded -sheet flanked by five -helices that belongs to the ribonuclease H superfamily. As such, this represents a new fold capable of binding FeMo-co, where the only previous example was that seen in dinitrogenase.

Received for publication, April 23, 2003 , and in revised form, May 14, 2003.

The atomic coordinates and structure factors (code 1P90) 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 National Institutes of Health Grants GM35332 (to P. L.) and AR35186 (to I. R.). Use of the Argonne National Laboratory Structural Biology Center beam-lines at the Advanced Photon Source was supported by the U.S. Department of Energy, Office of Basic Energy Research, under Contract No. W-31-109-ENG-38. 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.

These authors contributed equally to this work.

To whom correspondence may be addressed: Dept. of Plant & Microbial Biology, 211 Koshland Hall, University of California, Berkeley, CA 94720-3102. Tel.: 510-642-7171; Fax: 510-642-4612; E-mail: pludden{at}nature.berkeley.edu.

^¶ To whom correspondence may be addressed: Dept. of Biochemistry, 433 Babcock Dr., Madison, WI 53706. Tel.: 608-262-0437; Fax: 608-262-1319; E-mail: Ivan_Rayment{at}biochem.wisc.edu.

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				L. M. Rubio and P. W. Ludden Maturation of Nitrogenase: a Biochemical Puzzle J. Bacteriol., January 15, 2005; 187(2): 405 - 414. [Full Text] [PDF]

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