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J. Biol. Chem., Vol. 279, Issue 35, 37087-37094, August 27, 2004

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Crystal Structure of Yeast Ypr118w, a Methylthioribose-1-phosphate Isomerase Related to Regulatory eIF2B Subunits^*

Mario Bumann¶, Siamak Djafarzadeh¶, Anselm Erich Oberholzer¶||, Peter Bigler, Michael Altmann, Hans Trachsel, and Ulrich Baumann**

From the Department of Chemistry and Biochemistry, University of Berne, Freiestrasse 3, Berne CH-3012 and the Institute for Molecular Biology and Biochemistry, University of Berne, Bühlstrasse 28, Berne CH-3012 Switzerland

Ypr118w is a non-essential, low copy number gene product from Saccharomyces cerevisiae. It belongs to the PFAM family PF01008, which contains the -, -, and -subunits of eukaryotic translation initiation factor eIF2B, as well as proteins of unknown function from all three kingdoms. Recently, one of those latter proteins from Bacillus subtilis has been characterized as a 5-methylthioribose-1-phosphate isomerase, an enzyme of the methionine salvage pathway. We report here the crystal structure of Ypr118w, which reveals a dimeric protein with two domains and a putative active site cleft. The C-terminal domain resembles ribose-5-phosphate isomerase from Escherichia coli with a similar location of the active site. In vivo, Ypr118w protein is required for yeast cells to grow on methylthioadenosine in the absence of methionine, showing that Ypr118w is involved in the methionine salvage pathway. The crystal structure of Ypr118w reveals for the first time the fold of a PF01008 member and allows a deeper discussion of an enzyme of the methionine salvage pathway, which has in the past attracted interest due to tumor suppression and as a target of aniprotozoal drugs.

Received for publication, April 22, 2004 , and in revised form, June 21, 2004.

The atomic coordinates and structure factors (code 1W2W) 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 by the Swiss National Science Foundation Grants 31-55423.98 (to H. T.) and 31-67253.01 (to U. B.) and by the Berner Hochschulstiftung and the University of Berne. 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.

^|| Recipient of a Roche Research Foundation.

^** To whom correspondence should be addressed. Tel.: 41-31-631-4320; Fax: 41-31-631-4887; E-mail: ulrich.baumann{at}ibc.unibe.ch.

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