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Crystal structure of the YML079w protein from Saccharomyces cerevisiae reveals a new sequence family of the jelly-roll fold

¹ Institut de Biochimie et de Biophysique Moléculaire et Cellulaire, Centre National de la Recherche Scientifique-Unité Mixte de Recherche (CNRS-UMR 8619) and
² Institut de Génétique et Microbiologie (CNRS-UMR 8621), Université Paris-Sud, 91405 Orsay, France
³ Laboratoire d’Enzymologie et Biochimie Structurale (CNRS-UPR [Unité Propre de Recherche] 9063), 91198 Gif sur Yvette, France
⁴ Centre de Bioingénierie Gilbert Durand, UMR-CNRS 5504, UR-INRA 792, F-31077, Toulouse, France

(RECEIVED September 14, 2004; FINAL REVISION September 16, 2004; ACCEPTED September 16, 2004)

We determined the three-dimensional crystal structure of the protein YML079wp, encoded by a hypothetical open reading frame from Saccharomyces cerevisiae to a resolution of 1.75 Å. The protein has no close homologs and its molecular and cellular functions are unknown. The structure of the protein is a jelly-roll fold consisting of ten -strands organized in two parallel packed -sheets. The protein has strong structural resemblance to the plant storage and ligand binding proteins (canavalin, glycinin, auxin binding protein) but also to some plant and bacterial enzymes (epimerase, germin). The protein forms homodimers in the crystal, confirming measurements of its molecular mass in solution. Two monomers have their -sheet packed together to form the dimer. The presence of a hydrophobic ligand in a well conserved pocket inside the barrel and local sequence similarity with bacterial epimerases may suggest a biochemical function for this protein.

Keywords: jelly-roll motif; cupin superfamily; structural genomics; YML079wp; S. cerevisiae

Article and publication are at http://www.proteinscience.org/cgi/doi/10.1110/ps.041121305.

Reprint requests to: Herman van Tilbeurgh, Institut de Biochimie et de Biophysique Moléculaire et Cellulaire (CNRS-UMR 8619), Université Paris-Sud, Bât. 430, 91405 Orsay, France; e-mail: Herman.Van-Tilbeurgh{at}ibbmc.u-psud.fr; fax: +00-331-69-85-37-15.

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