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J. Biol. Chem., Vol. 281, Issue 19, 13762-13776, May 12, 2006

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The Crystal Structures of Dihydropyrimidinases Reaffirm the Close Relationship between Cyclic Amidohydrolases and Explain Their Substrate Specificity^*

Bernhard Lohkamp, Birgit Andersen, Jure Pikur, and Doreen Dobritzsch¹

From the Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-17177 Stockholm and the Department of Cell and Organism Biology, Lund University, SE-22362 Lund, Sweden

In eukaryotes, dihydropyrimidinase catalyzes the second step of the reductive pyrimidine degradation, the reversible hydrolytic ring opening of dihydropyrimidines. Here we describe the three-dimensional structures of dihydropyrimidinase from two eukaryotes, the yeast Saccharomyces kluyveri and the slime mold Dictyostelium discoideum, determined and refined to 2.4 and 2.05 Å, respectively. Both enzymes have a (/)₈-barrel structural core embedding the catalytic di-zinc center, which is accompanied by a smaller -sandwich domain. Despite loop-forming insertions in the sequence of the yeast enzyme, the overall structures and architectures of the active sites of the dihydropyrimidinases are strikingly similar to each other, as well as to those of hydantoinases, dihydroorotases, and other members of the amidohydrolase superfamily of enzymes. However, formation of the physiologically relevant tetramer shows subtle but nonetheless significant differences. The extension of one of the sheets of the -sandwich domain across a subunit-subunit interface in yeast dihydropyrimidinase underlines its closer evolutionary relationship to hydantoinases, whereas the slime mold enzyme shows higher similarity to the noncatalytic collapsin-response mediator proteins involved in neuron development. Catalysis is expected to follow a dihydroorotase-like mechanism but in the opposite direction and with a different substrate. Complexes with dihydrouracil and N-carbamyl--alanine obtained for the yeast dihydropyrimidinase reveal the mode of substrate and product binding and allow conclusions about what determines substrate specificity, stereoselectivity, and the reaction direction among cyclic amidohydrolases.

Received for publication, December 13, 2005 , and in revised form, February 6, 2006.

The atomic coordinates and structure factors (code 2fty, 2fvk, 2fvm, and 2ftw) 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 funds from the Swedish Research Council (to D. D. and J. P.), the Stiftelse Lars Hiertas Minne and Åke Wibergs Stiftelse foundations, and Karolinska Institutes Research Foundation. 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: Dept. of Medical Biochemistry and Biophysics, Karolinska Institutet, Tomtebodavägen 6, SE-17177 Stockholm, Sweden. Tel.: 46-8-524-87651; Fax: 46-8-32-7626; E-mail: Doreen.Dobritzsch{at}ki.se.

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