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J. Biol. Chem., Vol. 278, Issue 48, 48236-48244, November 28, 2003

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Crystal Structure of the Citrobacter freundii Dihydroxyacetone Kinase Reveals an Eight-stranded -Helical Barrel ATP-binding Domain^*

Christian Siebold, Ingrid Arnold, Luis F. Garcia-Alles, Ulrich Baumann¶, and Bernhard Erni¶

From the Departement für Chemie und Biochemie, Universität Bern, Freiestrasse 3, CH-3012 Bern, Switzerland

Dihydroxyacetone kinases are a sequence-conserved family of enzymes, which utilize two different phosphoryldonors, ATP in animals, plants and some bacteria, and a multiphosphoprotein of the phosphoenolpyruvate carbohydrate phosphotransferase system in bacteria. Here we report the 2.5-Å crystal structure of the homodimeric Citrobacter freundii dihydroxyacetone kinase complex with an ATP analogue and dihydroxyacetone. The N-terminal domain consists of two /-folds with a molecule of dihydroxyacetone covalently bound in hemiaminal linkage to the N2 of His-220. The C-terminal domain consists of a regular eight-helix -barrel. The eight helices form a deep pocket, which includes a tightly bound phospholipid. Only the lipid headgroup protrudes from the surface. The nucleotide is bound on the top of the barrel across from the entrance to the lipid pocket. The phosphate groups are coordinated by two Mg²⁺ ions to -carboxyl groups of aspartyl residues. The ATP binding site does not contain positively charged or aromatic groups. Paralogues of dihydroxyacetone kinase also occur in association with transcription regulators and proteins of unknown function pointing to biological roles beyond triose metabolism.

Received for publication, June 5, 2003 , and in revised form, August 28, 2003.

The atomic coordinates and structure factors (code 1UN8 and 1UN9) 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 Grant 3100-063420 from the Swiss National Science Foundation, a grant from the Secretaria de Estado de Educacion y Universidades (to L. F. G.-A.), and the Ciba-Geigy Jubiläumsstiftung. 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.

Present address: Division of Structural Biology, The Henry Wellcome Bldg. for Genomic Medicine, The University of Oxford, Roosevelt Dr., Oxford OX3 7BN, United Kingdom.

^¶ To whom correspondence may be addressed: Dept. für Chemie und Biochemie, Universität Bern, Freiestrasse 3, CH-3012 Bern, Switzerland. Tel.: 4131-631-43-46 or 4131-631-; Fax: 4131-631-48-87; E-mail: bernhard.erni{at}ibc.unibe.ch (B. E.) or ulrich.baumann{at}ibc.unibe.ch (U. B.).

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