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EDD, a novel phosphotransferase domain common to mannose transporter EIIA, dihydroxyacetone kinase, and DegV

¹ Howard Hughes Medical Institute and ² Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390–9050, USA

(RECEIVED September 10, 2004; FINAL REVISION October 18, 2004; ACCEPTED October 19, 2004)

Using a recently developed program (SCOPmap) designed to automatically assign new protein structures to existing evolutionary-based classification schemes, we identify a evolutionarily conserved domain (EDD) common to three different folds: mannose transporter EIIA domain (EIIA-man), dihydroxyacetone kinase (Dak), and DegV. Several lines of evidence support unification of these three folds into a single superfamily: statistically significant sequence similarity detected by PSI-BLAST; "closed structural grouping" using DALI Z-scores (each protein inside a group finds all other group members with scores higher than those to proteins outside the group) that includes only these proteins sharing a unique -helical hairpin at the C-terminus and excludes all other proteins with similar topology; similar domain fusions connect Dak and DegV, and genomic neighborhood organizations connect Dak and EIIA-man. Finally, both Dak and EIIA-man perform similar phosphotransfer reactions, suggesting a phosphotransferase activity for the DegV-like family of proteins, whose function other than lipid binding revealed in the crystal structure remains unknown.

Keywords: EDD domain; Dak1; Dak2; dihydroxyacetone kinase; DegV; mannose transporter EIIA; SCOPmap; homology detection; structure similarity; protein classification

Abbreviations: Dak, dihydroxyacetone kinase • EIIA-man, mannose transporter IIA domain superfamily • PEP, phosphoenolpyruvate • PTS, PEP, sugar phosphotransferase system • HPR, histidine-containing phosphoryl carrier protein • ATP, adenosine triphosphate • DegV, DegV-like protein fold

Article published online ahead of print. Article and publication date are at http://www.proteinscience.org/cgi/doi/10.1110/ps.041114805.

Reprint requests to: Nick V. Grishin, Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390–9050; e-mail: grishin{at}chop.swmed.edu; fax: (214) 648-9099.

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