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Originally published In Press as doi:10.1074/jbc.C000238200 on May 25, 2000

J. Biol. Chem., Vol. 275, Issue 32, 24608-24612, August 11, 2000
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Crystal Structure of dTDP-4-keto-6-deoxy-D-hexulose 3,5-Epimerase from Methanobacterium thermoautotrophicum Complexed with dTDP*

Dinesh ChristendatDagger §||, Vivian SaridakisDagger §, Akil DharamsiDagger §**, Alexei BochkarevDagger Dagger , Emil F. PaiDagger §, Cheryl H. ArrowsmithDagger §§§, and Aled M. EdwardsDagger §§§¶¶

From the Dagger  Division of Molecular and Structural Biology, Ontario Cancer Institute, Toronto, Ontario M5G 2M9, Canada, the § Department of Medical Biophysics,  Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario M5W 1L6, Canada, ** Integrated Proteomics Inc., Toronto, Ontario M5G 2M9, Canada, and the Dagger Dagger  Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, BRC-466, Oklahoma City, Oklahoma 73190

Deoxythymidine diphosphate (dTDP)-4-keto-6-deoxy-D-hexulose 3,5-epimerase (RmlC) is involved in the biosynthesis of dTDP-L-rhamnose, which is an essential component of the bacterial cell wall. The crystal structure of RmlC from Methanobacterium thermoautotrophicum was determined in the presence and absence of dTDP, a substrate analogue. RmlC is a homodimer comprising a central jelly roll motif, which extends in two directions into longer beta -sheets. Binding of dTDP is stabilized by ionic interactions to the phosphate group and by a combination of ionic and hydrophobic interactions with the base. The active site, which is located in the center of the jelly roll, is formed by residues that are conserved in all known RmlC sequence homologues. The conservation of the active site residues suggests that the mechanism of action is also conserved and that the RmlC structure may be useful in guiding the design of antibacterial drugs.

* Use of the Advanced Photon Source was supported by the United States Department of Energy, Basic Energy Sciences, Office of Science, under Contract W-31-109-Eng-38. Use of the BioCARS Sector 14 was supported by the National Institutes of Health, National Center for Research Resources, under Grant Number RR07707.The costs of publication of this article were defrayed in part by the payment of page charges. The article must therefore be hereby marked "advertisement" in accordance with 18 U.S.C. Section 1734 solely to indicate this fact.

The atomic coordinates and stucture factors (1EP0 and 1EPZ, for the native protein and its complex with dTDP, respectively) have been deposited in the Protein Data Bank, Research Collaboratory for Structural Bioinformatics, Rutgers University, New Brunswick, NJ (http://www.rcsb.org/).

|| Supported by the Banting and Best Institute fellowship.

§§ Medical Research Council of Canada Scientists.

¶¶ To whom correspondence should be addressed: Ontario Cancer Institute, 610 University Ave., Toronto, Ontario M5G 2M9, Canada. Tel.: 416-946-3435; Fax: 416-946-6529; E-mail: aled.edwards@ utoronto.ca.

Copyright © 2000 by The American Society for Biochemistry and Molecular Biology, Inc.
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