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RmlC, the third enzyme of dTDP-L-rhamnose pathway, is a new class of epimerase

Nature Structural Biology volume 7, pages 398–402 (2000)Cite this article

Abstract

Deoxythymidine diphosphate (dTDP)-l-rhamnose is the precursor of l-rhamnose, a saccharide required for the virulence of some pathogenic bacteria. dTDP-l-rhamnose is synthesized from glucose-1-phosphate and deoxythymidine triphosphate (dTTP) via a pathway involving four distinct enzymes. This pathway does not exist in humans and the enzymes involved in dTDP-l-rhamnose synthesis are potential targets for the design of new therapeutic agents. Here, the crystal structure of dTDP-6-deoxy-d-xylo-4-hexulose 3,5 epimerase (RmlC, EC5.1.3.13) from Salmonella enterica serovar Typhimurium was determined. The third enzyme of the rhamnose biosynthetic pathway, RmlC epimerizes at two carbon centers, the 3 and 5 positions of the sugar ring. The structure was determined by multiwavelength anomalous diffraction to a resolution of 2.17 Å. RmlC is a dimer and each monomer is formed mainly from two β-sheets arranged in a β-sandwich. The structure of a dTDP-phenol–RmlC complex shows the substrate-binding site to be located between the two β-sheets; this site is formed from residues of both monomers. Sequence alignments of other RmlC enzymes confirm that this region is very highly conserved. The enzyme is distinct structurally from other epimerases known and thus, is the first example of a new class of carbohydrate epimerase.

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Figure 1: a, The biosynthetic pathway of rhamnose.
Figure 2: Structure of RmlC.
Figure 3: a, Stereo view of the electron density for dTDP-phenol in monomer A.
Figure 4: a, Alignment of 19 RmlC sequences.

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Acknowledgements

This work was supported by the Wellcome Trust. The use of the CCLRC Daresbury Laboratory, UK, and ESRF-Grenoble facilities is gratefully acknowledged. We thank D. Sanders and W. Blankenfeldt for assistance.

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Authors and Affiliations

  1. Centre for Biomolecular Sciences, North Haugh, The University, St. Andrews, Fife, KY16 9ST, Scotland

    Marie-France Giraud, Robert A. Field, Christian Berlind & James H. Naismith

  2. Joint Structural Biology Group, European Synchrotron Radiation Facility, Grenoble Cedex, F-38043, France

    Gordon A. Leonard

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  1. Marie-France Giraud
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Correspondence to James H. Naismith.

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Giraud, MF., Leonard, G., Field, R. et al. RmlC, the third enzyme of dTDP-L-rhamnose pathway, is a new class of epimerase. Nat Struct Mol Biol 7, 398–402 (2000). https://doi.org/10.1038/75178

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