Isopentenyl pyrophosphate (IPP) is a common precursor for the synthesis of all isoprenoids, which have important functions in living organisms. IPP is produced by the mevalonate pathway in archaea, fungi, and animals. In contrast, IPP is synthesized by a mevalonate-independent pathway in most bacteria, algae, and plant plastids. 1-Deoxy-D-xylulose 5-phosphate synthase (DXS) catalyzes the first and the rate-limiting step of the mevalonateindependent pathway and is an attractive target for the development of novel antibiotics, antimalarials, and herbicides. We report here the first structural information on DXS, from Escherichia coli and Deinococcus radiodurans, in complex with the coenzyme thiamine pyrophosphate (TPP). The structure contains three domains (I, II, and III), each of which bears homology to the equivalent domains in transketolase and the E1 subunit of pyruvate dehydrogenase. However, DXS has a novel arrangement of these domains as compared with the other enzymes, such that the active site of DXS is located at the interface of domains I and II in the same monomer, whereas that of transketolase is located at the interface of the dimer. The coenzyme TPP is mostly buried in the complex, but the C-2 atom of its thiazolium ring is exposed to a pocket that is the substrate-binding site. The structures identify residues that may have important roles in catalysis, which have been confirmed by our mutagenesis studies.Isoprenoids are an extensive class of extraordinarily diverse natural products and have important functions in all living organisms (1-4). Isopentenyl pyrophosphate (IPP) 2 is a common precursor for the synthesis of all isoprenoids. Although it has long been known that IPP can be generated from the mevalonate pathway, recent studies have revealed a mevalonate-independent pathway for IPP biosynthesis in most bacteria, algae, and plant chloroplasts (2-9). This pathway is also called the MEP pathway because 2-C-methyl-D-erythritol 4-phosphate (MEP) is its first committed precursor. Because the mevalonate-independent pathway is absent in animals, it represents a promising target for the development of novel antibiotics, antimalarials, herbicides, and other drugs. The herbicide fosmidomycin functions by inhibiting an enzyme in this pathway (10), and it also has activity against malarial infection in an animal model (11).1-Deoxy-D-xylulose 5-phosphate synthase (DXS) catalyzes the first and the rate-limiting reaction in the mevalonate-independent pathway, the condensation of glyceraldehyde 3-phosphate (GAP), and pyruvate ( Fig. 1A) (5-8, 12-15). The 1-deoxy-D-xylulose 5-phosphate product is also used for the biosynthesis of thiamine (vitamin B 1 ) and pyridoxol (vitamin B 6 ) (16,17). The dxs gene is essential for Escherichia coli, and disruption of this gene in Arabidopsis produces an albino phenotype (13, 18) because of the lack of chlorophylls and carotenoids. These studies demonstrate the crucial role of DXS in bacteria and plants. Although absent in humans, dxs and the mevalonate-independent pathwa...
