2CâMethylâdâerythritolâ4âphosphate synthase, encoded by the ispC gene (also designated dxr), catalyzes the first committed step in the nonmevalonate isoprenoid biosynthetic pathway. The reaction involves the isomerization of 1âdeoxyâdâxylulose 5âphosphate, giving a branchedâchain aldose derivative that is subsequently reduced to 2Câmethylâdâerythritol 4âphosphate. The isomerization step has been proposed to proceed as an intramolecular rearrangement or a retroaldolâaldol sequence. We report the preparation of 13Câlabeled substrate isotopologs that were designed to optimize the detection of an exchange of putative cleavage products that might occur in the hypothetical retroaldolâaldol reaction sequence. In reaction mixtures containing large amounts of 2Câmethylâdâerythritolâ4âphosphate synthase from Escherichiaâcoli, Mycobacteriumâtuberculosis or Arabidopsisâthaliana, and a mixture of [1â13C1]â2Câmethylâdâerythritol 4âphosphate and [3â13C1]2Câmethylâdâerythritol 4âphosphate, the reversible reaction could be followed over thousands of reaction cycles. No fragment exchange could be detected by NMR spectroscopy, and the frequency of exchange, if any, is less than 5âp.p.m. per catalytic cycle. Hydroxyacetone, the putative second fragment expected from the retroaldol cleavage, was not incorporated into the enzyme product. In contrast to other reports, IspC did not catalyze the isomerisation of 1âdeoxyâdâxylulose 5âphosphate to give 1âdeoxyâlâribulose 5âphosphate under any conditions tested. However, we could show that the isomerization reaction proceeds at room temperature without a requirement for enzyme catalysis. Although a retroaldolâaldol mechanism cannot be ruled out conclusively, the data show that a retroldolâaldol reaction sequence would have to proceed with very stringent fragment containment that would apply to the enzymes from three genetically distant organisms.