The recently elucidated methylerythritol phosphate (MEP) pathway for isoprenoid biosynthesis is essential in eubacteria (including Escherichia coli), the malaria parasite, and plants, but is absent in animals. Therefore, the pathway enzymes are promising targets for the development of novel herbicides and antimicrobials that are potentially innocuous for humans. For an effective drug design, it is important to identify the residues required to preserve the structure and activity of the MEP pathway enzymes. Here, we report a genetic approach to identify such residues in E. coli. A strain harboring a synthetic operon that allows the production of isoprenoids through a MEP-independent pathway was used to screen for the otherwise lethal loss-of-function point mutations in the MEP pathway genes generated by ethylmethane sulfonate (EMS) mutagenesis. Besides confirming the role of residues involved in catalysis, our results define regions within several of the proteins with a potential key role for enzyme function.