The shikimate pathway links metabolism of carbohydrates to biosynthesis of aromatic compounds. In a sequence of seven steps, phosphoenolpyruvate and erythrose 4-phosphate are converted to chorismate, a precursor of the aromatic amino acids and many secondary aromatic metabolites. The shikimate pathway is essential for most bacteria and plants but absent in humans, making it an attractive target for the development of novel antibiotics. The third step in the pathway consists of the dehydration of dehydroquinate to dehydroshikimate. This reaction can be catalyzed by two enzyme families which utilize distinct mechanisms. The protein structure presented here is representative of the type I enzyme family.
This enzyme’s reaction mechanism is known to involve a covalent Schiff base intermediate. We previously obtained structures characterizing two covalent intermediate states of the enzyme (PDB codes: 3JS3 and 3M7W). To obtain insight in the substrate binding event, the Schiff base forming lysine-170 was mutated to methionine. Co-crystallization of this mutant protein with substrate, 3-dehydroquinic acid, produced this structure in which the substrate is observed non-covalently bound at the active site. The substrate’s ring core is similarly positioned within the active site compared to the covalent intermediates which demonstrates a similar mode of binding in the absence of covalent bond formation.