Structure Based Insight into the Mechanism of Type I Dehydroquinate Dehydratases

The biosynthetic shikimate pathway consists of seven enzymes that catalyze sequential reactions to generate chorismate, a critical branch point in the synthesis of the aromatic amino acids. The third enzyme in the pathway, dehydroquinate dehydratase (DHQD), catalyzes the dehydration of 3‐dehydroquinate to 3‐dehydroshikimate. We present 3 crystal structures of the type I DHQD from the intestinal pathogens Clostridium difficile and Salmonella typhimurium. Structures of the enzyme with substrate and two covalent intermediates provide snapshots of successive steps along the type I DHQD‐catalyzed reaction coordinate. Intermediate state structures reveal a reaction‐state‐dependent behavior of His143 – in which the residue assumes a conformation proximal to the site of catalytic dehydration only when the leaving group is intact. We speculate that His143 is likely to assume multiple roles in catalysis of the formation/hydrolysis of the covalent Schiff base intermediates and the catalytic dehydration event. The fact that the shikimate pathway is absent from humans makes the enzymes of the pathway potential targets for the development of nontoxic antimicrobials. The structures and mechanistic insight presented here may inform the design of type I DHQD enzyme inhibitors.