title: Insights into the mechanism of type I dehydroquinate dehydratases from structures of reaction intermediates.
abstract: 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 three crystal structures of the type I DHQD from the intestinal pathogens Clostridium difficile and Salmonella enterica. Structures of the enzyme with substrate and covalent pre- and post-dehydration reaction intermediates provide snapshots of successive steps along the type I DHQD-catalyzed reaction coordinate. These structures reveal that the position of the substrate within the active site does not appreciably change upon Schiff base formation. The intermediate state structures reveal a reaction state-dependent behavior of His-143 in which the residue adopts a conformation proximal to the site of catalytic dehydration only when the leaving group is present. We speculate that His-143 is likely to assume differing catalytic roles in each of its observed conformations. One conformation of His-143 positions the residue for the formation/hydrolysis of the covalent Schiff base intermediates, whereas the other conformation positions the residue for a role in 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 non-toxic antimicrobials. The structures and mechanistic insight presented here may inform the design of type I DHQD enzyme inhibitors.
authors.affiliation: Center for Structural Genomics of Infectious Diseases, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA.
authors.forename: Samuel H
authors.initials: SH
authors.lastname: Light
authors.forename: George
authors.initials: G
authors.lastname: Minasov
authors.forename: Ludmilla
authors.initials: L
authors.lastname: Shuvalova
authors.forename: Mark-Eugene
authors.initials: ME
authors.lastname: Duban
authors.forename: Michael
authors.initials: M
authors.lastname: Caffrey
authors.forename: Wayne F
authors.initials: WF
authors.lastname: Anderson
authors.forename: Arnon
authors.initials: A
authors.lastname: Lavie
mesh_terms: D001426:Bacterial Proteins; D002384:Catalysis; D020134:Catalytic Domain; D016360:Clostridioides difficile / Q000201:enzymology*; D018360:Crystallography, X-Ray; D006836:Hydro-Lyases / Q000737:chemistry* / Q000378:metabolism; D011485:Protein Binding; D011487:Protein Conformation; D011801:Quinic Acid / Q000031:analogs & derivatives / Q000737:chemistry / Q000378:metabolism; D019779:Salmonella enterica / Q000201:enzymology*; D012545:Schiff Bases; D012765:Shikimic Acid / Q000031:analogs & derivatives / Q000378:metabolism
chemical_list: C474477:3-dehydroquinic acid; D001426:Bacterial Proteins; D012545:Schiff Bases; D011801:Quinic Acid; C096387:3-dehydroshikimate; D012765:Shikimic Acid; D006836:Hydro-Lyases