title: Structures of the class D carbapenemase OXA-24 from Acinetobacter baumannii in complex with doripenem.
abstract: The emergence of class D β-lactamases with carbapenemase activity presents an enormous challenge to health practitioners, particularly with regard to the treatment of infections caused by Gram-negative pathogens such as Acinetobacter baumannii. Unfortunately, class D β-lactamases with carbapenemase activity are resistant to β-lactamase inhibitors. To better understand the details of the how these enzymes bind and hydrolyze carbapenems, we have determined the structures of two deacylation-deficient variants (K84D and V130D) of the class D carbapenemase OXA-24 with doripenem bound as a covalent acyl-enzyme intermediate. Doripenem adopts essentially the same configuration in both OXA-24 variant structures, but varies significantly when compared to the non-carbapenemase class D member OXA-1/doripenem complex. The alcohol of the 6α hydroxyethyl moiety is directed away from the general base carboxy-K84, with implications for activation of the deacylating water. The tunnel formed by the Y112/M223 bridge in the apo form of OXA-24 is largely unchanged by the binding of doripenem. The presence of this bridge, however, causes the distal pyrrolidine/sulfonamide group to bind in a drastically different conformation compared to doripenem bound to OXA-1. The resulting difference in the position of the side-chain bridge sulfur of doripenem is consistent with the hypothesis that the tautomeric state of the pyrroline ring contributes to the different carbapenem hydrolysis rates of OXA-1 and OXA-24. These findings represent a snapshot of a key step in the catalytic mechanism of an important class D enzyme, and might be useful for the design of novel inhibitors.
authors.affiliation: Department of Chemistry, Grand Valley State University, Allendale, MI 49401, USA.
authors.forename: Kyle D
authors.initials: KD
authors.lastname: Schneider
authors.forename: Caleb J
authors.initials: CJ
authors.lastname: Ortega
authors.forename: Nicholas A
authors.initials: NA
authors.lastname: Renck
authors.forename: Robert A
authors.initials: RA
authors.lastname: Bonomo
authors.forename: Rachel A
authors.initials: RA
authors.lastname: Powers
authors.forename: David A
authors.initials: DA
authors.lastname: Leonard
mesh_terms: D040981:Acinetobacter baumannii / Q000201:enzymology*; D019943:Amino Acid Substitution; D000900:Anti-Bacterial Agents / Q000737:chemistry* / Q000378:metabolism*; D015780:Carbapenems / Q000737:chemistry* / Q000378:metabolism*; D018360:Crystallography, X-Ray; D000077726:Doripenem; D008958:Models, Molecular; D050505:Mutant Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D020125:Mutation, Missense; D017434:Protein Structure, Tertiary; D001618:beta-Lactamases / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*
chemical_list: D000900:Anti-Bacterial Agents; D015780:Carbapenems; D050505:Mutant Proteins; D000077726:Doripenem; D001618:beta-Lactamases; C410345:beta-lactamase OXA-24