Crystal Structure of the OXA-48 β-Lactamase Reveals Mechanistic Diversity among Class D Carbapenemases

Abstract

Carbapenem-hydrolyzing class D beta-lactamases (CHDLs) are enzymes found in important Gram-negative pathogens (mainly Acinetobacter baumannii and Enterobacteriaceae) that confer resistance to beta-lactam antibiotics, and notably carbapenems. The crystal structure of the OXA-48 carbapenemase was determined at pH 7.5 and at a resolution of 1.9 A. Surprisingly, and by contrast with OXA-24, the only other CHDL of known crystal structure, the structure of OXA-48 was similar to OXA-10, an enzyme devoid of carbapenemase activity, indicating that the hydrolysis of these compounds could depend on subtle changes in the active site region. Moreover, the active site groove of OXA-48 was different from that of OXA-24 in shape, dimensions, and charge distribution. Molecular dynamics pointed to the functional relevance of residues located in or close to the beta5-beta6 loop and allowed us to propose a mechanism for carbapenem hydrolysis by OXA-48.

Hydrolytic Mechanism of OXA-58 Enzyme, a Carbapenem-hydrolyzing Class D β-Lactamase from Acinetobacter baumannii

“…7 and supplemental Fig. S3), which is similar to the loop conformation observed in OXA-24 and OXA-48 (15,18). The predicted topology of the active site in OXA-58 is narrower compared with the active site of OXA-10 and OXA-24.…”

“…Structural studies on OXA-24 revealed a hydrophobic cleft on the active site that might account for the preference of this enzyme for imipenem over oxacillin (15). However, this structural feature is not conserved in OXA-48 (18).…”

“…This catalytic role of a CO 2 molecule resolves the apparent discrepancy between the low catalytic efficiency reported for imipenem in literature and the measured resistance levels (39). Recent structural studies on two CHDLs, OXA-24 and OXA-48, show the conserved lysine residue to be carbamylated (16,18). It is plausible that the carbamylated lysine residue is mechanistically conserved among all OXA ␤-lactamases.…”

“…The structure reveals that OXA-48 lacks the hydrophobic cleft over the active site that is seen in OXA-24 and also that it has a differently shaped active site (18). It was reported that OXA-48 might employ a different catalytic mechanism (18).…”

“…Recently, the crystal structure of OXA-48, a CHDL prevalent in Klebsiella pneumoniae, was solved (18). The structure reveals that OXA-48 lacks the hydrophobic cleft over the active site that is seen in OXA-24 and also that it has a differently shaped active site (18).…”