8G2R

CRYSTAL STRUCTURE OF THE KPC-2 D179N VARIANT IN COMPLEX WITH AVIBACTAM

Summary for 8G2R

• Entry DOI: 10.2210/pdb8g2r/pdb
• Descriptor: Carbapenem-hydrolyzing beta-lactamase KPC, (2S,5R)-1-formyl-5-[(sulfooxy)amino]piperidine-2-carboxamide (3 entities in total)
• Functional Keywords: beta-lactamase, inhibitor, antibiotic resistance, hydrolase, hydrolase-antibiotic complex, hydrolase/antibiotic
• Biological source: Klebsiella pneumoniae
• Total number of polymer chains: 1
• Total formula weight: 28443.01

Authors

Alsenani, T.,van den Akker, F. (deposition date: 2023-02-06, release date: 2023-08-09, Last modification date: 2024-10-23)

Primary citation

Alsenani, T.A.,Viviani, S.L.,Papp-Wallace, K.M.,Bonomo, R.A.,van den Akker, F.
Exploring avibactam and relebactam inhibition of Klebsiella pneumoniae carbapenemase D179N variant: role of the Omega loop-held deacylation water.
Antimicrob.Agents Chemother., 67:e0035023-e0035023, 2023

PubMed Abstract: carbapenemase-2 (KPC-2) presents a clinical threat as this β-lactamase confers resistance to carbapenems. Recent variants of KPC-2 in clinical isolates contribute to concerning resistance phenotypes. expressing KPC-2 D179Y acquired resistance to the ceftazidime/avibactam combination affecting both the β-lactam and the β-lactamase inhibitor yet has lowered minimum inhibitory concentrations for all other β-lactams tested. Furthermore, expressing the KPC-2 D179N variant also manifested resistance to ceftazidime/avibactam yet retained its ability to confer resistance to carbapenems although significantly reduced. This structural study focuses on the inhibition of KPC-2 D179N by avibactam and relebactam and expands our previous analysis that examined ceftazidime resistance conferred by D179N and D179Y variants. Crystal structures of KPC-2 D179N soaked with avibactam and co-crystallized with relebactam were determined. The complex with avibactam reveals avibactam making several hydrogen bonds, including with the deacylation water held in place by Ω loop. These results could explain why the KPC-2 D179Y variant, which has a disordered Ω loop, has a decreased affinity for avibactam. The relebactam KPC-2 D179N complex revealed a new orientation of the diazabicyclooctane (DBO) intermediate with the scaffold piperidine ring rotated ~150° from the standard DBO orientation. The density shows relebactam to be desulfated and present as an imine-hydrolysis intermediate not previously observed. The tetrahedral imine moiety of relebactam interacts with the deacylation water. The rotated relebactam orientation and deacylation water interaction could potentially contribute to KPC-mediated DBO fragmentation. These results elucidate important differences that could aid in the design of novel β-lactamase inhibitors.

PubMed: 37750722
DOI: 10.1128/aac.00350-23

Experimental method

X-RAY DIFFRACTION (1.28 Å)