8TMR

Crystal structure of KPC-44 carbapenemase complexed with avibactam

Summary for 8TMR

• Entry DOI: 10.2210/pdb8tmr/pdb
• Related: 8TJM
• Descriptor: beta-lactamase, (2S,5R)-1-formyl-5-[(sulfooxy)amino]piperidine-2-carboxamide, PHOSPHATE ION, ... (5 entities in total)
• Functional Keywords: kpc carbapenemase, ceftazidime-avibactam resistance, hydrolase
• Biological source: Klebsiella pneumoniae
• Total number of polymer chains: 1
• Total formula weight: 30522.11

Authors

Sun, Z.,Palzkill, T.,Hu, L.,Lin, H.,Sankaran, B.,Wang, J.,Prasad, B. (deposition date: 2023-07-30, release date: 2023-12-06, Last modification date: 2023-12-27)

Primary citation

Sun, Z.,Lin, H.,Hu, L.,Neetu, N.,Sankaran, B.,Wang, J.,Prasad, B.V.V.,Palzkill, T.
Klebsiella pneumoniae carbapenemase variant 44 acquires ceftazidime-avibactam resistance by altering the conformation of active-site loops.
J.Biol.Chem., 300:105493-105493, 2023

PubMed Abstract: Klebsiella pneumoniae carbapenemase 2 (KPC-2) is an important source of drug resistance as it can hydrolyze and inactivate virtually all β-lactam antibiotics. KPC-2 is potently inhibited by avibactam via formation of a reversible carbamyl linkage of the inhibitor with the catalytic serine of the enzyme. However, the use of avibactam in combination with ceftazidime (CAZ-AVI) has led to the emergence of CAZ-AVI-resistant variants of KPC-2 in clinical settings. One such variant, KPC-44, bears a 15 amino acid duplication in one of the active-site loops (270-loop). Here, we show that the KPC-44 variant exhibits higher catalytic efficiency in hydrolyzing ceftazidime, lower efficiency toward imipenem and meropenem, and a similar efficiency in hydrolyzing ampicillin, than the WT KPC-2 enzyme. In addition, the KPC-44 variant enzyme exhibits 12-fold lower AVI carbamylation efficiency than the KPC-2 enzyme. An X-ray crystal structure of KPC-44 showed that the 15 amino acid duplication results in an extended and partially disordered 270-loop and also changes the conformation of the adjacent 240-loop, which in turn has altered interactions with the active-site omega loop. Furthermore, a structure of KPC-44 with avibactam revealed that formation of the covalent complex results in further disorder in the 270-loop, suggesting that rearrangement of the 270-loop of KPC-44 facilitates AVI carbamylation. These results suggest that the duplication of 15 amino acids in the KPC-44 enzyme leads to resistance to CAZ-AVI by modulating the stability and conformation of the 270-, 240-, and omega-loops.

PubMed: 38000656
DOI: 10.1016/j.jbc.2023.105493

Experimental method

X-RAY DIFFRACTION (1.37 Å)