7TB7

Crystal structure of D179N KPC-2 beta-lactamase

Summary for 7TB7

• Entry DOI: 10.2210/pdb7tb7/pdb
• Descriptor: Carbapenem-hydrolyzing beta-lactamase KPC, CITRIC ACID (3 entities in total)
• Functional Keywords: beta-lactamase, antibiotic resistance, hydrolase
• Biological source: Klebsiella pneumoniae
• Total number of polymer chains: 1
• Total formula weight: 28367.88

Authors

van den Akker, F.,Alsenani, T. (deposition date: 2021-12-21, release date: 2022-03-02, Last modification date: 2024-11-13)

Primary citation

Alsenani, T.A.,Viviani, S.L.,Kumar, V.,Taracila, M.A.,Bethel, C.R.,Barnes, M.D.,Papp-Wallace, K.M.,Shields, R.K.,Nguyen, M.H.,Clancy, C.J.,Bonomo, R.A.,van den Akker, F.
Structural Characterization of the D179N and D179Y Variants of KPC-2 beta-Lactamase: Omega-Loop Destabilization as a Mechanism of Resistance to Ceftazidime-Avibactam.
Antimicrob.Agents Chemother., 66:e0241421-e0241421, 2022

PubMed Abstract: Klebsiella pneumoniae carbapenemases (KPC-2 and KPC-3) present a global clinical threat, as these β-lactamases confer resistance to carbapenems and oxyimino-cephalosporins. Recent clinically identified KPC variants with substitutions at Ambler position D179, located in the Ω loop, are resistant to the β-lactam/β-lactamase inhibitor combination ceftazidime-avibactam, but susceptible to meropenem-vaborbactam. To gain insights into ceftazidime-avibactam resistance conferred by D179N/Y variants of KPC-2, crystal structures of these variants were determined. The D179N KPC-2 structure revealed that the change of the carboxyl to an amide moiety at position 179 disrupted the salt bridge with R164 present in wild-type KPC-2. Additional interactions were disrupted in the Ω loop, causing a decrease in the melting temperature. Shifts originating from N179 were also transmitted toward the active site, including ∼1-Å shifts of the deacylation water and interacting residue N170. The structure of the D179Y KPC-2 β-lactamase revealed more drastic changes, as this variant exhibited disorder of the Ω loop, with other flanking regions also being disordered. We postulate that the KPC-2 variants can accommodate ceftazidime because the Ω loop is displaced in D179Y or can be more readily displaced in D179N KPC-2. To understand why the β-lactamase inhibitor vaborbactam is less affected by the D179 variants than avibactam, we determined the crystal structure of D179N KPC-2 in complex with vaborbactam, which revealed wild-type KPC-2-like vaborbactam-active site interactions. Overall, the structural results regarding KPC-2 D179 variants revealed various degrees of destabilization of the Ω loop that contribute to ceftazidime-avibactam resistance, possible substrate-assisted catalysis of ceftazidime, and meropenem and meropenem-vaborbactam susceptibility.

PubMed: 35341315
DOI: 10.1128/aac.02414-21

Experimental method

X-RAY DIFFRACTION (0.99 Å)