3RXX

KPC-2 carbapenemase in complex with 3-NPBA

Summary for 3RXX

• Entry DOI: 10.2210/pdb3rxx/pdb
• Related: 3QXW
• Descriptor: Carbepenem-hydrolyzing beta-lactamase KPC, 3-NITROPHENYLBORONIC ACID (3 entities in total)
• Functional Keywords: inhibitor, beta-lactamase, hydrolase-hydrolase inhibitor complex, hydrolase/hydrolase inhibitor
• Biological source: Klebsiella pneumoniae
• Total number of polymer chains: 1
• Total formula weight: 28159.43

Authors

Ke, W.,van den Akker, F. (deposition date: 2011-05-10, release date: 2012-03-21, Last modification date: 2023-09-13)

Primary citation

Ke, W.,Bethel, C.R.,Papp-Wallace, K.M.,Pagadala, S.R.,Nottingham, M.,Fernandez, D.,Buynak, J.D.,Bonomo, R.A.,van den Akker, F.
Crystal structures of KPC-2 {beta}-lactamase in complex with 3-nitrophenyl boronic acid and the penam sulfone PSR-3-226.
Antimicrob.Agents Chemother., 56:2713-2718, 2012

PubMed Abstract: Class A carbapenemases are a major threat to the potency of carbapenem antibiotics. A widespread carbapenemase, KPC-2, is not easily inhibited by β-lactamase inhibitors (i.e., clavulanic acid, sulbactam, and tazobactam). To explore different mechanisms of inhibition of KPC-2, we determined the crystal structures of KPC-2 with two β-lactamase inhibitors that follow different inactivation pathways and kinetics. The first complex is that of a small boronic acid compound, 3-nitrophenyl boronic acid (3-NPBA), bound to KPC-2 with 1.62-Å resolution. 3-NPBA demonstrated a K(m) value of 1.0 ± 0.1 μM (mean ± standard error) for KPC-2 and blocks the active site by making a reversible covalent interaction with the catalytic S70 residue. The two boron hydroxyl atoms of 3-NPBA are positioned in the oxyanion hole and the deacylation water pocket, respectively. In addition, the aromatic ring of 3-NPBA provides an edge-to-face interaction with W105 in the active site. The structure of KPC-2 with the penam sulfone PSR-3-226 was determined at 1.26-Å resolution. PSR-3-226 displayed a K(m) value of 3.8 ± 0.4 μM for KPC-2, and the inactivation rate constant (k(inact)) was 0.034 ± 0.003 s(-1). When covalently bound to S70, PSR-3-226 forms a trans-enamine intermediate in the KPC-2 active site. The predominant active site interactions are generated via the carbonyl oxygen, which resides in the oxyanion hole, and the carboxyl moiety of PSR-3-226, which interacts with N132, N170, and E166. 3-NPBA and PSR-3-226 are the first β-lactamase inhibitors to be trapped as an acyl-enzyme complex with KPC-2. The structural and inhibitory insights gained here could aid in the design of potent KPC-2 inhibitors.

PubMed: 22330909
DOI: 10.1128/AAC.06099-11

Experimental method

X-RAY DIFFRACTION (1.62 Å)