9TEB

Crystal structure of Nocardia cyriacigeorgica, class A beta-lactamase, NCY-1 bound to Avibactam

Summary for 9TEB

• Entry DOI: 10.2210/pdb9teb/pdb
• Descriptor: Beta-lactamase, (2S,5R)-1-formyl-5-[(sulfooxy)amino]piperidine-2-carboxamide, CITRATE ANION, ... (4 entities in total)
• Functional Keywords: beta-lactamase, avibactam, nocardia, hydrolase
• Biological source: Nocardia cyriacigeorgica
• Total number of polymer chains: 1
• Total formula weight: 28398.33

Authors

Couston, J.,Le-Marchand, A.,Hodille, E.,Genestet, C.,Joannard, B.,Feuillard, J.,Benito, Y.,Dumitrescu, O.,Blaise, M. (deposition date: 2025-11-25, release date: 2026-03-18, Last modification date: 2026-04-01)

Primary citation

Couston, J.,Le Marchand, A.,Hodille, E.,Genestet, C.,Joannard, B.,Feuillard, J.,Benito, Y.,Dumitrescu, O.,Blaise, M.
NCY-1 beta-Lactamase Activity Correlates With Antimicrobial Susceptibility of a Clinical Strain of Nocardia cyriacigeorgica.
Microbiologyopen, 15:e70267-e70267, 2026

PubMed Abstract: Nocardiosis is an infectious disease caused by several Nocardia species, among which Nocardia cyriacigeorgica is one of the most frequently isolated species in the clinic. Albeit most isolates of this species are susceptible to standard treatment combining trimethoprim and sulfamethoxazole, resistance has been reported, necessitating alternative or combination therapies. β-lactam antibiotics are of particular interest in this context. In this study, we aimed to address the β-lactam susceptibility profile of a clinical strain of N. cyriacigeorgica and assessed whether it correlated with the enzymatic activity of purified β-lactamase of the strain. We herein established that the strain is highly susceptible to imipenem and ceftriaxone, moderately susceptible to meropenem and resistant to amoxicillin. The resistance could be counteracted by β-lactamase inhibitors from two distinct chemical classes: vaborbactam, and avibactam while clavulanate was less potent. We demonstrated that the β-lactam susceptibility of the strain is in direct line with the enzymatic activity of purified NCY-1, a class A β-lactamase. NCY-1 was indeed only active with amoxicillin but displayed poor activity towards other classes of β-lactams. The NCY-1 activity could be inhibited in vitro by vaborbactam, clavulanate, and avibactam. We consolidated these data by determining the high-resolution structure of NCY-1 bound to avibactam. The structural analysis supported a conserved inhibitor binding site among other Nocardia class A β-lactamases strongly suggesting a broad inhibition spectrum of avibactam across Nocardia species.

PubMed: 41860015
DOI: 10.1002/mbo3.70267

Experimental method

X-RAY DIFFRACTION (1.3 Å)