9ZO2
Toho-1 Beta Lactamase in complex with Avibactam
Summary for 9ZO2
| Entry DOI | 10.2210/pdb9zo2/pdb |
| Descriptor | Beta-lactamase, (2S,5R)-1-formyl-5-[(sulfooxy)amino]piperidine-2-carboxamide, (2S,5R)-7-oxo-6-(sulfooxy)-1,6-diazabicyclo[3.2.1]octane-2-carboxamide, ... (5 entities in total) |
| Functional Keywords | beta lacamtase antibiotic resistance, hydrolase |
| Biological source | Escherichia coli |
| Total number of polymer chains | 1 |
| Total formula weight | 28829.34 |
| Authors | |
| Primary citation | Williams, C.G.,Wang, S.,Carta, V.,Langan, P.S.,Thome, A.F.,Ramos, S.A.,Holmes, J.B.,Ghosh, R.K.,Weiss, K.L.,Beran, G.J.O.,Hartman, J.D.,Coates, L.,Rienstra, C.M.,Mueller, L.J. NMR crystallography reveals active-site protonation states of Toho-1 beta-lactamase in complex with avibactam. Proc.Natl.Acad.Sci.USA, 123:e2616547123-e2616547123, 2026 Cited by PubMed Abstract: The determination of active-site protonation states is critical for a full mechanistic understanding of enzyme catalysis and inhibition. Here, we employ NMR crystallography-the integrated combination of solid-state NMR spectroscopy, X-ray diffraction, and first-principles computational chemistry-to determine the protonation states of the active site of Toho-1 β-lactamase in complex with the non-β-lactam inhibitor avibactam. We report two X-ray crystal structures of the Toho-1:avibactam complex, along with high-field solid-state NMR measurements that enable near-complete backbone and side-chain resonance assignments. To overcome the computational scaling limits that have traditionally hindered NMR crystallography in large systems, we use an accelerated workflow in which machine-learning interatomic potentials enable efficient geometry refinement prior to density functional theory chemical shift calculations. For Toho-1, quantitative analysis of the active-site chemical shifts and chemical shift tensors using this hybrid protocol reveals that the key active-site side chains retain their canonical charge states in the presence of avibactam, with Lys73 and Lys234 protonated and positively charged, and Glu166 deprotonated and poised to function as a general base. Contrary to recent proposals suggesting that avibactam inhibits by suppressing essential proton transfers through p perturbations, our data point to a more direct chemical origin arising from the intrinsic resistance of the Ser70-avibactam carbamoyl linkage to hydrolysis. PubMed: 42743273DOI: 10.1073/pnas.2616547123 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1.15 Å) |
Structure validation
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