8YS5

Cryo-EM structure of the Helicobacter pylori OorDABC complex in the apo-form

Summary for 8YS5

• Entry DOI: 10.2210/pdb8ys5/pdb
• EMDB information: 39556
• Descriptor: 2-oxoglutarate:acceptor oxidoreductase, 2-oxoglutarate synthase subunit alpha, 2-oxoglutarate ferredoxin oxidoreductase subunit beta, ... (7 entities in total)
• Functional Keywords: oxoglutarate oxidoreductase, electron transport, tricarboxylic acid cycle, oxidoreductase
• Biological source: Helicobacter pylori; More
• Total number of polymer chains: 8
• Total formula weight: 212546.44

Authors

Lan, W.,Gao, Y.,Bi, H. (deposition date: 2024-03-22, release date: 2025-07-02, Last modification date: 2026-01-21)

Primary citation

Hang, X.,Lan, W.,Yanqiang, H.,Huang, H.,Zhang, M.,Zeng, L.,Shi, T.,Bai, Y.,Yang, Z.,Hu, S.,Wang, J.,Dong, L.,Tong, Q.,Jia, J.,Bi, S.,Xia, Q.,Gao, Y.,Bi, H.
2-oxoglutarate:acceptor oxidoreductase-catalyzed redox cycling effectively targets coccoid forms of Helicobacter pylori.
Nat Commun, 16:6965-6965, 2025

PubMed Abstract: Helicobacter pylori, a globally significant pathogen, plays a central etiological role in diverse gastric pathologies ranging from chronic gastritis and peptic ulcers to gastric adenocarcinoma. Although conventional antibiotics effectively inhibit or kill growing helical H. pylori, metabolically dormant coccoid forms of H. pylori exhibit considerable tolerance, posing a persistent and clinically significant challenge. Here, we report napabucasin (2-acetylfuro-1,4-naphthoquinone) as a redox-cycling antibiotic with potent bactericidal activity against both drug-resistant helical and coccoid forms of H. pylori. Notably, napabucasin does not induce acquired resistance in vitro and demonstrates superior efficacy compared to standard triple therapy in murine infection models. Mechanistic studies reveal that napabucasin acts through 2-oxoglutarate:acceptor oxidoreductase (OOR)-catalyzed futile redox cycling, generating bactericidal levels of reactive oxygen species (ROS). Compared to menaquinone 6, a proposed physiological electron acceptor, napabucasin exhibits enhanced oxidative capacity. Structural, biochemical, and microbiological analyses identify Leu44 and Lys46 within the OorD subunit as critical residues for napabucasin recognition and catalysis. These findings establish OOR-mediated redox cycling as a robust antimicrobial strategy that sustains endogenous ROS production to combat refractory H. pylori infections.

PubMed: 40730563
DOI: 10.1038/s41467-025-62477-4

Experimental method

ELECTRON MICROSCOPY (2.95 Å)