9SNK

CryoEM structure of NADH:quinone oxidoreductases YjlCD from Bacillus subtilis

Summary for 9SNK

• Entry DOI: 10.2210/pdb9snk/pdb
• EMDB information: 55048
• Descriptor: NADH dehydrogenase-like protein YjlD, YjlC, FLAVIN-ADENINE DINUCLEOTIDE, ... (10 entities in total)
• Functional Keywords: bacterial metabolism, bioenergetics, quinone, helical membrane plug-in, oxidoreductase
• Biological source: Bacillus subtilis subsp. subtilis str. 168; More
• Total number of polymer chains: 8
• Total formula weight: 249986.56

Authors

Osman, R.,Cherrier, M.V.,Nicolet, Y.,Juyoux, P.,Schoehn, G.,Seduk, F.,Garcia, P.S.,Bizien-Jaglin, L.,Botte, C.Y.,Kosta, A.,Lebrun, R.,Mate, M.J.,Pierrel, F.,Yamaryo-Botte, Y.,Walburger, A.,Magalon, A. (deposition date: 2025-09-11, release date: 2026-07-01)

Primary citation

Seduk, F.,Osman, R.,Garcia, P.S.,Bizien-Jaglin, L.,Juyoux, P.,Kosta, A.,Sauvage, S.,Mate, M.J.,Pierrel, F.,Lebrun, R.,Schoehn, G.,Yamaryo-Botte, Y.,Botte, C.Y.,Nicolet, Y.,Cherrier, M.V.,Walburger, A.,Magalon, A.
A Bacillales-specific tubular scaffold essential for NADH dehydrogenase activity.
Nat Commun, 2026

PubMed Abstract: Respiratory type II NADH:quinone oxidoreductases (NDH-II) are typically monotopic flavoproteins that make direct contact with the membrane to access the quinone pool. Here, we show that in Bacillus subtilis, one NDH-II, termed Ndh, assembles with the helical membrane plugin (HMP) protein YjlC and forms supramolecular fibers. Genetic and biochemical analyses demonstrate that Ndh and YjlC proteins are essential for NADH oxidation. Cryo-EM analysis reveals that YjlC forms a tubular scaffold onto which multiple Ndh subunits are regularly docked via their C-terminal domain, repurposed from its classical role in direct membrane binding. These fibers can extend up to ~1000 Å, creating a continuous hydrophobic tunnel filled with lipids and quinones, thereby mimicking the membrane environment. Comparative genomics unveils that this partnership arose exclusively within Bacillales through the recruitment of an ancestral HMP originally associated with sulfide:quinone reductases. Together, our findings uncover a lineage-specific structural adaptation in which NDH-II enzymes depend on an HMP scaffold, expanding their functional diversity beyond the classical monotopic paradigm.

PubMed: 42315832
DOI: 10.1038/s41467-026-74385-2

Experimental method

ELECTRON MICROSCOPY (2.59 Å)