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Structure paper

TitleA Bacillales-specific tubular scaffold essential for NADH dehydrogenase activity.
Journal, issue, pagesNat Commun, Vol. 17, Issue 1, Year 2026
Publish dateJun 18, 2026
AuthorsFarida Seduk / Rayan Osman / Pierre Simon Garcia / Lilou Bizien-Jaglin / Pauline Juyoux / Artemis Kosta / Salomé Sauvage / Maria J Maté / Fabien Pierrel / Régine Lebrun / Guy Schoehn / Yoshiki Yamaryo-Botté / Cyrille Y Botté / Yvain Nicolet / Mickael V Cherrier / Anne Walburger / Axel Magalon /
PubMed AbstractRespiratory 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 ...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.
External linksNat Commun / PubMed:42315832 / PubMed Central
MethodsEM (single particle)
Resolution2.59 - 3.61 Å
Structure data

55048

9snk

EMDB-55048, PDB-9snk:
CryoEM structure of NADH:quinone oxidoreductases YjlCD from Bacillus subtilis
Method: EM (single particle) / Resolution: 2.59 Å

EMDB-55049: CryoEM structure of NADH:quinone oxidoreductases YjlCD fiber's HMP extremity from Bacillus subtilis
Method: EM (single particle) / Resolution: 3.61 Å

EMDB-55050: CryoEM structure of NADH:quinone oxidoreductases YjlCD fiber's N-terminal extremity from Bacillus subtilis
Method: EM (single particle) / Resolution: 3.04 Å

Chemicals

ChemComp-FAD:
FLAVIN-ADENINE DINUCLEOTIDE / FAD*YM

ChemComp-SHV:
HEPTANOIC ACID

ChemComp-6NA:
HEXANOIC ACID

ChemComp-3PE:
1,2-Distearoyl-sn-glycerophosphoethanolamine / phospholipid*YM

ChemComp-LEA:
PENTANOIC ACID

ChemComp-GOL:
GLYCEROL

ChemComp-DKA:
DECANOIC ACID

ChemComp-HOH:
WATER

Source
  • bacillus subtilis subsp. subtilis str. 168 (bacteria)
KeywordsOXIDOREDUCTASE / Bacterial metabolism / Bioenergetics / Quinone / Helical Membrane Plug-in

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