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Cited by 24Metalloenzymes and iron-sulfur proteinsEnzyme Structure and FunctionATP Synthase and ATPases Research

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Molecular principles of redox-coupled sodium pumping of the ancient Rnf machinery

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Kumar, Anuj, Roth, Jennifer, Kim, Hyunho, Saura, Patricia, Bohn, Stefan, Reif-Trauttmansdorff, Tristan, Schubert, Anja, Kaila, Ville R. I., Schuller, Jan M., Müller, Volker·2025·Nature Communications
DOI 10.1038/s41467-025-57375-8PMC PMC11889175

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Abstract

The Rnf complex is the primary respiratory enzyme of several anaerobic prokaryotes that transfers electrons from ferredoxin to NAD + and pumps ions (Na + or H + ) across a membrane, powering ATP synthesis. Rnf is widespread in primordial organisms and the evolutionary predecessor of the Na + -pumping NADH-quinone oxidoreductase (Nqr). By running in reverse, Rnf uses the electrochemical ion gradient to drive ferredoxin reduction with NADH, providing low potential electrons for nitrogenases and CO 2 reductases. Yet, the molecular principles that couple the long-range electron transfer to Na + translocation remain elusive. Here, we resolve key functional states along the electron transfer pathway in the Na + -pumping Rnf complex from Acetobacterium woodii using redox-controlled cryo-electron microscopy that, in combination with biochemical functional assays and atomistic molecular simulations, provide key insight into the redox-driven Na + pumping mechanism. We show that the reduction of the unique membrane-embedded [2Fe2S] cluster electrostatically attracts Na + , and in turn, triggers an inward/outward transition with alternating membrane access driving the Na + pump and the reduction of NAD + . Our study unveils an ancient mechanism for redox-driven ion pumping, and provides key understanding of the fundamental principles governing energy conversion in biological systems.

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Metadata

Authors
Kumar, A., Roth, J., Kim, H., Saura, P., Bohn, S., Reif-Trauttmansdorff, T., Schubert, A., Kaila, V. R. I., Schuller, J. M., & Müller, V.
Affiliations
  • Goethe University Frankfurt (DE)
  • Stockholm University (SE)
  • Helmholtz Munich (DE)
  • Philipps University of Marburg (DE)
Corresponding author
  • Kaila, Ville R. I.
  • Schuller, Jan M.
  • Müller, Volker
ORCID
Venue
Nature Communications
Publisher
Springer Science and Business Media LLC
Published
2025-03-07
Volume
16
Issue
1
Pages
2302-2302
ISSN
2041-1723 (ISSN-L)
DOI
10.1038/s41467-025-57375-8
PMC
PMC11889175
OpenAlex
W4408167625
Cited by
24
References
2
Citations by year
2026: 13 · 2025: 11
FWCI
3.30
Type
journal article
Language
en
Open access
Licence
Locations
  • Nature Communications (publishedVersion, cc-by)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
  • Europe PMC (PubMed Central) (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • RePEc: Research Papers in Economics (submittedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
Funders
  • European Commission (101075992, HORIZON2020)
  • Deutsche Forschungsgemeinschaft (SCHU 3364/1-1)
  • Knut och Alice Wallenbergs Stiftelse (2019.0251)
  • Vetenskapsrådet
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Biochemistry › Metalloenzymes and iron-sulfur proteins
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Structural Biology › Enzyme Structure and Function
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › ATP Synthase and ATPases Research
Keywords
Rnf complex, NADH:quinone oxidoreductase, nuclear quadrupole resonance, Acetobacterium woodii, ferredoxin, [2Fe-2S] cluster, long-range electron transfer, ion translocation, electrochemical gradient, nitrogenase, evolution of respiration, energy conversion
MeSH terms
Bacterial Proteins, Electron Transport, Ferredoxins, NAD, Oxidation-Reduction, Quinone Reductases, Sodium, Ion Transport, Cryoelectron Microscopy, Acetobacterium, Molecular Dynamics Simulation

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