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

Anuj Kumar, Jennifer Roth, Hyunho Kim, Patricia Saura, Stefan Bohn, Tristan Reif-Trauttmansdorff, Anja Schubert, Ville R. I. Kaila (), Jan M. Schuller () and Volker Müller ()
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Anuj Kumar: Philipps-University of Marburg
Jennifer Roth: Johann Wolfgang Goethe University
Hyunho Kim: Stockholm University
Patricia Saura: Stockholm University
Stefan Bohn: Helmholtz Munich
Tristan Reif-Trauttmansdorff: Philipps-University of Marburg
Anja Schubert: Johann Wolfgang Goethe University
Ville R. I. Kaila: Stockholm University
Jan M. Schuller: Philipps-University of Marburg
Volker Müller: Johann Wolfgang Goethe University

Nature Communications, 2025, vol. 16, issue 1, 1-13

Abstract: 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 CO2 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.

Date: 2025
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DOI: 10.1038/s41467-025-57375-8

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