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

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.