Proton/sodium pumping pyrophosphatases: the last of the primary ion pumps

•Reviews structural understanding of H+/Na+-pumping pyrophosphatases (M-PPases).•Discusses structural and functional data and potential models of pumping.•Proposes adopting Ballesteros and Weinstein numbering to simplify M-PPase comparison. Membrane-bound pyrophosphatases (M-PPases) are homodimeric enzymes that couple the generation and utilization of membrane potentials to pyrophosphate (PPi) hydrolysis and synthesis. Since the discovery of the link between PPi use and proton transport in purple, non-sulphur bacteria in the 1960s, M-PPases have been found in all three domains of life and have been shown to have a crucial role in stress tolerance and in plant maturation. The discovery of sodium-pumping and sodium/proton-pumping M-PPases showed that the pumping specificity of these enzymes is not limited to protons, further suggesting that M-PPases are evolutionarily very ancient. The recent structures of two M-PPases, the Vigna radiata H+-pumping M-PPase and Thermotoga maritima Na+-pumping M-PPase, provide the basis for understanding the functional data. They show that M-PPases have a novel fold and pumping mechanism, different to the other primary pumps. This review discusses the current structural understanding of M-PPases and of ion selection among various M-PPases.