Membrane Na+-pyrophosphatases Can Transport Protons at Low Sodium Concentrations

Membrane-bound Na⁺-pyrophosphatase (Na⁺-PPase), working in parallel with the corresponding ATP-energized pumps, catalyzes active Na⁺ transport in bacteria and archaea. Each ∼75-kDa subunit of homodimeric Na⁺-PPase forms an unusual funnel-like structure with a catalytic site in the cytoplasmic part and a hydrophilic gated channel in the membrane. Here, we show that at subphysiological Na⁺ concentrations (<5 mm), the Na⁺-PPases of Chlorobium limicola, four other bacteria, and one archaeon additionally exhibit an H⁺-pumping activity in inverted membrane vesicles prepared from recombinant Escherichia coli strains. H⁺ accumulation in vesicles was measured with fluorescent pH indicators. At pH 6.2–8.2, H⁺ transport activity was high at 0.1 mm Na⁺ but decreased progressively with increasing Na⁺ concentrations until virtually disappearing at 5 mm Na⁺. In contrast, ²²Na⁺ transport activity changed little over a Na⁺ concentration range of 0.05–10 mm. Conservative substitutions of gate Glu²⁴² and nearby Ser²⁴³ and Asn⁶⁷⁷ residues reduced the catalytic and transport functions of the enzyme but did not affect the Na⁺ dependence of H⁺ transport, whereas a Lys⁶⁸¹ substitution abolished H⁺ (but not Na⁺) transport. All four substitutions markedly decreased PPase affinity for the activating Na⁺ ion. These results are interpreted in terms of a model that assumes the presence of two Na⁺-binding sites in the channel: one associated with the gate and controlling all enzyme activities and the other located at a distance and controlling only H⁺ transport activity. The inherent H⁺ transport activity of Na⁺-PPase provides a rationale for its easy evolution toward specific H⁺ transport.