Figure 4

Consensus sequences of the transmembrane segments of Na⁺-binding (top) and H⁺-binding (bottom) c subunits of prokaryotic F-type and V-type ATPases represented in the Sequence Logo format. The height of each letter is proportional to the frequency of the respective amino acid in the given position [105, 106]. Residue numbering in the top and bottom panels follows the c subunits from Ilyobacter tartaricus [47] and Escherichia coli, respectively. The residues shown on Fig. 3 are indicated with arrows. The logo was constructed based on an alignment of single-hairpin c subunits (see Additional File 1). The alignment of Na⁺-translocating c subunits also included 13 hairpin domains from the Methanopyrus kandleri ATP synthase (see text and ref. 50). Note that the conservation of the Na⁺-ligands (e.g. Gln/Glu32, Glu65, Ser/Thr66) is partly absent in H⁺-binding subunits. It is noteworthy that the sodium ligands did not disappear completely; in addition to the principal acidic (Glu or Asp) residue, some Na⁺ ligands are conserved in a variety of F-type and V-type H⁺-ATPases (see Additional File 1). This might reflect binding of the H₃O⁺ ion, rather than free proton, as first suggested by Boyer [107], in some enzymes, given that H₃O⁺ requires at least three coordination bonds [108].