ATP synthase (proton-translocating ATPase) (EC 3.6.3.14) [1,2] is a component of the cytoplasmic membrane of eubacteria, the inner membrane of mitochondria, and the thylakoid membrane of chloroplasts. The ATPase complex is composed of an oligomeric transmembrane sector, called CF(0), and a catalytic core, called coupling factor CF(1). The former acts as a proton channel; the latter is composed of five subunits, α, β, γ, delta and epsilon. The sequences of subunits α and β are related and both contain a nucleotide-binding site for ATP and ADP. The β chain has catalytic activity, while the α chain is a regulatory subunit.

Vacuolar ATPases [3] (V-ATPases) are responsible for acidifying a variety of intracellular compartments in eukaryotic cells. Like F-ATPases, they are oligomeric complexes of a transmembrane and a catalytic sector. The sequence of the largest subunit of the catalytic sector (70 Kd) is related to that of F-ATPase β subunit, while a 60 Kd subunit, from the same sector, is related to the F-ATPases α subunit [4].

Archaebacterial membrane-associated ATPases are composed of three subunits. The α chain is related to F-ATPases β chain and the β chain is related to F-ATPases α chain [4].

A protein highly similar to F-ATPase β subunits is found [5] in some bacterial apparatus involved in a specialized protein export pathway that proceeds without signal peptide cleavage. This protein is known as fliI in Bacillus and Salmonella, Spa47 (mxiB) in Shigella flexneri, HrpB6 in Xanthomonas campestris and yscN in Yersinia virulence plasmids.

In order to detect these ATPase subunits, we took a segment of ten amino-acid residues, containing two conserved serines, as a signature pattern. The first serine seems to be important for catalysis - in the ATPase α chain at least - as its mutagenesis causes catalytic impairment.