PROSITE documentation PDOC00137
ATP synthase alpha and beta subunits signature


ATP synthase (proton-translocating ATPase) (EC [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.


F-ATPase α and β subunits, V-ATPase 70 Kd subunit and the archaebacterial ATPase α subunit also contain a copy of the ATP-binding motifs A and B (see <PDOC00017>).

Last update:

April 2006 / Pattern revised.


Technical section

PROSITE method (with tools and information) covered by this documentation:

ATPASE_ALPHA_BETA, PS00152; ATP synthase alpha and beta subunits signature  (PATTERN)


1AuthorsFutai M. Noumi T. Maeda M.
TitleATP synthase (H+-ATPase): results by combined biochemical and molecular biological approaches.
SourceAnnu. Rev. Biochem. 58:111-136(1989).
PubMed ID2528322

2AuthorsSenior A.E.
TitleATP synthesis by oxidative phosphorylation.
SourcePhysiol. Rev. 68:177-231(1988).
PubMed ID2892214

3AuthorsNelson N.
TitleStructure, molecular genetics, and evolution of vacuolar H+-ATPases.
SourceJ. Bioenerg. Biomembr. 21:553-571(1989).
PubMed ID2531737

4AuthorsGogarten J.P. Kibak H. Dittrich P. Taiz L. Bowman E.J. Bowman B.J. Manolson M.F. Poole R.J. Date T. Oshima T.
TitleEvolution of the vacuolar H+-ATPase: implications for the origin of eukaryotes.
SourceProc. Natl. Acad. Sci. U.S.A. 86:6661-6665(1989).
PubMed ID2528146

5AuthorsDreyfus G. Williams A.W. Kawagishi I. Macnab R.M.
TitleGenetic and biochemical analysis of Salmonella typhimurium FliI, a flagellar protein related to the catalytic subunit of the F0F1 ATPase and to virulence proteins of mammalian and plant pathogens.
SourceJ. Bacteriol. 175:3131-3138(1993).
PubMed ID8491729

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