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* ATP synthase alpha and beta subunits signature *
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ATP synthase (proton-translocating ATPase) (EC 3.6.1.34) [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,  alpha,  beta,  gamma,  delta  and  epsilon.  The
sequences of   subunits  alpha  and  beta  are  related  and  both  contain  a
nucleotide-binding site  for  ATP  and  ADP.  The  alpha  chain  has catalytic
activity, while the beta 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 beta subunit, while a 60 Kd subunit, from the same sector, is related
to the F-ATPases alpha subunit [4].

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

A protein  highly  similar  to  F-ATPase  beta  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  and HrpB6 in
Xanthomonas campestris.

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 alpha chain at
least - as its mutagenesis causes catalytic impairment.

-Consensus pattern: P-[SAP]-[IV]-[DNH]-x(3)-S-x-S
                    [The first S is a putative active site residue]
-Sequences known to belong to this class detected by the pattern: ALL,  except
 for the  archaebacterium  Sulfolobus  acidocaldarius ATPase alpha chain where
 the first Ser is replaced by Gly.
-Other sequence(s) detected in SWISS-PROT: 10.

-Note: F-ATPase  alpha  and  beta  subunits,  V-ATPase  70  Kd subunit and the
 archaebacterial ATPase alpha  subunit also  contain a copy of the ATP-binding
 motifs A and B (see the relevant section).

-Last update: June 1994 / Pattern and text revised.

[ 1] Futai M., Noumi T., Maeda M.
     Annu. Rev. Biochem. 58:111-136(1989).
[ 2] Senior A.E.
     Physiol. Rev. 68:177-231(1988).
[ 3] Nelson N.
     J. Bioenerg. Biomembr. 21:553-571(1989).
[ 4] Gogarten J.P., Kibak H., Dittrich P., Taiz L., Bowman E.J., Bowman B.J.,
     Manolson M.F., Poole R.J., Date T., Oshima T., Konishi J., Denda K.,
     Yoshida M.
     Proc. Natl. Acad. Sci. U.S.A. 86:6661-665(1989).
[ 5] Dreyfus G., Williams A.W., Kawagishi I., MacNab R.M.
     J. Bacteriol. 175:3131-3138(1993).