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), which acts as a proton channel, and a catalytic core, termed coupling factor CF(1).

The CF(0) c subunit (also called protein 9, proteolipid, or subunit III) [3,4] is a highly hydrophobic protein of about 8 Kd which has been implicated in the proton-conducting activity of ATPase. Structurally subunit c consist of two long terminal hydrophobic regions, which probably span the membrane, and a central hydrophilic region. N,N'-dicyclohexylcarbodiimide (DCCD) can bind covalently to subunit c and thereby abolish the ATPase activity. DCCD binds to a specific glutamate or aspartate residue which is located in the middle of the second hydrophobic region near the C-terminus of the protein.

We derived a signature pattern which includes the DCCD-binding residue.