The catalytic nucleotide binding subunit (subunit A) of the vacuolar proton-translocating ATPase (or V-ATPase) is homologous to the -subunit of the F-ATPase but contains a 90-amino acid insert not present in the -subunit, termed the nonhomologous region. We previously demonstrated that mutations in this region lead to changes in coupling of proton transport and ATPase activity and to inhibition of in vivo dissociation of the V-ATPase complex, an important regulatory mechanism (Shao, E., Nishi T., Kawasaki-Nishi, S., and The vacuolar proton-translocating ATPases (V-ATPases) 1 are a family of ATP-dependent proton pumps that couple the hydrolysis of ATP to proton movement across the membrane (1-8). This proton movement results in acidification of intracellular compartments, which in turn is critical for cellular processes such as receptor-mediated endocytosis, the processing and degradation of macromolecules, intracellular trafficking of lysosomal enzymes, coupled transport of small molecules, and entry of certain envelope viruses (1). For certain specialized cells such as renal intercalated cells, osteoclasts, macrophages, and insect goblet cells, V-ATPases are present on the plasma membrane and function in processes such as renal acidification, bone resorption, pH homeostasis, and coupled potassium transport (9 -12).The V-ATPases are multisubunit complexes composed of two functional domains (1-8). The soluble V 1 domain is responsible for ATP hydrolysis and contains eight different subunits (subunits A-H) with molecular masses 70 -13 kDa. The integral V 0 domain is responsible for proton translocation and contains six different subunits (subunits a, d, e, c, cЈ, and cЉ) with molecular masses of 100 -10 kDa. The 10-kDa subunit e, previously identified in bovine and insect (13,14), has recently been shown to be essential for function of the yeast V-ATPase (15). Both the 70-kDa A subunit and the 60-kDa B subunit of V 1 possess nucleotide binding sites (16,17), with the catalytic nucleotide binding sites located on subunit A (18). The V-ATPases structurally resemble the F-ATPases (proton-driven ATP synthases) of mitochondria, chloroplasts, and bacteria (19 -23). The A and B subunits of the V-ATPases share ϳ25% amino acid sequence identity with the -and ␣-subunits of the F-ATPases, respectively (24 -28). Sequence alignment of the A subunit and the -subunit reveals a 90-amino acid region (termed the nonhomologous domain), which is present in the A subunit but which is absent from the -subunit (24 -27). Although not conserved between the V and F-ATPases, this region is highly conserved among V-ATPase A subunit sequences (24 -27).We have previously demonstrated by site-directed mutagenesis of the VMA1 gene that encodes subunit A in yeast that changes in the nonhomologous domain can alter coupling of proton transport and ATPase activity (29). We have also observed that mutations in this domain are able to block in vivo dissociation of the V-ATPase in response to glucose depletion (29). Reversible dissociation of the ...