The vacuolar membrane ATPase (V-ATPase) 1 of the yeast Saccharomyces cerevisiae belongs to the vacuolar-type (V-type) proton pump (1-7). The V-type ATPase acidifies various endomembrane organelles in eucaryotic cells, including the Golgi apparatus, lysosomes, coated vesicles, and chromaffin granules (8). This type of proton pump is also found in the plasma membrane of certain specialized cells (9). Organelle acidification and/or membrane energization by the V-type ATPase is important for such processes as receptor-mediated endocytosis, protein sorting, zymogen activation, and solute uptake into a specific organelle (8,10,11).The V-type ATPase consists of two structural domains, V 1 and V 0 , both of which are composed of several different subunits (4,7,12). The peripheral V 1 domain possesses the nucleotide binding site(s) required for ATP hydrolysis (5,7,12,13). The integral V 0 domain translocates protons across the membrane and anchors the peripheral V 1 domain to the membrane (4, 7, 12). The yeast V-ATPase is composed of at least seven V 1 subunits (69, 60,54,42,32,27, and 14 kDa) and three V 0 subunits (100, 36, and 17 kDa) (14 -26). The 36-kDa subunit is not an integral membrane protein but stably associates with the V 0 subcomplex and thus is considered to be a nonintegral component of the V 0 domain (20,27). Recently, another essential subunit of 13 kDa was identified (28). The membrane disposition of this subunit has not yet been unambiguously determined.Yeast cells also express genes that encode proteins with sequence similarity to the 100-kDa (Vph1p) and the 17-kDa (Vma3p) 2 V-ATPase subunits (29 -31). STV1 encodes a polypeptide of 102 kDa with 54% amino acid identity to Vph1p (14,29). Stv1p is localized to nonvacuolar membranes, possibly endosomal and/or Golgi membrane, and is not required for vacuolar membrane V-ATPase activity. Overexpression of Stv1p induces mislocalization of this protein to the vacuolar membrane and can partially complement the phenotypes associated with the loss of V-ATPase activity in ⌬vph1 mutant cells (29). From these observations, it has been proposed that yeast cells possess another V-type ATPase acidifying organelles (containing Stv1p) other than vacuoles and that the 100-kDa subunit isoforms are responsible for targeting of the V-type ATPases to different organelles (29).VMA11 and VMA16 genes can encode polypeptides of 17 and