The newly identified specific V-ATPase inhibitor, salicylihalamide A, is distinct from any previously identified V-ATPase inhibitors in that it inhibits only mammalian V-ATPases, but not those from yeast or other fungi (Boyd, M. R., Farina, C., Belfiore, P., Gagliardi, S., Kim Acidification of intracellular compartments of eukaryotes is essential for many cellular processes, including receptor-mediated endocytosis, protein degradation in lysosomes, processing of hormones, uptake, and storage of neurotransmitters, and entry of many viruses into cells. The control of pH within these intracellular compartments is mediated by vacuolar H ϩ -translocating ATPases, which acidify organelles of both constitutive and regulated secretory pathways (1-5). V-ATPases 1 are also found in the plasma membrane of certain cells where they are responsible for cell type-specific processes, including urinary acidification and osteoclast-mediated bone resorption (6, 7). The V-type ATPases are among the most widely distributed ATP-driven ion pumps in nature, present in all eukaryotic cells and in various bacteria. Within eukaryotic cells, the structure of these proton pumps is highly conserved from yeast to human, as a multiple subunit complex with a molecular mass exceeding 850 kDa. They contain at least 13 different subunits with various copy numbers, which are organized into two distinct domains, a peripheral V 1 domain that is the catalytic sector and a transmembrane V 0 domain that constitutes the proton channel.V-pumps are regulated at various levels from transcription and protein synthesis to the regulation of its enzymatic activity through a variety of mechanisms. The most unique regulation mechanism for V-pumps is the reversible dissociation and association of V 1 and V 0 in response to energy demand, which has been extensively studied and clearly demonstrated in yeast and tobacco hornworm (8 -10). However, whether this reversible dissociation and association of V-ATPase domains exists in mammals as a regulatory mechanism and, if it does, how this process is regulated, is not clear at the present.During the past two decades, the importance of this class of ATPases for many critical cellular functions has become increasingly appreciated. Furthermore, the elucidation of the physiological role of V-pumps has revealed the important role these proteins play in a wide array of pathological processes, such as osteoporosis (6), certain renal diseases (7, 11), HIV infection (12), and tumor metastasis (5). The food vacuole of certain parasites is acidified by V-type proton pumps, and disruption of the acidification of this intracellular compartment results in death of the organism. Thus, the V-type pumps are potential targets for the development of pharmacological agents to treat a variety of diseases.Because of the importance of V-ATPases as a potential therapeutic target, the mechanism by which inhibitors of V-ATPase interfere with pump function has become an area of great scientific interest. Over the past 15 years a few specific VATP...