Crystal structure of yeast V1-ATPase in the autoinhibited state

Vacuolar ATPases (V-ATPases) are essential proton pumps that acidify the lumen of subcellular organelles in all eukaryotic cells and the extracellular space in some tissues. V-ATPase activity is regulated by a unique mechanism referred to as reversible disassembly, wherein the soluble catalytic sector, V-1, is released from the membrane and its MgATPase activity silenced. The crystal structure of yeast V-1 presented here shows that activity silencing involves a large conformational change of subunit H, with its C-terminal domain rotating similar to 150 degrees from a position near the membrane in holo V-ATPase to a position at the bottom of V-1 near an open catalytic site. Together with biochemical data, the structure supports a mechanistic model wherein subunit H inhibits ATPase activity by stabilizing an open catalytic site that results in tight binding of inhibitory ADP at another site.