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The vacuole-type ATPases (V-ATPases) exist in various intracellular compartments of eukaryotic cells to regulate physiological processes by controlling the acidic environment. The crystal structure of the subunit C of Thermus thermophilus V-ATPase, homologous to eukaryotic subunit d of V-ATPases, has been determined at 1.95-Å resolution and located into the holoenzyme complex structure obtained by single particle analysis as suggested by the results of subunit cross-linking experiments. The result shows that V-ATPase is substantially longer than the related F-type ATPase, due to the insertion of subunit C between the V₁ (soluble) and the V_o (membrane bound) domains. Subunit C, attached to the V_o domain, seems to have a socket like function in attaching the central-stalk subunits of the V₁ domain. This architecture seems essential for the reversible association/dissociation of the V₁ and the V_o domains …