The soluble portion of the Escherichia coli F 1 F 0 ATP synthase (ECF 1 ) and E. coli F 1 F 0 ATP synthase (ECF 1 F 0 ) have been isolated from a novel mutant ␥Y205C. ECF 1 isolated from this mutant had an ATPase activity 3.5-fold higher than that of wild-type enzyme and could be activated further by maleimide modification of the introduced cysteine. This effect was not seen in ECF 1 F 0 . The mutation partly disrupts the F 1 to F 0 interaction, as indicated by a reduced efficiency of proton pumping. ECF 1 containing the mutation ␥Y205C was bound to the membrane-bound portion of the E. coli F 1 F 0 ATP synthase (ECF 0 ) isolated from mutants cA39C, cQ42C, cP43C, and cD44C to reconstitute hybrid enzymes. Cu Cross-linking of ␥ to ⑀ had only a minimal effect on ATP hydrolysis. The reactivity of the Cys at ␥ 205 showed a nucleotide dependence of reactivity to maleimides in both ECF 1 and ECF 1 F 0 , which was lost in ECF 1 when the ⑀ subunit was removed. Our results show that there is close interaction of the ␥ and ⑀ subunits for the fulllength of the stalk region in ECF 1 F 0 . We argue that this interaction controls the coupling between nucleotide binding sites and the proton channel in ECF 1 F 0 .F 1 F 0 type ATP synthases play a key role in oxidative phosphorylation and photophosphorylation. The F 1 , which can be detached from the F 0 and studied separately, is a complex of five different types of subunits called ␣, , ␥, ␦, and ⑀ that are present in the molar ratio 3:3:1:1:1. The F 0 part in the Escherichia coli enzyme is composed of three different subunits: a, b, and c in the molar ratio 1:2:10 -12 (1-4). Electron microscopy first showed that the ␣ and  subunits are arranged hexagonally and alternate around a central cavity in which the ␥ subunit is located (5-7). Biochemical studies place the ⑀ subunit (nomenclature for the E. coli enzyme) at the bottom of the ␣ 3  3 ␥ core complex (4, 8) in the stalk region, which is a 40 -45-Å-long structure that links the F 1 to the F 0 part (9, 10).The recently published high resolution structure of a major part of the beef heart F 1 molecule confirms the above-described arrangement of the ␣, , and ␥ subunits and adds important details (11). In particular, it shows the ␥ subunit arranged with a long C-terminal ␣-helix extending from the top of the ␣ and  subunits into the stalk region. A shorter N-terminal ␣-helix is also present, running from the catalytic site region into the stalk region. These two ␣ helices form a coiled coil. A third short ␣-helix of the ␥ subunit (residues 83-99 in the E. coli sequence) is inclined at about 45°to the two larger helices at the bottom of the F 1 as it becomes the stalk. Approximately half of the ␥ subunit is unresolved in the structure, presumably because it is disordered in the crystal form.Recently, we observed cross-linking between a Cys introduced at position 44 of the polar loop of the c subunits and a site or sites on the ␥ subunit in the region between residues 202 and 230 (12). This result implies that the ␥ subunit exte...