Vacuolar ATPase (V-ATPase) of Enterococcus hirae is composed of a soluble functional domain V-1 (A(3)B(3)DF) and an integral membrane domain V-o (ac), where V1 and Vo domains are connected by a central stalk, composed of D-, F-, and d-subunits; and two peripheral stalks (E-and G-subunits). We identified 120 interacting residues of A(3)B(3) heterohexamer with D-subunit in DF heterodimer in the crystal structures of A(3)B(3) and A(3)B(3)DF. In our previous study, we reported 10 mutants of E. hirae V-1-ATPase, which showed lower binding affinities of DF with A(3)B(3) complex leading to higher initial specific ATPase activities compared to the wild-type. In this study, we identified a mutation of A-subunit (LV(476-7)AA) at its C-terminal domain resulting in the A(3)B(3) complex with higher binding affinities for wild-type or mutant DF heterodimers and lower initial ATPase activities compared to the wild-type A(3)B(3) complex, consistent with our previous proposal of reciprocal relationship between the ATPase activity and the protein-protein binding affinity of DF axis to the A(3)B(3) catalytic domain of E. hirae V-ATPase. These observations suggest that the binding of DF axis at the contact region of A(3)B(3) rotary ring is relevant to its rotation activity.