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The ϵ subunit of bacterial and chloroplast FoF1-ATP synthases modulates their ATP hydrolysis activity. Here, we report the crystal structure of the ATP-bound ϵ subunit from a thermophilic Bacillus PS3 at 1.9-Å resolution. The C-terminal two α-helices were folded into a hairpin, sitting on the β sandwich structure, as reported for Escherichia coli. A previously undescribed ATP binding motif, I(L)DXXRA, recognizes ATP together with three arginine and one glutamate residues. The E. coli e subunit binds ATP in a similar manner, as judged on NMR. We also determined solution structures of the C-terminal domain of the PS3 ϵ subunit and relaxation parameters of the whole molecule by NMR. The two helices fold into a hairpin in the presence of ATP but extend in the absence of ATP. The latter structure has more helical regions and is much more flexible than the former. These results suggest that the ϵ C- terminal domain can undergo an arm-like motion in response to an ATP concentration change and thereby contribute to regulation of FoF1-ATP synthase [ABSTRACT FROM AUTHOR]