Tentoxin, a natural cyclic tetrapeptide produced by phytopathogenic fungi from the Alternaria species affects the catalytic function of the chloroplast F-1-ATPase in certain sensitive species of plants. In this study, we show that the uncompetitive inhibitor tentoxin binds to the alphabeta-interface of the chloroplast F-1-ATPase in a cleft localized at betaAsp-83. Most of the binding site is located on the noncatalytic a-subunit. The crystal structure of the tentoxin-inhibited CF1-complex suggests that the inhibitor is hydrogen bonded to Asp-83 in the catalytic beta-subunit but forms hydrophobic contacts with residues Ile-63, Leu-65, Val-75, Tyr-237, Leu-238, and Met-274 in the adjacent a-subunit. Except for minor changes around the tentoxin-binding site, the structure of the chloroplast alpha(3)beta(3)-core complex is the same as that determined with the native chloroplast ATPase. Tentoxin seems to act by inhibiting intersubunit contacts at the alphabeta-interface and by blocking the interconversion of binding sites in the catalytic mechanism.