The molecular description of the mechanism of F 1 -ATPase is based mainly on high-resolution structures of the enzyme from mitochondria, coupled with direct observations of rotation in bacterial enzymes. During hydrolysis of ATP, the rotor turns counterclockwise (as viewed from the membrane domain of the intact enzyme) in 120°steps. Because the rotor is asymmetric, at any moment the three catalytic sites are at different points in the catalytic cycle. In a "ground-state" structure of the bovine enzyme, one site (β E ) is devoid of nucleotide and represents a state that has released the products of ATP hydrolysis. A second site (β TP ) has bound the substrate, magnesium. ATP, in a precatalytic state, and in the third site (β DP ), the substrate is about to undergo hydrolysis. Three successive 120°turns of the rotor interconvert the sites through these three states, hydrolyzing three ATP molecules, releasing the products and leaving the enzyme with two bound nucleotides. A transition-state analog structure, F 1 -TS, displays intermediate states between those observed in the ground state. For example, in the β DP -site of F 1 -TS, the terminal phosphate of an ATP molecule is undergoing in-line nucleophilic attack by a water molecule. As described here, we have captured another intermediate in the catalytic cycle, which helps to define the order of substrate release. In this structure, the β E -site is occupied by the product ADP, but without a magnesium ion or phosphate, providing evidence that the nucleotide is the last of the products of ATP hydrolysis to be released.catalytic mechanism | magnesium release | nucleotide release H igh-resolution structures of F 1 -ATPase from bovine heart and yeast mitochondria have provided the molecular basis for the catalytic mechanism of ATP synthesis and hydrolysis by F 1 F oATPase (1-10). During ATP synthesis, a mechanical rotation of the γ-subunit driven by the transmembrane proton-motive force, exerted on a ring of C-subunits in the F o membrane domain of the intact enzyme, takes each of the three β-subunits in its catalytic domain through the states represented by the β TP -, β DP -, and β Esubunits, thereby synthesizing three ATP molecules during each 360°rotation (1, 11). Hydrolysis of ATP reverses the direction of rotation, and protons are ejected from the mitochondrial matrix into the intermembrane space through the F o domain of the enzyme (12, 13). The rotation of the γ-subunit is not continuous, but it proceeds in 120°steps consisting of 90°and 30°substeps (14). The ground-state structure of F 1 -ATPase (denoted F 1 -GS) probably represents the state of the enzyme at the end of the complete 120°rotary step.Attempts have been made to access structures that represent conformations of β-subunits that are intermediate between the three conformations in the ground-state structure by inhibiting the enzyme in various ways. However, many of the inhibitors arrest the catalytic cycle in the ground state (15-17), except that the natural inhibitor protein IF 1 arrests bovine F ...