The 3 × 120° rotary mechanism of Paracoccus denitrificans F(1)-ATPase is different from that of the bacterial and mitochondrial F(1)-ATPases

The rotation of Paracoccus denitrificans F(1)-ATPase (PdF(1)) was studied using single-molecule microscopy. At all concentrations of adenosine triphosphate (ATP) or a slowly hydrolyzable ATP analog (ATPγS), above or below K(m), PdF(1) showed three dwells per turn, each separated by 120°. Analysis of dwell time between steps showed that PdF(1) executes binding, hydrolysis, and probably product release at the same dwell. The comparison of ATP binding and catalytic pauses in single PdF(1) molecules suggested that PdF(1) executes both elementary events at the same rotary position. This point was confirmed in an inhibition experiment with a nonhydrolyzable ATP analog (AMP-PNP). Rotation assays in the presence of adenosine diphosphate (ADP) or inorganic phosphate at physiological concentrations did not reveal any obvious substeps. Although the possibility of the existence of substeps remains, all of the datasets show that PdF(1) is principally a three-stepping motor similar to bacterial vacuolar (V(1))-ATPase from Thermus thermophilus. This contrasts with all other known F(1)-ATPases that show six or nine dwells per turn, conducting ATP binding and hydrolysis at different dwells. Pauses by persistent Mg-ADP inhibition or the inhibitory ζ-subunit were also found at the same angular position of the rotation dwell, supporting the simplified chemomechanical scheme of PdF(1). Comprehensive analysis of rotary catalysis of F(1) from different species, including PdF(1), suggests a clear trend in the correlation between the numbers of rotary steps of F(1) and F(o) domains of F-ATP synthase. F(1) motors with more distinctive steps are coupled with proton-conducting F(o) rings with fewer proteolipid subunits, giving insight into the design principle the F(1)F(o) of ATP synthase.