Effect of epsilon subunit on the nucleotide binding to the catalytic sites of F-1-ATPase from the thermophilic Bacillus PS3 (TF1) has been tested by using alpha(3)beta(3)gamma and alpha(3)beta(3)gamma epsilon complexes of TF1 containing beta Tyr341 to Trp substitution. The nucleotide binding was assessed with fluorescence quenching of the introduced Trp. The presence of the E subunit weakened ADP binding to each catalytic site, especially to the highest affinity site. This effect was also observed when GDP or IDP was used. The ratio of the affinity of the lowest to the highest nucleotide binding sites had changed two orders of magnitude by the c subunit. The differences may relate to the energy required for the binding change in the ATP synthesis reaction and contribute to the efficient ATP synthesis. (C) 2009 Elsevier Inc. All rights reserved.