ATP synthase of yeast: structural insight into the different inhibitory potencies of two regulatory peptides and identification of a new potential regulator

Mitochondrial ATP synthases, the major producers of ATP in higher eukaryotic cells, are known to be regulated by a peptide designated IF1. In contrast, in yeast three such peptides have been identified, IF1 and STF1, which inhibit the reverse ATPase reaction, and STF2, a modulator of the action of these inhibitors. Despite significant homology to IF1, STF1 exhibits less than half (∼40%) its inhibitory potency. The two-fold purpose of this bioinformatic study was to gain structural insight into the different inhibitory potencies of IF1 and STF1 and to determine to what extent yeast are unique in employing multiple peptides to regulate the ATP synthase. Sequence and secondary structural analyses and comparison with the known structure of bovine IF1 predicted a dimeric structure for yeast STF1 in which the C-terminal regions form a coiled-coil. Moreover, sequence comparisons showed that within this C-terminal region a conserved acidic residue (Asp 59) in yeast IF1 is replaced by Asn in STF1. In the known structure of bovine IF1, predicted to be very similar to that of yeast IF1, the residue Glu 68 corresponding to Asp 59 participates in the formation of a four-residue conserved acidic cluster in the middle of the coiled-coil in the C-terminal region. It is deduced here that this acidic cluster is likely to be important in the regulation of IF1ʹs inhibitory capacity and that replacement of conserved Asp 59 by Asn in STF1 may reduce its potency. Although other homologs to the inhibitors IF1 and STF1 were not found in searches of available eukaryotic genomes, including human, a new homolog, named STF3, with 65% identity to the modulator STF2, was discovered within the yeast genome and identified to be expressed by searching the yeast EST database. Thus, yeast appears unique in regulating the ATP synthase by involving multiple peptides (IF1, STF1, STF2, and perhaps STF3).