The amino acid sequence of all but a few N-terminal residues of the β subunit of rat liver ATP synthase has been determined from cDNA clones. Rat liver F1-β is shown to contain 17 amino acid differences from that reported for F1-β of bovine heart, 2 differences of which involve differences in charge. This may account in part for the observation that bovine heart F1binds nucleotides with much greater affinity than the rat liver enzyme. Rat liver F1-β also contains homologous regions with another nucleotide binding protein, adenylate kinase, for which high-resolution structural studies are available. Adjacent to one of these homologous regions is an eight amino acid stretch which bears striking homology to the phosphorylation region of the (Na+,K+)-ATPase. The combination of these two homology regions may constitute at least part of a nucleotide binding domain in F1-β. Significantly, both rat liver and bovine heart β contain these regions of homology, whereas the 17 amino acid differences between the two enzymes lie outside this region. The possibility of a second nucleotide binding domain which differs between the two enzymes is discussed. A cDNA clone containing all the regions of homology as well as 11 of the 17 amino acid differences between the bovine heart and rat liver β subunits has been ligated into the bacterial expression vector pKK223-3. After transformation of a protease-deficient strain of Escherichia coli, this cDNA clone is expressed as a 36-kilodalton protein. Finally, further cDNA library screening and primer extension analysis using several oligonucleotide probes generated cDNAs which always terminated prior to that region of the β gene coding for the N-terminal region. A strong secondary structure of regulatory significance may, therefore, be a unique characteristic of the rat liver mRNA coding for the F1-β subunit in this region.
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