Transcription of the vacuolar aminopeptidase yscI (APE1) gene in Saccharomyces cerevisiae has previously been suggested to require the participation of a cis upstream activation sequence (UAS) involved in carbon catabolite repression that responds to glucose. To determine the structure of the APE1 UAS element, we used the 18-bp sequence 5'-ATGAATTAGTCAGCTTCT-3' as the DNA-binding site. Using gel mobility shift assays, we have identified a 78 kDa protein from yeast that binds specifically to both single and double-stranded forms of the UAS DNA-binding site. We have also identified a 48 kDa heterodimer from yeast that binds specifically to the single-stranded form of the UAS and whose DNA binding activity is remarkably heat stable. Even though the APE1 UAS contains a consensus sequence for the binding of the yeast activator protein yAP1, the two DNA-protein complexes could still be detected in a strain bearing a deletion in the YAP1 gene.