Contacts of the ABF1 protein of Saccharomyces cerevisiae with a DNA binding site at MATa.

The ABF1 protein of Saccharomyces cerevisiae is a multifunctional DNA-binding protein that is required for cell viability. The ABF1 protein has previously been shown to bind to a number of yeast sequences having a consensus of: 5'-A/G TC A/G C/T C/T NNNNACG-3'. A heretofore undiscovered ABF1-binding site was found in the MATa region. We have used missing contact analysis of this ABF1-binding site to show that removal of the conserved bases, as well as of some bases which are not conserved, reduces binding. We have probed contacts of ABF1 with the DNA-binding site using dimethyl sulfate and potassium permanganate and find that the protein makes extensive contacts with both the major and minor grooves. Ethylation interference studies indicate that numerous phosphate contacts are also important for ABF1 binding. Interference studies indicate that the ABF1 protein is also in close proximity to the DNA that is 5' and 3' of the conserved bases of the binding site. The extensive DNA contacts exhibited by ABF1 may play a role in the protein-induced bending of the DNA target (McBroom, L. D. B., and Sadowski, P. D. (1994) J. Biol. Chem. 169, 16461-16468).