A novel feature of DNA recognition: A mutant Gcn4p bZip peptide with dual DNA binding specificities dependent of half-site spacing

Homodimeric DNA-binding proteins with relaxed half-site spacing requirement s for their DNA targets have been described. As an example, the yeast trans criptional activator Gcn4p binds in vitro equally well to the AP1 site (5'A (4)T(3)G(2)A(1)C(0)T(1')C(2')A(3')T(4')3') and the ATF/CREB site (5'A(4)T(3 )G(2)A(1)C(0)G(0')T(1')C(2')A(3')T(4')3'), which have identical but differe ntly spaced half-site blocks. We describe a novel feature for the bZip clas s of DNA-binding proteins. The N-14: mutant of a Gcn4p-derived bZip peptide shows a diametrically opposed base-pair recognition specificity depending on the half-site spacing of its DNA target: on pseudo-palindromic, AP1 site -like binding sites, guanine is required in position 2 for proper binding; in contrast, on palindromic, ATF/CREB site-like targets, position 2 must be cytosine to prevent a loss of binding. Modeling studies suggest that the d ifferent base-pair requirements on differently spaced DNA targets are due t o minimal alterations of the distances between the relevant atoms of the N- 14 side-chain and the corresponding target groups on the DNA. Although the N-14 peptide does not have a natural counterpart, its behavior hints at the possibility that dual binding modi dependent on half-site spacing may occu r also for natural homodimeric DNA-binding proteins. (C) 1999 Academic Pres s.