Mutant bZip-DNA complexes with four quasi-identical protein-DNA interfaces.EMBO J. 1996 Feb 01; 15(3):598-606.EJ
The complex between the yeast transcriptional activator GCN4 and the palindromic ATF/CREB site 5'- A4T3G2A1C0*G0'T1'C2'A3'T4'-3' shows dyad symmetry. The basic region of GCN4 contains a segment of 18 amino acids with a partially palindromic sequence: N-LKRARNTEA*ARRSRARKL-C. Symmetric residues are underlined. Apart from the ATF/CREB site, GCN4 also binds well to the symmetric variants with guanine in position 4 (5'-G4T3G2A1C0*G0'T1'C2'A3'C4'-3') or thymine in position 0 (5'-A4T3G2A1T0*A0'T1'C2'A3'T4'-3'). The half-sites of these sequences can be regarded as short pseudo-palindromes with central guanine 2/cytosine 2' base pairs. We investigated whether the geometry of the peptide of the basic region of GCN4 could be functionally related to the pseudo-palindromic character of some target half-sites. Since inspection of the X-ray structures of GCN4-DNA complexes reveals that several amino acid-DNA interactions are symmetric within the wild-type half-complexes, we introduced mutations into a GCN4 bZip peptide that improve the symmetry of the peptide. We found that most of the constructs retain specific DNA recognition. For one mutant, we conclude that it is not only capable of forming DNA complexes showing the well-known overall dyad symmetry, but that the protein-DNA interface of each half-complex can be divided further into two quasi-identical, quasi-symmetric substructures.