Detailed analysis of the basic domain of the E2F1 transcription factor indicates that it is unique among bHLH proteins.

The E2F1 transcription factor binds to sites within the promoters of a number of cell cycle regulated genes through a basic-helix-loop-helix motif (bHLH). It is shown here that the basic region of E2F1 is distinct from that of all other bHLH proteins. The center of the basic region contains a helix breaking proline-glycine pair, (P122, G123), implying a turn within this region. This is in contrast to the known bHLH containing proteins where the basic region is alpha-helical. Substitution of P122 and G123 with alanines results in a significant reduction in DNA binding levels, with the predicted formation of an alpha-helix. Also in contrast to other bHLH proteins, mutations generated in conserved basic residues of E2F1 do not effect DNA binding. In addition, a single leucine (191) between helix no. 2 and the leucine zipper is required for DNA binding while the leucine zipper itself is not necessary. Finally, E2F1 interacts with all of the G-residues in the sequence GGCGGGAAA while the A-residues are not required for DNA binding. The uniqueness of the E2F1 DNA binding domain is likely to play a role in its binding a DNA site that is distinct from that of all other bHLH proteins (CACGTG).