Single amino acid substitutions alter helix-loop-helix protein specificity for bases flanking the core CANNTG motif.

While all basic region/helix-loop-helix (bHLH) proteins bind the consensus CANNTG motif, other factors must be involved in determining regulatory specificity. In this report we show that bases outside this core 6 bp are involved in determining the specificity of binding. Thus, binding of the yeast bHLH protein PHO4, but not CPF-1, is inhibited by the presence of a T residue immediately 5' to their common CACGTG recognition sequence. PHO4 binding specificity is altered by mutation at any of three different positions in the basic region, including a single Glu to Asp substitution. The significance of these data for DNA-binding and transcription regulation by the bHLH family of transcription factors is discussed.