Crystal structure of PHO4 bHLH domain-DNA complex: Flanking base recognition

The crystal structure of a DNA-binding domain of PHO4 complexed with DNA at 2.8 Angstrom resolution revealed that the domain folds into a basic-helix-loop-helix (bHLH) motif with a long but compact loop that contains a short alpha-helical segment, This helical structure positions a tryptophan residue into an aromatic cluster so as to make the loop compact, PHO4 binds to DNA as a homodimer with direct reading of both the core E-box sequence CACGTG and its 3'-flanking bases, The 3'-flanking bases GG are recognized by Arg2 and His5, The residues involved in the E-box recognition are Bis5, Glu9 and Arg13, as already reported for bHLH/Zip proteins MAX and USF, and are different from those recognized by bHLH proteins MyoD and E47, although PHO4 is a bHLH protein.