Background
Gal4p is a transcriptional activator in Saccharomyces cerevisiae that regulates the expression of genes to coordinate the response to the carbon source galactose.
Gal4p is an 881-amino-acid protein with a Zn cluster-type DNA-binding domain, a linker domain, a dimerization domain, and two acidic activation domains.
The structure of the DNA-binding domain(1d66), the dimerization domain (1hbw), and the activation domain (3bts) has been solved separately. There is a structure of the DNA-binding and dimerization domains as one unit as well (3coq).
Pioneering studies on Gal4p from the Ptashne laboratory shaped our understanding of eukaryotic transcriptional activation, and Gal4p derivatives, along with their cognate promoters, continue to be used as tools by investigators preforming research in yeast.
DNA Recognition by Gal4p
Each monomer of the protein dimer has 3 alpha helices.
The protein binds as a dimer to a symmetrical 17-base-pair sequence. Specifically, the consensus Gal4p-binding site is a 17-mer of sequence conforming to the motif below, which has the key feature of CGG triplets at the 5' ends, separated by 11 bps, or 5′-CGG-N11-CCG-3′.
5'-CGGNNNNNNNNNNNCCG-3'
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3'-CGGNNNNNNNNNNNGGC-5'
The DNA binding domain uses six Cys residues to coordinate the binding of two ions of zinc (Zn(II)). (In the crystal structure 1d66, the zinc ions are actually represented by other members of the same group on the periodic table, the heavier cadmium ions.) The Zn-binding motif lets the structure accomplish more with fewer amino acids, the metals lending an "economy of structure", arranging two small helices to recognize a specific DNA site. Two lysines (17 and 18) make direct base contacts in the DNA major groove with the specified CGG triplets.
A C G T
Despite only making base-specific contacts at the ends, Ga14p is mostly in contact with the DNA for its entire span of the binding site.
The third, large helix of each dimer subunit interacts with the other by arranging hydrophobic residues in the contact region. Note the abundance of gray residues in the central stem protruding from a site roughly above the center of the DNA binding site. The dimer interface is more fully explored in a later publication with an expanded structure, see 3coq.
The conformation of the linker connecting each dimerization helix and the metal-binding domains determines the preferred total number of bases between the triplets.
