GAL4 is a protein commonly found in yeast that is an active participant of transcription of genes required for catabolism of galactose. The protein binds to DNA and then actively recruits RNA polymerase to the promoter region of the DNA. The DNA binds as a symmetrical diamer as can be seen above in the model. Each subunit contains a zinc ion, which is the metal binding domain. The zinc ion is coordinated by six cystine amino acids. The metal ion forms the metal binding domain, which lies in the major groove. It is therefore called the recognition module. The diamer binds to DNA at a site that is about 17 base pairs long and has a consensus sequence of CCG at each end. This means that the consensus sequences lie about one and a half turns away from each other.
To view the two dimers and the DNA strand in separate colors click the following button.
To more easily view the protein-DNA complex as a cartoon view click the button below
A better way to visualize the overall structure of the protein-DNA complex is via the spacefilling model.
In this view only the hydrogen bonds within the alpha helices of the protein are shown. The hydrogen bonds between the protein and the DNA and within the DNA double helix are not visible. This may be because many of the hydrogen bonds between the Gal4 protein and DNA are facilitated by water. Since there are no water molecules in this rendition, the hydrogen bond interactions are not displayed.
Click the following button to remove DNA and view a single dimer of the Gal4 protein.
By viewing one dimer of Gal4, the helices of the protein are more apparant. One monomer binds to the other monomer at the top of the protein to form a cross-link. This cross-linkage occurs above the minor groove of the DNA strand. The active site seen here at the bottom of the protein binds within the major grove of the DNA to the concensus sequence CCG. This binding occurs via the zinc binding domain. The zinc binding is similar to the zinc-finder.