3D Structure of Gal4

CPK Color Scheme

On this page, you can see a portion of the Gal4 homodimer bound to a double-stranded DNA molecule. Gal4 is a transcription factor that is involved in galactose metabolism (1). To function, Gal4 binds DNA in a sequence specific manner and activates transcription (1). While it spins, notice the two macromolecules: the protein (blue) and the DNA (red).

Reset this protein-DNA complex.

Notice the similarity between the two amino acid chains (blue and green).  The Gal4 transcription factor binds DNA as a homodimer (two identical subunits form a complex that binds the DNA molecule).  This feature of Gal4 is essential to function (1). 

Look closely at the DNA-binding domain (residues 7-40, Orange).  Gal4 interacts with the DNA with this short DNA-binding motif.  Notice the way the ends of the Gal4 molecule fit into the major grooves of the DNA. 

Look closely at the interaction with DNA.  Notice the zinc ions (green) that are present!  Gal4 has a DNA-binding motif that is known as a zinc-finger motif, due to the presence of zinc ions in the complex (1).  Zinc fingers are one of many DNA binding motifs that have been identified (2). 

How many base pairs does this protein recognize?  Although this Gal4 molecule is bound to a 20 base pair sequence of DNA, studies have shown that it recognizes a specific 17 base pair sequence (3 of the base pairs shown here are therefore not nocessary for recognition) (1). 

Also notice the molecule (white) that is situated between the protein and DNA.  This molecule is known as MPD, or methyl-pentadiol.  It is a commonly used reagent in crystallizing proteins, but not part of the structure in vivo.

Now look at the rest of the protein (blue).

Notice how the two subunits interact with one another.  The dimerization domain (residues 50-94, yellow) of each chain intertwine another holding the dimer together (1).  This has been shown to be important in proper DNA binding of Gal4.  When it is a monomore it binds with a significantly lower affinity (see Gal4 Information) (1). 

What other domain is necessary for a functioning transcription factor?  The activation domain is not actually shown here.  This domain is imoportant in the actual initiation of transcription, but was not part of the structure used for this Jmol tutorial.  The activation domain would be attached to the ends of this portion of Gal4 (yellow).


1.    Hong M, Fitzgerald M, Harper S, Lueo C, Speicher D, Marmorstein R. Structural basis for dimerization in DNA recognition by Gal4. Structure 2008; 16: 1019-1026.
2.    Marmorstein R, Carey M, Ptashne M, Harrison S. DNA recognition by GAL4: structure of a protein-DNA complex. Nature 1992; 256; 408-414.

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