Transcriptional activator GCN4/DNA complex
Saccharomyces cerevisiae (Baker's yeast)
Helices not only are maybe the most compact motif in protein structures, they are also capable, due to their structure to have a janus face. When looking down the axis of a helix, the amino acids forming a helix may be arranged in such a way that all hydrophilic residues point to one half of the helix and that all hydrophobic residues point to the other half. Such helices are called amphipathic and are a common motif for membrane proteins. A very prominent example of an amphipathic helix is the leucine zipper motif. If every eighth residue in a helix, one, eight, 15 etc is a leucine, then all the leucines in the helix will appear lined up in the same direction when looking down the helix axis. In a protein such a leucine zipper domain is often preceded by a region with basic residues, the basic region that binds DNA. This arrangement is called the basic region-leucine zipper motif (bZIP). The two helices of a bZIP have a tendency to twist around each other forming a coiled coil arrangement.
In the example here we see is the leucine zipper motif of GCN4 together with a DNA double helix. The two helices of the bZIP extend from the DNA almost at a right angle to the DNA helical axis. The arrangement, when looking at it from the side, strongly resembles a pair of tweezers or a pair of scissors gripping an object, the DNA. Remarkable is the length of this helices, being about 75-85 A long. The shape of the DNA creates two typical grooves, called the minor (shallow) and the major (deep) groove. The two helices tightly embed themselves into the major grooves of the DNA allowing them to get a tight grip of the DNA.
Protein Data Bank (PDB)
author: Arno Paehler