Below are examples of different types of DNA-binding proteins. The most common and best studied DNA-binding proteins are the Zinc finger proteins, the Helix-turn-helix proteins, and the Leucine zipper proteins.
|TATA Box Binding Prtn||The TATA box binding protein is a subunit of the eukaryotic transcription factor, TFIID. This protein is somewhat unusual in that its TBP-binding domain binds to the minor groove of DNA.|
|Zinc finger domain||This domain is common in eukaryotic DNA-binding proteins. It was first noticed in the eukaryotic transcription factor, TFIIIA. TFIIIA contains 9 repeated modules, each of which contains two Cysteine and two Histidine residues. These four residues chelate one Zn++ ion. Each finger is bound in the major groove of B-DNA.|
|Helix-turn-helix domain||This motif was first noticed as a feature of the crystal structure of the bacteriophage l Cro protein. The structure of this small regulatory protein contained two a-helices separated by 34 Ã… - the pitch of a DNA double helix. Model building studies showed that these two a-helices would fit into two successive major grooves. As the structures of a number of other bacterial regulatory proteins (the CRP protein and the bacteriophage l cI repressor) were solved, the same structural motif - called a helix-turn-helix - was observed. It consists of two a-helices separated by a short turn (it is not a b turn). One helix binds to recognition elements within the major groove of DNA; the other helps to keep the binding helix properly positioned with respect to the rest of the molecule. This motif, common in bacterial DNA-binding proteins, also occurs in the eukaryotic homeobox proteins.|
|Leucine Zipper domains||This domain is an important feature of many eukaryotic regulatory proteins. Leucine is an hydrophobic amino acid. When it occurs at every seventh position of an a-helix, the aliphatic side-chains are all oriented on the same side of the helix and they can interact with another such helix to form a coiled coil type of structure. The GCN4 transcription activator in yeast is a dimer in which the leucine zipper region helps to position the two basic regions that bind to the DNA recognition sequence.|
|Helix-Loop-Helix binding motif||A variation of the leucine zipper, the basic DNA-binding helices are connected to the dimerization helices by a short loop.|