The DNA binding motifs are an integral part of the DNA binding proteins. However, it only helps the protein bind to the DNA and the function of the protein once it binds to the DNA is controlled by another part of the protein which may not be present when the structure of the DNA binding protein was determined.

LEUCINE ZIPPER MOTIF:

Leucine zipper motif is composed of two alpha helices which interact with each other causing dimerization. The alpha helix is a periodic repeat of Leucine residue at every seventh position and consists of approximately 30-40 aminoacids. This causes the formation of heptad repeats. Other hydrophobic aminoacids are positioned to be on the outer surface with the alpha helices with Leucine in the interior forming an amphipathic zipper region.

The zipper domain plays a crucial role in protein dimerization. The R-groups of the Leucine residues protrude from the alpha helical regions and this interacts with the R-groups of Leucine from the other dimmer to form a homo or heterodimer. This allows the dimmers to be stabilized and form a tight dimeric complex.

Examples for Leucine zipper motifs are found in proteins such as c-Myc and C/EBP. Yeast Gcn4 protein is found to have a Leucine Zipper motif in which the same motif is responsible for dimerization and DNA binding. Homodimers and Heterodimers are found to recognize and bind to different sequences. It is also found in regulatory proteins such as fos, CRE binding protein, jun etc in mammals.

This protein interaction may help to enhance the association of separate DNA binding domains with their target. DNA recognition involves interaction between DNA and argenines and lysine through non specific interaction. However specific interaction also occurs via side chains other than arginine and lysine.

ZINC FINGER MOTIF

These are zinc coordinated DNA binding motifs. The zinc finger was the second DNA binding motif discovered. Zinc finger motifs are small, independently folded domains which coordinates one or more zinc ions for stabilizing the structure. The process is mediated through cysteine and/or histidine residues. There are a number of Zinc fingers which vary in structure and function. These motifs are found to play crucial roles in DNA- or RNA-binding, protein-protein interactions and membrane association.

There are many types of zinc fingers. The most frequent are the C2H2-type, the CCHC-type, the PHD-type and the RING-type.

a. C2H2 Fingers:
This was first discovered in the protein TFIII A. It is a positive regulator of RNA transcription requiring zinc for activity. The transcription factor was discovered to regulate the expression of genes coding for 5S RNA. Each TFIII A molecule contains 9 zinc ions in closely spaced cysteine- cysteine residues. This is followed by histidine-histidine pair 12 -13 amino acids later. The arrangement is always at the same relative positions. The protein containing zinc fingers are positioned on the surface of DNA helix with successive fingers placed alternatively in one turn in the major groove. TFIII zinc finger contacts about 5 bp of DNA and are important in the action of steroid hormones.
C2H2 Fingers occur in clusters and forms a compact globular domain intercalated with a Zinc ion held together by the Cys and His residues. There are 12 alpha helices with an irregular beta sheet and the zinc ion is found in between. It has about 23 to 26 residues. These alpha helical structures are found in the major groove of DNA.

b. C2C2 Fingers:
This class of motifs is found in nuclear receptors which are ligand activated transcription factors which are involved in response to stimuli such as steroid hormones, vitamin D etc. The domains for binding are made of 70 to 80 aminoacids and have two zinc ions. These zinc ions are tetrahedrally coordinated by four cysteine residues. There are two similar loops. The zinc ion binds to the two cysteine residues at the start of loop and with another two cysteine residues at the N-terminal end of the helices.

c. C4-type zinc fingers:
These are characterized by 4 cysteine residues coordinating the zinc ion. There is no sequence similarity and the distance between the binding cysteine residues are not conserved. These are found in some of the nuclear receptors.
Examples include the UvrA subfamily of ABC transporters, clpX chaperones, and recR family in archaea and bacteria.

d. Atypical zinc fingers:
Atypical zinc fingers are derived from a consensus sequence, which can bind to the zinc ion. Some sequences replace Cys by His residue. In some others, the distance between the two residues is varied.

C- x(5), C-x(10,14)-H, H-x(2)-H, H-x(6)-H etc are some examples of such altered sequences.
Here C stands for Cysteine residue and H is for Histidine residue.

e. Degenerate zinc fingers:
These are also derived from consensus sequences and cannot bind to zinc ion. In such zinc fingers, the Cysteine residues are replaced by aminoacids other than Histidine. The distance between the residues is also not like the atypical zinc fingers. In some cases, the sequence is truncated.

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