Different DNA binding motifs

HELIX-TURN-HELIX MOTIF;

The helix turn helix motif is present in many prokaryotes and eukaryotic DNA binding protein. The HTH motif was the first DNA binding structure to be identified. The motif is made up  of alpha-helices separated by beta-turn, made up of four amino acid, the second of which is usually glycine. This turn, in conjunction with the first alpha-helix, position. The second helix on the surface of the protein in an orientation that unable it to fit inside the major groove of DNA molecule. This second alpha-helix is known as recognition helix. The HTH is usually 20 or 50 amino acids in length as is just a small part of the protein as a whole. 

The homeodomain is an extended HTH motif passed by protein encoded by homeotic gene. It is made up of highly conserved domain of 60 amino acids encoded by 180 bp DNA sequence called homeobox. It has three alpha helices and helices 2 and 3 separated by beta-turn. Helices 3, which is 17 amino acid residue long act as recognition helix and bind to major groove of DNA. Helix 1 make contact with the minor groove.

HELIX-LOOP-HELIX MOTIF:

The helix-loop-helix (HLH) motif is involved in both DNA binding and protein dimerization. The HLH motif is composed of two region of alpha-helix of 15 to 16 residue separated by region of variable length, which form loop between two helices. Length of connecting loop varies from 12 to 28 amino acid residues. This motif is quite similar to leucine zipper motif.

LEUCINE ZIPPER MOTIF:

Leucine zipper motif (Lzip) mediates both DNA binding and dimerization. Two distinct right handed alpha-helices participate in the formation of homo or hetero dimer structure. N-terminal DNA binding domain is rich in positively charged amino acid residues. C-terminal dimerization domain is 30-40 amino acids long with leucine at every seventh position. The leucine zipper domain is necessary for protein dimerization. Two alpha-helices in parallel wind around each other to form a coiled coil structure. The leucine residue end up with their R group protruding from the helical domain in which the leucine residue reside. The protruding R-group are thought to interdigitate with leucine R group of another leucine zipper domain, thus stablishing homo- or hetero- dimerization.

ZINC FINGER:

Zinc-coordinated DNA binding motif are called zinc-finger motif. There are several type of zinc finger motif. The most widely occurring zinc finger motif in eukaryotes is the Lys2-His2 (C2-H2) zinc finger, which was first discovered in a transcription factor called TFIIA that regulate the transcription of gene for 5S rRNA. This class of zinc finger occur in cluster. Each finger is 130 amino acids long and is characterized by pair of Cys and His that always occur at the same relative portion.

It form compact, globular domain in which a zinc ion is coordinated tetrahedrally by Cys and His residue. The zinc is essential for correct folding and DNA binding. NMR and X-ray studies shown that C2H2 finger is a compact globular domain composed of 12 residue alpha-helix packed against irregular beta-sheet, with the zinc in between. The alpha-helix of each finger lie in major groove and contact three base pairs.