3.13. DNA-binding domain
A DNA-binding domain is a protein structure that has a high affinity for DNA. It is an independently folded protein domain. A DBD can recognize a specific DNA sequence (a recognition sequence).DNA recognition by the DBD can occur at the major or minor groove of DNA, or at the sugar-phosphate DNA backbone.
Types of DNA-binding domains
1. Helix-turn-helix domain
The first DNA-binding protein motif to be recognized was helix-turn-helix which was originally identified in bacterial proteins. It is constructed from two α helices connected by a short extended chain of amino acids, which constitutes the “turn” The C-terminal helix is called the recognition helix because it fits into the major groove of DNA; its amino acid side chains, which differ from protein to protein, play an important part in recognizing the specific DNA sequence to which the protein binds.
This domain is characteristic of DNA - binding proteins containing a 60- amino acid homeodomain which is encoded by a sequence called the homeobox. In the Antennapedia transcription factor of Drosophila , this domain consists of four α - helices in which helices II and III are at right angles to each other and are separated by a characteristic β - turn.
The characteristic helix -turn helix structure is also found in bacteriophage DNA - binding proteins such as the phage A cro repressor , lac and trp repressors, and cAMP receptor proteins , CRP.
2. Zinc finger domain
The zinc finger domain is generally between 23 and 28 amino acids long and is stabilized by coordinating zinc ions with regularly spaced zinc-coordinating residues (either histidines or cysteines). This domain exists in two forms. The C2H2 zinc finger has a loop of 12 amino acids anchored by two cysteine and two histidine residues that tetrahedrally co-ordinate a zinc ion. This motifs folds into a compact structure comprising two β - strands and one α- helix, the latter binding in the major groove of DNA. The α- helical region contains conserved basic amino acids which are responsible for interacting with the DNA. This structure is repeated nine times in TFIIIA, the RNA Pol III transcription factors. Usually, three or more C2H2 zinc fingers are required for DNA binding.
A related motif, in which the zinc ion is co-ordinated by four cysteine residues, occur in over 100 steroid hormone receptor transcription factors. These factors consist of homo- or hetero- dimers, in which each monomer contains two C4 zinc finger motifs.
3. Leucine zipper
Leucine zipper proteins contain a hydrophobic leucine residue at every seventh position in a region that is often at the C-terminal part of the DNA- binding domain. These leucines lie in an α- helical region and the regular repeat of these residues forms a hydrophobic surface on one side of the α - helix with a leucine every second turn of the helix. These leucines are responsible for dimerizatin through interactions between hydrophobic faces of the α - helices. This interaction forms a coiled - coil structure. bZIP transcription factor contain a basic DNA- binding domain N- terminal to the leucine zipper. This is present on an α - helix which is a continuation from the leucine zipper α - helical C- terimal domain. The N- terminal basic domains of each helix form a symmeterical structure in which each basic domain lies along the DNA in opposite directions, interacting with a symmetrical DNA recognition site so that the protein in effect forms a clamp around the DNA. The leucine zipper is also used as a dimerization domain in proteins that use DNA- binding domains other than the basic domain, including some homeodomain proteins.
4. HELIX- LOOP- HELIX DOMAIN
The overall structure of this domain is similar to the leucine zipper , except that a non helical loop of polypeptide chain separates two α- helices in each monomeric protein. hydrophobic residues on one side of the C-terminal α- helix allow dimerization. this structure is found in the MyoD family of proteins. As with the leucine zipper , the HLH motif is often found adjacent to a basic domain that requires dimerization for DNA- binding. With both basic HLH proteins and bZIP proteins the formation of heterodimers allows much greater diversity and complexity in the transcription factor repertoire.