DNA-binding domains are included in many proteins involved in the regulation of gene expression (including transcription factors), proteins involved in the packaging of DNA within the nucleus (such as histones), nucleic acid dependent-polymerases involved in DNA replication and transcription, or any of many accessory proteins which are involved in these processes.
Sequence-specific DNA-binding proteins generally interact with the major groove of B-DNA, because it exposes more functional groups that identify a base pair.
The specificity of DNA-binding proteins can be identified using a technique called "DNA Footprinting".
Types of DNA-binding domains
Originally discovered in bacteria, this motif is commonly found in repressor proteins and is about 20 amino acids long. In eukaryotes, the homeodomain is comprised of 3 helices, of which the third recognizes the DNA (aka recognition helix). They are common in proteins that regulate developmental processes.
This domain is 30 amino acids long and consists of a recognition helix and a 2-strand beta-sheet. The domain also contains four regularly spaced ligands for Zinc (either histidines or cysteines). The Zn ion stabilizes the 3D structure of the domain. Each finger contains one Zn ion and recognizes a specific triplet of DNA basepairs.
Leucine zipper domain (bZIP)
The leucine zipper contains an alpha helix with a leucine at every 7th amino acid. If two such helices find one another, the leucines can interact as the teeth in a zipper, allowing dimerization of two proteins. When binding to the DNA, basic amino acid residues bind to the sugar-phosphate backbone while the helices sit in the major grooves.
Winged helix (WH)
Consisting of about 110 amino acids, the domain has four helices and a two-strand beta-sheet.
First discovered in the ETS oncogene, the domain is 85-90 amino acids long and is folded into a structure with 3 helices and a 4-strand beta-sheet, where the third helix is the recognition helix. ETS proteins are transcription factors that are activated via phosphorylation by the MAP kinases.
This domain is found in some transcription factors and is characterized by two α helices connected by a loop. One helix is typically smaller and due to the flexibility of the loop, allows dimerization by folding and packing against another helix. The larger helix typically contains the DNA binding regions.
Unusual DNA binding domains
The domain consists of a beta-sheet structure with large connecting loops, which serve to recognize either DNA major grooves or antigens. Usually found in immunoglobulin proteins, they are also present in Stat proteins of the cytokine pathway. This is likely due to the fact that the cytokine pathway evolved relatively recently and has made use of systems that were already functional, rather than creating its own.
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