DNA-binding domain

A DNA-binding domain (DBD) includes any protein motif that binds to double- or single-stranded DNA with affinity to a specific sequence or set thereof or a general affinity to DNA.

Explanation

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

Helix-turn-helix

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.

Zinc finger

File:1r4o.png

Crystallographic structure (PDB 1R4O) of a dimer of the zinc finger containing DBD of the glucocorticoid receptor (top) bound to DNA (bottom). Zinc atoms are represented by grey spheres and the coordinating cysteine sidechains are depicted as sticks.

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.

ETS domain

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.

Helix-loop-helix

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

Immunoglobulin Fold

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.

External links

• Table of DNA-binding motifs
• MeSH DNA+Footprinting
• MeSH DNA-Binding+Proteins

it:DNA-binding protein