DNA-binding domain

[3] Originally discovered in bacteria, the helix-turn-helix motif is commonly found in repressor proteins and is about 20 amino acids long.

[7] In transcription factors these domains are often found in arrays (usually separated by short linker sequences) and adjacent fingers are spaced at 3 basepair intervals when bound to DNA.

The basic leucine zipper (bZIP) domain is found mainly in eukaryotes and to a limited extent in bacteria.

Consisting of about 110 amino acids, the winged helix (WH) domain has four helices and a two-strand beta-sheet.

The basic helix-loop-helix (bHLH) domain is found in some transcription factors and is characterized by two alpha helices (α-helixes) connected by a loop.

HMG-box domains are found in high mobility group proteins which are involved in a variety of DNA-dependent processes like replication and transcription.

[12] The immunoglobulin domain (InterPro: IPR013783) consists of a beta-sheet structure with large connecting loops, which serve to recognize either DNA major grooves or antigens.

The B3 DBD (InterPro: IPR003340, SCOP 117343) is found exclusively in transcription factors from higher plants and restriction endonucleases EcoRII and BfiI and typically consists of 100-120 residues.

It includes seven beta sheets and two alpha helices, which form a DNA-binding pseudobarrel protein fold.

[17] Related proteins are found in bacterial plant pathogen Ralstonia solanacearum,[18] the fungal endosymbiont Burkholderia rhizoxinica[19] and two as-yet unidentified marine-microorganisms.

[20] The DNA binding code and the structure of the repeat array is conserved between these groups, referred to collectively as the TALE-likes.

Example of a DNA-binding domain in the context of a protein. The N-terminal DNA-binding domain (labeled) of Lac repressor is regulated by a C-terminal regulatory domain (labeled). The regulatory domain binds an allosteric effector molecule (green). The allosteric response of the protein is communicated from the regulatory domain to the DNA binding domain through the linker region. [ 2 ]
DNA contacts of different types of DNA-binding domains
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.