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A DNA-binding domain (DBD) is an independently folded protein domain that contains at least one structural motif that recognizes double- or single-stranded DNA.A DBD can recognize a specific DNA sequence (a recognition sequence) or have a general affinity to DNA. [1]
DNA-binding proteins are proteins that have DNA-binding domains and thus have a specific or general affinity for single- or double-stranded DNA. [ 3 ] [ 4 ] [ 5 ] 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 .
DNA contacts of different types of DNA-binding domains. DNA binding sites are a type of binding site found in DNA where other molecules may bind. DNA binding sites are distinct from other binding sites in that (1) they are part of a DNA sequence (e.g. a genome) and (2) they are bound by DNA-binding proteins.
Helix-turn-helix is a DNA-binding domain (DBD). The helix-turn-helix (HTH) is a major structural motif capable of binding DNA. Each monomer incorporates two α helices, joined by a short strand of amino acids, that bind to the major groove of DNA. The HTH motif occurs in many proteins that regulate gene expression
In molecular biology, binding domain is a protein domain which binds to a specific atom or molecule, such as calcium or DNA.A protein domain is a part of a protein sequence and a tertiary structure that can change or evolve, function, and live by itself independent of the rest of the protein chain. [1]
Activator DNA-binding domains come in a variety of conformations, including the helix-turn-helix, zinc finger, and leucine zipper among others. [1] [2] [3] These DNA-binding domains are specific to a certain DNA sequence, allowing activators to turn on only certain genes.
The B3 DNA binding domain (DBD) is a highly conserved domain found exclusively in transcription factors (≥40 species) (Pfam PF02362) combined with other domains (InterPro: IPR003340). It consists of 100-120 residues, includes seven beta strands and two alpha helices that form a DNA-binding pseudobarrel protein fold ( SCOP 117343 ); it ...
The dimerization domain binds to other LexA polypeptides to form dumbbell shaped dimers. The DNA-binding domain is a variant form of the helix-turn-helix DNA binding motif, [4] and is usually located at the N-terminus of the protein. [1] This domain is bound to an SOS box upstream of SOS response genes until DNA damage stimulates ...