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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 .
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] Upon binding, proteins may undergo a ...
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
For example, acetylation has been seen to increase the activity of some activators through mechanisms such as increasing DNA-binding affinity. [1] On the other hand, ubiquitination decreases the activity of activators, as ubiquitin marks proteins for degradation after they have performed their respective functions.
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.
Most Pax genes contain a homeobox and a paired domain that also binds DNA to increase binding specificity, though some Pax genes have lost all or part of the homeobox sequence. [46] Pax genes function in embryo segmentation, nervous system development, generation of the frontal eye fields, skeletal development, and formation of face structures.
For example, there are two PstI recognition sites in the following DNA sequence fragment, starting at base 9 and 31 respectively. A recognition sequence is a specific sequence, usually very short (less than 10 bases). Depending on the degree of specificity of the protein, a DNA-binding protein can bind to more than one specific sequence.