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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 ]
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 conformational change. Binding domains are essential for the function of many proteins.
Structure and domain organization of NOD2, a human NOD-like receptor. The nucleotide-binding oligomerization domain-like receptors, or NOD-like receptors (NLRs) (also known as nucleotide-binding leucine-rich repeat receptors), [1] are intracellular sensors of pathogen-associated molecular patterns (PAMPs) that enter the cell via phagocytosis or pores, and damage-associated molecular patterns ...
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 .
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.
The Rossmann fold is a tertiary fold found in proteins that bind nucleotides, such as enzyme cofactors FAD, NAD +, and NADP +.This fold is composed of alternating beta strands and alpha helical segments where the beta strands are hydrogen bonded to each other forming an extended beta sheet and the alpha helices surround both faces of the sheet to produce a three-layered sandwich.
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.
The NBD (nucleotide binding domain) consists of two lobes with a deep cleft between them, at the bottom of which nucleotide (ATP and ADP) binds. The exchange of ATP and ADP leads to conformational changes in the other two domains. Substrate binding domain – is composed of a 15 kDa β sheet subdomain