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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] One or more DNA-binding domains are often part of a larger protein consisting of further protein domains with differing function. The ...
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 ...
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-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 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
The main class of R-genes consist of a nucleotide binding domain (NB) and a leucine rich repeat (LRR) domain(s) and are often referred to as (NB-LRR) R-genes or NLRs. [1] Generally, the NB domain binds either ATP/ADP or GTP/GDP. The LRR domain is often involved in protein-protein interactions as well as ligand binding.