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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 distinct group of DNA-binding proteins are the DNA-binding proteins that specifically bind single-stranded DNA. In humans, replication protein A is the best-understood member of this family and is used in processes where the double helix is separated, including DNA replication, recombination and DNA repair. [18]
The authors were able to show that the motif has DNA binding activity. A similar approach is commonly used by modern protein domain databases such as Pfam : human curators would select a pool of sequences known to be related and use computer programs to align them and produce the motif profile (Pfam uses HMMs , which can be used to identify ...
This motif is seen in transcription factors. Zinc finger Two beta strands with an alpha helix end folded over to bind a zinc ion. Important in DNA binding proteins. Helix-turn-helix Two α helices joined by a short strand of amino acids and found in many proteins that regulate gene expression. [12] Nest Extremely common.
Thus a consensus sequence is a model for a putative DNA binding site: it is obtained by aligning all known examples of a certain recognition site and defined as the idealized sequence that represents the predominant base at each position. All the actual examples shouldn't differ from the consensus by more than a few substitutions, but counting ...
The helix-turn-helix motif is a DNA-binding motif. The recognition and binding to DNA by helix-turn-helix proteins is done by the two α helices, one occupying the N-terminal end of the motif, the other at the C-terminus. In most cases, such as in the Cro repressor, the second helix contributes most to DNA recognition, and hence it is often ...
E-box binding proteins play a major role in regulating transcriptional activity. These proteins usually contain the basic helix-loop-helix protein structural motif, which allows them to bind as dimers. [10] This motif consists of two amphipathic α-helices, separated by a small sequence of amino acids, that form one or
Homeodomain proteins function as transcription factors due to the DNA binding properties of the conserved HTH motif. Homeodomain proteins are considered to be master control genes, meaning that a single protein can regulate expression of many target genes. Homeodomain proteins direct the formation of the body axes and body structures during ...