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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]
One part of the domain contains a region that mediates sequence specific DNA binding properties and the leucine zipper that is required to hold together (dimerize) two DNA binding regions. The DNA binding region comprises a number of basic amino acids such as arginine and lysine. Proteins containing this domain are transcription factors. [1] [2]
TRANSFAC: a database about eukaryotic transcription factors, their genomic binding sites and DNA-binding profiles; JASPAR: a database of manually curated, non-redundant transcription factor binding profiles. MetOSite: a database about methionine sulfoxidation sites and its functional roles in proteins [35]
The Protein Data Bank (PDB) is a database of 3D structure data for large biological molecules, such as proteins, DNA, and RNA. PDB is managed by an international organization called the Worldwide Protein Data Bank , which is composed of several local organizations, as. PDBe, PDBj, RCSB, and BMRB.
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 ]
TDP-43 is a transcriptional repressor that binds to chromosomally integrated TAR DNA and represses HIV-1 transcription. In addition, this protein regulates alternate splicing of the CFTR gene. In particular, TDP-43 is a splicing factor binding to the intron8/exon9 junction of the CFTR gene and to the intron2/exon3 region of the apoA-II gene.
This DNA binding domain has a consensus DNA sequence 5’-CATTCCA/T-3’ that is called the MCAT element. [11] The three dimensional structure of the TEA domain has been identified. [9] Its conformation is close to that of the homeodomain and contains 3 α helixes (H1, H2 and H3). It is the H3 helix that enables TEAD proteins to bind DNA. [12]
The Protein Data Bank (PDB) [1] is a database for the three-dimensional structural data of large biological molecules such as proteins and nucleic acids, ...