How does TBP bind to DNA

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The TATA box binding protein (TBP)

The eukaryotic promoter differs considerably from the promoters of the prokaryotes. It comprises a TATA box, a GC box, a CCAAT box and another typical sequence element. The TATA box represents an AT-rich section with a length of 29-34 bp and, as a starting point for certain transcription factors, helps to find the starting point of the gene to be transcribed. Proteins that bind to this section of DNA are called TATA box-binding proteins (TATA-box binding proteins or TBP).

The TATA box-binding proteins differ in structure and mode of operation from conventional bacterial transcription factors. At the C-terminus there are two homologous, 88 amino acid-length sections that are responsible for the strong binding of the transcription factor to the DNA. Both amino acid sequences each occupy an α-helix and a 5-stranded antiparallel β-sheet structure, the two sheets being arranged to form a 10-strand β-sheet. This protein part takes the form of a saddle, the DNA-binding, concave underside of which emerges from the β-sheet. The helices on the top do not take part in protein-DNA interactions. In interactions between protein and DNA, the saddle lies over the small and large furrows of the TATA box sequence and bends the nucleic acid strand to a 100 ° -tipped kink. The DNA helix unwinds and embeds itself tightly in the saddle. A phenylalanine residue is inserted between the first and last base pairs of the TATA box to prevent the DNA from rewinding through a stabilizing stacking of the nucleotide bases.

The interactions between TBP and DNA are mainly hydrophobic and occur between 15 amino acids of the β-sheets and the sugar components of the nucleotide bases. Hydrogen bridges are only formed between the phosphate-containing backbone of the TATA box and the lysine and arginine side chains at the ends of the bound DNA segment. So it is not surprising that there are no water molecules between TBP and DNA, but they can play an important role in other protein-DNA interactions.

A TBP does not acquire its specificity from the section of protein that lies over the small groove in the DNA. Interactions occurring here only identify the DNA as a binding partner. In contrast, the interactions with the TATA box center located in the major groove are sequence-specific. Two asparagines and two tryptophans form hydrogen bonds. The four amino acids are divided into two palindromically opposite domains and are therefore able to interact well with the quasi-palindromically arranged base pairs of the DNA double strand.

The TBP lies like a saddle over the DNA strand.