TATA-Binding Protein (TBP): How It Binds to DNA

TATA-binding protein (TBP) is a crucial component of the transcription machinery in eukaryotic cells, playing a pivotal role in the initiation of gene transcription. By recognizing and binding to the TATA box, TBP facilitates the assembly of the transcriptional machinery, which is essential for the initiation of gene transcription.

Recognition of the TATA Box

The TATA box is a consensus sequence (TATAAA) found in many eukaryotic promoters, and TBP specifically recognizes and binds to it. This binding is critical for the initiation of transcription by RNA polymerase II. By recognizing the TATA box, TBP provides the necessary platform for the assembly of the transcriptional machinery, ensuring the precise initiation of gene transcription.

Structural Conformation of TBP

TBP has a distinctive saddle-shaped structure that allows it to fit around the DNA helix. When TBP binds to the TATA box, it induces a significant bend in the DNA, a process facilitated by the projection of four bulky phenylalanine residues into the minor groove. This bending is crucial as it facilitates the recruitment of other transcription factors and RNA polymerase II to form the pre-initiation complex.

Interaction with DNA

TBP interacts with the DNA through hydrogen bonds and van der Waals forces, primarily making contact with the phosphate backbone and the bases of the DNA. This interaction stabilizes the binding and ensures the proper positioning of TBP for its role in transcription.

Formation of the Pre-Initiation Complex

Once TBP is bound to the TATA box, it serves as a platform for the assembly of additional transcription factors and RNA polymerase II. This assembly leads to the formation of the pre-initiation complex, which is essential for the initiation of gene transcription.

Role of TBP-Associated Factors (TAFs)

In addition to TBP, TBP-associated factors (TAFs) can also interact with TBP and the DNA, further stabilizing the complex and enhancing the recruitment of the transcriptional machinery. TAFs play a crucial role in the formation of the pre-initiation complex and ensure the efficient initiation of transcription.

TBP binds with the negatively charged phosphates in the DNA backbone through positively charged lysine and arginine amino acid residues. The sharp bend in the DNA is produced through the projection of four bulky phenylalanine residues into the minor groove, creating a precise fit between TBP and the TATA sequence.

This process can be visualized as the surfaces of the two macromolecules matching almost ideally in topology and charges to fit together, with TBP inserting peptides between the double-stranded DNA, thus distorting and entangling the two strands.

For more details on how TBP binds to DNA, you can refer to the Wikipedia article.