TBP binding to DNA

The largest TAP included in TFIID has an inhibitory action on TBP binding to DNA. The structure of a domain located in the N-terminus of D. melanogaster TAF230 complexed with S.cerevisiae TBP was obtained by NMR... 

TBP binding to DNA is directional such that the same protein surface is always pointed toward the transcriptional start site. 

FIGURE 11.20 Model of yeast TATA-binding protein (TBP) binding to DNA. The DNA... 

The sharp bend of DNA at the TATA box induced by TBP binding is favorable for the formation of the complete DNA control module in particular, for the interaction of specific transcription factors with TFIID. Since these factors may bind to DNA several hundred base pairs away from the TATA box, and at the same time may interact with TBP through one or several TAFs, there must be several protein-DNA interactions within this module that distort the regular B-DNA structure (see Figure 9.2). The DNA bend caused by the binding of TBP to the TATA box is one important step to bring activators near to the site of action of RNA polymerase. 

TFIIA and TFIIB bind to both TBP and DNA Flomeodomain proteins are involved in the development of many eucaryotic organisms Monomers of homeodomain proteins bind to DNA through a heltx-turn-helix motif In vivo specificity of homeodomain... 

TBP binds to the TATA box in the minor groove of DNA (most transcription factors bind in the major groove) and causes an approximately 100-degree bend or kink of the DNA helix. This bending is thought to facilitate the interaction of TBP-associated factors with other components of the transcription initiation complex and possibly with factors bound to upstream elements. Although defined as a component of class II gene promoters, TBP, by virtue of its association with... 

Recently, a family of related proteins has been identified in metazoa, the TBP-like proteins or TLPs [16], which are also able to bind to DNA, albeit not to the consensus TATA boxes. The physiological role of TLPs is an area of intense research, and some proposals suggest that it sequesters other general transcription factors (such as TFIIA), thereby repressing RNApol-II transcription mediated by TBP [17]. 

Ternary complexes formed by TBP, DNA and TFIIA or TFIIB have also been crystallized [27-32] and their structures are available in the PDB and NDB (see Table 1). These complexes display practically the same mode of interaction between TBP and the DNA moiety as found in the corresponding binary complexes. They also explain the inability of TFIIB to bind to DNA on its own, as it is found to contact the DNA upstream and downstream of TBP, an impossible feat in a straight DNA molecule. This feature places TBP among the architectural transcription factors, together with DBF, HMG, SRY and LEFl... 

N. Pastor and H. Weinstein. Sidechain dynamics and seuqence specific TBP binding to TATA box DNA. Biophys. J. 76 (1999) A387. 

The proposed structure of TBP bound to DNA based on X-ray crystallography data. (A) A monomer of TBP appears to form a protein "saddle" that sits atop the DNA helix. (B) TBP-binding to the TATA box causes a bend in the DNA double helix. 

The biochemical structure of yeast TBP bound to DNA has been determined by X-ray crystallography and two very interesting observations have been made. The first is that TBP has an internal pseudo-dimer interaction between two adjacent protein domains, forming a "saddle" structure that binds DNA (Figure 24. 7). The exposed surface of TBP in this configuration serves as a contact area for a variety of other transcription factors. 

A prototypical RNA pol II-dependent eukaryotic promoter. Three classes of transcription factors are schematically represented the TFII auxiliary factors (TFIIF, TFIIJ, TFIIH, etc.), TBP with its associated factors (TAFs), and various transcriptional regulatory factors which bind to DNA sequences called response elements (RE). See Chapter 24 for more information about TBP and the RNA pol II holoenzyme. 

TFIID (which contains the TATA-box binding protein, TBP) binds to the TATA box. TFIIA and TFIIB then bind, followed by recruitment of RNA polymerase II and TFIIF. TFIIH and TFIIE then bind to form the preinitiation complex (PIC). Kinases phosphorylate the C-terminal domain of Pol II, leading to the open complex in which the DNA strands are separated. RNA is produced during elongation as Pol II and TFIIF leave the promoter and the other general transcription factors behind. Pol II dissociates during the termination phase, and the CTD is dephosphorylated. Pol II/TFIIF is then recycled to bind to another promoter. 

The co-crystal structure of the TBP-DNA complex shows that TBP binds to the minor groove of the TATA element and introduces a sharp bend in the DNA (Kim and Burley, 1994 Kim et al., 1993a Kim et al., 1993b). This is mediated by insertion of two pairs of phenylalanine residues in between the first two and between the last two base pairs of the TATAAA sequence. The minor groove is thus widened and fit to the concave surface of the saddle. The particular wrapping of DNA around the nucleosome can affect the disposition of the minor groove and the TATA element, and this can affect the ability of TBP to bind in the context of a nucleosome (Imbalzano et al., 1994). The bend in DNA could also serve other purposes such as... 

TBP has been cloned from many organisms, ranging from archeabacteria 4, 5) to humans (see (6) for a review). Crystallographic determinations of TBP structures from archeabacteria (7), yeast (5), and plants (6) reveal the same architecture a molecular saddle with a near two-fold symmetry axis. TBP has also been crystallized in complex with DNA (9-72), and in ternary complexes with two other basic transcription factors, TFIIA (75, 14) and TFIIB (75). In all the crystallized complexes, TBP binds to 8 basepairs in the minor groove of the DNA encoding a characteristic TA repeat. The underside of the TBP saddle is the binding interface with the DNA. This interface is mostly hydrophobic, but 6 hydrogen bonds have been identified in the crystal structures. 

They involve the interactions between Thr and Asn residues and the two central basepairs of the TATA box. While TBP does not change its conformation drastically upon binding to DNA, the geometry of the DNA, which is practically identical in all the crystallized complexes, has two kinks that are caused by the partial insertion of two pairs of Phe residues at the first and last basepair steps of the TATA box. These insertions result in a bend of -90° between the DNA preceding the TATA box and the stretch following it. The DNA is unwound in these complexes, and the minor groove is widened. 

The absence of a distinguishing feature among the calculated average structures of the various dodecamers moved the search for the selectivity determinants for TBP binding to the analysis of more local properties of the DNA oligomers, both bound to TBP and free. 

Most sequence-specific regulatory proteins bind to their DNA targets by presenting an a helix or a pair of antiparallel p strands to the major groove of DNA. Recognition of the TATA box by TBP is therefore exceptional it utilizes a concave pleated sheet protein surface that interacts with the minor groove of DNA. Since the minor groove has very few sequence-specific... 

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