TBP binding

TBP binds in the minor groove and induces large structural changes in 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. 

TBP-TATA box complexes are known A p sheet in TBP forms the DNA-binding site TBP binds in the minor groove and induces large structural changes in DNA The interaction area between TBP and the TATA box is mainly hydrophobic Functional implications of the distortion of DNA by TBP... 

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... 

Bellorini M, Moncollin V, D lncalci M, Mongelli N, Mantovani R. (1995) Distamycin A and tallimustine inhibit TBP binding and basal in vitro transcription. Nucleic Acids Res 23 1657-1663. 

There are also indications that the composition of TFIID is not fixed, but may vary depending on the detailed structure of the promoter. This idea is corroborated by the isolation of a transcription-competent TFIID that supports transcription without requiring TBP binding (Apone Green, 1998). 

Kraus, R. J., Murray, E. E Wiley, S. R., Zink, N. M Loritz, K., Gelembiuk, G. W. Mertz, J. E. (1996). Experimentally determined weight matrix definitions of the initiator and TBP binding site elements of promoters. Nucleic Acids Res 24,1531-9. 

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 binds slowly to DNA (kg = 10 M l s-1) [46], and dissociates even more slowly (for very stable complexes, the lifetime of the complex can exceed two hours) [47]. The need for this remarkable stability of the TBP-DNA complex has been rationalized in terms of its being a launching pad for multiple rounds of transcription [2]. The fact that TBP binds more slowly than would be allowed by diffusion has lead to much discussion in the field [48]. The mechanisms that have been advanced to explain this are as follows a) the limiting step is breaking up the TBP dimers that exist in solution before... 

The populations shown in Figure 6 agree with the way MLP was parsed, and further support for this idea comes from experiments where DNA is made more flexible by including mismatches and bulges in the sequence [62], For these sequences, TBP binds preferentially in the direction predicted by Kim and Burley and Suzuki. 

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

J. Bernues, P. Carrera and F. Azorin. TBP binds the transcriptionally inactive TA5 sequence but the resulting complex is not efficiently recognised by TFIIB and TFIIA. Nucleic Acids Res. 24 (1996) 2950-8. 

Binding of antibody to T4-E decreases enzyme activity. The unbound T4-enzyme conjugate, on the other hand, is active and catalyzes the oxidation of glucose-6-phosphate with simultaneous reduction of NAD-t to NADH. The rate of increase of absorbance at 340 nm is inversely proportional to the number of unsaturated TBP binding sites. Test results are expressed as percent of T uptake using a calibration curve or a mathematical function. Manual and automated versions of this assay are commercially available. ... 

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