Transcription factors structure

Pabo, C.O., Sauer, R.T. Transcription factors structural families and principles for DNA recognition. 

Schuller, H.-J., Richter, K., Hoffmann, B., Ebbert, R., and Schweizer, E., 1995, DNA binding site of the yeast heteromeric Ino2p/Ino4p basic helix-loop-helix transcription factor Structural requirements as defined by saturation mutagenesis. FEBS Lett. 370 149-152. 

C. O. Pabo and R T. Sauer. Transcription factors Structural families and principles of DNA recognition. Annu Rev Biochem, 61, 1053-1095, 1992. 

ZINC-CONTAINING TRANSCRIPTION FACTORS STRUCTURAL ZINC SITES... 

Chen FE, Ghosh G Regulation of DNA binding by Rel/NF-kB transcription factors Structural views. Oncogene 1999 18 6845-6852. 

K. Yamasaki, T. Kigawa, M. Seki, K. Shinozaki and S. Yokoyama, DNA-Binding Domains of Plant-Specific Transcription Factors Structure, Function, and Evolution, Trends Plant ScL, 2013,18, 267. 

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 are two basal transcription factors that are involved in the nucleation stages of the preinitiation complex by binding to the TBP-TATA box complex. Crystal structures of the ternary complex TFIIA-TBP-TATA box have been determined by the groups of Paul Sigler, Yale University, and Timothy Richmond, ETH, Zurich, and that of the TFIIB-TBP-TATA box by Stephen Burley and collaborators. The TBP-DNA interactions and the distortions of the DNA structure are essentially the same in these ternary complexes as in the binary TBP-TATA complex. 

Figure 9.12 Schematic diagram of the structure of the heterodimeric yeast transcription factor Mat a2-Mat al bound to DNA. Both Mat o2 and Mat al are homeodomains containing the helix-turn-helix motif. The first helix in this motif is colored blue and the second, the recognition helix, is red. (a) The assumed structure of the Mat al homeodomain in the absence of DNA, based on Its sequence similarity to other homeodomains of known structure, (b) The structure of the Mat o2 homeodomain. The C-terminal tail (dotted) is flexible in the monomer and has no defined structure, (c) The structure of the Mat a 1-Mat a2-DNA complex. The C-terminal domain of Mat a2 (yellow) folds into an a helix (4) in the complex and interacts with the first two helices of Mat a2, to form a heterodimer that binds to DNA. (Adapted from B.J. Andrews and M.S. Donoviel, Science 270 251-253, 1995.)...

Burley, S.K., Boeder, R.G. Biochemistry and structural biology of transcription factor IID. Anna. Rev. Bioehem. 

The coiled-coil structure of the leucine zipper motif is not the only way that homodimers and heterodimers of transcription factors are formed. As we saw in Chapter 3 when discussing the RNA-binding protein ROP, the formation of a four-helix bundle structure is also a way to achieve dimerization, and the helix-loop-helix (HLH) family of transcription factors dimerize in this manner. In these proteins, the helix-loop-helix region is preceded by a sequence of basic amino acids that provide the DNA-binding site (Figure 10.23), and... 

Figure 10.24 Structure of a monomer of the DNA-binding domain of the transcription factor MyoD. The domain, which belongs to the b/HLH family, comprises two a helices joined by a loop region. The basic region (blue) and the first helix HI (red) of the helix-loop-helLx region form one continous a helix. (Adapted from P.C.M. Ma et al.. Cell 77 451-459, 1994.)...

Helix-loop-helix (b/HLH) transcription factors are either heterodimers or homodimers with basic a-helical DNA-binding regions that lie across the major groove, rather than along it, and these helices extend into the four-helix bundle that forms the dimerization region. A modification of the b/HLH structure is seen in some transcription factors (b/HLH/zip) in which the four-helix bundle extends into a classic leucine zipper. 

Glover, J.N.M., Harrison, S.C. Crystal structure of the het-erodimeric bZIP transcription factor c-Fos-c-Jun bound to DNA. Nature 373 257-261, 1995. 

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