DNA-binding sites

The two homologous repeats, each of 88 amino acids, at both ends of the TBP DNA-binding domain form two stmcturally very similar motifs. The two motifs each comprise an antiparallel p sheet of five strands and two helices (Figure 9.4). These two motifs are joined together by a short loop to make a 10-stranded p sheet which forms a saddle-shaped molecule. The loops that connect p strands 2 and 3 of each motif can be visualized as the stirmps of this molecular saddle. The underside of the saddle forms a concave surface built up by the central eight strands of the p sheet (see Figure 9.4a). Side chains from this side of the P sheet, as well as residues from the stirrups, form the DNA-binding site. No a helices are involved in the interaction area, in contrast to the situation in most other eucaryotic transcription factors (see below). 

By examining some of the over one thousand tumor-causing point mutations of p53 in the light of its structure, we can identify features of p53 that are necessary for tumor suppression. The amino acids most frequently changed in cancer cells are at or near the protein-DNA interface residues that are infrequently mutated, if at all, are in general far from the DNA-binding site. 

DNA-binding site specificity among the C -zinc cluster family of transcription factors is achieved by the linker regions... 

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... 

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... 

Kroeger, P.E., Morimoto, R.L (1994). Selection of new HSFI and HSF2 DNA-binding sites reveals difference in trimer cooperativity. Mol. Cell. Biol. 14, 7592-7603. ... 

Proteins with the helix-turn-helix or leucine zipper motifs form symmetric dimers, and their respective DNA binding sites are symmetric palindromes. In proteins with the zinc finger motif, the binding site is repeated two to nine times. These features allow for cooperative interactions between binding sites and enhance the degree and affinity of binding. 

Rothmel, RK, DL Shinbarger, MR Parsek, TL Aldrich, AM Chakrabarty (1991) Functional analysis of the Pseudomonas putida regulatory protein CatR transcriptional studies and determination of the CatR DNA-binding site by hydroxyl-radical footprinting. J Bacterial 173 4717-4724. 

The DNA binding site of Fur was predicted and then found to be in the N-terminal domain in an unusual helix-turn-helix motif (Holm et ah, 1994 Stojiljkovic and Hantke, 1995). The structure of Fur still remains to be determined and attempts to crystallize the protein have so far been unsuccessful. 

Dolenc, J. Oostenbrink, C. Koller, J. van Gunsteren, W.F., Molecular dynamics simulations and free energy calculations of netropsin and distamycin binding to an AAAAA DNA binding site, Nucl. Acids Res. 2005, 33, 725-733. 

Two types of DNA binding sites. Two different spectroscopically distinct types of binding sites have been identified utilizing absorption, fluorescence and linear dichroism data on non-covalent (6), and covalent (7) pyrene-like metabolite model compound-DNA complexes. 

The major goals of recent studies of the physical binding to DNA of BP and DMBA metabolites and metabolite models are to determine (1) the magnitudes of the binding constants, (2) the conformations of physical complexes which are formed and the nature of DNA binding sites, (3) how DNA structure and environment influence physical binding, (4) how the structure of hydrocarbon metabolites influences physical binding properties, (5) whether the... 

ACTIVATION OF TRANSCRIPTION by soluble hormones. The hormone is carried to its site of action by a carrier protein in the blood. The hormone crosses the membrane (by itself) and binds to a soluble receptor. A conformation change induced by hormone binding causes the receptor to expose its DNA binding site. This site binds to a specific sequence in the DNA upstream of genes that are to be activated for transcription. The transcription activation occurs through another domain of the protein that binds to components of the RNA polymerase complex. 

The X-ray crystallographic structure from the mouse protein Zif268 and a consensus DNA-binding site has been determined at 2.1-A resolution, as reported by the authors of reference 27. In this complex, the zinc fingers bind in the major groove of B-DNA and wrap part way around the double helix. Each zinc-finger... 

Matsen, S. and Shiverick, K., The Ah receptor recognizes DNA binding sites for the B cell transcription factor BSAP A possible mechanism for dioxin-mediated alteration of CD 19 gene expression in human B lymphocytes, Biochem. Biophys. Res. Comm., 212, 27, 1995. 

Wu et al. (1998) noted that doxombicin-induced apoptosis in lymphoid cells was blocked by pepstatin A, which is an inhibitor of cathepsin D. These investigators also observed that cathepsin D was induced through p53 DNA-binding sites at the cathepsin D promoter. Moreover, they have foimd that, compared to fibroblasts from wild-type mice, cathepsin D-/- fibroblasts from gene knock-out mice exhibited increased resistance to death caused by doxombicin. Also, in semm-deprived rat PC 12 cells undergoing apoptosis, the amoimt of cathepsin B has been observed to decline, while the level of cathepsin D increased (Shibata et al, 1998), and, in our laboratory (Kagedal et al, 2001), the same phenomenon was recently seen in human fibroblasts exposed to naphthazarin. 

Ribbon view of the R. capsulatus IHF protein bound to its DNA binding site upstream from hupS gene... 

Southgate CD, Green MR. The HlV-1 Tat protein activates transcription from an upstream DNA-binding site implications for Tat function. Genes Dev 1991 5(12B) 2496-2507. 

The C-terminal domain (85 amino acid residues, not completely denatured at 90 °C) of the so-called a subunit of the RNAP from the extremely thermophilic eubacterium T. thermophilus (Tt) has been expressed uniformly N/ C-labelled and structurally characterized by the NMR spectroscopy. The tertiary structure of the domain, comprising a helical turn and four helices, was found to be almost identical to that of the corresponding domain from the mesophilic E. coli, despite 32% sequence homology. The interaction of the Tt domain with a variety of DNAs at 37 °C and 50 °C was investigated by chemical shift perturbation of the NMR signals and the DNA binding site was localized. ... 

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