Transcription factor binding domains

See also Eukaryotic Transcription, Transcription Factor Binding Domains... 

See also RNA Polymerase I Transcription, RNA Polymerase III Transcription, RNA Polymerase II Transcription, Chromatin Structure and Transcription, Eukaryotic Transcription. Termination of Eukaryotic Transcription, Chromatin Remodeling, Transcription Factor Binding Domains... 

It is believed that many transcription factors bind DNA as dimers ( dimeric transcription factors) in either the same or opposite orientation. The DNA sites therefore can look like two direct repeat sequences or like palindromes. The interaction of the subunits with each other must obviously be specific and be mediated by dimerization domains. Specificity and stability of the dimers (dimeric transcription factors) is mostly promoted by hydrophobic or ionic inteiphases, e.g. a... 

To influence the activity of RNA polymerase, transcription factors bind to DNA at enhancer sites and/or promoter sites. Four different structures of these factors are known. They possess structures that allow specific binding to DNA. They are given names that indicate the key protein domains that encourage this binding, as follows ... 

Fig. 7. Schematic representation of the domain organizadon, as well as ligand-, receptor-, and co-receptor-binding preferences of the semaphorins and their neuronal receptors. The individual domains are labeled. PSI, Plexin/Semaphorin//ntegrin domain IPX, /mmunoglobulin-like domain found in Plexins (and Met) and in some Transcription factors CUB, domain homologous to complement-binding factors Clr and Cls FV/VIII, domain homologous to coagulation factor V and VIII (also known as F5/8 type C or discoidin domain) MAM, Meprin/A5/fi domain SP, Sex-Plexin domain. Semaphorins, plexins and scatter-factor receptors (MET) share a common semaphorin domain (black heptagon).

Figure 1 The classic yeast two-hybrid method and derivatives, (a) Schematic diagram of the yeast two-hybrid approach, describing an interaction between protein X and protein Y. Protein X is fused to a transcription factor DNA-binding domain (the "bait" construct), and protein Y is fused to a transcription factor activation domain (the "prey" construct), (b) High-throughput applications of the yeast two-hybrid method use mating of haploid strains carrying bait and prey, respectively. Hybrids can be mated in arrayed formats (as shown) or as libraries, (c) The reverse two-hybrid method uses a counter-selectable marker to indicate loss of protein interaction because of disruption by an inhibitor protein/small molecule ("/" illustrated in the diagram) or mutation(s) in proteins X and/or Y.

Key Words Motif discovery sequence motif sequence pattern protein domain multiple alignment position-specific scoring matrix PSSM position-specific weight matrix PWM transcription factor-binding site transcription factor promoter protein features. 

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). 

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