Paired-domain containing transcription

A leucine zipper is a structural motif present in a large class of transcription factors. These dimeric proteins contain two extended alpha helices that grip the DNA molecule much like a pair of scissors at adjacent major grooves. The coiled-coil dimerization domain contains precisely spaced leucine residues which are required for the interaction of the two monomers. Some DNA-binding proteins with this general motif contain other hydrophobic amino acids in these positions hence, this structural motif is generally called a basic zipper. 

The DNA-binding domain of the yeast GCN4 transcription factor mentioned earlier is a leucine-zipper domain. X-ray crystallographic analysis of complexes between DNA and the GCN4 DNA-binding domain has shown that the dimeric protein contains two extended a helices that grip the DNA molecule, much like a pair of scissors, at two ad-... 

There is good evidence for independent chromosomal domains of about 50- to 100-thousand base pairs (50100 kb) of DNA. In such a domain, the ends of the domain are anchored so that the domain may be torsionally constrained, even though the chromosome is linear. One domain can contain any or all of the elements of chromatin structure already mentioned. The current hypothesis is that the ends of the domains are anchored to a large, stable protein structure, called the nuclear matrix (in interphase) or the nuclear scaffold (in metaphase). In some cases, one domain may represent one independently controlled transcriptional unit. The possibility of DNA becoming supercoiled within a torsionally constrained domain is discussed in Chapter 2. 

In addition to independent DNA binding and activation sequences, many eukaryotic transcription factors also contain dimerization domains, which are sequences required for subunit interactions. Most prokaryotic DNA binding proteins bind to an inverted repeat DNA sequence as homodimers. However, many eukaryotic transcription factors are members of multi-gene families, and because of conserved structural properties in the dimer interface of the proteins, two related proteins can often form heterodimers. Since these related proteins may have subtle differences in their DNA binding domains, such heterodimer pairings can create discrete DNA binding specificities. 

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