Protein prokaryotic regulators

In the previous chapter we discussed DNA-binding proteins that regulate transcription in prokaryotes. The principles that govern recognition between proteins in eukaryotes show some similarities and some differences. In both cases specific recognition is dominated by interactions that take place in the major groove of the DNA. The specific interactions usually involve H bond formation... 

The biggest difference between transcription in prokaryotes and eukaryotes is the sheer number of proteins associated with the eukaryotic version of the process. Any protein that regulates transcription but is not itself a subunit of RNA polymerase is a transcription factor. There are many transcription factors for eukaryotic transcription, as we shall see. The molecular mass of the entire complex of Pol II and all of the associated factors exceeds 2.5 million Da. 

Regulation in eukaryotes is much more complicated. Prokaryotic regulation is controlled by the choice of G-subunit, the nature of the promoters, and the use of repressors/inducers. In eukaryotes, there are many more promoter elements, transcription factors, and coactivators. In addition, the DNA must be released from histone proteins, so transcription of DNA is linked to histone modifications. 

In cyclic nucleotide-regulated channels, this domain serves as a high-affinity binding site for 3-5 cyclic monophosphates. The CNBD of channels has a significant sequence similarity to the CNBD of most other classes of eukaryotic cyclic nucleotide receptors and to the CNBD of the prokaryotic catabolite activator protein (CAP). The primary sequence of CNBDs consists of approximately 120 amino acid residues forming three a-helices (oA-aC) and eight (3-strands ( 31- 38). 

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