E. coli RNA Polymerase is α2ββ'ω there are three eukaryotic RNA Polymerases. Binding of the RNA polymerase to the gene is highly regulated and requires lots of protein factors even for genes active in all cells. Transcription in eukaryotes requires the assembly of the RNA Polymerase into a very large initiation complex at the gene promoter. This is controlled by a large number of factors that effect both the packaging of the DNA and the binding of the polymerase.
|Mg+ Ion||Important in catalysis of phosphodiester bond attack.|
|CTD||The carboxy terminal domain is very important for RNA processing. You have a protein and a peptide repeat and its serines can be phosphorylatd and then bind the RNA transcript and do RNA processing like cap, polyadenylation and more. CTD = (Tyr-Ser-Pro-Thr-Ser-Pro-Ser)n → n = ~26 in yeast, 52 in mammals Ser2 and Ser5 are phosphorylated and dephosphorylated.|
RNA Polymerase II General Transcription Factors
Pol II requires the RNA polymerase II General Transcription Factors (Pol II GTFs) to transcribe virtually all eukaryotic protein coding genes. Purified RNA polymerase II cannot initiate transcription from a promoter without the assistance these proteins: (TFIIA); TFIIB; TFIID; TFIIE; TFIIF; TFIIH. These are required along with Pol II to transcribe virtually all eukaryotic protein coding genes.
Within TFIID is a TATA-box binding domain that binds the TATA-box; next, TFIIA binds upstream to TFIID and then TFIIB downstream to TFIID. This multi-protein complex binds RNA Pol II (forming the basal transcription complex) and transcription initiates. In genes without a TATA box, an initiator element binds TBP instead but without sequence specificity.
|TFIID||Subunit. is TBP. TBP is associated with several other subunits in the general transcription factor TFIID. These are called TBP-Associated Factors, or TAFs. There is an anti-TBP that blocks initiation of transcription.|
|TFIIH||TFIIH is a large General Transcription Factor (GTF) of 9 subunits, nearly as large as Pol II. Two of the subunits are homologous to DNA helicases, enzymes that use energy from ATP hydrolysis to separate the strands of a DNA double helix. One of the subunits is a kinase that phosphorylates Ser5 of the Pol II large subunit C-terminal domain (CTD) heptapeptide repeat (Tyr-Ser-Pro-Thr-Ser-Pro-Ser).|