E2’s ion binding sites are exposed to the exterior of the cell and it has low affinity for Na+ but high affinity for K+

#Id: 2402

#Unit 3. Fundamental Processes

TF11S displays little similarity in sequence or structure to the Gre factors, but it binds to the same part of the enzyme, the RNA polymerase secondary channel (pore). 

#Id: 2403

#Unit 3. Fundamental Processes

The cleavage activity is intrinsic to RNA polymerase itself, it is stimulated greatly by accessory factors that are ubiquitous in the three biological kingdoms. There are two such factors in E. coli, GreA and GreB, and eukaryotic RNA polymerase II uses TFIIS for the same purpose. 

#Id: 2404

#Unit 3. Fundamental Processes

The Gre factors/TF11S enable the polymerase to cleave a few ribonucleotides from the 3' terminus of the RNA product, thereby allowing the catalytic site of RNA polymerase to be realigned with the 3' -OH.

#Id: 2405

#Unit 3. Fundamental Processes

An arrested RNA polymerase can restart transcription by cleaving the RNA transcript to generate a new 3' end.

#Id: 2406

#Unit 3. Fundamental Processes

RNA polymerase performs two proofreading functions on that growing transcript

pyrophosphorolytic editing

hydrolytic editing

#Id: 2407

#Unit 3. Fundamental Processes

In the Pyrophosphorolytic editing, the enzyme uses its active site, in a simple back-reaction, to catalyze the removal of an incorrectly inserted ribonucleotide, by reincorporation of PPi.