RNA polymerase-2

Function

• RNA polymerase 2 transcribes genes into mRNA at ~ 50 bases/sec
• synthesis of mRNA, snRNAs U1-U5 & U7
• at the start of transcription, a single stranded DNA template strand of the promoter is positioned within the central active site cleft of RNA polymerase 2
• a bridging helix emanates from POLR2A & crosses the cleft near the catalytic site & is thought to promote translocation of RNA polymerase 2 by acting as a ratchet that moves the RNA-DNA hybrid through the active site by switching from straight to bent conformations at each step of nucleotide addition
• during transcription elongation, RNA polymerase 2 moves on the template as the transcript elongates
• elongation is influenced by the phosphorylation status of the C-terminal domain (CTD) of POLR2A which serves as a platform for assembly of factors that regulate transcription initiation, elongation, termination & mRNA processing
• binding of ribonucleoside triphosphate to the RNA polymerase 2 transcribing complex probably involves a two- step mechanism
• initial binding seems to occur at the entry (E) site & involves a Mg+2 temporarily coordinated by 3 conserved Asp of the two largest RNA polymerase 2 subunits (POLR2A & POLR2B)
• the ribonucleoside triphosphate is transferred by a rotation to the nucelotide addition (A) site for pairing with the template DNA
• the catalytic A site involves 3 conserved Asp of POLR2A permanently coordinating a 2nd Mg+2
• RNA polymerase 2 interacts with accessory proteins that modulate transcription including:
  • elongation factor ELL2
  • transcription elongation factors necessary for efficient RNA polymerase 2 transcription elongation past template- encoded arresting sites
• holoenzyme contains RNA polymerase 2 elongator complex

Structure

• 12 subunits
• yeast RNA polymerase 2 complex consists of 12 subunits all of which have been cloned
• in mammalian systems many subunit genes have not yet been cloned
• 2 largest subunits comprise at least part of the catalytic site, but the functions of other subunits are not yet clear
• consist of core element with a central large cleft, a clamp element that moves to open & close the cleft & jaws that are thought to grab the incoming DNA template
• the RNA polymerase 2 core element consists of POLR2A & POLR2B (2 largest subunits)

More general terms

• RNA polymerase
• phosphoprotein
• regulatory molecule

More specific terms

• RNA polymerase-2 yeast holoenzyme

Additional terms

• RNA polymerase 2 elongator complex
• RNA polymerase II elongation factor ELL2 (ELL2)
• RNA polymerase II elongation factor ELL; eleven-nineteen lysine-rich leukemia protein (ELL, C19orf17)
• transcription

Component of

• transcriptional initiation complex

Components

• RNA polymerase II subunit A C-terminal domain phosphatase; TFIIF-associating CTD phosphatase (CTDP1, FCP1)
• RNA polymerase II elongation factor ELL3 (ELL3)
• TBP-associated factor 2N; RNA-binding protein 56; RBP56; TAF15 RNA polymerase 2; TATA box-binding protein-associated factor 68-kd (TAF2N)