page_title: RNA polymerase II
section_title: Kinetics
hierarchical_section_title: RNA polymerase II / Kinetics
caption_attribution_description: Ribbon diagram of Saccharomyces cerevisiae RNA polymerase II in complex with α-amanitin (red). Active site magnesium ion visible in pink near center.Created using PyMOL (http://pymol.sourceforge.net) and GIMP. Style and orientation made to match http://www.pnas.org/content/vol99/issue3/images/large/pq0326646002.jpeg. Legend &#160;&#160; RNA polymerase II &#160;&#160; Active site magnesium ion &#160;&#160; &#945;-amanitin &#160;&#160; Zinc ions
context_page_description: RNA polymerase II is a multiprotein complex that transcribes DNA into precursors of messenger RNA and most small nuclear RNA and microRNA. It is one of the three RNAP enzymes found in the nucleus of eukaryotic cells. A 550 kDa complex of 12 subunits, RNAP II is the most studied type of RNA polymerase. A wide range of transcription factors are required for it to bind to upstream gene promoters and begin transcription.
context_section_description: Enzymes can catalyze up to several million reactions per second. Enzyme rates depend on solution conditions and substrate concentration. Like other enzymes POLR2 has a saturation curve and a maximum velocity (Vₘₐₓ). It has a Kₘ (substrate concentration required for one-half Vₘₐₓ) and a kcat (the number of substrate molecules handled by one active site per second). The specificity constant is given by kcat/Kₘ. The theoretical maximum for the specificity constant is the diffusion limit of about 10⁸ to 10⁹ (M⁻¹s⁻¹), where every collision of the enzyme with its substrate results in catalysis. In yeast, mutation in the Trigger-Loop domain of the largest subunit can change the kinetics of the enzyme.
  Bacterial RNA polymerase, a relative of RNA Polymerase II, switches between inactivated and activated states by translocating back and forth along the DNA. Concentrations of [NTP]eq = 10 μM GTP, 10 μM UTP, 5 μM ATP and 2.5 μM CTP, produce a mean elongation rate, turnover number, of ~1 bp (NTP)⁻¹ for bacterial RNAP, a relative of RNA polymerase II.
  RNA polymerase II undergoes extensive co-transcriptional pausing during transcription elongation. This pausing is especially pronounced at nucleosomes, and arises in part through the polymerase entering a transcriptionally incompetent backtracked state. The duration of these pauses ranges from seconds to minutes or longer, and exit from long-lived pauses can be promoted by elongation factors such as TFIIS. In turn, the transcription rate influences whether the histones of transcribed nucleosomes are evicted from chromatin, or reinserted behind the transcribing polymerase.
caption: RNA Polymerase II gray. Alpha-amanitin interaction (red).
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