RNA polymerase II makes the mRNA that ribosomes read. It grips duplex DNA in a cleft, unwinds one turn, then pairs the template strand with a growing RNA chain. A bridge helix and a trigger loop sit at the active site and check each incoming nucleotide. After each bond the enzyme moves one base along the template, and the new RNA leaves through a separate groove.
12
Rpb1 to Rpb12: a ten-subunit core plus the Rpb4-Rpb7 pair. Rpb1 and Rpb2 build the cleft and the active site.
9 base pairs
The hybrid runs from the active site at nearly a right angle to the entering DNA.
2
One metal stays bound; the second may exchange during synthesis.
~3.8 kb per minute
Elongation rate in human cells
18Measured over long human genes, about 63 nucleotides per second.
varies by gene
Elongation rate, genome-wide
19Pol II speeds up along a gene and slows at exons. Rates differ widely between genes.
~4 x 10^-6 per base
Transcription error rate
20Measured transcriptome-wide in Caenorhabditis elegans mRNA.
backtrack by one position
A misincorporated base frays, the enzyme backtracks, and the same active site cuts off the RNA end that holds the error.
a leucine moves ~13 A
Measured between the wedged and closed positions of the trigger loop.