RNA Polymerase II
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RNA polymerase II is responsible for making mRNA (messenger RNA) from a DNA
template. It is a complex of proteins that helps to
stabilize, transcribe, and separate the RNA/DNA hybrid that
is formed during transcription.
For more information see
Biochemistry Online: Chapter 5D - Binding and the Control of Gene
II. General Structure
Cartoon and Wireframe
beta-pleated sheets in yellow and the alpha helixes in pink.
Numerous magnesium ions
(blue balls) are observed
to bind to the polymerase surface. They may play a role in the binding
and bending of DNA, which is thought to be wrapped around the
polymerase as transcription proceeds.
Notice the DNA
(red wireframe)/RNA (cyan wireframe) hybrid located between the Purple and
Maroon subunits of the protein. Purple
= Sub-unit A, Maroon = Sub-unit B (Additional
colors delineate the different subunits of the protein)
Purple= LID, Green= RUDDER, Orange= FORKLOOP,
Yellow = important side chains: 252 &
264a, 318 & 320a, and 471
& 476b amino acids.
Active Site with RNA/DNA
RNA= Red, DNA=
The three parts (see above) of the active site are key to RNA/DNA strand
separation. The LID acts to dislodge the RNA from the DNA strand.
The RUDDER interacts with the DNA to help prevent re-annealing of the RNA/DNA hybrid. The FORKLOOP extends down the length of the RNA to help restrict the region of strand separation.
Surface at center of
sphere (diameter of water molecule).
Surface at contact with a 1.2 A sphere.
Map of Electrostatic Potential
of Subunits A and B.
Red = Negative, Blue = Positive. Notice the RNA/DNA hybrid in the
positively charged pocket (blue). This is because of the DNA/RNA backbone
which is negatively charged by the phosphates that comprise the phosphodiester bond.