RNA Polymerase II
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I. Introduction
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
Transcription
II. General Structure
Wireframe
Cartoon and Wireframe
Notice the
beta-pleated sheets in yellow and the alpha helixes in pink.
Cartoon.
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.
Subunits.
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)
Active
Site.
Purple= LID, Green= RUDDER, Orange= FORKLOOP,
Yellow = important side chains: 252 &
264a, 318 & 320a, and 471
& 476b amino acids.
Active Site with RNA/DNA
Hybrid.
RNA= Red, DNA=
Blue.
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.
Solvent
Accessible Surface.
Surface at center of
1.2 A
sphere (diameter of water molecule).
Solvent
Excluded
Protein Surface.
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.