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

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.