RNA Polymerase II

This is a default text for your page RNA Polymerase II. Click above on edit this page to modify. Be careful with the < and > signs.

You may include any references to papers as in: the use of JSmol in Proteopedia ^[1] or to the article describing Jmol ^[2] to the rescue.

Overview

RNA polymerase (RNAP) II

The is an Rpb1 segment that translocates the DNA-RNA combination at the end of each cycle of catalysis.

Structural Components

The clamp swings to trap the DNA in the cleft. Further along, the wall sends the DNA template through the cleft in approximately a 90° turn. Both the clamp and wall are parts of the Rpb2 subunit. Further along in the process, the rudder separates the newly synthesized RNA strand from the DNA template. The DNA reforms into a double helix as it leaves RNA pol II.

Other components of RNA pol II include the following:

The jaw is the opening through which DNA enters. The funnel is what the NTP’s travel through to be incorporated into the growing RNA strand, and the pore is the end of the funnel. The is an Rpb1 segment that translocates the DNA-RNA combination at the end of each cycle of catalysis.

This is a sample scene created with SAT to by Group, and another to make of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.

Mechanism of Action

Alpha Amanitin

α-Amanitin is a bicyclinc octapeptide that adheres tightly with RNAP II, which blocks the elongation steps. α-amanitin binds in the funnel and interacts with the bridge helix and adjacent Rpb1, but it does not inhibit the RNA pol II’s interaction with NTP. Instead, α-amanitin likely challenges the bridge’s conformational change that is necessary for the purposed RNAP translocation step. α-Amanitin, found in the poisonous mushroom death cap, leads to death after several days. This time frame aligns with the rate at which mRNA’s and proteins turnover.

Modifications