Alpha-amanitin is toxic substance from the poisonous mushroom Amanita phalloides that causes severe human health problems and can be fatal (9).  This substance is a specific inhibitor of RNAPII and is known to interfere with the enzyme’s transcription mechanism.  As described above, Rpb1 and Rpb2 form a cleft in which DNA enters and binds to.  Rpb1 also projects an alpha helix (“bridge helix”) across this cleft forming a bridge-like structure between the two subunits.  This alpha helix serves to separate pore 1 from pore 2, which both lead downwards into a funnel-shaped cavity.  a-amanitin binds beneath this bridge helix and occupies the funnel-shaped cavity (View 1).  Residues from both the bridge helix and an adjacent region of Rpb1 located on the Rpb2 side of the cleft interact with a-amanitin.  The strongest of these interactions is a hydrogen bond between a-amanitin’s hydroxyproline 2 and Glu-A822 of the bridge helix (View 2 shows a close up of these interactions).  All of these interactions keep a-amanitin tightly bound within the funnel-shaped cavity and closest to the Rpb2-side of the cleft. 

During translocation, RNAPII moves down the DNA one nucleotide at a time in order to expose a new site for synthesis.  This process also causes the bridge helix to move.  Bridge helix residues are known to interact with both the first DNA nucleotide that is base-paired with RNA and the second unpaired DNA nucleotide.  Glu-A822 is a prime example for one of these residues.

a-amanitin drastically lowers the transcription rate of RNAPII.  This substance disrupts Glu-A822 and other residue interactions with the DNA and also prevents movement of the bridge helix.