Alpha amanitin, a molecule isolated from the “death cap” mushroom, is the potent known inhibitor of RNA polymerase. α-amanitin inhibits both the initiation and elongation stages of transcription. The inhibitor binds to RNA polymerase between the two largest subunits, Rpb1 and Rpb2. The cleft that forms between these two subunits is connected by a helix bridge, and α-amanitin binds just beneath this bridge. The key hydrogen bonding occurs between amanitin and residues 726, 767-769, and 822 of the largest RNA polymerase subunit, Rpb1. There is also a hydrogen bonding interaction with residue 763 of Rpb2. This binding position allows α-amanitin to restrict the movement of the helix bridge. It does not, however, allow α-amanitin to interfere directly with the entry of nucleotides into the active site or with the formation of phosphodiester bonds. Amanitin does severely reduce the rate of translocation of RNA polymerase. The translocation reduces from thousands of nucleotides a minute to only a few. The reduced rate of translocation is a result of the constraint placed on the bridge helix by the binding of amanitin. The alpha helix bridge must be able to move in order for the entire RNA polymerase complex to move along the DNA strand. When α-amanitin is bound beneath the bridge helix, it is unable to make the required bend to cause the translocation. Transcription is severely inhibited as a result of this prevention of translocation. (
Bushnell, et al, 2002)
The buttons below the image show the location of the alpha amanitin binding site within Rpb1 (blue) and Rpb2 (green), as well as the key residues (red) that interact with amanitin.