Jmol pdb file is 1K83

This is the structure of alpha-amanitin

This shows how alpha-amanitin fits under the bridge helix


            Now that we have the layout of how RNAPII works during transcription, we can look at what causes changes in the normal function of transcription with inhibitors such as α-amanitin. α-Amanitin is the most potent and specific known inhibitor of the RNAPII enzyme [1], [2]. α-Amanitin (Show structure) is produced by the poisonous mushroom Amanita phalloides which is also called the destroying angel. This is actually such a potent inhibitor to RNAPII that more than a hundred deaths result worldwide from the ingestion of the poisonous mushroom. Ingestion of the mushroom will usually kill humans by destroying the liver and damaging the kidneys [2]. Bushnell et al. showed that the binding site of α-amanitin is located beneath the bridge helix (Bridge Helix) in a funnel shaped cavity in the RNAPII structure known as pore 1. The RNAPII residues that interact with α-amanitin are primarily located on that bridge helix and in fact there is a strong hydrogen bond formed between the bridge helix and α-amanitin.

What actually happens is α-amanitin will penetrate pore 1 and regulate translocation and stop elongation at or before translocation occurs [2].The binding of α-amanitin does not affect NTP loading into the active site because it sits too far away from the active site [1], [2]. How it prevents translocation is that the bridge helix needs flex in order to allow DNA movement. Since α-amanitin is associating with the bridge helix, it prevents this flexing and thus prevents DNA translocation [1], [2]. Gong et al. showed that depending on when α-amanitin associates with RNAPII will determine how it inhibits the enzyme. At some points, they are allowed to form a single phosphodiester bond but the α-amanitin will inhibit the next bond addition cycle. Other studies have shown that α-amanitin can allow for multiple phosphodiester bonds to form but the elongation rates are highly reduced [2]. This could have happened by the hydrogen bond between α-amanitin and the bridge helix being broken which would have allowed for the translocation of the DNA, and the enzyme would become resistant through a single bond addition cycle before inhibition was restored [2].

[1] Bushnell, D.A.; Cramer, P.; Kornberg, R.D. Structural basis of transcription: α-Amanitin-RNA polymerase II cocrystal at 2.8 Å resolution. PNAS. 5 February 2002. 99, 1218-1222.

[2] Gong, X.Q.; Nedialkov, Y.A.; Burton, Z.F. α-Amanitin Blocks Translocation by Human RNA Polymerase II. The Journal of Biological Chemistry. 19 April, 2004. 279, 27422-27427.

Effect of Alpha-Amanitin