Alpha-amanitin is a mushroom-derived cyclic peptide containing eight amino acid residues. It inhibits RNA polymerase II, making it a molecular tool for studying transcription as well as a naturally occurring toxin. Its small residue count coexists with a constrained ring-and-bridge chemical structure.[ref]
Alpha-Amanitin in PubChem. CID 9543442, Description and structural identity
A structural experiment soaked RNA polymerase II transcription elongation complex crystals with alpha-amanitin. The inhibitor trapped a state resolved at in which the entering DNA base lay above a shifted RNA polymerase bridge helix instead of occupying the normal templating position. The authors interpreted this as a possible intermediate in the polymerase's movement along DNA.[ref]
Structural basis of transcription inhibition by alpha-amanitin and implications for RNA polymerase II translocation by Florian Brueckner and Patrick Cramer. 2008, abstract: crystal soaking, resolution and proposed translocation intermediate
This illustrates how blocking a moving enzyme can reveal part of its reaction cycle. A trapped structure identifies a physically accessible arrangement; establishing how frequently that arrangement occurs during uninhibited transcription requires kinetic evidence as well. Inhibition of RNA polymerase II should also be specified by assay conditions rather than treated as a universal claim about every RNA polymerase.[ref]
Role of DNA-Dependent RNA Polymerase III in the Transcription of the tRNA and 5S RNA Genes by Roberto Weinmann and Robert G. Roeder. 1974, polymerase-dependent alpha-amanitin inhibition comparisons
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