Structural basis for transcription inhibition by tagetitoxin

Tagetitoxin (Tgt) inhibits plastid-encoded, bacterial and some eukaryotic RNA polymerases (RNAPs) by an unknown mechanism. A 2.4Å-resolution structure of the Thermus thermophilus RNAP/Tgt complex revealed that Tgt-binding site within the RNAP secondary channel overlaps with that of the stringent control effector ppGpp, which partially protects RNAP from Tgt inhibition. Tgt binding is mediated exclusively through polar interactions with the β and β′ residues whose substitutions confer resistance to Tgt in vitro. Importantly, a Tgt phosphate, together with two active site acidic residues, coordinates the third Mg2+ ion distinct from the two catalytic metal ions. We show that Tgt inhibits all RNAP catalytic reactions and propose a mechanism in which the Tgt-bound Mg2+ ion plays a key role in stabilization of an inactive transcription intermediate. This and other recent studies suggest that Mg-mediated remodeling of the active site could be a common theme in the regulation of catalysis by nucleic acid enzymes.