Unified two-metal mechanism of RNA synthesis and degradation by RNA polymerase

In DNA‐dependent RNA polymerases, reactions of RNA synthesis and degradation are performed by the same active center (in contrast to DNA polymerases in which they are separate). We propose a unified catalytic mechanism for multisubunit RNA polymerases based on the analysis of its 3′–5′ exonuclease reaction in the context of crystal structure. The active center involves a symmetrical pair of Mg2+ ions that switch roles in synthesis and degradation. One ion is retained permanently and the other is recruited ad hoc for each act of catalysis. The weakly bound Mg2+ is stabilized in the active center in different modes depending on the type of reaction: during synthesis by the β,γ‐phosphates of the incoming substrate; and during hydrolysis by the phosphates of a non‐base‐paired nucleoside triphosphate. The latter mode defines a transient, non‐specific nucleoside triphosphate‐binding site adjacent to the active center, which may serve as a gateway for polymerization of substrates.