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 Mg(2+) 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 Mg(2+) is stabilized in the active center in different modes depending on the type of reaction: during synthesis by the beta,gamma-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.
Sosunov
Vasily
V
Public Health Research Institute, 225 Warren Street, Newark, NJ 07103, USA.
Sosunova
Ekaterina
E
Mustaev
Arkady
A
Bass
Irina
I
Nikiforov
Vadim
V
Goldfarb
Alex
A
D001665:Binding Sites; D002384:Catalysis; D012321:DNA-Directed RNA Polymerases / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D006863:Hydrogen-Ion Concentration; D006868:Hydrolysis; D008958:Models, Molecular; D011755:Pyrophosphatases / Q000494:pharmacology; D012313:RNA / Q000096:biosynthesis* / Q000378:metabolism
D012313:RNA; D012321:DNA-Directed RNA Polymerases; D011755:Pyrophosphatases