Journal
EMBO JOURNAL
Volume 22, Issue 9, Pages 2234-2244Publisher
OXFORD UNIV PRESS
DOI: 10.1093/emboj/cdg193
Keywords
catalytic magnesium; exonuclease; RNA polymerase; stimulating NTP; two-metal mechanism
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Funding
- NIGMS NIH HHS [GM30717, GM49242, R01 GM030717] Funding Source: Medline
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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 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.
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