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Citation
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HERO ID
3123415
Reference Type
Journal Article
Title
An active site rearrangement within the Tetrahymena group I ribozyme releases nonproductive interactions and allows formation of catalytic interactions
Author(s)
Sengupta, RN; Van Schie, SNS; Giambasu, G; Dai, Q; Yesselman, JD; York, D; Piccirilli, JA; Herschlag, D
Year
2016
Is Peer Reviewed?
1
Journal
R N A
ISSN:
1355-8382
Volume
22
Issue
1
Page Numbers
32-48
Language
English
PMID
26567314
DOI
10.1261/rna.053710.115
Web of Science Id
WOS:000368967600004
Abstract
Biological catalysis hinges on the precise structural integrity of an active site that binds and transforms its substrates and meeting this requirement presents a unique challenge for RNA enzymes. Functional RNAs, including ribozymes, fold into their active conformations within rugged energy landscapes that often contain misfolded conformers. Here we uncover and characterize one such "off-pathway" species within an active site after overall folding of the ribozyme is complete. The Tetrahymena group I ribozyme (E) catalyzes cleavage of an oligonucleotide substrate (S) by an exogenous guanosine (G) cofactor. We tested whether specific catalytic interactions with G are present in the preceding E•S•G and E•G ground-state complexes. We monitored interactions with G via the effects of 2'- and 3'-deoxy (-H) and -amino (-NH(2)) substitutions on G binding. These and prior results reveal that G is bound in an inactive configuration within E•G, with the nucleophilic 3'-OH making a nonproductive interaction with an active site metal ion termed MA and with the adjacent 2'-OH making no interaction. Upon S binding, a rearrangement occurs that allows both -OH groups to contact a different active site metal ion, termed M(C), to make what are likely to be their catalytic interactions. The reactive phosphoryl group on S promotes this change, presumably by repositioning the metal ions with respect to G. This conformational transition demonstrates local rearrangements within an otherwise folded RNA, underscoring RNA's difficulty in specifying a unique conformation and highlighting Nature's potential to use local transitions of RNA in complex function.
Keywords
active site; conformational change; metal ion; noncoding RNA; RNA catalysis
Tags
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Ammonia, Oral - Problem Formulation
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