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The structural basis for recognition of the PreQ0 metabolite by an unusually small riboswitch aptamer domain.


ABSTRACT: Riboswitches are RNA elements that control gene expression through metabolite binding. The preQ(1) riboswitch exhibits the smallest known ligand-binding domain and is of interest for its economical organization and high affinity interactions with guanine-derived metabolites required to confer tRNA wobbling. Here we present the crystal structure of a preQ(1) aptamer domain in complex with its precursor metabolite preQ(0). The structure is highly compact with a core that features a stem capped by a well organized decaloop. The metabolite is recognized within a deep pocket via Watson-Crick pairing with C15. Additional hydrogen bonds are made to invariant bases U6 and A29. The ligand-bound state confers continuous helical stacking throughout the core fold, thus providing a platform to promote Watson-Crick base pairing between C9 of the decaloop and the first base of the ribosome-binding site, G33. The structure offers insight into the mode of ribosome-binding site sequestration by a minimal RNA fold stabilized by metabolite binding and has implications for understanding the molecular basis by which bacterial genes are regulated.

SUBMITTER: Spitale RC 

PROVIDER: S-EPMC2670106 | biostudies-literature | 2009 Apr

REPOSITORIES: biostudies-literature

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The structural basis for recognition of the PreQ0 metabolite by an unusually small riboswitch aptamer domain.

Spitale Robert C RC   Torelli Andrew T AT   Krucinska Jolanta J   Bandarian Vahe V   Wedekind Joseph E JE  

The Journal of biological chemistry 20090304 17


Riboswitches are RNA elements that control gene expression through metabolite binding. The preQ(1) riboswitch exhibits the smallest known ligand-binding domain and is of interest for its economical organization and high affinity interactions with guanine-derived metabolites required to confer tRNA wobbling. Here we present the crystal structure of a preQ(1) aptamer domain in complex with its precursor metabolite preQ(0). The structure is highly compact with a core that features a stem capped by  ...[more]

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