The structural basis for recognition of the preQ0 metabolite by an unusually small riboswitch aptamer domain

Robert C. Spitale, Andrew T. Torelli, Jolanta Krucinska, Vahe Bandarian, Joseph E. Wedekind

Research output: Contribution to journalArticle

64 Citations (Scopus)

Abstract

Riboswitches are RNA elements that control gene expression through metabolite binding. The preQ1 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 preQ1 aptamer domain in complex with its precursor metabolite preQ0. 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.

Original languageEnglish (US)
Pages (from-to)11012-11016
Number of pages5
JournalJournal of Biological Chemistry
Volume284
Issue number17
DOIs
StatePublished - Apr 24 2009

Fingerprint

Riboswitch
Metabolites
Ribosomes
Binding Sites
RNA
Ligands
N,N-dimethyl-3,3-diphenyl-1-methylallylamine
Bacterial Genes
Guanine
Transfer RNA
Base Pairing
Hydrogen
Gene Expression
Gene expression
Hydrogen bonds
Genes
Crystal structure

ASJC Scopus subject areas

  • Biochemistry
  • Cell Biology
  • Molecular Biology

Cite this

The structural basis for recognition of the preQ0 metabolite by an unusually small riboswitch aptamer domain. / Spitale, Robert C.; Torelli, Andrew T.; Krucinska, Jolanta; Bandarian, Vahe; Wedekind, Joseph E.

In: Journal of Biological Chemistry, Vol. 284, No. 17, 24.04.2009, p. 11012-11016.

Research output: Contribution to journalArticle

Spitale, Robert C. ; Torelli, Andrew T. ; Krucinska, Jolanta ; Bandarian, Vahe ; Wedekind, Joseph E. / The structural basis for recognition of the preQ0 metabolite by an unusually small riboswitch aptamer domain. In: Journal of Biological Chemistry. 2009 ; Vol. 284, No. 17. pp. 11012-11016.
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