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Title: Structural insights into recognition of ;#8203;c-di-AMP by the ;#8203;ydaO riboswitch

;  [1]
  1. (NYUSM)
Publication Date:
Research Org.:
Argonne National Lab. (ANL), Argonne, IL (United States). Advanced Photon Source (APS)
Sponsoring Org.:
OSTI Identifier:
Resource Type:
Journal Article
Resource Relation:
Journal Name: Nat. Chem. Biol.; Journal Volume: 10; Journal Issue: 08, 2014
Country of Publication:
United States

Citation Formats

Gao, Ang, and Serganov , Alexander. Structural insights into recognition of ;#8203;c-di-AMP by the ;#8203;ydaO riboswitch. United States: N. p., 2014. Web. doi:10.1038/nchembio.1607.
Gao, Ang, & Serganov , Alexander. Structural insights into recognition of ;#8203;c-di-AMP by the ;#8203;ydaO riboswitch. United States. doi:10.1038/nchembio.1607.
Gao, Ang, and Serganov , Alexander. Mon . "Structural insights into recognition of ;#8203;c-di-AMP by the ;#8203;ydaO riboswitch". United States. doi:10.1038/nchembio.1607.
title = {Structural insights into recognition of ;#8203;c-di-AMP by the ;#8203;ydaO riboswitch},
author = {Gao, Ang and Serganov , Alexander},
abstractNote = {},
doi = {10.1038/nchembio.1607},
journal = {Nat. Chem. Biol.},
number = 08, 2014,
volume = 10,
place = {United States},
year = {Mon Aug 25 00:00:00 EDT 2014},
month = {Mon Aug 25 00:00:00 EDT 2014}
  • Glycine riboswitches regulate gene expression by feedback modulation in response to cooperative binding to glycine. Here, we report on crystal structures of the second glycine-sensing domain from the Vibrio cholerae riboswitch in the ligand-bound and unbound states. This domain adopts a three-helical fold that centers on a three-way junction and accommodates glycine within a bulge-containing binding pocket above the junction. Glycine recognition is facilitated by a pair of bound Mg{sup 2+} cations and governed by specific interactions and shape complementarity with the pocket. A conserved adenine extrudes from the binding pocket and intercalates into the junction implying that glycine bindingmore » in the context of the complete riboswitch could impact on gene expression by stabilizing the riboswitch junction and regulatory P1 helix. Analysis of riboswitch interactions in the crystal and footprinting experiments indicates that adjacent glycine-sensing modules of the riboswitch could form specific interdomain interactions, thereby potentially contributing to the cooperative response.« less
  • The bacterial second messenger c-di-GMP is used in many species to control essential processes that allow the organism to adapt to its environment. The c-di-GMP riboswitch (GEMM) is an important downstream target in this signaling pathway and alters gene expression in response to changing concentrations of c-di-GMP. The riboswitch selectively recognizes its second messenger ligand primarily through contacts with two critical nucleotides. However, these two nucleotides are not the most highly conserved residues within the riboswitch sequence. Instead, nucleotides that stack with c-di-GMP and that form tertiary RNA contacts are the most invariant. Biochemical and structural evidence reveals that themore » most common natural variants are able to make alternative pairing interactions with both guanine bases of the ligand. Additionally, a high-resolution (2.3 {angstrom}) crystal structure of the native complex reveals that a single metal coordinates the c-di-GMP backbone. Evidence is also provided that after transcription of the first nucleotide on the 3{prime}-side of the P1 helix, which is predicted to be the molecular switch, the aptamer is functional for ligand binding. Although large energetic effects occur when several residues in the RNA are altered, mutations at the most conserved positions, rather than at positions that base pair with c-di-GMP, have the most detrimental effects on binding. Many mutants retain sufficient c-di-GMP affinity for the RNA to remain biologically relevant, which suggests that this motif is quite resilient to mutation.« less