The Structure of the Guanidine-II Riboswitch

Lin Huang; Jia Wang; David M. J. Lilley

doi:10.1016/j.chembiol.2017.05.014

The Structure of the Guanidine-II Riboswitch

Lin Huang, Jia Wang, David M. J. Lilley (Lead / Corresponding author)

Research output: Contribution to journal › Article › peer-review

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Abstract

The guanidine-II (mini-ykkC) riboswitch is the smallest of the guanidine-responsive riboswitches, comprising two stem loops of similar sequence. We have solved high-resolution crystal structures of both stem loops for the riboswitch from Gloeobacter violaceus. The stem loops have a strong propensity to dimerize by intimate loop-loop interaction. The dimerization creates specific binding pockets for two guanidine molecules, explaining their cooperative binding. Within the binding pockets the ligands are hydrogen bonded to a guanine at O6 and N7, and to successive backbone phosphates. Additionally they are each stacked upon a guanine nucleobase. One side of the pocket has an opening to the solvent, slightly lowering the specificity of ligand binding, and structures with bound methylguanidine, aminoguanidine, and agmatine show how this is possible.

Original language	English
Pages (from-to)	695-702.e2
Number of pages	10
Journal	Cell Chemical Biology
Volume	24
Issue number	6
Early online date	18 May 2017
DOIs	https://doi.org/10.1016/j.chembiol.2017.05.014
Publication status	Published - 22 Jun 2017

Keywords

Gene regulation
RNA structure
X-ray crystallography
riboregulation

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10.1016/j.chembiol.2017.05.014Licence: CC BY

Final Published Version
Copyright 2017 The Authors. Published by Elsevier Ltd. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).
Final published version, 2.3 MBLicence: CC BY

Dynamics of Eukaryotic Junction-Resolving Enzyme GEN1 - DNA Junction Interactions
Lilley, D. (Investigator)
Biotechnology and Biological Sciences Research Council
1/10/16 → 30/09/19
Project: Research
Fluorescence Resonance Energy Transfer as a Rich Source of Orientational Information in Nucleic Acid Structure
Lilley, D. (Investigator)
Engineering and Physical Sciences Research Council
1/09/12 → 30/06/16
Project: Research

Lilley, David
- Molecular Cell and Developmental Biology - Professor of Molecular Biology
Person: Academic

Cite this

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title = "The Structure of the Guanidine-II Riboswitch",

abstract = "The guanidine-II (mini-ykkC) riboswitch is the smallest of the guanidine-responsive riboswitches, comprising two stem loops of similar sequence. We have solved high-resolution crystal structures of both stem loops for the riboswitch from Gloeobacter violaceus. The stem loops have a strong propensity to dimerize by intimate loop-loop interaction. The dimerization creates specific binding pockets for two guanidine molecules, explaining their cooperative binding. Within the binding pockets the ligands are hydrogen bonded to a guanine at O6 and N7, and to successive backbone phosphates. Additionally they are each stacked upon a guanine nucleobase. One side of the pocket has an opening to the solvent, slightly lowering the specificity of ligand binding, and structures with bound methylguanidine, aminoguanidine, and agmatine show how this is possible.",

keywords = "Gene regulation, RNA structure, X-ray crystallography, riboregulation",

author = "Lin Huang and Jia Wang and Lilley, {David M. J.}",

note = "Funding: Cancer Research UK (program grant A18604).",

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doi = "10.1016/j.chembiol.2017.05.014",

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T1 - The Structure of the Guanidine-II Riboswitch

AU - Huang, Lin

AU - Wang, Jia

AU - Lilley, David M. J.

N1 - Funding: Cancer Research UK (program grant A18604).

PY - 2017/6/22

Y1 - 2017/6/22

N2 - The guanidine-II (mini-ykkC) riboswitch is the smallest of the guanidine-responsive riboswitches, comprising two stem loops of similar sequence. We have solved high-resolution crystal structures of both stem loops for the riboswitch from Gloeobacter violaceus. The stem loops have a strong propensity to dimerize by intimate loop-loop interaction. The dimerization creates specific binding pockets for two guanidine molecules, explaining their cooperative binding. Within the binding pockets the ligands are hydrogen bonded to a guanine at O6 and N7, and to successive backbone phosphates. Additionally they are each stacked upon a guanine nucleobase. One side of the pocket has an opening to the solvent, slightly lowering the specificity of ligand binding, and structures with bound methylguanidine, aminoguanidine, and agmatine show how this is possible.

AB - The guanidine-II (mini-ykkC) riboswitch is the smallest of the guanidine-responsive riboswitches, comprising two stem loops of similar sequence. We have solved high-resolution crystal structures of both stem loops for the riboswitch from Gloeobacter violaceus. The stem loops have a strong propensity to dimerize by intimate loop-loop interaction. The dimerization creates specific binding pockets for two guanidine molecules, explaining their cooperative binding. Within the binding pockets the ligands are hydrogen bonded to a guanine at O6 and N7, and to successive backbone phosphates. Additionally they are each stacked upon a guanine nucleobase. One side of the pocket has an opening to the solvent, slightly lowering the specificity of ligand binding, and structures with bound methylguanidine, aminoguanidine, and agmatine show how this is possible.

KW - Gene regulation

KW - RNA structure

KW - X-ray crystallography

KW - riboregulation

U2 - 10.1016/j.chembiol.2017.05.014

DO - 10.1016/j.chembiol.2017.05.014

M3 - Article

C2 - 28529131

SN - 2451-9456

VL - 24

SP - 695-702.e2

JO - Cell Chemical Biology

JF - Cell Chemical Biology

IS - 6

ER -

The Structure of the Guanidine-II Riboswitch

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Projects

Dynamics of Eukaryotic Junction-Resolving Enzyme GEN1 - DNA Junction Interactions

Fluorescence Resonance Energy Transfer as a Rich Source of Orientational Information in Nucleic Acid Structure

Profiles

Lilley, David

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