The Structure of the Guanidine-II Riboswitch

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

Research output: Contribution to journalArticle

11 Citations (Scopus)
93 Downloads (Pure)

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 languageEnglish
Pages (from-to)695-702.e2
Number of pages10
JournalCell Chemical Biology
Volume24
Issue number6
Early online date18 May 2017
DOIs
Publication statusPublished - 22 Jun 2017

Fingerprint

Riboswitch
Guanidine
Guanine
Methylguanidine
Agmatine
Inverted Repeat Sequences
Ligands
Dimerization
Hydrogen
Crystal structure
Phosphates
Molecules

Keywords

  • Gene regulation
  • RNA structure
  • X-ray crystallography
  • riboregulation

Cite this

@article{6261f5c6956e49989660a9ab8444c1e4,
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).",
year = "2017",
month = "6",
day = "22",
doi = "10.1016/j.chembiol.2017.05.014",
language = "English",
volume = "24",
pages = "695--702.e2",
journal = "Cell Chemical Biology",
issn = "2451-9456",
publisher = "Elsevier",
number = "6",

}

The Structure of the Guanidine-II Riboswitch. / Huang, Lin; Wang, Jia; Lilley, David M. J. (Lead / Corresponding author).

In: Cell Chemical Biology, Vol. 24, No. 6, 22.06.2017, p. 695-702.e2.

Research output: Contribution to journalArticle

TY - JOUR

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

VL - 24

SP - 695-702.e2

JO - Cell Chemical Biology

JF - Cell Chemical Biology

SN - 2451-9456

IS - 6

ER -