Structure and ligand binding of the glutamine-II riboswitch

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

Research output: Contribution to journalArticle

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Abstract

We have determined the structure of the glutamine-II riboswitch ligand binding domain using X-ray crystallography. The structure was solved using a novel combination of homology modeling and molecular replacement. The structure comprises three coaxial helical domains, the central one of which is a pseudoknot with partial triplex character. The major groove of this helix provides the binding site for L-glutamine, which is extensively hydrogen bonded to the RNA. Atomic mutation of the RNA at the ligand binding site leads to loss of binding shown by isothermal titration calorimetry, explaining the specificity of the riboswitch. A metal ion also plays an important role in ligand binding. This is directly bonded to a glutamine carboxylate oxygen atom, and its remaining inner-sphere water molecules make hydrogen bonding interactions with the RNA.

Original languageEnglish
Pages (from-to)7666-7675
Number of pages10
JournalNucleic Acids Research
Volume47
Issue number14
Early online date19 Jun 2019
DOIs
Publication statusPublished - 22 Aug 2019

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Riboswitch
Glutamine
RNA
Ligands
Binding Sites
Calorimetry
X Ray Crystallography
Hydrogen Bonding
Hydrogen
Metals
Ions
Oxygen
Mutation
Water

Cite this

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title = "Structure and ligand binding of the glutamine-II riboswitch",
abstract = "We have determined the structure of the glutamine-II riboswitch ligand binding domain using X-ray crystallography. The structure was solved using a novel combination of homology modeling and molecular replacement. The structure comprises three coaxial helical domains, the central one of which is a pseudoknot with partial triplex character. The major groove of this helix provides the binding site for L-glutamine, which is extensively hydrogen bonded to the RNA. Atomic mutation of the RNA at the ligand binding site leads to loss of binding shown by isothermal titration calorimetry, explaining the specificity of the riboswitch. A metal ion also plays an important role in ligand binding. This is directly bonded to a glutamine carboxylate oxygen atom, and its remaining inner-sphere water molecules make hydrogen bonding interactions with the RNA.",
author = "Lin Huang and Jia Wang and Watkins, {Andrew M.} and Rhiju Das and Lilley, {David M. J.}",
note = "Funding Cancer Research UK [A18604 to D.M.J.L.]; U.S. National Institutes of Health [R21 CA219847, R35 GM122579 to R.D.]. The open access publication charge for this paper has been waived by Oxford University Press – NAR Editorial Board members are entitled to one free paper per year in recognition of their work on behalf of the journal. Conflict of interest statement. None declared.{\circledC} The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research.",
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Structure and ligand binding of the glutamine-II riboswitch. / Huang, Lin; Wang, Jia; Watkins, Andrew M.; Das, Rhiju; Lilley, David M. J. (Lead / Corresponding author).

In: Nucleic Acids Research, Vol. 47, No. 14, 22.08.2019, p. 7666-7675.

Research output: Contribution to journalArticle

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T1 - Structure and ligand binding of the glutamine-II riboswitch

AU - Huang, Lin

AU - Wang, Jia

AU - Watkins, Andrew M.

AU - Das, Rhiju

AU - Lilley, David M. J.

N1 - Funding Cancer Research UK [A18604 to D.M.J.L.]; U.S. National Institutes of Health [R21 CA219847, R35 GM122579 to R.D.]. The open access publication charge for this paper has been waived by Oxford University Press – NAR Editorial Board members are entitled to one free paper per year in recognition of their work on behalf of the journal. Conflict of interest statement. None declared.© The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research.

PY - 2019/8/22

Y1 - 2019/8/22

N2 - We have determined the structure of the glutamine-II riboswitch ligand binding domain using X-ray crystallography. The structure was solved using a novel combination of homology modeling and molecular replacement. The structure comprises three coaxial helical domains, the central one of which is a pseudoknot with partial triplex character. The major groove of this helix provides the binding site for L-glutamine, which is extensively hydrogen bonded to the RNA. Atomic mutation of the RNA at the ligand binding site leads to loss of binding shown by isothermal titration calorimetry, explaining the specificity of the riboswitch. A metal ion also plays an important role in ligand binding. This is directly bonded to a glutamine carboxylate oxygen atom, and its remaining inner-sphere water molecules make hydrogen bonding interactions with the RNA.

AB - We have determined the structure of the glutamine-II riboswitch ligand binding domain using X-ray crystallography. The structure was solved using a novel combination of homology modeling and molecular replacement. The structure comprises three coaxial helical domains, the central one of which is a pseudoknot with partial triplex character. The major groove of this helix provides the binding site for L-glutamine, which is extensively hydrogen bonded to the RNA. Atomic mutation of the RNA at the ligand binding site leads to loss of binding shown by isothermal titration calorimetry, explaining the specificity of the riboswitch. A metal ion also plays an important role in ligand binding. This is directly bonded to a glutamine carboxylate oxygen atom, and its remaining inner-sphere water molecules make hydrogen bonding interactions with the RNA.

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