The Structure of the Guanidine-II Riboswitch

Cell Chemical Biology
Lin HuangDavid M J Lilley

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.

Citations

Jul 14, 2017·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Sha GongWenbing Zhang
Mar 7, 2018·Proceedings of the National Academy of Sciences of the United States of America·Ali A KermaniRandy B Stockbridge
Apr 24, 2018·ELife·Robert A Battaglia, Ailong Ke
Apr 27, 2018·Wiley Interdisciplinary Reviews. RNA·Robert A Battaglia, Ailong Ke
May 15, 2020·Nucleic Acids Research·Jiří ČernýBohdan Schneider
Jun 11, 2020·Nucleic Acids Research·Lin HuangDavid M J Lilley
Aug 29, 2020·Nucleic Acids Research·Christine WuebbenOlav Schiemann
Sep 2, 2020·Biochemical Society Transactions·Elizabeth C GrayMichelle M Meyer
Jun 27, 2020·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Charles Bou-Nader, Jinwei Zhang
Aug 19, 2018·Nature Chemical Biology·Alla Peselis, Alexander Serganov
Jun 20, 2019·Nucleic Acids Research·Lin HuangDavid M J Lilley
Apr 18, 2019·Nature Chemical Biology·Robert J TrachmanAdrian R Ferré-D'Amaré
Mar 25, 2019·BMC Microbiology·Shira StavRonald R Breaker
Nov 29, 2020·Nature Communications·Ali A KermaniRandy B Stockbridge
Nov 26, 2020·Nucleic Acids Research·Felina LenkeitZasha Weinberg
Aug 15, 2020·Chembiochem : a European Journal of Chemical Biology·Oliver BinasHarald Schwalbe
Jan 23, 2021·RSC Medicinal Chemistry·G PadroniA E Hargrove
Feb 17, 2021·Molecular Microbiology·Malte SinnJörg S Hartig
Aug 8, 2018·Microbiology Spectrum·Thea S Lotz, Beatrix Suess
Aug 17, 2021·Frontiers in Microbiology·Ingrid M KeselerPeter D Karp
Dec 23, 2017·Biochemistry·Erica A Frankel, Philip C Bevilacqua
Nov 26, 2020·Biochemistry·Hubert SalvailRonald R Breaker

❮ Previous
Next ❯

Methods Mentioned

BETA
electrophoresis

Software Mentioned

5NEX
Coot
REDO
5NEQ
refine
MOLPROBITY
Phenix AutoSol
Autosol
Phenix

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.