Structural basis for ligand binding to the guanidine-II riboswitch

Reiss, Caroline W.; Strobel, Scott A.

doi:10.1261/rna.061804.117

Structural basis for ligand binding to the guanidine-II riboswitch

Journal Article · Fri Jun 09 00:00:00 EDT 2017 · RNA

DOI:https://doi.org/10.1261/rna.061804.117· OSTI ID:1430335

Reiss, Caroline W. ^[1]; Strobel, Scott A. ^[1]

Yale Univ., New Haven, CT (United States)

The guanidine-II riboswitch, also known as mini-ykkC, is a conserved mRNA element with more than 800 examples in bacteria. It consists of two stem–loops capped by identical, conserved tetraloops that are separated by a linker region of variable length and sequence. Like the guanidine-I riboswitch, it controls the expression of guanidine carboxylases and SugE-like genes. The guanidine-II riboswitch specifically binds free guanidinium cations and functions as a translationally controlled on-switch. Here we report the structure of a P2 stem–loop from the Pseudomonas aeruginosa guanidine-II riboswitch aptamer bound to guanidine at 1.57 Å resolution. The hairpins dimerize via the conserved tetraloop, which also contains the binding pocket. Two guanidinium molecules bind near the dimerization interface, one in each tetraloop. The guanidinium cation is engaged in extensive hydrogen bonding to the RNA. Contacts include the Hoogsteen face of a guanine base and three nonbridging phosphate oxygens. Cation–π interactions and ionic interactions also stabilize ligand binding. Finally, the guanidine-II riboswitch utilizes the same recognition strategies as the guanidine-I riboswitch while adopting an entirely different and much smaller RNA fold.

Research Organization:: Argonne National Laboratory (ANL), Argonne, IL (United States). Advanced Photon Source (APS)

Sponsoring Organization:: National Institutes of Health (NIH); USDOE Office of Science (SC)

OSTI ID:: 1430335

Journal Information:: RNA, Journal Name: RNA Journal Issue: 9 Vol. 23; ISSN 1355-8382

Publisher:: Cambridge University PressCopyright Statement

Country of Publication:: United States

Language:: ENGLISH

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Structure and ligand binding of the glutamine-II riboswitch Huang, Lin; Wang, Jia; Watkins, Andrew M. Nucleic Acids Research, Vol. 47, Issue 14 https://doi.org/10.1093/nar/gkz539	journal	June 2019
Acting in tandem Battaglia, Robert A.; Ke, Ailong eLife, Vol. 7 https://doi.org/10.7554/elife.36489	journal	April 2018
Structure and functional reselection of the Mango-III fluorogenic RNA aptamer Trachman, Robert J.; Autour, Alexis; Jeng, Sunny C. Y. Nature Chemical Biology, Vol. 15, Issue 5 https://doi.org/10.1038/s41589-019-0267-9	journal	April 2019
Guanidinium export is the primal function of SMR family transporters Kermani, Ali A.; Macdonald, Christian B.; Gundepudi, Roja Proceedings of the National Academy of Sciences, Vol. 115, Issue 12 https://doi.org/10.1073/pnas.1719187115	journal	March 2018
Guanidine Riboswitch-Regulated Efflux Transporters Protect Bacteria against Ionic Liquid Toxicity Higgins, Douglas A.; Gladden, John M.; Kimbrel, Jeff A. Journal of Bacteriology, Vol. 201, Issue 13 https://doi.org/10.1128/jb.00069-19	journal	April 2019
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59 BASIC BIOLOGICAL SCIENCES
RNA
guanidine
hairpin
kissing loop
riboswitch
tetraloop

Structural basis for ligand binding to the guanidine-II riboswitch

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