5U3G

Structure of the Dickeya dadantii ykkC riboswitch bound to guanidinium

Summary for 5U3G

• Entry DOI: 10.2210/pdb5u3g/pdb
• Descriptor: ykkC riboswitch, MAGNESIUM ION, GUANIDINE, ... (5 entities in total)
• Functional Keywords: riboswitch, ykkc, guanidine, guanidinium, rna
• Biological source: Dickeya dadantii
• Total number of polymer chains: 1
• Total formula weight: 28595.11

Authors

Battaglia, R.A.,Price, I.R.,Ke, A. (deposition date: 2016-12-02, release date: 2017-02-01, Last modification date: 2024-03-06)

Primary citation

Battaglia, R.A.,Price, I.R.,Ke, A.
Structural basis for guanidine sensing by the ykkC family of riboswitches.
RNA, 23:578-585, 2017

PubMed Abstract: Regulation of gene expression by encoded riboswitches is a prevalent theme in bacteria. Of the hundreds of riboswitch families identified, the majority of them remain as orphans, without a clear ligand assignment. The orphan family was recently characterized as guanidine-sensing riboswitches. Herein we present a 2.3 Å crystal structure of the guanidine-bound riboswitch from The riboswitch folds into a boot-shaped structure, with a coaxially stacked P1/P2 stem forming the boot, and a 3'-P3 stem-loop forming the heel. Sophisticated base-pairing and cross-helix tertiary contacts give rise to the ligand-binding pocket between the boot and the heel. The guanidine is recognized in its positively charged guanidinium form, in its sp hybridization state, through a network of coplanar hydrogen bonds and by a cation-π stacking contact on top of a conserved guanosine residue. Disruption of these contacts resulted in severe guanidinium-binding defects. These results provide the structural basis for specific guanidine sensing by riboswitches and pave the way for a deeper understanding of guanidine detoxification-a previously unappreciated aspect of bacterial physiology.

PubMed: 28096518
DOI: 10.1261/rna.060186.116

Experimental method

X-RAY DIFFRACTION (2.3 Å)