5u3g

Publication Abstract from PubMed

Regulation of gene expression by cis-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 ykkC orphan family was recently characterized as guanidine-sensing riboswitches. Herein we present a 2.04 A crystal structure of the guanidine-bound ykkC riboswitch from Dickeya dadantii. The riboswitch folds into a boot-shaped structure, with a co-axially 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 sp2 hybridization state, through a network of coplanar hydrogen bonds and by a cation-pi 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 ykkC riboswitches, and pave the way for a deeper understanding of guanidine detoxification - a previously unappreciated aspect of bacterial physiology.

Structural Basis for Guanidine Sensing by the ykkC Family of Riboswitches.,Battaglia RA, Price IR, Ke A RNA. 2017 Jan 17. pii: rna.060186.116. doi: 10.1261/rna.060186.116. PMID:28096518^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.