Structural basis for guanidine sensing by the ykkC family of riboswitches

Battaglia, Robert A.; Price, Ian R.; Ke, Ailong

doi:10.1261/rna.060186.116

Title: Structural basis for guanidine sensing by the ykkC family of riboswitches

Journal Article · Tue Jan 17 00:00:00 EST 2017 · RNA

DOI:https://doi.org/10.1261/rna.060186.116· OSTI ID:1430300

Battaglia, Robert A. ^[1]; Price, Ian R. ^[1]; Ke, Ailong ^[1]

Cornell Univ., Ithaca, NY (United States)

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. In this work, we present a 2.3 Å crystal structure of the guanidine-bound ykkC riboswitch from Dickeya dadantii. 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 sp² 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 ykkC riboswitches and pave the way for a deeper understanding of guanidine detoxification—a previously unappreciated aspect of bacterial physiology.

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

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

Grant/Contract Number:: AC02-06CH11357; R41 GM103403; S10 RR029205

OSTI ID:: 1430300

Journal Information:: RNA, Vol. 23, Issue 4; ISSN 1355-8382

Publisher:: Cambridge University PressCopyright Statement

Country of Publication:: United States

Language:: ENGLISH

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Cited by: 35 works

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