{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,30]],"date-time":"2026-09-30T16:12:25Z","timestamp":1790784745646,"version":"4.1.0"},"reference-count":32,"publisher":"Cold Spring Harbor Laboratory","issue":"4","funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health\/National Institute of General Medical Sciences","doi-asserted-by":"publisher","award":["GM118174"],"award-info":[{"award-number":["GM118174"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["P41 GM103403"],"award-info":[{"award-number":["P41 GM103403"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"NIH-ORIP HEI","doi-asserted-by":"publisher","award":["S10 RR029205"],"award-info":[{"award-number":["S10 RR029205"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["RNA"],"published-print":{"date-parts":[[2017,4]]},"abstract":"<jats:p>Regulation of gene expression by <jats:italic>cis-<\/jats:italic>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 <jats:italic>ykkC<\/jats:italic> orphan family was recently characterized as guanidine-sensing riboswitches. Herein we present a 2.3 \u00c5 crystal structure of the guanidine-bound <jats:italic>ykkC<\/jats:italic> riboswitch from <jats:italic>Dickeya dadantii<\/jats:italic>. The riboswitch folds into a boot-shaped structure, with a coaxially stacked P1\/P2 stem forming the boot, and a 3\u2032-P3 stem\u2013loop 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<jats:sup>2<\/jats:sup> hybridization state, through a network of coplanar hydrogen bonds and by a cation\u2013\u03c0 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 <jats:italic>ykkC<\/jats:italic> riboswitches and pave the way for a deeper understanding of guanidine detoxification\u2014a previously unappreciated aspect of bacterial physiology.<\/jats:p>","DOI":"10.1261\/rna.060186.116","type":"journal-article","created":{"date-parts":[[2017,1,18]],"date-time":"2017-01-18T03:11:24Z","timestamp":1484709084000},"page":"578-585","source":"Crossref","is-referenced-by-count":49,"title":["Structural basis for guanidine sensing by the <i>ykkC<\/i> family of riboswitches"],"prefix":"10.1261","volume":"23","author":[{"given":"Robert A.","family":"Battaglia","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ian R.","family":"Price","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ailong","family":"Ke","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"246","published-online":{"date-parts":[[2017,1,17]]},"reference":[{"key":"2021112105592289000_23.4.578.1","doi-asserted-by":"publisher","DOI":"10.1107\/S0907444909052925"},{"key":"2021112105592289000_23.4.578.2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.0308014101"},{"key":"2021112105592289000_23.4.578.3","doi-asserted-by":"publisher","DOI":"10.1038\/nature03037"},{"key":"2021112105592289000_23.4.578.4","doi-asserted-by":"crossref","first-page":"11608","DOI":"10.1021\/jp407339v","article-title":"Non-covalent interactions: complexes of guanidinium with DNA and RNA nucleobases","volume":"117","year":"2013","journal-title":"J Phys Chem B"},{"key":"2021112105592289000_23.4.578.5","doi-asserted-by":"publisher","DOI":"10.1016\/j.molcel.2011.08.024"},{"key":"2021112105592289000_23.4.578.6","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1214024109"},{"key":"2021112105592289000_23.4.578.7","doi-asserted-by":"publisher","DOI":"10.1107\/S0907444910007493"},{"key":"2021112105592289000_23.4.578.8","doi-asserted-by":"crossref","first-page":"501","DOI":"10.1016\/S0021-9258(18)73944-6","article-title":"Sulfhydryl groups in proteins. II","volume":"125","year":"1938","journal-title":"J Biol Chem"},{"key":"2021112105592289000_23.4.578.9","doi-asserted-by":"publisher","DOI":"10.1016\/j.str.2013.09.001"},{"key":"2021112105592289000_23.4.578.10","doi-asserted-by":"publisher","DOI":"10.1128\/JB.182.8.2311-2313.2000"},{"key":"2021112105592289000_23.4.578.11","doi-asserted-by":"publisher","DOI":"10.1107\/S0907444909047337"},{"key":"2021112105592289000_23.4.578.12","doi-asserted-by":"publisher","DOI":"10.1016\/j.ymeth.2004.03.027"},{"key":"2021112105592289000_23.4.578.13","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkt057"},{"key":"2021112105592289000_23.4.578.14","doi-asserted-by":"publisher","DOI":"10.1038\/nsmb.1494"},{"key":"2021112105592289000_23.4.578.15","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/29.13.2860"},{"key":"2021112105592289000_23.4.578.16","doi-asserted-by":"publisher","DOI":"10.1038\/nsmb710"},{"key":"2021112105592289000_23.4.578.17","doi-asserted-by":"publisher","DOI":"10.4161\/rna.8.1.13865"},{"key":"2021112105592289000_23.4.578.18","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btl470"},{"key":"2021112105592289000_23.4.578.19","first-page":"1","article-title":"Metabolism of free guanidine in bacteria is regulated by a widespread riboswitch class","volume":"65","year":"2017","journal-title":"Mol Cell"},{"key":"2021112105592289000_23.4.578.20","doi-asserted-by":"publisher","DOI":"10.1007\/BF00197809"},{"key":"2021112105592289000_23.4.578.21","doi-asserted-by":"publisher","DOI":"10.1107\/S0021889804018047"},{"key":"2021112105592289000_23.4.578.22","doi-asserted-by":"publisher","DOI":"10.1016\/j.mib.2003.08.005"},{"key":"2021112105592289000_23.4.578.23","doi-asserted-by":"crossref","first-page":"908","DOI":"10.1016\/j.bbagrm.2014.02.012","article-title":"Themes and variations in riboswitch structure and function","volume":"1839","year":"2014","journal-title":"Biochim Biophys Acta"},{"key":"2021112105592289000_23.4.578.24","doi-asserted-by":"crossref","first-page":"931","DOI":"10.1016\/j.bbagrm.2014.05.013","article-title":"Common themes and differences in SAM recognition among SAM riboswitches","volume":"1839","year":"2014","journal-title":"Biochim Biophys Acta"},{"key":"2021112105592289000_23.4.578.25","doi-asserted-by":"publisher","DOI":"10.1016\/j.molcel.2015.02.016"},{"key":"2021112105592289000_23.4.578.26","doi-asserted-by":"crossref","first-page":"195","DOI":"10.1016\/j.str.2016.11.020","article-title":"Structural basis for ligand binding to the guanidine-I riboswitch","volume":"25","year":"2017","journal-title":"Structure"},{"key":"2021112105592289000_23.4.578.27","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2012.12.024"},{"key":"2021112105592289000_23.4.578.28","doi-asserted-by":"publisher","DOI":"10.1107\/S0907444909038360"},{"key":"2021112105592289000_23.4.578.29","doi-asserted-by":"publisher","DOI":"10.1038\/nsmb.1702"},{"key":"2021112105592289000_23.4.578.30","doi-asserted-by":"publisher","DOI":"10.1021\/ja036166s"},{"key":"2021112105592289000_23.4.578.31","doi-asserted-by":"publisher","DOI":"10.1186\/gb-2010-11-3-r31"},{"key":"2021112105592289000_23.4.578.32","doi-asserted-by":"crossref","first-page":"2197","DOI":"10.1002\/ejic.200200278","article-title":"Metal ligand aromatic cation\u2212\u03c0 interactions","volume":"2003","year":"2003","journal-title":"Eur J Inorg Chem"}],"container-title":["RNA"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/syndication.highwire.org\/content\/doi\/10.1261\/rna.060186.116","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,11,21]],"date-time":"2021-11-21T14:24:15Z","timestamp":1637504655000},"score":1,"resource":{"primary":{"URL":"http:\/\/rnajournal.cshlp.org\/lookup\/doi\/10.1261\/rna.060186.116"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2017,1,17]]},"references-count":32,"journal-issue":{"issue":"4","published-online":{"date-parts":[[2017,3,16]]},"published-print":{"date-parts":[[2017,4]]}},"alternative-id":["10.1261\/rna.060186.116"],"URL":"https:\/\/doi.org\/10.1261\/rna.060186.116","relation":{},"ISSN":["1355-8382","1469-9001"],"issn-type":[{"value":"1355-8382","type":"print"},{"value":"1469-9001","type":"electronic"}],"subject":[],"published":{"date-parts":[[2017,1,17]]}}}