{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,9]],"date-time":"2026-06-09T02:26:36Z","timestamp":1780971996468,"version":"3.54.1"},"reference-count":48,"publisher":"Oxford University Press (OUP)","issue":"12","license":[{"start":{"date-parts":[[2021,6,14]],"date-time":"2021-06-14T00:00:00Z","timestamp":1623628800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["32022039"],"award-info":[{"award-number":["32022039"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["31870810"],"award-info":[{"award-number":["31870810"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["91940302"],"award-info":[{"award-number":["91940302"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["91640104"],"award-info":[{"award-number":["91640104"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["31670826"],"award-info":[{"award-number":["31670826"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Zhejiang Province","award":["LR19C050003"],"award-info":[{"award-number":["LR19C050003"]}]},{"DOI":"10.13039\/501100012226","name":"Fundamental Research Funds for the Central Universities","doi-asserted-by":"publisher","award":["2017QN81010"],"award-info":[{"award-number":["2017QN81010"]}],"id":[{"id":"10.13039\/501100012226","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004835","name":"Zhejiang University","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100004835","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002428","name":"Austrian Science Fund","doi-asserted-by":"publisher","award":["P31691"],"award-info":[{"award-number":["P31691"]}],"id":[{"id":"10.13039\/501100002428","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002428","name":"Austrian Science Fund","doi-asserted-by":"publisher","award":["F8011-B"],"award-info":[{"award-number":["F8011-B"]}],"id":[{"id":"10.13039\/501100002428","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001821","name":"Vienna Science and Technology Fund","doi-asserted-by":"publisher","award":["LS17-003"],"award-info":[{"award-number":["LS17-003"]}],"id":[{"id":"10.13039\/501100001821","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004955","name":"Austrian Research Promotion Agency","doi-asserted-by":"publisher","award":["West Austrian BioNMR 858017"],"award-info":[{"award-number":["West Austrian BioNMR 858017"]}],"id":[{"id":"10.13039\/501100004955","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,7,9]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Riboswitches are conserved functional domains in mRNA that mostly exist in bacteria. They regulate gene expression in response to varying concentrations of metabolites or metal ions. Recently, the NMT1 RNA motif has been identified to selectively bind xanthine and uric acid, respectively, both are involved in the metabolic pathway of purine degradation. Here, we report a crystal structure of this RNA bound to xanthine. Overall, the riboswitch exhibits a rod-like, continuously stacked fold composed of three stems and two internal junctions. The binding-pocket is determined by the highly conserved junctional sequence J1 between stem P1 and P2a, and engages a long-distance Watson\u2013Crick base pair to junction J2. Xanthine inserts between a G\u2013U pair from the major groove side and is sandwiched between base triples. Strikingly, a Mg2+ ion is inner-sphere coordinated to O6 of xanthine and a non-bridging oxygen of a backbone phosphate. Two further hydrated Mg2+ ions participate in extensive interactions between xanthine and the pocket. Our structure model is verified by ligand binding analysis to selected riboswitch mutants using isothermal titration calorimetry, and by fluorescence spectroscopic analysis of RNA folding using 2-aminopurine-modified variants. Together, our study highlights the principles of metal ion-mediated ligand recognition by the xanthine riboswitch.<\/jats:p>","DOI":"10.1093\/nar\/gkab486","type":"journal-article","created":{"date-parts":[[2021,5,27]],"date-time":"2021-05-27T08:35:32Z","timestamp":1622104532000},"page":"7139-7153","source":"Crossref","is-referenced-by-count":31,"title":["Insights into xanthine riboswitch structure and metal ion-mediated ligand recognition"],"prefix":"10.1093","volume":"49","author":[{"given":"Xiaochen","family":"Xu","sequence":"first","affiliation":[{"name":"Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michaela","family":"Egger","sequence":"additional","affiliation":[{"name":"Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innsbruck\u00a06020, Austria"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hao","family":"Chen","sequence":"additional","affiliation":[{"name":"Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Karolina","family":"Bartosik","sequence":"additional","affiliation":[{"name":"Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innsbruck\u00a06020, Austria"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ronald","family":"Micura","sequence":"additional","affiliation":[{"name":"Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innsbruck\u00a06020, Austria"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Aiming","family":"Ren","sequence":"additional","affiliation":[{"name":"Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2021,6,14]]},"reference":[{"key":"2021070901253917000_B1","doi-asserted-by":"crossref","first-page":"a003566","DOI":"10.1101\/cshperspect.a003566","article-title":"Riboswitches and the RNA world","volume":"4","author":"Breaker","year":"2012","journal-title":"Cold Spring Harb. Perspect. Biol."},{"key":"2021070901253917000_B2","doi-asserted-by":"crossref","first-page":"17","DOI":"10.1016\/j.cell.2012.12.024","article-title":"A decade of riboswitches","volume":"152","author":"Serganov","year":"2013","journal-title":"Cell"},{"key":"2021070901253917000_B3","doi-asserted-by":"crossref","first-page":"194501","DOI":"10.1016\/j.bbagrm.2020.194501","article-title":"Riboswitch regulation mechanisms: RNA, metabolites and regulatory proteins","volume":"1863","author":"B\u00e9dard","year":"2020","journal-title":"Biochim. Biophys. Acta Gene Regul. Mech."},{"key":"2021070901253917000_B4","doi-asserted-by":"crossref","first-page":"455","DOI":"10.1146\/annurev-biophys-070816-034042","article-title":"Long-range interactions in riboswitch control of gene expression","volume":"46","author":"Jones","year":"2017","journal-title":"Annu. Rev. Biophys."},{"key":"2021070901253917000_B5","doi-asserted-by":"crossref","first-page":"a003533","DOI":"10.1101\/cshperspect.a003533","article-title":"Riboswitches: structures and mechanisms","volume":"3","author":"Garst","year":"2011","journal-title":"Cold Spring Harb. Perspect. Biol."},{"key":"2021070901253917000_B6","doi-asserted-by":"crossref","first-page":"7331","DOI":"10.1039\/D0CS00617C","article-title":"Fundamental studies of functional nucleic acids: aptamers, riboswitches, ribozymes and DNAzymes","volume":"49","author":"Micura","year":"2020","journal-title":"Chem. Soc. Rev."},{"key":"2021070901253917000_B7","doi-asserted-by":"crossref","first-page":"112","DOI":"10.1016\/j.sbi.2015.02.007","article-title":"Multiple conformational states of riboswitches fine-tune gene regulation","volume":"30","author":"F\u00fcrtig","year":"2015","journal-title":"Curr. Opin. Struct. Biol."},{"key":"2021070901253917000_B8","doi-asserted-by":"crossref","first-page":"1339","DOI":"10.1021\/ar200035g","article-title":"The dynamic nature of RNA as key to understanding riboswitch mechanisms","volume":"44","author":"Haller","year":"2011","journal-title":"Acc. Chem. Res."},{"key":"2021070901253917000_B9","doi-asserted-by":"crossref","first-page":"1043","DOI":"10.1016\/S1074-5521(02)00224-7","article-title":"Genetic control by a metabolite binding mRNA","volume":"9","author":"Nahvi","year":"2002","journal-title":"Chem. Biol."},{"key":"2021070901253917000_B10","doi-asserted-by":"crossref","first-page":"952","DOI":"10.1038\/nature01145","article-title":"Thiamine derivatives bind messenger RNAs directly to regulate bacterial gene expression","volume":"419","author":"Winkler","year":"2002","journal-title":"Nature"},{"key":"2021070901253917000_B11","doi-asserted-by":"crossref","first-page":"747","DOI":"10.1016\/S0092-8674(02)01134-0","article-title":"Sensing small molecules by nascent RNA: a mechanism to control transcription in bacteria","volume":"111","author":"Mironov","year":"2002","journal-title":"Cell"},{"key":"2021070901253917000_B12","doi-asserted-by":"crossref","first-page":"15908","DOI":"10.1073\/pnas.212628899","article-title":"An mRNA structure that controls gene expression by binding FMN","volume":"99","author":"Winkler","year":"2002","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"key":"2021070901253917000_B13","doi-asserted-by":"crossref","first-page":"995","DOI":"10.1261\/rna.061234.117","article-title":"Riboswitch diversity and distribution","volume":"23","author":"McCown","year":"2017","journal-title":"RNA"},{"key":"2021070901253917000_B14","doi-asserted-by":"crossref","first-page":"141","DOI":"10.1016\/j.tibs.2016.09.009","article-title":"A new view into the regulation of purine metabolism: the purinosome","volume":"42","author":"Pedley","year":"2017","journal-title":"Trends Biochem. Sci."},{"key":"2021070901253917000_B15","doi-asserted-by":"crossref","first-page":"96","DOI":"10.1016\/j.mib.2021.01.017","article-title":"The ever-expanding world of bacterial cyclic oligonucleotide second messengers","volume":"60","author":"Yoon","year":"2021","journal-title":"Curr. Opin. Microbiol."},{"key":"2021070901253917000_B16","doi-asserted-by":"crossref","first-page":"282","DOI":"10.1002\/prot.1093","article-title":"Adenine recognition: a motif present in ATP-, CoA-, NAD-, NADP-, and FAD-dependent proteins","volume":"44","author":"Denessiouk","year":"2001","journal-title":"Proteins"},{"key":"2021070901253917000_B17","doi-asserted-by":"crossref","first-page":"243","DOI":"10.1016\/j.tibs.2004.03.007","article-title":"S-Adenosylmethionine: nothing goes to waste","volume":"29","author":"Fontecave","year":"2004","journal-title":"Trends Biochem. Sci."},{"key":"2021070901253917000_B18","doi-asserted-by":"crossref","first-page":"577","DOI":"10.1016\/S0092-8674(03)00391-X","article-title":"Riboswitches control fundamental biochemical pathways in Bacillus subtilis and other bacteria","volume":"113","author":"Mandal","year":"2003","journal-title":"Cell"},{"key":"2021070901253917000_B19","doi-asserted-by":"crossref","first-page":"29","DOI":"10.1038\/nsmb710","article-title":"Adenine riboswitches and gene activation by disruption of a transcription terminator","volume":"11","author":"Mandal","year":"2004","journal-title":"Nat. Struct. Mol. Biol."},{"key":"2021070901253917000_B20","doi-asserted-by":"crossref","first-page":"317","DOI":"10.1016\/j.molcel.2015.01.001","article-title":"An ancient riboswitch class in bacteria regulates purine biosynthesis and one-carbon metabolism","volume":"57","author":"Kim","year":"2015","journal-title":"Mol. Cell"},{"key":"2021070901253917000_B21","doi-asserted-by":"crossref","first-page":"16092","DOI":"10.1073\/pnas.0705884104","article-title":"Guanine riboswitch variants from Mesoplasma florum selectively recognize 2\u2032-deoxyguanosine","volume":"104","author":"Kim","year":"2007","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"key":"2021070901253917000_B22","doi-asserted-by":"crossref","first-page":"E2077","DOI":"10.1073\/pnas.1619581114","article-title":"Bioinformatic analysis of riboswitch structures uncovers variant classes with altered ligand specificity","volume":"114","author":"Weinberg","year":"2017","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"key":"2021070901253917000_B23","doi-asserted-by":"crossref","first-page":"e33908","DOI":"10.7554\/eLife.33908","article-title":"Tandem riboswitches form a natural Boolean logic gate to control purine metabolism in bacteria","volume":"7","author":"Sherlock","year":"2018","journal-title":"Elife"},{"key":"2021070901253917000_B24","doi-asserted-by":"crossref","first-page":"401","DOI":"10.1021\/acs.biochem.8b00617","article-title":"Variant bacterial riboswitches associated with nucleotide hydrolase genes sense nucleoside diphosphates","volume":"58","author":"Sherlock","year":"2019","journal-title":"Biochemistry"},{"key":"2021070901253917000_B25","doi-asserted-by":"crossref","first-page":"675","DOI":"10.1261\/rna.074997.120","article-title":"Former orphan riboswitches reveal unexplored areas of bacterial metabolism, signaling, and gene control processes","volume":"26","author":"Sherlock","year":"2020","journal-title":"RNA"},{"key":"2021070901253917000_B26","doi-asserted-by":"crossref","first-page":"960","DOI":"10.1261\/rna.075218.120","article-title":"A bacterial riboswitch class senses xanthine and uric acid to regulate genes associated with purine oxidation","volume":"26","author":"Yu","year":"2020","journal-title":"RNA"},{"key":"2021070901253917000_B27","doi-asserted-by":"crossref","first-page":"947","DOI":"10.1038\/nsb1197-947","article-title":"Crystal Structure of the protein drug urate oxidase-inhibitor complex at 2.05 \u00c5 resolution","volume":"4","author":"Collo\u0107h","year":"1997","journal-title":"Nat. Struct. Biol."},{"key":"2021070901253917000_B28","doi-asserted-by":"crossref","first-page":"115","DOI":"10.1007\/978-1-59745-558-9_9","article-title":"Preparation and crystallization of riboswitch-ligand complexes","volume":"540","author":"Pikovskaya","year":"2009","journal-title":"Methods Mol. Biol."},{"key":"2021070901253917000_B29","doi-asserted-by":"crossref","first-page":"213","DOI":"10.1107\/S0907444909052925","article-title":"PHENIX: a comprehensive Python-based system for macromolecular structure solution","volume":"66","author":"Adams","year":"2010","journal-title":"Acta Crystallogr. D Biol. Crystallogr."},{"key":"2021070901253917000_B30","doi-asserted-by":"crossref","first-page":"2126","DOI":"10.1107\/S0907444904019158","article-title":"Coot: model-building tools for molecular graphics","volume":"60","author":"Emsley","year":"2004","journal-title":"Acta Crystallogr. D. Biol. Crystallogr."},{"key":"2021070901253917000_B31","doi-asserted-by":"crossref","first-page":"240","DOI":"10.1107\/S0907444996012255","article-title":"Refinement of macromolecular structures by the maximum-likelihood method","volume":"53","author":"Murshudov","year":"1997","journal-title":"Acta Crystallogr. D. Biol. Crystallogr."},{"key":"2021070901253917000_B32","doi-asserted-by":"crossref","first-page":"896","DOI":"10.1002\/cbic.200700057","article-title":"Ligand-induced folding of the adenosine deaminase A-riboswitch and implications on riboswitch translational control","volume":"8","author":"Rieder","year":"2007","journal-title":"Chembiochem"},{"key":"2021070901253917000_B33","doi-asserted-by":"crossref","first-page":"16161","DOI":"10.1021\/ja2063583","article-title":"A powerful approach for the selection of 2-Aminopurine substitution sites to investigate RNA folding","volume":"133","author":"Souli\u00e8re","year":"2011","journal-title":"J. Am. Chem. Soc."},{"key":"2021070901253917000_B34","doi-asserted-by":"crossref","first-page":"1375","DOI":"10.1016\/j.str.2015.05.016","article-title":"Global RNA fold and molecular recognition for a pfl riboswitch bound to ZMP, a master regulator of One-Carbon metabolism","volume":"23","author":"Ren","year":"2015","journal-title":"Structure"},{"key":"2021070901253917000_B35","doi-asserted-by":"crossref","first-page":"829","DOI":"10.1016\/j.chembiol.2015.06.007","article-title":"Metal ion-mediated nucleobase recognition by the ZTP riboswitch","volume":"22","author":"Trausch","year":"2015","journal-title":"Chem. Biol."},{"key":"2021070901253917000_B36","doi-asserted-by":"crossref","first-page":"679","DOI":"10.1038\/nsmb.3073","article-title":"Recognition of the bacterial alarmone ZMP through long-distance association of two RNA subdomains","volume":"22","author":"Jones","year":"2015","journal-title":"Nat. Struct. Mol. Biol."},{"key":"2021070901253917000_B37","doi-asserted-by":"crossref","first-page":"1167","DOI":"10.1038\/nature04740","article-title":"Structural basis for gene regulation by a thiamine pyrophosphate-sensing riboswitch","volume":"441","author":"Serganov","year":"2006","journal-title":"Nature"},{"key":"2021070901253917000_B38","doi-asserted-by":"crossref","first-page":"1208","DOI":"10.1126\/science.1128451","article-title":"Structure of the eukaryotic thiamine pyrophosphate riboswitch with its regulatory ligand","volume":"312","author":"Thore","year":"2006","journal-title":"Science"},{"key":"2021070901253917000_B39","doi-asserted-by":"crossref","first-page":"1459","DOI":"10.1016\/j.str.2006.07.008","article-title":"Crystal structures of the Thi-Box riboswitch bound to thiamine pyrophosphate analogs reveal adaptive RNA-Small molecule recognition","volume":"14","author":"Edwards","year":"2006","journal-title":"Structure"},{"key":"2021070901253917000_B40","doi-asserted-by":"crossref","first-page":"233","DOI":"10.1038\/nature07642","article-title":"Coenzyme recognition and gene regulation by a flavin mononucleotide riboswitch","volume":"458","author":"Serganov","year":"2009","journal-title":"Nature"},{"key":"2021070901253917000_B41","doi-asserted-by":"crossref","first-page":"887","DOI":"10.1038\/s41589-018-0114-4","article-title":"ykkC riboswitches employ an add-on helix to adjust specificity for polyanionic ligands","volume":"14","author":"Peselis","year":"2018","journal-title":"Nat. Chem. Biol."},{"key":"2021070901253917000_B42","doi-asserted-by":"crossref","first-page":"e36381","DOI":"10.7554\/eLife.36381","article-title":"Structures of two aptamers with differing ligand specificity reveal ruggedness in the functional landscape of RNA","volume":"7","author":"Knappenberger","year":"2018","journal-title":"eLife"},{"key":"2021070901253917000_B43","doi-asserted-by":"crossref","first-page":"878","DOI":"10.1261\/rna.074898.120","article-title":"Structure and ligand binding of the ADP-binding domain of the NAD(+) riboswitch","volume":"26","author":"Huang","year":"2020","journal-title":"RNA"},{"key":"2021070901253917000_B44","doi-asserted-by":"crossref","first-page":"12394","DOI":"10.1093\/nar\/gkaa1029","article-title":"Structural distinctions between NAD+ riboswitch domains 1 and 2 determine differential folding and ligand binding","volume":"48","author":"Chen","year":"2020","journal-title":"Nucleic Acids Res."},{"key":"2021070901253917000_B45","doi-asserted-by":"crossref","first-page":"85","DOI":"10.1038\/nature11152","article-title":"Fluoride ion encapsulation by Mg2+ ions and phosphates in a fluoride riboswitch","volume":"486","author":"Ren","year":"2012","journal-title":"Nature"},{"key":"2021070901253917000_B46","doi-asserted-by":"crossref","first-page":"493","DOI":"10.18388\/abp.2004_3587","article-title":"Xanthine, xanthosine and its nucleotides: solution structures of neutral and ionic forms, and relevance to substrate properties in various enzyme systems and metabolic pathways","volume":"51","author":"Kulikowska","year":"2004","journal-title":"Acta Biochim. Polonica"},{"key":"2021070901253917000_B47","doi-asserted-by":"crossref","first-page":"2740","DOI":"10.3390\/molecules25122740","article-title":"Excited-state proton transfer in 8-azapurines I: a kinetic analysis of 8-azaxanthine fluorescence","volume":"25","author":"Wierzchowski","year":"2020","journal-title":"Molecules"},{"key":"2021070901253917000_B48","doi-asserted-by":"crossref","first-page":"857","DOI":"10.1016\/j.str.2009.04.009","article-title":"Adaptive ligand binding by the purine riboswitch in the recognition of guanine and adenine analogs","volume":"17","author":"Gilbert","year":"2009","journal-title":"Struct.\/Folding Des."}],"container-title":["Nucleic Acids Research"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/nar\/article-pdf\/49\/12\/7139\/38885947\/gkab486.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"http:\/\/academic.oup.com\/nar\/article-pdf\/49\/12\/7139\/38885947\/gkab486.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,7,9]],"date-time":"2021-07-09T03:49:12Z","timestamp":1625802552000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/nar\/article\/49\/12\/7139\/6298625"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2021,6,14]]},"references-count":48,"journal-issue":{"issue":"12","published-online":{"date-parts":[[2021,6,14]]},"published-print":{"date-parts":[[2021,7,9]]}},"URL":"https:\/\/doi.org\/10.1093\/nar\/gkab486","relation":{"has-review":[{"id-type":"doi","id":"10.3410\/f.740293348.793588931","asserted-by":"object"}]},"ISSN":["0305-1048","1362-4962"],"issn-type":[{"value":"0305-1048","type":"print"},{"value":"1362-4962","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2021,7,9]]},"published":{"date-parts":[[2021,6,14]]}}}