{"database":"biostudies-literature","file_versions":[],"scores":null,"additional":{"submitter":["Xu X"],"funding":["Fundamental Research Funds for the Central Universities","Austrian Science Fund FWF","Austrian Research Promotion Agency","National Natural Science Foundation of China","National Key Research and Development Project of China","Zhejiang University","outstanding youth fund of Zhejiang Province"],"pagination":["54-67"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC9841397"],"repository":["biostudies-literature"],"omics_type":["Unknown"],"volume":["51(1)"],"pubmed_abstract":["Riboswitches are conserved non-coding domains in bacterial mRNA with gene regulation function that are essential for maintaining enzyme co-factor metabolism. Recently, the pnuC RNA motif was reported to selectively bind nicotinamide adenine dinucleotide (NAD+), defining a novel class of NAD+ riboswitches (NAD+-II) according to phylogenetic analysis. To reveal the three-dimensional architecture and the ligand-binding mode of this riboswitch, we solved the crystal structure of NAD+-II riboswitch in complex with NAD+. Strikingly and in contrast to class-I riboswitches that form a tight recognition pocket for the adenosine diphosphate (ADP) moiety of NAD+, the class-II riboswitches form a binding pocket for the nicotinamide mononucleotide (NMN) portion of NAD+ and display only unspecific interactions with the adenosine. We support this finding by an additional structure of the class-II RNA in complex with NMN alone. The structures define a novel RNA tertiary fold that was further confirmed by mutational analysis in combination with isothermal titration calorimetry (ITC), and 2-aminopurine-based fluorescence spectroscopic folding studies. Furthermore, we truncated the pnuC RNA motif to a short RNA helical scaffold with binding affinity comparable to the wild-type motif to allude to the potential of engineering the NAD+-II motif for biotechnological applications."],"journal":["Nucleic acids research"],"pubmed_title":["Structure-based investigations of the NAD+-II riboswitch."],"pmcid":["PMC9841397"],"funding_grant_id":["BioNMR 858017","32022039","91940302","P 31691","91640104","P31691","2021YFC2300300","F8011-B","2017QN81010","31870810","LR19C050003"],"pubmed_authors":["Micura R","Egger M","Li C","Chen H","Xu X","Ren A"],"additional_accession":[]},"is_claimable":false,"name":"Structure-based investigations of the NAD+-II riboswitch.","description":"Riboswitches are conserved non-coding domains in bacterial mRNA with gene regulation function that are essential for maintaining enzyme co-factor metabolism. Recently, the pnuC RNA motif was reported to selectively bind nicotinamide adenine dinucleotide (NAD+), defining a novel class of NAD+ riboswitches (NAD+-II) according to phylogenetic analysis. To reveal the three-dimensional architecture and the ligand-binding mode of this riboswitch, we solved the crystal structure of NAD+-II riboswitch in complex with NAD+. Strikingly and in contrast to class-I riboswitches that form a tight recognition pocket for the adenosine diphosphate (ADP) moiety of NAD+, the class-II riboswitches form a binding pocket for the nicotinamide mononucleotide (NMN) portion of NAD+ and display only unspecific interactions with the adenosine. We support this finding by an additional structure of the class-II RNA in complex with NMN alone. The structures define a novel RNA tertiary fold that was further confirmed by mutational analysis in combination with isothermal titration calorimetry (ITC), and 2-aminopurine-based fluorescence spectroscopic folding studies. Furthermore, we truncated the pnuC RNA motif to a short RNA helical scaffold with binding affinity comparable to the wild-type motif to allude to the potential of engineering the NAD+-II motif for biotechnological applications.","dates":{"release":"2023-01-01T00:00:00Z","publication":"2023 Jan","modification":"2026-05-28T22:53:06.541Z","creation":"2025-04-06T11:12:11.506Z"},"accession":"S-EPMC9841397","cross_references":{"pubmed":["36610789"],"doi":["10.1093/nar/gkac1227"]}}