{"doi":"10.1261/rna.078824.121","title":"An uncommon [K<sup>+</sup>(Mg<sup>2+</sup>)<sub>2</sub>] metal ion triad imparts stability and selectivity to the Guanidine-I riboswitch","abstract":"The widespread ykkC -I riboswitch class exemplifies divergent riboswitch evolution. To analyze how natural selection has diversified its versatile RNA fold, we determined the X-ray crystal structure of the Burkholderia sp. TJI49 ykkC -I subtype-1 (Guanidine-I) riboswitch aptamer domain. Differing from the previously reported structures of orthologs from Dickeya dadantii and Sulfobacillus acidophilus , our Burkholderia structure reveals a chelated K + ion adjacent to two Mg 2+ ions in the guanidine-binding pocket. Thermal melting analysis shows that K + chelation, which induces localized conformational changes in the binding pocket, improves guanidinium-RNA interactions. Analysis of ribosome structures suggests that the [K + (Mg 2+ ) 2 ] ion triad is uncommon. It is, however, reminiscent of metal ion clusters found in the active sites of ribozymes and DNA polymerases. Previous structural characterization of ykkC -I subtype-2 RNAs, which bind the effector ligands ppGpp and PRPP, indicate that in those paralogs, an adenine responsible for K + chelation in the Burkholderia Guanidine-I riboswitch is replaced by a pyrimidine. This mutation results in a water molecule and Mg 2+ ion binding in place of the K + ion. Thus, our structural analysis demonstrates how ion and solvent chelation tune divergent ligand specificity and affinity among ykkC -I riboswitches.","journal":"RNA","year":2021,"id":193047,"datarank":0.5037465872789829,"base_score":2.4849066497880004,"endowment":2.4849066497880004,"self_citation_contribution":0.37273599746820013,"citation_network_contribution":0.1310105898107828,"self_endowment_contribution":0.37273599746820013,"citer_contribution":0.1310105898107828,"corpus_percentile":null,"corpus_rank":null,"citation_count":11,"citer_count":10,"citers_with_citation_signal":7,"citers_with_endowment":7,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9485,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2021-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":321054,"name":"A.R. Ferré-D′Amaré","orcid":"0000-0003-4549-1619","position":1,"is_corresponding":false},{"id":478452,"name":"Robert J. Trachman","orcid":"0000-0001-7459-2457","position":0,"is_corresponding":true}],"reference_count":47,"raw_metadata":{"citation_network_status":"fetched"},"created_at":"2026-07-18T23:49:47.463744Z","pmid":"34257148","pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}