{"doi":"10.1261/rna.074377.119","title":"Substrate analogs that trap the 2′-phospho-ADP-ribosylated RNA intermediate of the Tpt1 (tRNA 2′-phosphotransferase) reaction pathway","abstract":"The enzyme Tpt1 removes an internal RNA 2′-PO 4 via a two-step reaction in which: (i) the 2′-PO 4 attacks NAD + to form an RNA-2′-phospho-(ADP-ribose) intermediate and nicotinamide; and (ii) transesterification of the ADP-ribose O2″ to the RNA 2′-phosphodiester yields 2′-OH RNA and ADP-ribose-1″,2″-cyclic phosphate. Because step 2 is much faster than step 1, the ADP-ribosylated RNA intermediate is virtually undetectable under normal circumstances. Here, by testing chemically modified nucleic acid substrates for activity with bacterial Tpt1 enzymes, we find that replacement of the ribose-2′-PO 4 nucleotide with arabinose-2′-PO 4 selectively slows step 2 of the reaction pathway and results in the transient accumulation of high levels of the reaction intermediate. We report that replacing the NMN ribose of NAD + with 2′-fluoroarabinose (thereby eliminating the ribose O2″ nucleophile) results in durable trapping of RNA-2′-phospho-(ADP-fluoroarabinose) as a “dead-end” product of step 1. Tpt1 enzymes from diverse taxa differ in their capacity to use ara-2″F-NAD + as a substrate.","journal":"RNA","year":2020,"id":106067,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":7,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9529,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2020-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":512408,"name":"Leonora Abdullahu","orcid":"0000-0002-8132-9726","position":1,"is_corresponding":false},{"id":512815,"name":"Annum Munir","orcid":null,"position":2,"is_corresponding":false},{"id":512816,"name":"Adam Katolik","orcid":null,"position":3,"is_corresponding":false},{"id":512409,"name":"Masad J. Damha","orcid":"0000-0002-4458-1623","position":4,"is_corresponding":false},{"id":409034,"name":"Stewart Shuman","orcid":"0000-0001-5034-6438","position":5,"is_corresponding":false},{"id":512407,"name":"Swathi Dantuluri","orcid":"0000-0002-9923-1655","position":0,"is_corresponding":true}],"reference_count":25,"raw_metadata":null,"created_at":"2026-07-18T23:12:23.770754Z","pmid":"31932322","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":[]}