Substrate analogs that trap the 2′-phospho-ADP-ribosylated RNA intermediate of the Tpt1 (tRNA 2′-phosphotransferase) reaction pathway
- Swathi Dantuluri1,
- Leonora Abdullahu2,
- Annum Munir1,
- Adam Katolik2,
- Masad J. Damha2 and
- Stewart Shuman1
- 1Molecular Biology Program, Sloan-Kettering Institute, New York, New York 10065, USA
- 2Department of Chemistry, McGill University, Montreal, Quebec H3A0B8, Canada
- Corresponding authors: s-shuman{at}ski.mskcc.org, masad.damha{at}mcgill.ca
Abstract
The enzyme Tpt1 removes an internal RNA 2′-PO4 via a two-step reaction in which: (i) the 2′-PO4 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′-PO4 nucleotide with arabinose-2′-PO4 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.
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Article is online at http://www.rnajournal.org/cgi/doi/10.1261/rna.074377.119.
- Received December 17, 2019.
- Accepted January 10, 2020.
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