Structures of RNA phosphotransferase Tpt1 reveal distinct binding modes for an RNA 2′-PO₄splice junction versus a 5′-PO₄mononucleotide

Tpt1 is a widely distributed enzyme that removes an internal RNA 2'-phosphate by transfer to NAD⁺, via a two-step reaction in which: (i) the RNA 2'-PO₄ attacks NAD⁺ to form an RNA-2'-phospho-(ADP-ribose) intermediate and expel nicotinamide; and (ii) the ADP-ribose O2″ attacks the RNA 2'-phosphodiester to form 2'-OH RNA and ADP-ribose-1″,2″-cyclic phosphate products. Tpt1 can also execute a single-step ADP-ribosyltransferase reaction at a 5'-monophosphate nucleic acid terminus that installs a 5'-phospho-ADP-ribose cap structure. Here we present crystal structures of Tpt1 bound to an RNA containing an internal 2'-PO₄ mark (the substrate for the canonical Tpt1 pathway) and in a complex with 5'-AMP. We find that Tpt1 has distinct binding modes, whereby the RNA 2'-PO₄ and the AMP 5'-PO₄ are engaged by the same set of active site amino acids, but the 2'-PO₄ nucleoside and the 5'-nucleoside occupy different sites on the enzyme.