8TKB

tRNA 2-phosphotransferase (Tpt1) from Pyrococcus horikoshii in complex with 5'-AMP

Summary for 8TKB

• Entry DOI: 10.2210/pdb8tkb/pdb
• Related: 8TFI
• Descriptor: Probable RNA 2'-phosphotransferase, ADENOSINE MONOPHOSPHATE, POTASSIUM ION, ... (6 entities in total)
• Functional Keywords: trna 2'-phosphotransferase, tpt1, trna splicing, 5'-amp, amp, transferase
• Biological source: Pyrococcus horikoshii OT3
• Total number of polymer chains: 1
• Total formula weight: 21961.21

Authors

Jacewicz, A.,Dantuluri, S.,Shuman, S. (deposition date: 2023-07-25, release date: 2024-06-19, Last modification date: 2025-07-16)

Primary citation

Jacewicz, A.,Damha, M.J.,Shuman, S.
Structures of RNA phosphotransferase Tpt1 reveal distinct binding modes for an RNA 2'-PO 4 splice junction versus a 5'-PO 4 mononucleotide.
Rna, 31:916-922, 2025

PubMed Abstract: 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'-PO 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'-PO 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'-PO and the AMP 5'-PO are engaged by the same set of active site amino acids, but the 2'-PO nucleoside and the 5'-nucleoside occupy different sites on the enzyme.

PubMed: 40324821
DOI: 10.1261/rna.080444.125

Experimental method

X-RAY DIFFRACTION (1.71 Å)