8TG5

tRNA 2'-phosphotransferase (Tpt1) from Pyrococcus horikoshii in complex with branched 2'-PO4 RNA

Summary for 8TG5

• Entry DOI: 10.2210/pdb8tg5/pdb
• Related: 8TFI
• Descriptor: Probable RNA 2'-phosphotransferase, (2S,3R,4R,5S)-2-(6-amino-9H-purin-9-yl)-4-{[(S)-{[(2R,3S,4R,5S)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl]oxy}-5-({[(S)-{[(2R,3R,4S,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-2-(hydroxymethyl)oxolan-3-yl]oxy}(hydroxy)phosphoryl]oxy}methyl)oxolan-3-yl dihydrogen phosphate (non-preferred name), POTASSIUM ION, ... (5 entities in total)
• Functional Keywords: trna 2'-phosphotransferase, tpt1, trna splicing, branched rna, 2'-po4 rna, transferase
• Biological source: Pyrococcus horikoshii OT3
• Total number of polymer chains: 1
• Total formula weight: 22029.40

Authors

Jacewicz, A.,Dantuluri, S.,Shuman, S. (deposition date: 2023-07-12, release date: 2024-06-05, Last modification date: 2024-06-26)

Primary citation

Jacewicz, A.,Dantuluri, S.,Shuman, S.
Structural basis for Tpt1-catalyzed 2'-PO 4 transfer from RNA and NADP(H) to NAD.
Proc.Natl.Acad.Sci.USA, 120:e2312999120-e2312999120, 2023

PubMed Abstract: Tpt1 is an essential agent of fungal and plant tRNA splicing that removes an internal RNA 2'-phosphate generated by tRNA ligase. Tpt1 also removes the 2'-phosphouridine mark installed by Ark1 kinase in the V-loop of archaeal tRNAs. Tpt1 performs a two-step reaction in which the 2'-PO attacks NAD to form an RNA-2'-phospho-(ADP-ribose) intermediate, and transesterification of the ADP-ribose O2″ to the RNA 2'-phosphodiester yields 2'-OH RNA and ADP-ribose-1″,2″-cyclic phosphate. Here, we present structures of archaeal Tpt1 enzymes, captured as product complexes with ADP-ribose-1″-PO, ADP-ribose-2″-PO, and 2'-OH RNA, and as substrate complexes with 2',5'-ADP and NAD, that illuminate 2'-PO junction recognition and catalysis. We show that archaeal Tpt1 enzymes can use the 2'-PO-containing metabolites NADP and NADPH as substrates for 2'-PO transfer to NAD. A role in 2'-phospho-NADP(H) dynamics provides a rationale for the prevalence of Tpt1 in taxa that lack a capacity for internal RNA 2'-phosphorylation.

PubMed: 37883434
DOI: 10.1073/pnas.2312999120

Experimental method

X-RAY DIFFRACTION (2 Å)