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Structure paper

TitleThe molecular basis of tRNA selectivity by human pseudouridine synthase 3.
Journal, issue, pagesMol Cell, Vol. 84, Issue 13, Page 2472-22489.e8, Year 2024
Publish dateJul 11, 2024
AuthorsTing-Yu Lin / Leon Kleemann / Jakub Jeżowski / Dominika Dobosz / Michał Rawski / Paulina Indyka / Grzegorz Ważny / Rahul Mehta / Andrzej Chramiec-Głąbik / Łukasz Koziej / Tristan Ranff / Christian Fufezan / Mateusz Wawro / Jakub Kochan / Joanna Bereta / Sebastian A Leidel / Sebastian Glatt /
PubMed AbstractPseudouridine (Ψ), the isomer of uridine, is ubiquitously found in RNA, including tRNA, rRNA, and mRNA. Human pseudouridine synthase 3 (PUS3) catalyzes pseudouridylation of position 38/39 in tRNAs. ...Pseudouridine (Ψ), the isomer of uridine, is ubiquitously found in RNA, including tRNA, rRNA, and mRNA. Human pseudouridine synthase 3 (PUS3) catalyzes pseudouridylation of position 38/39 in tRNAs. However, the molecular mechanisms by which it recognizes its RNA targets and achieves site specificity remain elusive. Here, we determine single-particle cryo-EM structures of PUS3 in its apo form and bound to three tRNAs, showing how the symmetric PUS3 homodimer recognizes tRNAs and positions the target uridine next to its active site. Structure-guided and patient-derived mutations validate our structural findings in complementary biochemical assays. Furthermore, we deleted PUS1 and PUS3 in HEK293 cells and mapped transcriptome-wide Ψ sites by Pseudo-seq. Although PUS1-dependent sites were detectable in tRNA and mRNA, we found no evidence that human PUS3 modifies mRNAs. Our work provides the molecular basis for PUS3-mediated tRNA modification in humans and explains how its tRNA modification activity is linked to intellectual disabilities.
External linksMol Cell / PubMed:38996458 / PubMed Central
MethodsEM (single particle)
Resolution2.66 - 6.5 Å
Structure data

16917

9f9q

EMDB-16917: Human apo pseudouridine synthase 3 (PUS3)
PDB-9f9q: Human apo pseudouridine synthase 3 (PUS3 D118A mutant)
Method: EM (single particle) / Resolution: 6.5 Å

16926

8okd

EMDB-16926, PDB-8okd:
Human pseudouridine synthase 3 and tRNA-Gln
Method: EM (single particle) / Resolution: 3.1 Å

19830

9enb

EMDB-19830, PDB-9enb:
Human pseudouridine synthase 3 (PUS3 R116A mutant) and two tRNA-Gln
Method: EM (single particle) / Resolution: 2.66 Å

19831

9enc

EMDB-19831, PDB-9enc:
Human pseudouridine synthase 3 (PUS3 R116A mutant) and one tRNA-Gln
Method: EM (single particle) / Resolution: 3.36 Å

19832

9ene

EMDB-19832, PDB-9ene:
Human pseudouridine synthase 3 (PUS3 D118A mutant) and two tRNA-Arg
Method: EM (single particle) / Resolution: 3.15 Å

19833

9enf

EMDB-19833, PDB-9enf:
Human pseudouridine synthase 3 (PUS3 D118A mutant) and two pre-tRNA-Arg
Method: EM (single particle) / Resolution: 2.97 Å

EMDB-19834: Human pseudouridine synthase 3 (PUS3 R116A mutant)
Method: EM (single particle) / Resolution: 4.49 Å

EMDB-19835: Human pseudouridine synthase 3 (PUS3 K119A mutant)
Method: EM (single particle) / Resolution: 5.15 Å

EMDB-19836: Human pseudouridine synthase 3 (wild type)
Method: EM (single particle) / Resolution: 4.02 Å

Chemicals

ChemComp-MG:
Unknown entry

Source
  • homo sapiens (human)
KeywordsRNA BINDING PROTEIN / RNA modification / pseudouridylation / tRNA / homodimer

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