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TitleMechanistic basis for PYROXD1-mediated protection of the human tRNA ligase complex against oxidative inactivation.
Journal, issue, pagesNat Struct Mol Biol, Vol. 32, Issue 7, Page 1205-1212, Year 2025
Publish dateMar 11, 2025
AuthorsLuuk Loeff / Alena Kroupova / Igor Asanović / Franziska M Boneberg / Moritz M Pfleiderer / Luca Riermeier / Alexander Leitner / Andrè Ferdigg / Fabian Ackle / Javier Martinez / Martin Jinek /
PubMed AbstractThe metazoan tRNA ligase complex (tRNA-LC) has essential roles in tRNA biogenesis and unfolded protein response. Its catalytic subunit RTCB contains a conserved active-site cysteine that is ...The metazoan tRNA ligase complex (tRNA-LC) has essential roles in tRNA biogenesis and unfolded protein response. Its catalytic subunit RTCB contains a conserved active-site cysteine that is susceptible to metal ion-induced oxidative inactivation. The flavin-containing oxidoreductase PYROXD1 preserves the activity of human tRNA-LC in a NAD(P)H-dependent manner, but its protective mechanism remains elusive. Here, we report a cryogenic electron microscopic structure of the human RTCB-PYROXD1 complex, revealing that PYROXD1 directly interacts with the catalytic center of RTCB through its carboxy-terminal tail. NAD(P)H binding and FAD reduction allosterically control PYROXD1 activity and RTCB recruitment, while reoxidation of PYROXD1 enables timed release of RTCB. PYROXD1 interaction is mutually exclusive with Archease-mediated RTCB guanylylation, and guanylylated RTCB is intrinsically protected from oxidative inactivation. Together, these findings provide a mechanistic framework for the protective function of PYROXD1 that maintains the activity of the tRNA-LC under aerobic conditions.
External linksNat Struct Mol Biol / PubMed:40069351 / PubMed Central
MethodsEM (single particle)
Resolution3.3 Å
Structure data

17127

8orj

EMDB-17127, PDB-8orj:
Cryo-EM structure of human tRNA ligase RTCB in complex with human PYROXD1.
Method: EM (single particle) / Resolution: 3.3 Å

Chemicals

ChemComp-MG:
Unknown entry

ChemComp-NAD:
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / NAD*YM

ChemComp-FDA:
DIHYDROFLAVINE-ADENINE DINUCLEOTIDE

Source
  • homo sapiens (human)
KeywordsLIGASE / tRNA ligase / PYROXD1 / RTCB / Flavoprotein

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