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TitleStructural basis for aminoacylation of cellular modified tRNALys3 by human lysyl-tRNA synthetase.
Journal, issue, pagesNucleic Acids Res, Vol. 53, Issue 5, Year 2025
Publish dateFeb 27, 2025
AuthorsSwapnil C Devarkar / Christina R Budding / Chathuri Pathirage / Arundhati Kavoor / Cassandra Herbert / Patrick A Limbach / Karin Musier-Forsyth / Yong Xiong /
PubMed AbstractThe average eukaryotic transfer ribonucleic acid (tRNA) contains 13 post-transcriptional modifications; however, their functional impact is largely unknown. Our understanding of the complex tRNA ...The average eukaryotic transfer ribonucleic acid (tRNA) contains 13 post-transcriptional modifications; however, their functional impact is largely unknown. Our understanding of the complex tRNA aminoacylation machinery in metazoans also remains limited. Herein, using a series of high-resolution cryo-electron microscopy (cryo-EM) structures, we provide the mechanistic basis for recognition and aminoacylation of fully modified cellular tRNALys3 by human lysyl-tRNA synthetase (h-LysRS). The tRNALys3 anticodon loop modifications S34 (mcm5s2U) and R37 (ms2t6A) play an integral role in recognition by h-LysRS. Modifications in the T-, variable-, and D-loops of tRNALys3 are critical for ordering the metazoan-specific N-terminal domain of LysRS. The two catalytic steps of tRNALys3 aminoacylation are structurally ordered; docking of the 3'-CCA end in the active site cannot proceed until the lysyl-adenylate intermediate is formed and the pyrophosphate byproduct is released. Association of the h-LysRS-tRNALys3 complex with a multi-tRNA synthetase complex-derived peptide shifts the equilibrium toward the 3'-CCA end "docked" conformation and allosterically increases h-LysRS catalytic efficiency. The insights presented here have broad implications for understanding the role of tRNA modifications in protein synthesis, the human aminoacylation machinery, and the growing catalog of metabolic and neurological diseases linked to it.
External linksNucleic Acids Res / PubMed:40036503 / PubMed Central
MethodsEM (single particle)
Resolution2.8 - 3.1 Å
Structure data

47094

9dow

EMDB-47094, PDB-9dow:
h-LysRS bound to unmodified tRNA-Lys3 (Undocked State, AMP bound)
Method: EM (single particle) / Resolution: 3.1 Å

47100

9dpa

EMDB-47100, PDB-9dpa:
Human LysRS bound to unmodified tRNA-Lys3 (3'-CCA Docked State, AMP bound)
Method: EM (single particle) / Resolution: 3.0 Å

47101

9dpb

EMDB-47101, PDB-9dpb:
Human LysRS bound to unmodified tRNA-Lys3 (Undocked State, AMPCPP bound)
Method: EM (single particle) / Resolution: 2.9 Å

47106

9dpl

EMDB-47106, PDB-9dpl:
Human LysRS bound to cellular modified tRNA-Lys3 and AIMP2
Method: EM (single particle) / Resolution: 2.8 Å

Chemicals

ChemComp-LYS:
LYSINE

ChemComp-AMP:
ADENOSINE MONOPHOSPHATE / AMP*YM

ChemComp-NA:
Unknown entry

ChemComp-APC:
DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER / AMP-CPP, energy-carrying molecule analogue*YM

ChemComp-MG:
Unknown entry

Source
  • homo sapiens (human)
KeywordsTRANSLATION / LysRS / undocked state / unmodified tRNALys3 / aminoacylation / docked state / tRNA-Lys3 / tRNALys3 / AMPCPP / tRNA / multi-tRNA synthetase complex

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