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TitleAnticodon loop remodeling and D-stem shape drive the specific recognition of ANN-decoding tRNAs for t6A modification.
Journal, issue, pagesNucleic Acids Res, Vol. 54, Issue 11, Year 2026
Publish dateJun 8, 2026
AuthorsAna Kutchuashvili / Erik Scheleen / George Guynes / Junzhou Wu / Chi-Kong Chan / Peter Dedon / Dirk Iwata-Reuyl / Manal A Swairjo /
PubMed AbstractN6-threonylcarbamoyladenosine (t6A) is a universal transfer RNA (tRNA) modification essential for translational fidelity. The modification is installed at position 37 of ANN-decoding tRNAs (N is A, ...N6-threonylcarbamoyladenosine (t6A) is a universal transfer RNA (tRNA) modification essential for translational fidelity. The modification is installed at position 37 of ANN-decoding tRNAs (N is A, U, G, or C) by transfer of a threonylcarbamoyl moiety from a pathway intermediate, catalyzed in bacteria by the TsaBD complex. Despite the strict requirement for the 36-UAA-38 sequence in substrate tRNAs, the structural basis for this specificity has remained unclear. We determined cryo-EM structures of the Thermotoga maritima t6A synthase bound to unmodified and to natively modified tRNA carrying the t6A37 modification, at a nominal resolution of 3.2 Å. In both structures, A37 is positioned in the active site, and the anticodon loop is remodeled into a zig-zag conformation not previously observed in tRNA, stabilized by conserved interactions with the RNA backbone at the TsaD/TsaB interface. The wobble and middle anticodon bases occupy shallow surface pockets without base-specific contacts, explaining tolerance to base identity at these positions. In contrast, U36 and A38 are recognized indirectly through formation of a base triple with U32. Additional D-stem contacts provide a second mode of indirect readout. Together with mutagenesis data, the structures reveal the molecular basis for restriction of t6A37 to ANN-decoding tRNAs and the requirement for A38.
External linksNucleic Acids Res / PubMed:42312490 / PubMed Central
MethodsEM (single particle)
Resolution3.2 Å
Structure data

77046

13fn

EMDB-77046, PDB-13fn:
Thermotoga maritima threonylcarbamoyl transfer complex (TsaB2D) in complex with Escherichia coli tRNA(THR)
Method: EM (single particle) / Resolution: 3.2 Å

77048

13fo

EMDB-77048, PDB-13fo:
Thermotoga maritima threonylcarbamoyl transfer complex (TsaB2D) in complex with Thermotoga maritima tRNA(LYS)
Method: EM (single particle) / Resolution: 3.2 Å

Chemicals

ChemComp-MG:
Unknown entry

Source
  • thermotoga maritima (bacteria)
  • escherichia coli (E. coli)
KeywordsRNA BINDING PROTEIN/RNA / TsaB2D2 / threonylcarbamoyl transfer complex / tRNA / t6A / N6-threonylcarbamoyl adenosine / t6A37 / transfer-RNA / BIOSYNTHETIC PROTEIN / BIOSYNTHETIC PROTEIN-RNA complex / RNA BINDING PROTEIN / RNA BINDING PROTEIN-RNA complex

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