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Structure paper

TitleStructures of the ribosome bound to EF-Tu-isoleucine tRNA elucidate the mechanism of AUG avoidance.
Journal, issue, pagesNat Struct Mol Biol, Year 2024
Publish dateMar 27, 2024
AuthorsMariia Yu Rybak / Matthieu G Gagnon /
PubMed AbstractThe frequency of errors upon decoding of messenger RNA by the bacterial ribosome is low, with one misreading event per 1 × 10 codons. In the universal genetic code, the AUN codon box specifies ...The frequency of errors upon decoding of messenger RNA by the bacterial ribosome is low, with one misreading event per 1 × 10 codons. In the universal genetic code, the AUN codon box specifies two amino acids, isoleucine and methionine. In bacteria and archaea, decoding specificity of the AUA and AUG codons relies on the wobble avoidance strategy that requires modification of C34 in the anticodon loop of isoleucine transfer RNA (tRNA). Bacterial tRNA with 2-lysylcytidine (lysidine) at the wobble position deciphers AUA while avoiding AUG. Here we report cryo-electron microscopy structures of the Escherichia coli 70S ribosome complexed with elongation factor thermo unstable (EF-Tu) and isoleucine-tRNA in the process of decoding AUA and AUG. Lysidine in tRNA excludes AUG by promoting the formation of an unusual Hoogsteen purine-pyrimidine nucleobase geometry at the third position of the codon, weakening the interactions with the mRNA and destabilizing the EF-Tu ternary complex. Our findings elucidate the molecular mechanism by which tRNA specifically decodes AUA over AUG.
External linksNat Struct Mol Biol / PubMed:38538914
MethodsEM (single particle)
Resolution2.8 - 3.1 Å
Structure data

29819

8g7p

EMDB-29819, PDB-8g7p:
Structure of the Escherichia coli 70S ribosome in complex with EF-Tu and Ile-tRNAIle(LAU) bound to the cognate AUA codon (Structure I)
Method: EM (single particle) / Resolution: 2.9 Å

29820

8g7q

EMDB-29820, PDB-8g7q:
Structure of the Escherichia coli 70S ribosome in complex with EF-Tu and Ile-tRNAIle(LAU) bound to the near-cognate AUG codon (Structure II)
Method: EM (single particle) / Resolution: 3.1 Å

29821

8g7r

EMDB-29821, PDB-8g7r:
Structure of the Escherichia coli 70S ribosome in complex with A-site tRNAIle(LAU) bound to the cognate AUA codon (Structure III)
Method: EM (single particle) / Resolution: 2.8 Å

29822

8g7s

EMDB-29822, PDB-8g7s:
Structure of the Escherichia coli 70S ribosome in complex with P-site tRNAIle(LAU) bound to the cognate AUA codon (Structure IV)
Method: EM (single particle) / Resolution: 3.1 Å

Chemicals

ChemComp-MG:
Unknown entry

ChemComp-K:
Unknown entry

ChemComp-ILE:
ISOLEUCINE / Isoleucine

ChemComp-GCP:
PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER / GMP-PCP, energy-carrying molecule analogue*YM

ChemComp-ZN:
Unknown entry

ChemComp-HOH:
WATER / Water

ChemComp-PAR:
PAROMOMYCIN / Antimicrobial, medication*YM / Paromomycin

Source
  • escherichia coli (E. coli)
  • escherichia phage t4 (virus)
KeywordsRIBOSOME / Elongation factor Tu / lysidine 34 / cryo-EM / tRNA / paromomycin

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