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TitleA tRNA modification with aminovaleramide facilitates AUA decoding in protein synthesis.
Journal, issue, pagesNat Chem Biol, Vol. 21, Issue 4, Page 522-531, Year 2025
Publish dateSep 19, 2024
AuthorsKenjyo Miyauchi / Satoshi Kimura / Naho Akiyama / Kazuki Inoue / Kensuke Ishiguro / Thien-Son Vu / Veerasak Srisuknimit / Kenta Koyama / Gosuke Hayashi / Akiko Soma / Asuteka Nagao / Mikako Shirouzu / Akimitsu Okamoto / Matthew K Waldor / Tsutomu Suzuki /
PubMed AbstractModified tRNA anticodons are critical for proper mRNA translation during protein synthesis. It is generally thought that almost all bacterial tRNAs use a modified cytidine-lysidine (L)-at the first ...Modified tRNA anticodons are critical for proper mRNA translation during protein synthesis. It is generally thought that almost all bacterial tRNAs use a modified cytidine-lysidine (L)-at the first position (34) of the anticodon to decipher the AUA codon as isoleucine (Ile). Here we report that tRNAs from plant organelles and a subset of bacteria contain a new cytidine derivative, designated 2-aminovaleramididine (avaC). Like L34, avaC34 governs both Ile-charging ability and AUA decoding. Cryo-electron microscopy structural analyses revealed molecular details of codon recognition by avaC34 with a specific interaction between its terminal amide group and an mRNA residue 3'-adjacent to the AUA codon. These findings reveal the evolutionary variation of an essential tRNA modification and demonstrate the molecular basis of AUA decoding mediated by a unique tRNA modification.
External linksNat Chem Biol / PubMed:39300229 / PubMed Central
MethodsEM (single particle)
Resolution2.25 - 2.47 Å
Structure data

39577

8yuo

EMDB-39577, PDB-8yuo:
E. coli 70S ribosome complexed with P. putida tRNAIle2 at the A-site and P-site
Method: EM (single particle) / Resolution: 2.25 Å

39578

8yup

EMDB-39578, PDB-8yup:
E. coli 70S ribosome complexed with P. putida tRNAIle2 and A4 mRNA
Method: EM (single particle) / Resolution: 2.39 Å

39579

8yuq

EMDB-39579, PDB-8yuq:
E. coli 70S ribosome complexed with P. putida tRNAIle2 and dA4 mRNA
Method: EM (single particle) / Resolution: 2.41 Å

39580

8yur

EMDB-39580, PDB-8yur:
E. coli 70S ribosome complexed with P. putida tRNAIle2 and Am4 mRNA
Method: EM (single particle) / Resolution: 2.47 Å

39581

8yus

EMDB-39581, PDB-8yus:
E. coli 70S ribosome complexed with P.putida tRNAIle2 and A(F)4 mRNA
Method: EM (single particle) / Resolution: 2.43 Å

Chemicals

ChemComp-MG:
Unknown entry

Source
  • escherichia coli (E. coli)
  • pseudomonas putida nbrc 14164 (bacteria)
  • escherichia coli bw25113 (bacteria)
KeywordsRIBOSOME / tRNA modification / decoding

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