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TitleStructural insights into the decoding capability of isoleucine tRNAs with lysidine and agmatidine.
Journal, issue, pagesNat Struct Mol Biol, Year 2024
Publish dateMar 27, 2024
AuthorsNaho Akiyama / Kensuke Ishiguro / Takeshi Yokoyama / Kenjyo Miyauchi / Asuteka Nagao / Mikako Shirouzu / Tsutomu Suzuki /
PubMed AbstractThe anticodon modifications of transfer RNAs (tRNAs) finetune the codon recognition on the ribosome for accurate translation. Bacteria and archaea utilize the modified cytidines, lysidine (L) and ...The anticodon modifications of transfer RNAs (tRNAs) finetune the codon recognition on the ribosome for accurate translation. Bacteria and archaea utilize the modified cytidines, lysidine (L) and agmatidine (agmC), respectively, in the anticodon of tRNA to decipher AUA codon. L and agmC contain long side chains with polar termini, but their functions remain elusive. Here we report the cryogenic electron microscopy structures of tRNAs recognizing the AUA codon on the ribosome. Both modifications interact with the third adenine of the codon via a unique C-A geometry. The side chains extend toward 3' direction of the mRNA, and the polar termini form hydrogen bonds with 2'-OH of the residue 3'-adjacent to the AUA codon. Biochemical analyses demonstrated that AUA decoding is facilitated by the additional interaction between the polar termini of the modified cytidines and 2'-OH of the fourth mRNA residue. We also visualized cyclic N-threonylcarbamoyladenosine (ctA), another tRNA modification, and revealed a molecular basis how ctA contributes to efficient decoding.
External linksNat Struct Mol Biol / PubMed:38538915
MethodsEM (single particle)
Resolution2.32 - 2.69 Å
Structure data

35001

8hsp

EMDB-35001, PDB-8hsp:
E. coli 70S ribosome complexed with tRNA_Ile2 bearing L34 and t6A37 in classical state
Method: EM (single particle) / Resolution: 2.32 Å

35020

8htz

EMDB-35020, PDB-8htz:
E. coli 70S ribosome complexed with H. marismortui tRNA_Ile2 bearing agm2C34 in classical state
Method: EM (single particle) / Resolution: 2.4 Å

35022

8hu1

EMDB-35022, PDB-8hu1:
E. coli 70S ribosome complexed with tRNA_Ile2 bearing L34 and ct6A37 in classical state
Method: EM (single particle) / Resolution: 2.69 Å

Chemicals

ChemComp-MG:
Unknown entry

ChemComp-K:
Unknown entry

Source
  • escherichia coli (E. coli)
  • escherichia coli bw25113 (bacteria)
  • haloarcula marismortui (Halophile)
KeywordsRIBOSOME / tRNA modification / decoding

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