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The structural basis for specific decoding of AUA by isoleucine tRNA on the ribosome.

Voorhees RM, Mandal D, Neubauer C, Köhrer C, RajBhandary UL, Ramakrishnan V - Nat. Struct. Mol. Biol. (2013)

Bottom Line: Decoding of the AUA isoleucine codon in bacteria and archaea requires modification of a C in the anticodon wobble position of the isoleucine tRNA.Here, we report the crystal structure of the archaeal tRNA2(Ile), which contains the modification agmatidine in its anticodon, in complex with the AUA codon on the 70S ribosome.The structure illustrates how agmatidine confers codon specificity for AUA over AUG.

View Article: PubMed Central - PubMed

Affiliation: Medical Research Council Laboratory of Molecular Biology, Cambridge, UK.

ABSTRACT
Decoding of the AUA isoleucine codon in bacteria and archaea requires modification of a C in the anticodon wobble position of the isoleucine tRNA. Here, we report the crystal structure of the archaeal tRNA2(Ile), which contains the modification agmatidine in its anticodon, in complex with the AUA codon on the 70S ribosome. The structure illustrates how agmatidine confers codon specificity for AUA over AUG.

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The role of the agmatidine modification in decoding. A) Comparison of the A3•agm2C wobble pair with a canonical G3-C34 Watson-Crick base pair (grey) and an A3•C34 mismatch (cyan), both observed in the wobble position 12. B) Interaction of the terminal amine of the agmatidine modification on the A-site tRNA with the backbone of a downstream mRNA residue important for stabilizing the codon-anticodon interaction.
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Figure 2: The role of the agmatidine modification in decoding. A) Comparison of the A3•agm2C wobble pair with a canonical G3-C34 Watson-Crick base pair (grey) and an A3•C34 mismatch (cyan), both observed in the wobble position 12. B) Interaction of the terminal amine of the agmatidine modification on the A-site tRNA with the backbone of a downstream mRNA residue important for stabilizing the codon-anticodon interaction.

Mentions: Instead, the configuration at the wobble position is more similar to the A3•C34 mismatch observed for binding of the tRNATrp-derived Hirsh suppressor tRNA to the UGA stop codon than to a canonical wobble or Watson-Crick interaction 12 (Fig. 2a). Interestingly, a similar geometry of the A3•agm2C34 base pair is maintained in the P site of the ribosome as well. Formation of this interaction requires a shift in both the mRNA and tRNA, which is in contrast to previous studies where the mRNA remained stationary while interacting with several modified cognate anticodons 20. The Watson-Crick interactions at the first and second positions of the codon-anticodon helix appear unaffected by this distorted geometry in the wobble position.


The structural basis for specific decoding of AUA by isoleucine tRNA on the ribosome.

Voorhees RM, Mandal D, Neubauer C, Köhrer C, RajBhandary UL, Ramakrishnan V - Nat. Struct. Mol. Biol. (2013)

The role of the agmatidine modification in decoding. A) Comparison of the A3•agm2C wobble pair with a canonical G3-C34 Watson-Crick base pair (grey) and an A3•C34 mismatch (cyan), both observed in the wobble position 12. B) Interaction of the terminal amine of the agmatidine modification on the A-site tRNA with the backbone of a downstream mRNA residue important for stabilizing the codon-anticodon interaction.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3672977&req=5

Figure 2: The role of the agmatidine modification in decoding. A) Comparison of the A3•agm2C wobble pair with a canonical G3-C34 Watson-Crick base pair (grey) and an A3•C34 mismatch (cyan), both observed in the wobble position 12. B) Interaction of the terminal amine of the agmatidine modification on the A-site tRNA with the backbone of a downstream mRNA residue important for stabilizing the codon-anticodon interaction.
Mentions: Instead, the configuration at the wobble position is more similar to the A3•C34 mismatch observed for binding of the tRNATrp-derived Hirsh suppressor tRNA to the UGA stop codon than to a canonical wobble or Watson-Crick interaction 12 (Fig. 2a). Interestingly, a similar geometry of the A3•agm2C34 base pair is maintained in the P site of the ribosome as well. Formation of this interaction requires a shift in both the mRNA and tRNA, which is in contrast to previous studies where the mRNA remained stationary while interacting with several modified cognate anticodons 20. The Watson-Crick interactions at the first and second positions of the codon-anticodon helix appear unaffected by this distorted geometry in the wobble position.

Bottom Line: Decoding of the AUA isoleucine codon in bacteria and archaea requires modification of a C in the anticodon wobble position of the isoleucine tRNA.Here, we report the crystal structure of the archaeal tRNA2(Ile), which contains the modification agmatidine in its anticodon, in complex with the AUA codon on the 70S ribosome.The structure illustrates how agmatidine confers codon specificity for AUA over AUG.

View Article: PubMed Central - PubMed

Affiliation: Medical Research Council Laboratory of Molecular Biology, Cambridge, UK.

ABSTRACT
Decoding of the AUA isoleucine codon in bacteria and archaea requires modification of a C in the anticodon wobble position of the isoleucine tRNA. Here, we report the crystal structure of the archaeal tRNA2(Ile), which contains the modification agmatidine in its anticodon, in complex with the AUA codon on the 70S ribosome. The structure illustrates how agmatidine confers codon specificity for AUA over AUG.

Show MeSH