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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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Decoding of the Ile AUA codon in prokaryotes. A) Post-transcriptional modification of C34 with either lysine or agmatine switches the amino acid and codon specificity of tRNA2Ile from Met to Ile. B) Chemically, the bacterial and archaeal agmatidine and lysidine modifications are very similar, suggesting they play similar roles in decoding of the AUA codon. C) The crystal structure of the archaeal tRNA2Ile bound to its cognate AUA codon on the ribosome, demonstrates that a single hydrogen bonding interaction between A3 (red) and agm2C (purple) forms in the wobble position.
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Figure 1: Decoding of the Ile AUA codon in prokaryotes. A) Post-transcriptional modification of C34 with either lysine or agmatine switches the amino acid and codon specificity of tRNA2Ile from Met to Ile. B) Chemically, the bacterial and archaeal agmatidine and lysidine modifications are very similar, suggesting they play similar roles in decoding of the AUA codon. C) The crystal structure of the archaeal tRNA2Ile bound to its cognate AUA codon on the ribosome, demonstrates that a single hydrogen bonding interaction between A3 (red) and agm2C (purple) forms in the wobble position.

Mentions: Genetically, tRNA2Ile contains a CAU anticodon, which alone, is perfectly complementary to the AUG Met codon. However, modification of C34 to k2C34 in bacteria switches both the amino acid and codon specificity of the tRNA; the k2C34-modified tRNA is acylated by Ile-tRNA synthetase and decodes the minor AUA Ile codon, while simultaneously rejecting the AUG Met codon 13 (Fig. 1a,b). The enzymes responsible for introducing this modification were later shown to be highly conserved and essential in bacteria 14. Recently, it was found that archaea use an analogous modification, known as agmatidine (agm2C), in the wobble position of tRNA2Ile (refs. 15-17), suggesting that the requirement for a post-transcriptional modification to discriminate between AUA and AUG codons is conserved across all kingdoms of biology 18. In order to understand how lysidine and agmatidine, which are derived from cytidine, can base pair specifically with A of the AUA Ile codon but not with G of the AUG Met codon is, we decided to study the interaction of tRNA2Ile with its cognate codon on the 70S ribosome.


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)

Decoding of the Ile AUA codon in prokaryotes. A) Post-transcriptional modification of C34 with either lysine or agmatine switches the amino acid and codon specificity of tRNA2Ile from Met to Ile. B) Chemically, the bacterial and archaeal agmatidine and lysidine modifications are very similar, suggesting they play similar roles in decoding of the AUA codon. C) The crystal structure of the archaeal tRNA2Ile bound to its cognate AUA codon on the ribosome, demonstrates that a single hydrogen bonding interaction between A3 (red) and agm2C (purple) forms in the wobble position.
© Copyright Policy
Related In: Results  -  Collection

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Figure 1: Decoding of the Ile AUA codon in prokaryotes. A) Post-transcriptional modification of C34 with either lysine or agmatine switches the amino acid and codon specificity of tRNA2Ile from Met to Ile. B) Chemically, the bacterial and archaeal agmatidine and lysidine modifications are very similar, suggesting they play similar roles in decoding of the AUA codon. C) The crystal structure of the archaeal tRNA2Ile bound to its cognate AUA codon on the ribosome, demonstrates that a single hydrogen bonding interaction between A3 (red) and agm2C (purple) forms in the wobble position.
Mentions: Genetically, tRNA2Ile contains a CAU anticodon, which alone, is perfectly complementary to the AUG Met codon. However, modification of C34 to k2C34 in bacteria switches both the amino acid and codon specificity of the tRNA; the k2C34-modified tRNA is acylated by Ile-tRNA synthetase and decodes the minor AUA Ile codon, while simultaneously rejecting the AUG Met codon 13 (Fig. 1a,b). The enzymes responsible for introducing this modification were later shown to be highly conserved and essential in bacteria 14. Recently, it was found that archaea use an analogous modification, known as agmatidine (agm2C), in the wobble position of tRNA2Ile (refs. 15-17), suggesting that the requirement for a post-transcriptional modification to discriminate between AUA and AUG codons is conserved across all kingdoms of biology 18. In order to understand how lysidine and agmatidine, which are derived from cytidine, can base pair specifically with A of the AUA Ile codon but not with G of the AUG Met codon is, we decided to study the interaction of tRNA2Ile with its cognate codon on the 70S ribosome.

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