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Related Concept Videos

tRNA Activation02:26

tRNA Activation

Aminoacyl-tRNA synthetases are present in both eukaryotes and bacteria. Though eukaryotes have 20 different aminoacyl-tRNA synthetases to couple to 20 amino acids, many bacteria do not have genes for all of these aminoacyl-tRNA synthetases. Despite this, they still use all 20 amino acids to synthesize their proteins. For instance, some bacteria do not have the gene encoding the enzyme that couples glutamine with its partner tRNA. In these organisms, one enzyme adds glutamic acid to all of the...
tRNA Activation02:26

tRNA Activation

Aminoacyl-tRNA synthetases are present in both eukaryotes and bacteria. Though eukaryotes have 20 different aminoacyl-tRNA synthetases to couple to 20 amino acids, many bacteria do not have genes for all of these aminoacyl-tRNA synthetases. Despite this, they still use all 20 amino acids to synthesize their proteins. For instance, some bacteria do not have the gene encoding the enzyme that couples glutamine with its partner tRNA. In these organisms, one enzyme adds glutamic acid to all of the...
Transfer RNA Synthesis02:36

Transfer RNA Synthesis

One of the unique features of tRNA is the presence of modified bases. In some tRNAs, modified bases account for nearly 20% of the total bases in the molecule. Altogether, these unusual bases protect the tRNA from enzymatic degradation by RNases.
Each of these chemical modifications is carried by a specific enzyme, post-transcription. All of these enzymes have unique base and site-specificity. Methylation, the most common chemical modification, is carried by at least nine different enzymes, with...
Transfer RNA Synthesis02:36

Transfer RNA Synthesis

One of the unique features of tRNA is the presence of modified bases. In some tRNAs, modified bases account for nearly 20% of the total bases in the molecule. Altogether, these unusual bases protect the tRNA from enzymatic degradation by RNases.
Each of these chemical modifications is carried by a specific enzyme, post-transcription. All of these enzymes have unique base and site-specificity. Methylation, the most common chemical modification, is carried by at least nine different enzymes, with...
Improving Translational Accuracy02:07

Improving Translational Accuracy

Base complementarity between the three base pairs of mRNA codon and the tRNA anticodon is not a failsafe mechanism. Inaccuracies can range from a single mismatch to no correct base pairing at all. The free energy difference between the correct and nearly correct base pairs can be as small as 3 kcal/ mol. With complementarity being the only proofreading step, the estimated error frequency would be one wrong amino acid in every 100 amino acids incorporated. However, error frequencies observed in...
Initiation of Translation02:33

Initiation of Translation

Initiating translation is complex because it involves multiple molecules. Initiator tRNA, ribosomal subunits, and eukaryotic initiation factors (eIFs) are all required to assemble on the initiation codon of mRNA. This process consists of several steps that are mediated by different eIFs.
First, the initiator tRNA must be selected from the pool of elongator tRNAs by eukaryotic initiation factor 2 (eIF2). The initiator tRNA (Met-tRNAi) has conserved sequence elements including modified bases at...

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Related Experiment Video

Updated: May 28, 2026

Protein-tRNA Agarose Gel Retardation Assays for the Analysis of the N6-threonylcarbamoyladenosine TcdA Function
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Protein-tRNA Agarose Gel Retardation Assays for the Analysis of the N6-threonylcarbamoyladenosine TcdA Function

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Structural basis of tRNA agmatinylation essential for AUA codon decoding.

Takuo Osawa1, Satoshi Kimura, Naohiro Terasaka

  • 1Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Ibaraki, Japan.

Nature Structural & Molecular Biology
|October 18, 2011
PubMed
Summary

The enzyme TiaS modifies a specific cytidine in archaeal tRNA to agmatidine, crucial for accurate genetic code reading. Structural studies reveal a novel kinase module and the mechanism of agmatidine synthesis.

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Isolation of Translating Ribosomes Containing Peptidyl-tRNAs for Functional and Structural Analyses
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Isolation of Translating Ribosomes Containing Peptidyl-tRNAs for Functional and Structural Analyses

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Related Experiment Videos

Last Updated: May 28, 2026

Protein-tRNA Agarose Gel Retardation Assays for the Analysis of the N6-threonylcarbamoyladenosine TcdA Function
08:03

Protein-tRNA Agarose Gel Retardation Assays for the Analysis of the N6-threonylcarbamoyladenosine TcdA Function

Published on: June 21, 2017

Genome-wide Analysis of Aminoacylation (Charging) Levels of tRNA Using Microarrays
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Genome-wide Analysis of Aminoacylation (Charging) Levels of tRNA Using Microarrays

Published on: June 18, 2010

Isolation of Translating Ribosomes Containing Peptidyl-tRNAs for Functional and Structural Analyses
11:19

Isolation of Translating Ribosomes Containing Peptidyl-tRNAs for Functional and Structural Analyses

Published on: February 25, 2011

Area of Science:

  • Molecular Biology
  • Structural Biology
  • Biochemistry

Background:

  • Accurate decoding of the genetic code relies on modified nucleosides in transfer RNA (tRNA).
  • The archaeal tRNA(Ile2) anticodon contains cytidine at position 34 (C34), which is modified to 2-agmatinylcytidine (agm(2)C), also known as agmatidine.
  • This modification is essential for the precise translation of the AUA codon.

Purpose of the Study:

  • To elucidate the structural basis of agmatidine synthesis by tRNA(Ile)-agm(2)C synthetase (TiaS).
  • To reveal the molecular mechanism of C34 activation and agmatidine formation.
  • To understand how TiaS distinguishes between tRNA(Ile2) and tRNA(Met).

Main Methods:

  • X-ray crystallography was used to determine the structures of the Archaeoglobus fulgidus TiaS-tRNA(Ile2) complex.
  • Structures were obtained in the presence of ATP, or AMPCPP and agmatine.

Main Results:

  • The crystal structures revealed a previously unrecognized kinase module within TiaS, responsible for C34 phosphorylation.
  • In the presence of agmatine, C34 is positioned near the ATP analog (AMPCPP) in the kinase module's active site.
  • The structures illustrate the critical role of agmatine in orienting C34 for activation and subsequent agmatidine synthesis.

Conclusions:

  • TiaS utilizes a kinase module to activate C34 via phosphorylation before agmatine conjugation.
  • Agmatine is essential for the correct positioning of C34 within the TiaS active site, facilitating the modification.
  • These findings provide detailed insights into the structural dynamics governing agmatidine formation and tRNA recognition.