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Related Concept Videos

RNA Structure01:19

RNA Structure

The basic structure of RNA consists of a string of ribonucleotides attached by phosphodiester bonds. Although most RNA is single-stranded, it can form complex secondary and tertiary structures. Such structures play essential roles in the regulation of transcription and translation.
Different Types of RNA Have the Same Basic Structure
There are three main types of ribonucleic acid (RNA) involved in protein synthesis: messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). All three...
RNA Structure01:23

RNA Structure

Overview
The basic structure of RNA consists of a five-carbon sugar and one of four nitrogenous bases. Although most RNA is single-stranded, it can form complex secondary and tertiary structures. Such structures play essential roles in the regulation of transcription and translation.
Different Types of RNA Have the Same Basic Structure
There are three main types of ribonucleic acid (RNA): messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). All three RNA types consist of a...
RNA Structure01:23

RNA Structure

Overview
The basic structure of RNA consists of a five-carbon sugar and one of four nitrogenous bases. Although most RNA is single-stranded, it can form complex secondary and tertiary structures. Such structures play essential roles in the regulation of transcription and translation.
Different Types of RNA Have the Same Basic Structure
There are three main types of ribonucleic acid (RNA): messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). All three RNA types consist of a...
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...

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Comparative RNA Structure Analysis of Nascent and Mature Transcripts in Saccharomyces cerevisiae
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Tertiary structure checkpoint at anticodon loop modification in tRNA functional maturation.

Sakurako Goto-Ito1, Takuhiro Ito, Mitsuo Kuratani

  • 1Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, Tokyo, Japan.

Nature Structural & Molecular Biology
|September 15, 2009
PubMed
Summary
This summary is machine-generated.

Archaeal Trm5 enzyme modifies guanosine at position 37 (G37) in transfer RNA (tRNA). Its D1 domain recognizes the tRNA

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Area of Science:

  • Molecular Biology
  • Structural Biology
  • Biochemistry

Background:

  • Transfer RNA (tRNA) precursors require maturation, including nucleotide modifications and folding into an L-shaped tertiary structure.
  • N1-methylguanosine at position 37 (m1G37), located 3' to the anticodon, is crucial for translational fidelity and efficiency.
  • The Trm5 enzyme is responsible for introducing the m1G37 modification in archaea and eukaryotes for all tRNAs with G37.

Purpose of the Study:

  • To elucidate the structural basis of Trm5's recognition and modification of tRNA.
  • To understand the role of Trm5 in ensuring tRNA tertiary structure formation during maturation.

Main Methods:

  • X-ray crystallography was employed to determine the structures of archaeal Trm5 (aTrm5) in complex with tRNA(Leu) and tRNA(Cys).
  • Biochemical assays were used to assess the enzyme's kinetic parameters and substrate recognition.

Main Results:

  • The crystal structures reveal that the D2-D3 domains of aTrm5 directly recognize and modify guanosine at position 37 (G37), independent of specific tRNA sequences.
  • The D1 domain interacts with the outer corner of the tRNA, recognizing the completed L-shaped tertiary structure.
  • This interaction by D1 significantly lowers the Michaelis constant (K(m)) for tRNA, facilitating catalysis by the D2-D3 domains.

Conclusions:

  • Archaeal Trm5 acts as a tertiary structure checkpoint in tRNA maturation, ensuring proper folding before modification.
  • The dual-domain recognition mechanism allows Trm5 to modify G37 efficiently only in correctly folded tRNAs.
  • This study provides critical structural insights into the precise regulation of tRNA modification by Trm5.