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Related Concept Videos

Regulation of the Unfolded Protein Response01:31

Regulation of the Unfolded Protein Response

Inositol-requiring kinase one or IRE1 is the most conserved eukaryotic unfolded protein response (UPR) receptor. It is a type I transmembrane protein kinase receptor with a distinctive site-specific RNase activity. As the binding mechanics of the misfolded proteins with the N-terminal domain of IRE-1 are unclear, three binding models — direct, indirect, and allosteric -- are proposed for receptor activation. Nevertheless, it is known that once a misfolded protein associates with IRE1, it...
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The organelle-specific signaling sequences direct proteins synthesized in the cytosol to their final destination like ER, mitochondria, peroxisomes, etc. Some of the proteins directed to ER are then trafficked via vesicles to other organelles within the cell or the extracellular environment through the Golgi complex. For example, the rough ER synthesizes soluble proteins for transportation to the lysosomes or secretion out of the cell. It can also synthesize transmembrane proteins that can...
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Sec61 protein conducting channel
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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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Leaky Scanning

During most eukaryotic translation processes, the small 40S ribosome subunit scans an mRNA from its 5' end until it encounters the first start AUG codon. The large 60S ribosomal subunit then joins the smaller one to initiate protein synthesis. The location of the translation initiation is largely determined by the nucleotides near the start codon as there may be multiple translation initiation sites present on the mRNA.  Marilyn Kozak discovered that the sequence RCCAUGG (where R stands for...

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De novo Identification of Actively Translated Open Reading Frames with Ribosome Profiling Data
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Structural insights into eRF3 and stop codon recognition by eRF1.

Zhihong Cheng1, Kazuki Saito, Andrey V Pisarev

  • 1Cancer and Developmental Cell Biology Division, Institute of Molecular and Cell Biology, Agency for Science, Technology, and Research (A*STAR), Singapore, Singapore.

Genes & Development
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Eukaryotic translation termination involves release factors eRF1 and eRF3. Their interaction, revealed by structural studies, shows eRF1 adopting a tRNA-like shape and highlights key residues for factor function and stop codon recognition.

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Area of Science:

  • Molecular Biology
  • Structural Biology
  • Biochemistry

Background:

  • Eukaryotic translation termination is a critical process.
  • It is mediated by eukaryotic release factor 1 (eRF1) and eukaryotic release factor 3 (eRF3).
  • These factors cooperate for efficient stop codon recognition and polypeptide release.

Purpose of the Study:

  • To elucidate the structural basis of eRF1 and eRF3 interaction.
  • To understand the conformational changes in eRF1 upon eRF3 binding.
  • To investigate the roles of specific residues and ATP binding in termination.

Main Methods:

  • X-ray crystallography of eRF1/eRF3 complexes.
  • Small-angle X-ray scattering (SAXS) of eRF1/eRF3/GTP.
  • Site-directed mutagenesis and functional assays.

Main Results:

  • Crystal structures revealed eRF1 conformational changes upon eRF3 binding, resembling tRNA.
  • SAXS indicated contact between eRF1's M domain and eRF3's GTPase domain.
  • Mutations in eRF1 (e.g., Arg192) and analysis of the ATP-binding site elucidated roles in GTPase activity and stop codon recognition.

Conclusions:

  • The eRF1-eRF3 interaction induces significant conformational changes in eRF1.
  • Specific residues and ATP binding are crucial for the cooperative function of these release factors.
  • Structural insights provide a mechanistic understanding of eukaryotic translation termination.