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The term ribozyme is used for RNA that can act as an enzyme. Ribozymes are mainly found in selected viruses, bacteria, plant organelles, and lower eukaryotes. Ribozymes were first discovered in 1982 when Tom Cech’s laboratory observed Group I introns acting as enzymes. This was shortly followed by the discovery of another ribozyme, Ribonulcease P, by Sid Altman’s laboratory. Both Cech and Altman received the Nobel Prize in chemistry in 1989 for their work on ribozymes.
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One of the common DNA damages is the chemical alteration of single bases by alkylation, oxidation, or deamination. The altered bases cause mispairing and strand breakage during replication. This type of damage causes minimal change to the DNA double helix structure and can be repaired by the base excision repair (BER) pathways. BER corrects damaged DNA sequences by removing the damaged base and restoring the original base sequence using the complementary strand as a template.
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Structures of 5'-3' Exoribonucleases.

Jeong Ho Chang1, Song Xiang2, Liang Tong1

  • 1Department of Biological Sciences, Columbia University, New York, NY, USA.

The Enzymes
|May 12, 2016
PubMed
Summary

5-3 Exoribonucleases (XRNs) are crucial for RNA regulation. Recent crystal structures reveal their conserved domains and active sites, uncovering a novel mRNA capping surveillance mechanism.

Keywords:
Dom3ZNonsense-mediated decayRai1Rat1Transcription terminationXrn1Xrn2mRNA cappingmRNA turnover

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Area of Science:

  • Biochemistry
  • Molecular Biology
  • Structural Biology

Background:

  • 5'-3' Exoribonucleases (XRNs) are essential enzymes involved in diverse cellular processes including RNA processing, decay, and transcription.
  • XRNs possess two highly conserved regions, CR1 and CR2, critical for their function.
  • Cytoplasmic Xrn1 and nuclear Xrn2/Rat1 are key examples found in yeast and animals, with XRNs present across most eukaryotes.

Purpose of the Study:

  • To elucidate the structural basis of 5'-3' Exoribonuclease (XRN) function.
  • To investigate the role of conserved regions CR1 and CR2 in enzyme activity and specificity.
  • To understand the mechanism of mRNA 5'-end capping quality surveillance mediated by XRNs and their partners.

Main Methods:

  • X-ray crystallography was employed to determine the structures of Xrn1 and Rat1.
  • Bioinformatic analysis was used to compare conserved regions and identify structural homologies.
  • Biochemical assays were performed to characterize the enzymatic activity and substrate specificity of XRNs.

Main Results:

  • Crystal structures revealed that the conserved regions CR1 and CR2 form a single, large domain in XRNs.
  • CR1 exhibits structural homology to the FEN superfamily of nucleases.
  • CR2 acts as a gatekeeper, restricting access to the active site and ensuring exclusive 5'-3' exoribonuclease activity. The structure of Rai1 revealed an active site involved in mRNA capping quality surveillance.

Conclusions:

  • The structural insights into XRNs provide a detailed understanding of their enzymatic mechanisms and substrate specificity.
  • The identified structural homology of CR1 to FEN nucleases sheds light on the evolutionary origins of XRNs.
  • The discovery of a novel mRNA 5'-end capping quality surveillance mechanism highlights the critical role of XRNs in maintaining RNA homeostasis.