Related Experiment Video

Updated: Jul 3, 2026

Novel RNA-Binding Proteins Isolation by the RaPID Methodology
11:19

Novel RNA-Binding Proteins Isolation by the RaPID Methodology

Published on: September 30, 2016

The RRM domain of poly(A)-specific ribonuclease has a noncanonical binding site for mRNA cap analog recognition

Takashi Nagata1, Sakura Suzuki, Ryuta Endo

  • 1Systems and Structural Biology Center, Yokohama Institute, RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Japan.

Nucleic Acids Research
|July 22, 2008
PubMed

Insights

Poly(A)-specific ribonuclease (PARN) binds mRNA caps via a novel mechanism. This discovery advances understanding of mRNA degradation and gene regulation.

Area of Science:

  • Biochemistry
  • Molecular Biology
  • Structural Biology

Background:

  • Poly(A) tail degradation is vital for mRNA regulation and quality control.
  • Poly(A)-specific ribonuclease (PARN) is a key enzyme in mRNA deadenylation and translation regulation.
  • PARN's interaction with the mRNA cap structure (m(7)GpppG) is critical for stimulating deadenylation.

Purpose of the Study:

  • To elucidate the structural basis of the interaction between the cap-binding domain of mouse PARN and the m(7)GpppG cap analog.
  • To reveal the novel cap-binding mode employed by PARN.

Main Methods:

  • Solution structure determination of the mouse PARN cap-binding domain (PARN RRM).
  • Structural analysis of the PARN RRM in complex with the m(7)GpppG cap analog.

Main Results:

  • The PARN RRM adopts a unique structure with an alpha-helical extension.
  • A distinctive tryptophan residue (Trp468) in the PARN RRM directly interacts with the N(7)-methyl guanosine of the cap analog.
  • This interaction reveals a novel cap-binding mode, differing from canonical RNA recognition motif (RRM) domains.

Conclusions:

  • The study reveals a unique cap-binding mechanism by PARN, mediated by specific structural features.
  • This finding provides new insights into the regulation of mRNA deadenylation and posttranscriptional gene control.

More Related Videos

An Oligonucleotide-based Tandem RNA Isolation Procedure to Recover Eukaryotic mRNA-Protein Complexes09:45

An Oligonucleotide-based Tandem RNA Isolation Procedure to Recover Eukaryotic mRNA-Protein Complexes

Published on: August 18, 2018

Sample Preparation for Mass Spectrometry-based Identification of RNA-binding Regions10:52

Sample Preparation for Mass Spectrometry-based Identification of RNA-binding Regions

Published on: September 28, 2017

Related Concept Videos

Types of RNA01:23

Types of RNA

Overview
Three main types of RNA are involved in protein synthesis: messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). These RNAs perform diverse functions and can be broadly classified as protein-coding or non-coding RNA. Non-coding RNAs play important roles in the regulation of gene expression in response to developmental and environmental changes. Non-coding RNAs in prokaryotes can be manipulated to develop more effective antibacterial drugs for human or animal use.
RNA...
Types of RNA01:20

Types of RNA

Three main types of RNA are involved in protein synthesis: messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). These RNAs perform diverse functions and can be broadly classified as protein-coding or non-coding RNA. Non-coding RNAs play important roles in regulating gene expression in response to developmental and environmental changes. Non-coding RNAs in prokaryotes can be manipulated to develop more effective antibacterial drugs for human or animal use.
RNA Performs Diverse...
Riboswitches01:56

Riboswitches

Riboswitches are non-coding mRNA domains that regulate the transcription and translation of downstream genes without the help of proteins. Riboswitches bind directly to a metabolite and can form unique stem-loop or hairpin structures in response to the amount of the metabolite present. They have two distinct regions – a metabolite-binding aptamer and an expression platform.
The aptamer has high specificity for a particular metabolite which allows riboswitches to specifically regulate...
Nucleic Acids02:43

Nucleic Acids

Nucleic acids are the most important macromolecules for the continuity of life. They carry the cell's genetic blueprint and carry instructions for its functioning.
DNA and RNA
The two main types of nucleic acids are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). DNA is the genetic material in all living organisms, ranging from single-celled bacteria to multicellular mammals. It is in the nucleus of eukaryotes and in the organelles, chloroplasts, and mitochondria. In prokaryotes, the...
Nucleic acids02:43

Nucleic acids

Nucleic acids are the most important macromolecules for the continuity of life. They carry the cell's genetic blueprint and carry instructions for its functioning.
DNA and RNA
The two main types of nucleic acids are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). DNA is the genetic material in all living organisms, ranging from single-celled bacteria to multicellular mammals. It is in the nucleus of eukaryotes and in the organelles, chloroplasts, and mitochondria. In prokaryotes, the...
Eukaryotic RNA Polymerases00:58

Eukaryotic RNA Polymerases

RNA Polymerase (RNAP) is conserved in all animals, with bacterial, archaeal, and eukaryotic RNAPs sharing significant sequence, structural, and functional similarities. Among the three eukaryotic RNAPs, RNA Polymerase II is most similar to bacterial RNAP in terms of both structural organization and folding topologies of the enzyme subunits. However, these similarities are not reflected in their mechanism of action.
All three eukaryotic RNAPs require specific transcription factors, of which the...