3D45

Crystal structure of mouse PARN in complex with m7GpppG


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.334 
  • R-Value Work: 0.299 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural basis of m(7)GpppG binding to poly(A)-specific ribonuclease.

Wu, M.Nilsson, P.Henriksson, N.Niedzwiecka, A.Lim, M.K.Cheng, Z.Kokkoris, K.Virtanen, A.Song, H.

(2009) Structure 17: 276-286

  • DOI: 10.1016/j.str.2008.11.012

  • PubMed Abstract: 
  • Poly(A)-specific ribonuclease (PARN) is a homodimeric, processive, and cap-interacting 3' exoribonuclease that efficiently degrades eukaryotic mRNA poly(A) tails. The crystal structure of a C-terminally truncated PARN in complex with m(7)GpppG reveal ...

    Poly(A)-specific ribonuclease (PARN) is a homodimeric, processive, and cap-interacting 3' exoribonuclease that efficiently degrades eukaryotic mRNA poly(A) tails. The crystal structure of a C-terminally truncated PARN in complex with m(7)GpppG reveals that, in one subunit, m(7)GpppG binds to a cavity formed by the RRM domain and the nuclease domain, whereas in the other subunit, it binds almost exclusively to the RRM domain. Importantly, our structural and competition data show that the cap-binding site overlaps with the active site in the nuclease domain. Mutational analysis demonstrates that residues involved in m(7)G recognition are crucial for cap-stimulated deadenylation activity, and those involved in both cap and poly(A) binding are important for catalysis. A modeled PARN, which shows that the RRM domain from one subunit and the R3H domain from the other subunit enclose the active site, provides a structural foundation for further studies to elucidate the mechanism of PARN-mediated deadenylation.


    Organizational Affiliation

    Institute of Molecular and Cell Biology, Proteos, Singapore; Department of Biological Sciences, National University of Singapore, Singapore.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Poly(A)-specific ribonuclease PARN
A, B
507Mus musculusMutation(s): 0 
Gene Names: Parn
EC: 3.1.13.4
Find proteins for Q8VDG3 (Mus musculus)
Go to UniProtKB:  Q8VDG3
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GDP
Query on GDP

Download SDF File 
Download CCD File 
A, B
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
 Ligand Interaction
7MG
Query on 7MG

Download SDF File 
Download CCD File 
A, B
7N-METHYL-8-HYDROGUANOSINE-5'-MONOPHOSPHATE
C11 H18 N5 O8 P
ZMWJGXGSWZFZPJ-KQYNXXCUSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
7MGKd: 2100 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.334 
  • R-Value Work: 0.299 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 58.013α = 90.00
b = 128.350β = 90.00
c = 176.844γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
ADSCdata collection
SCALAdata scaling
MOSFLMdata reduction
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2008-05-13 
  • Released Date: 2009-03-17 
  • Deposition Author(s): Wu, M., Song, H.

Revision History 

  • Version 1.0: 2009-03-17
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance
  • Version 1.2: 2018-01-24
    Type: Structure summary