3D45

Crystal structure of mouse PARN in complex with m7GpppG


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.334 
  • R-Value Work: 0.299 
  • R-Value Observed: 0.300 

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Ligand Structure Quality Assessment 


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
  • Primary Citation of Related Structures:  
    3D45

  • 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 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 ...

    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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Poly(A)-specific ribonuclease PARNA, B507Mus musculusMutation(s): 0 
Gene Names: Parn
EC: 3.1.13.4
UniProt
Find proteins for Q8VDG3 (Mus musculus)
Explore Q8VDG3 
Go to UniProtKB:  Q8VDG3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8VDG3
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GDP
Query on GDP

Download Ideal Coordinates CCD File 
D [auth A],
F [auth B]
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
 Ligand Interaction
7MG
Query on 7MG

Download Ideal Coordinates CCD File 
C [auth A],
E [auth B]
7N-METHYL-8-HYDROGUANOSINE-5'-MONOPHOSPHATE
C11 H18 N5 O8 P
ZMWJGXGSWZFZPJ-KQYNXXCUSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
7MG PDBBind:  3D45 Kd: 2100 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.334 
  • R-Value Work: 0.299 
  • R-Value Observed: 0.300 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.013α = 90
b = 128.35β = 90
c = 176.844γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
ADSCdata collection
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

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