3CTR

Crystal structure of the RRM-domain of the poly(A)-specific ribonuclease PARN bound to m7GTP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.210 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal structure of the RRM domain of poly(A)-specific ribonuclease reveals a novel m(7)G-cap-binding mode.

Monecke, T.Schell, S.Dickmanns, A.Ficner, R.

(2008) J.Mol.Biol. 382: 827-834

  • DOI: 10.1016/j.jmb.2008.07.073

  • PubMed Abstract: 
  • Poly(A)-specific ribonuclease (PARN) is a processive 3'-exoribonuclease involved in the decay of eukaryotic mRNAs. Interestingly, PARN interacts not only with the 3' end of the mRNA but also with its 5' end as PARN contains an RRM domain that specifi ...

    Poly(A)-specific ribonuclease (PARN) is a processive 3'-exoribonuclease involved in the decay of eukaryotic mRNAs. Interestingly, PARN interacts not only with the 3' end of the mRNA but also with its 5' end as PARN contains an RRM domain that specifically binds both the poly(A) tail and the 7-methylguanosine (m(7)G) cap. The interaction of PARN with the 5' cap of mRNAs stimulates the deadenylation activity and enhances the processivity of this reaction. We have determined the crystal structure of the PARN-RRM domain with a bound m(7)G triphosphate nucleotide, revealing a novel binding mode for the m(7)G cap. The structure of the m(7)G binding pocket is located outside of the canonical RNA-binding surface of the RRM domain and differs significantly from that of other m(7)G-cap-binding proteins. The crystal structure also shows a remarkable conformational flexibility of the RRM domain, leading to a perfect exchange of two alpha-helices with an adjacent protein molecule in the crystal lattice.


    Organizational Affiliation

    Abteilung für Molekulare Strukturbiologie, Institut für Mikrobiologie und Genetik, GZMB, Georg-August-Universität Göttingen, 37077 Göttingen, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Poly(A)-specific ribonuclease PARN
A
101Homo sapiensMutation(s): 0 
Gene Names: PARN (DAN)
EC: 3.1.13.4
Find proteins for O95453 (Homo sapiens)
Go to Gene View: PARN
Go to UniProtKB:  O95453
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MGP
Query on MGP

Download SDF File 
Download CCD File 
A
7-METHYL-GUANOSINE-5'-TRIPHOSPHATE
C11 H19 N5 O14 P3
DKVRNHPCAOHRSI-KQYNXXCUSA-O
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
MGPKd: 6940 nM BINDINGMOAD
MGPKd: 6940 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.210 
  • Space Group: I 41 2 2
Unit Cell:
Length (Å)Angle (°)
a = 81.107α = 90.00
b = 81.107β = 90.00
c = 78.058γ = 90.00
Software Package:
Software NamePurpose
MAR345dtbdata collection
REFMACrefinement
HKL-2000data scaling
SHELXEmodel building
HKL-2000data reduction
SHELXCDphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-07-29
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2013-11-06
    Type: Data collection
  • Version 1.3: 2017-10-25
    Type: Refinement description