4L2H

Structure of a catalytically inactive PARG in complex with a poly-ADP-ribose fragment


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.46 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.138 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Visualization of poly(ADP-ribose) bound to PARG reveals inherent balance between exo- and endo-glycohydrolase activities.

Barkauskaite, E.Brassington, A.Tan, E.S.Warwicker, J.Dunstan, M.S.Banos, B.Lafite, P.Ahel, M.Mitchison, T.J.Ahel, I.Leys, D.

(2013) Nat Commun 4: 2164-2164

  • DOI: 10.1038/ncomms3164

  • PubMed Abstract: 
  • Poly-ADP-ribosylation is a post-translational modification that regulates processes involved in genome stability. Breakdown of the poly(ADP-ribose) (PAR) polymer is catalysed by poly(ADP-ribose) glycohydrolase (PARG), whose endo-glycohydrolase activi ...

    Poly-ADP-ribosylation is a post-translational modification that regulates processes involved in genome stability. Breakdown of the poly(ADP-ribose) (PAR) polymer is catalysed by poly(ADP-ribose) glycohydrolase (PARG), whose endo-glycohydrolase activity generates PAR fragments. Here we present the crystal structure of PARG incorporating the PAR substrate. The two terminal ADP-ribose units of the polymeric substrate are bound in exo-mode. Biochemical and modelling studies reveal that PARG acts predominantly as an exo-glycohydrolase. This preference is linked to Phe902 (human numbering), which is responsible for low-affinity binding of the substrate in endo-mode. Our data reveal the mechanism of poly-ADP-ribosylation reversal, with ADP-ribose as the dominant product, and suggest that the release of apoptotic PAR fragments occurs at unusual PAR/PARG ratios.


    Organizational Affiliation

    Cancer Research UK, Paterson Institute for Cancer Research, University of Manchester, Wilmslow Road, Manchester M20 4BX, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Poly(ADP-ribose) glycohydrolase
A
477Tetrahymena thermophilaMutation(s): 1 
Find proteins for I6L8L7 (Tetrahymena thermophila)
Go to UniProtKB:  I6L8L7
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AR6
Query on AR6

Download SDF File 
Download CCD File 
A
[(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL [HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE
C15 H23 N5 O14 P2
SRNWOUGRCWSEMX-ZQSHOCFMSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.46 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.138 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 55.928α = 90.00
b = 75.713β = 90.00
c = 138.957γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-07-24
    Type: Initial release
  • Version 1.1: 2013-08-07
    Type: Database references
  • Version 1.2: 2013-08-21
    Type: Database references