3UEL

Crystal structure of the catalytic domain of rat poly (ADP-ribose) glycohydrolase bound to ADP-HPD


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.245 
  • R-Value Observed: 0.247 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Structure of mammalian poly(ADP-ribose) glycohydrolase reveals a flexible tyrosine clasp as a substrate-binding element.

Kim, I.K.Kiefer, J.R.Ho, C.M.Stegeman, R.A.Classen, S.Tainer, J.A.Ellenberger, T.

(2012) Nat Struct Mol Biol 19: 653-656

  • DOI: 10.1038/nsmb.2305
  • Primary Citation of Related Structures:  
    3UEK, 3UEL

  • PubMed Abstract: 
  • Reversible post-translational modification by poly(ADP-ribose) (PAR) regulates chromatin structure, DNA repair and cell fate in response to genotoxic stress. PAR glycohydrolase (PARG) removes PAR chains from poly ADP-ribosylated proteins to restore protein function and release oligo(ADP-ribose) chains to signal damage ...

    Reversible post-translational modification by poly(ADP-ribose) (PAR) regulates chromatin structure, DNA repair and cell fate in response to genotoxic stress. PAR glycohydrolase (PARG) removes PAR chains from poly ADP-ribosylated proteins to restore protein function and release oligo(ADP-ribose) chains to signal damage. Here we report crystal structures of mammalian PARG and its complex with a substrate mimic that reveal an open substrate-binding site and a unique 'tyrosine clasp' enabling endoglycosidic cleavage of branched PAR chains.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Poly(ADP-ribose) glycohydrolaseA, B, C588Rattus norvegicusMutation(s): 0 
Gene Names: Parg
EC: 3.2.1.143
UniProt
Find proteins for Q9QYM2 (Rattus norvegicus)
Explore Q9QYM2 
Go to UniProtKB:  Q9QYM2
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
A1R (Subject of Investigation/LOI)
Query on A1R

Download Ideal Coordinates CCD File 
D [auth A], E [auth B], F [auth C]5'-O-[(S)-{[(S)-{[(2R,3R,4S)-3,4-DIHYDROXYPYRROLIDIN-2-YL]METHOXY}(HYDROXY)PHOSPHORYL]OXY}(HYDROXY)PHOSPHORYL]ADENOSINE
C15 H24 N6 O12 P2
NDQDTBCXPOIQGT-UHNJQBFTSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
A1R BindingDB:  3UEL IC50: min: 100, max: 1400 (nM) from 5 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.245 
  • R-Value Observed: 0.247 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 130.773α = 90
b = 195.989β = 90
c = 163.45γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
SOLVEphasing
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-05-23
    Type: Initial release
  • Version 1.1: 2012-07-18
    Changes: Database references