3UEL | pdb_00003uel

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

• PDB DOI: https://doi.org/10.2210/pdb3UEL/pdb

• Classification: HYDROLASE
• Organism(s): Rattus norvegicus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-10-30 Released: 2012-05-23 
• Deposition Author(s): Kim, I.K., Kiefer, J.R., Stegemann, R.A., Classen, S., Tainer, J.A., Ellenberger, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 
  0.274 (Depositor), 0.278 (DCC) 
• R-Value Work: 
  0.245 (Depositor), 0.248 (DCC) 
• R-Value Observed: 
  0.247 (Depositor) 

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

• PubMed: 22609859 
• DOI: https://doi.org/10.1038/nsmb.2305
• Primary Citation 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. 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.

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 204.97 kDa 
• Atom Count: 11,952 
• Modeled Residue Count: 1,563 
• Deposited Residue Count: 1,764 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Poly(ADP-ribose) glycohydrolase	A, B, C	588	Rattus norvegicus	Mutation(s): 0  Gene Names: Parg EC: 3.2.1.143
UniProt
Find proteins for Q9QYM2 (Rattus norvegicus) Explore Q9QYM2  Go to UniProtKB:  Q9QYM2

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1R	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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free:  0.274 (Depositor), 0.278 (DCC) 
• R-Value Work:  0.245 (Depositor), 0.248 (DCC) 
• R-Value Observed: 0.247 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 130.773	α = 90
b = 195.989	β = 90
c = 163.45	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
SOLVE	phasing
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-05-23 
Deposition Author(s): Kim, I.K., Kiefer, J.R., Stegemann, R.A., Classen, S., Tainer, J.A., Ellenberger, T.

Revision History  

• Version 1.0: 2012-05-23
  Type: Initial release
  
• Version 1.1: 2012-07-18
  Changes: Database references
• Version 1.2: 2024-02-28
  Changes: Data collection, Database references, Derived calculations