4L2H | pdb_00004l2h

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

• PDB DOI: https://doi.org/10.2210/pdb4L2H/pdb

• Classification: HYDROLASE
• Organism(s): Tetrahymena thermophila
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2013-06-04 Released: 2013-07-24 
• Deposition Author(s): Brassington, A., Dunstan, M.S., Leys, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.46 Å
• R-Value Free: 
  0.177 (Depositor), 0.180 (DCC) 
• R-Value Work: 
  0.138 (Depositor), 0.147 (DCC) 
• R-Value Observed: 
  0.140 (Depositor) 

Starting Model: experimental

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

• PubMed: 23917065 
• DOI: https://doi.org/10.1038/ncomms3164
• Primary Citation Related Structures: 
  4L2H


• 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 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.

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

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 57 kDa 
• Atom Count: 4,186 
• Modeled Residue Count: 436 
• Deposited Residue Count: 477 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Poly(ADP-ribose) glycohydrolase	A	477	Tetrahymena thermophila	Mutation(s): 1  EC: 3.2.1.143 (PDB Primary Data), 3.2.2 (UniProt)
UniProt
Find proteins for I6L8L7 (Tetrahymena thermophila) Explore I6L8L7  Go to UniProtKB:  I6L8L7

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AR6	B [auth A], C [auth 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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.46 Å
• R-Value Free:  0.177 (Depositor), 0.180 (DCC) 
• R-Value Work:  0.138 (Depositor), 0.147 (DCC) 
• R-Value Observed: 0.140 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.928	α = 90
b = 75.713	β = 90
c = 138.957	γ = 90

Software Package:

Software Name	Purpose
PHASER	phasing
REFMAC	refinement
XDS	data reduction
XDS	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-07-24 
Deposition Author(s): Brassington, A., Dunstan, M.S., Leys, D.

Revision History  

• Version 1.0: 2013-07-24
  Type: Initial release
  
• Version 1.1: 2013-08-07
  Changes: Database references
• Version 1.2: 2013-08-21
  Changes: Database references
• Version 1.3: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary