4EPQ | pdb_00004epq

canonical poly(ADP-ribose) glycohydrolase RBPI inhibitor complex from Tetrahymena thermophila

• PDB DOI: https://doi.org/10.2210/pdb4EPQ/pdb

• Classification: HYDROLASE/INHIBITOR
• Organism(s): Tetrahymena thermophila
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-04-17 Released: 2012-06-13 
• Deposition Author(s): Dunstan, M.S., Leys, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.231 (Depositor), 0.227 (DCC) 
• R-Value Work: 
  0.165 (Depositor), 0.166 (DCC) 
• R-Value Observed: 
  0.168 (Depositor) 

Starting Model: experimental

Literature

Structure and mechanism of a canonical poly(ADP-ribose) glycohydrolase.

Dunstan, M.S., Barkauskaite, E., Lafite, P., Knezevic, C.E., Brassington, A., Ahel, M., Hergenrother, P.J., Leys, D., Ahel, I.

(2012) Nat Commun 3: 878-878

• PubMed: 22673905 
• DOI: https://doi.org/10.1038/ncomms1889
• Primary Citation Related Structures: 
  4EPP, 4EPQ


• PubMed Abstract: 
  

  Poly(ADP-ribosyl)ation is a reversible post-translational protein modification involved in the regulation of a number of cellular processes including DNA repair, chromatin structure, mitosis, transcription, checkpoint activation, apoptosis and asexual development. The reversion of poly(ADP-ribosyl)ation is catalysed by poly(ADP-ribose) (PAR) glycohydrolase (PARG), which specifically targets the unique PAR (1''-2') ribose-ribose bonds. Here we report the structure and mechanism of the first canonical PARG from the protozoan Tetrahymena thermophila. In addition, we reveal the structure of T. thermophila PARG in a complex with a novel rhodanine-containing mammalian PARG inhibitor RBPI-3. Our data demonstrate that the protozoan PARG represents a good model for human PARG and is therefore likely to prove useful in guiding structure-based discovery of new classes of PARG inhibitors.

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Organizational Affiliation: 
• Manchester Interdisciplinary Biocentre, Princess Street 131, M1 7DN, Manchester, 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: 56.4 kDa 
• Atom Count: 3,718 
• Modeled Residue Count: 439 
• 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): 0  EC: 3.2.2 (UniProt), 3.2.1.143 (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
0RR	B [auth A]	3-{(5Z)-5-[5-chloro-1-(2,6-dichlorobenzyl)-2-oxo-1,2-dihydro-3H-indol-3-ylidene]-4-oxo-2-thioxo-1,3-thiazolidin-3-yl}propanoic acid C21 H13 Cl3 N2 O4 S2 YESAJFJEXWEXAO-ZCXUNETKSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.231 (Depositor), 0.227 (DCC) 
• R-Value Work:  0.165 (Depositor), 0.166 (DCC) 
• R-Value Observed: 0.168 (Depositor) 

Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.68	α = 90
b = 80.68	β = 90
c = 89.42	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-06-13 
Deposition Author(s): Dunstan, M.S., Leys, D.

Revision History  

• Version 1.0: 2012-06-13
  Type: Initial release
  
• Version 1.1: 2012-08-29
  Changes: Database references
• Version 1.2: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description