4J5S | pdb_00004j5s

TARG1 (C6orf130), Terminal ADP-ribose Glycohydrolase 1 ADP-ribose complex

• PDB DOI: https://doi.org/10.2210/pdb4J5S/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2013-02-09 Released: 2013-03-27 
• Deposition Author(s): Schellenberg, M.J., Appel, C.D., Krahn, J., Williams, R.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 
  0.175 (Depositor), 0.182 (DCC) 
• R-Value Work: 
  0.137 (Depositor), 0.147 (DCC) 
• R-Value Observed: 
  0.139 (Depositor) 

Literature

Deficiency of terminal ADP-ribose protein glycohydrolase TARG1/C6orf130 in neurodegenerative disease.

Sharifi, R., Morra, R., Appel, C.D., Tallis, M., Chioza, B., Jankevicius, G., Simpson, M.A., Matic, I., Ozkan, E., Golia, B., Schellenberg, M.J., Weston, R., Williams, J.G., Rossi, M.N., Galehdari, H., Krahn, J., Wan, A., Trembath, R.C., Crosby, A.H., Ahel, D., Hay, R., Ladurner, A.G., Timinszky, G., Williams, R.S., Ahel, I.

(2013) EMBO J 32: 1225-1237

• PubMed: 23481255 
• DOI: https://doi.org/10.1038/emboj.2013.51
• Primary Citation Related Structures: 
  4J5Q, 4J5R, 4J5S


• PubMed Abstract: 
  

  Adenosine diphosphate (ADP)-ribosylation is a post-translational protein modification implicated in the regulation of a range of cellular processes. A family of proteins that catalyse ADP-ribosylation reactions are the poly(ADP-ribose) (PAR) polymerases (PARPs). PARPs covalently attach an ADP-ribose nucleotide to target proteins and some PARP family members can subsequently add additional ADP-ribose units to generate a PAR chain. The hydrolysis of PAR chains is catalysed by PAR glycohydrolase (PARG). PARG is unable to cleave the mono(ADP-ribose) unit directly linked to the protein and although the enzymatic activity that catalyses this reaction has been detected in mammalian cell extracts, the protein(s) responsible remain unknown. Here, we report the homozygous mutation of the c6orf130 gene in patients with severe neurodegeneration, and identify C6orf130 as a PARP-interacting protein that removes mono(ADP-ribosyl)ation on glutamate amino acid residues in PARP-modified proteins. X-ray structures and biochemical analysis of C6orf130 suggest a mechanism of catalytic reversal involving a transient C6orf130 lysyl-(ADP-ribose) intermediate. Furthermore, depletion of C6orf130 protein in cells leads to proliferation and DNA repair defects. Collectively, our data suggest that C6orf130 enzymatic activity has a role in the turnover and recycling of protein ADP-ribosylation, and we have implicated the importance of this protein in supporting normal cellular function in humans.

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Organizational Affiliation: 
• Biomedical Sciences Division, Human Genetics Research Centre, St George's University of London, London, UK. [e-mail]

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)

Biological Assembly 4  

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

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 69.21 kDa 
• Atom Count: 5,783 
• Modeled Residue Count: 567 
• Deposited Residue Count: 584 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
O-acetyl-ADP-ribose deacetylase 1	A, B, C, D	146	Homo sapiens	Mutation(s): 0  Gene Names: OARD1, C6orf130 EC: 3.5.1 (PDB Primary Data), 3.2.2 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y530 (Homo sapiens) Explore Q9Y530  Go to UniProtKB:  Q9Y530
PHAROS:  Q9Y530 GTEx:  ENSG00000124596

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZZC	BA [auth D], E [auth A], N [auth B], X [auth C]	[(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL [[(2R,3R)-2,3-DIHYDROXY-4-OXO-PENTOXY]-OXIDO-PHOSPHORYL] PHOSPHATE C15 H21 N5 O13 P2 IZTPERUWNZCNNH-GHVQHMAVSA-L
SBE	O [auth B]	1,3,2-DIOXABOROLAN-2-OL C2 H5 B O3 ZBEDLGKSWBORBS-UHFFFAOYSA-N
BO4	F [auth A]	BORATE ION B H4 O4 KCFLOKKYWBPKFN-UHFFFAOYSA-N
EDO	AA [auth C], DA [auth D], EA [auth D], FA [auth D], GA [auth D], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], Q [auth B], R [auth B], S [auth B], T [auth B], U [auth B], V [auth B], W [auth B], Z [auth C]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL	CA [auth D], G [auth A], P [auth B], Y [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free:  0.175 (Depositor), 0.182 (DCC) 
• R-Value Work:  0.137 (Depositor), 0.147 (DCC) 
• R-Value Observed: 0.139 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.375	α = 90
b = 56.221	β = 94.47
c = 73.788	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
DENZO	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-03-27 
Deposition Author(s): Schellenberg, M.J., Appel, C.D., Krahn, J., Williams, R.S.

Revision History  

• Version 1.0: 2013-03-27
  Type: Initial release
  
• Version 1.1: 2013-05-01
  Changes: Database references
• Version 1.2: 2013-07-03
  Changes: Database references
• Version 1.3: 2024-10-09
  Changes: Data collection, Database references, Derived calculations, Structure summary