4J5R

TARG1 (C6orf130), Terminal ADP-ribose Glycohydrolase 1 bound to ADP-HPD


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.25 Å
  • R-Value Free: 0.153 
  • R-Value Work: 0.118 
  • R-Value Observed: 0.120 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


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

  • DOI: https://doi.org/10.1038/emboj.2013.51
  • Primary Citation of 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.


  • Organizational Affiliation

    Biomedical Sciences Division, Human Genetics Research Centre, St George's University of London, London, UK. rsharifi@sgul.ac.uk


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
O-acetyl-ADP-ribose deacetylase 1
A, B
146Homo sapiensMutation(s): 0 
Gene Names: OARD1C6orf130
EC: 3.5.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y530 (Homo sapiens)
Explore Q9Y530 
Go to UniProtKB:  Q9Y530
PHAROS:  Q9Y530
GTEx:  ENSG00000124596 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Y530
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1R
Query on A1R

Download Ideal Coordinates CCD File 
C [auth A],
I [auth B]
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
EDO
Query on EDO

Download Ideal Coordinates CCD File 
F [auth A]
G [auth A]
H [auth A]
K [auth B]
L [auth B]
F [auth A],
G [auth A],
H [auth A],
K [auth B],
L [auth B],
M [auth B],
N [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
J [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.25 Å
  • R-Value Free: 0.153 
  • R-Value Work: 0.118 
  • R-Value Observed: 0.120 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.803α = 90
b = 72.004β = 90
c = 81.919γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description