4J5S

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.137 

wwPDB Validation 3D Report Full Report


This is version 1.2 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: 10.1038/emboj.2013.51
  • Primary Citation of Related Structures:  4J5Q, 4J5R

  • 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) polymera ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
O-acetyl-ADP-ribose deacetylase 1
A, B, C, D
146Homo sapiensGene Names: OARD1 (C6orf130)
EC: 3.5.1.-
Find proteins for Q9Y530 (Homo sapiens)
Go to Gene View: OARD1
Go to UniProtKB:  Q9Y530
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A, B, C, D
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
ZZC
Query on ZZC

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Download CCD File 
A, B, C, D
[(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
 Ligand Interaction
EDO
Query on EDO

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Download CCD File 
A, B, C, D
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
SBE
Query on SBE

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Download CCD File 
B
1,3,2-DIOXABOROLAN-2-OL
C2 H5 B O3
ZBEDLGKSWBORBS-UHFFFAOYSA-N
 Ligand Interaction
BO4
Query on BO4

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Download CCD File 
A
BORATE ION
B H4 O4
KCFLOKKYWBPKFN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.137 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 73.375α = 90.00
b = 56.221β = 94.47
c = 73.788γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
PHASERphasing
SCALEPACKdata scaling
HKL-2000data collection
DENZOdata reduction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-03-27
    Type: Initial release
  • Version 1.1: 2013-05-01
    Type: Database references
  • Version 1.2: 2013-07-03
    Type: Database references