The structure and catalytic mechanism of a poly(ADP-ribose) glycohydrolase


Post-translational modification of proteins by poly(ADP-ribosyl)ation regulates many cellular pathways that are critical for genome stability, including DNA repair, chromatin structure, mitosis and apoptosis1. Poly(ADP-ribose) (PAR) is composed of repeating ADP-ribose units linked via a unique glycosidic ribose–ribose bond, and is synthesized from NAD by PAR polymerases1,2. PAR glycohydrolase (PARG) is the only protein capable of specific hydrolysis of the ribose–ribose bonds present in PAR chains; its deficiency leads to cell death3,4. Here we show that filamentous fungi and a number of bacteria possess a divergent form of PARG that has all the main characteristics of the human PARG enzyme. We present the first PARG crystal structure (derived from the bacterium Thermomonospora curvata), which reveals that the PARG catalytic domain is a distant member of the ubiquitous ADP-ribose-binding macrodomain family5,6. High-resolution structures of T. curvata PARG in complexes with ADP-ribose and the PARG inhibitor ADP-HPD, complemented by biochemical studies, allow us to propose a model for PAR binding and catalysis by PARG. The insights into the PARG structure and catalytic mechanism should greatly improve our understanding of how PARG activity controls reversible protein poly(ADP-ribosyl)ation and potentially of how the defects in this regulation are linked to human disease.

Access options

Rent or Buy article

Get time limited or full article access on ReadCube.


All prices are NET prices.

Figure 1: Phylogeny and functional relationship between DUF2263 and canonical-type PARGs.
Figure 2: PAR hydrolytic activities of divergent and canonical PARGs.
Figure 3: T. curvata PARG crystal structure in complex with ADP-ribose.
Figure 4: Structural basis of PAR glycohydrolysis.

Accession codes

Primary accessions

Protein Data Bank

Data deposits

Atomic coordinates and structure factors have been deposited with the Protein Data Bank under accession codes 3SIG, 3SIH, 3SII and 3SIJ.


  1. 1

    Hakmé, A., Wong, H. K., Dantzer, F. & Schreiber, V. The expanding field of poly(ADP-ribosyl)ation reactions. EMBO Rep. 9, 1094–1100 (2008)

    Article  Google Scholar 

  2. 2

    D’Amours, D., Desnoyers, S., D’Silva, I. & Poirier, G. G. Poly(ADP-ribosyl)ation reactions in the regulation of nuclear functions. Biochem. J. 342, 249–268 (1999)

    Article  Google Scholar 

  3. 3

    Koh, D. W. et al. Failure to degrade poly(ADP-ribose) causes increased sensitivity to cytotoxicity and early embryonic lethality. Proc. Natl Acad. Sci. USA 101, 17699–17704 (2004)

    ADS  CAS  Article  Google Scholar 

  4. 4

    Hanai, S. et al. Loss of poly(ADP-ribose) glycohydrolase causes progressive neurodegeneration in Drosophila melanogaster . Proc. Natl Acad. Sci. USA 101, 82–86 (2004)

    ADS  CAS  Article  Google Scholar 

  5. 5

    Karras, G. I. et al. The macro domain is an ADP-ribose binding module. EMBO J. 24, 1911–1920 (2005)

    CAS  Article  Google Scholar 

  6. 6

    Till, S. & Ladurner, A. G. Sensing NAD metabolites through macro domains. Front. Biosci. 14, 3246–3258 (2009)

    CAS  Article  Google Scholar 

  7. 7

    Patel, C. N., Koh, D. W., Jacobson, M. K. & Oliveira, M. A. Identification of three critical acidic residues of poly(ADP-ribose) glycohydrolase involved in catalysis: determining the PARG catalytic domain. Biochem. J. 388, 493–500 (2005)

    CAS  Article  Google Scholar 

  8. 8

    Panda, S., Poirier, G. G. & Kay, S. A. tej defines a role for poly(ADP-ribosyl)ation in establishing period length of the Arabidopsis circadian oscillator. Dev. Cell 3, 51–61 (2002)

    CAS  Article  Google Scholar 

  9. 9

    Koh, D. W. et al. Identification of an inhibitor binding site of poly(ADP-ribose) glycohydrolase. Biochemistry 42, 4855–4863 (2003)

    CAS  Article  Google Scholar 

  10. 10

    Ahel, I. et al. Poly(ADP-ribose)-binding zinc finger motifs in DNA repair/checkpoint proteins. Nature 451, 81–85 (2008)

    ADS  CAS  Article  Google Scholar 

  11. 11

    Kothe, G. O., Kitamura, M., Masutani, M., Selker, E. U. & Inoue, H. PARP is involved in replicative aging in Neurospora crassa . Fungal Genet. Biol. 47, 297–309 (2010)

    CAS  Article  Google Scholar 

  12. 12

    Semighini, C. P., Savoldi, M., Goldman, G. H. & Harris, S. D. Functional characterization of the putative Aspergillus nidulans poly(ADP-ribose) polymerase homolog PrpA. Genetics 173, 87–98 (2006)

    CAS  Article  Google Scholar 

  13. 13

    Hassa, P. O. & Hottiger, M. O. The diverse biological roles of mammalian PARPS, a small but powerful family of poly-ADP-ribose polymerases. Front. Biosci. 13, 3046–3082 (2008)

    CAS  Article  Google Scholar 

  14. 14

    Tao, Z., Gao, P. & Liu, H. W. Studies of the expression of human poly(ADP-ribose) polymerase-1 in Saccharomyces cerevisiae and identification of PARP-1 substrates by yeast proteome microarray screening. Biochemistry 48, 11745–11754 (2009)

    CAS  Article  Google Scholar 

  15. 15

    Lin, W., Ame, J. C., Aboul-Ela, N., Jacobson, E. L. & Jacobson, M. K. Isolation and characterization of the cDNA encoding bovine poly(ADP-ribose) glycohydrolase. J. Biol. Chem. 272, 11895–11901 (1997)

    CAS  Article  Google Scholar 

  16. 16

    Kustatscher, G., Hothorn, M., Pugieux, C., Scheffzek, K. & Ladurner, A. G. Splicing regulates NAD metabolite binding to histone macroH2A. Nature Struct. Mol. Biol. 12, 624–625 (2005)

    CAS  Article  Google Scholar 

  17. 17

    Ahel, D. et al. Poly(ADP-ribose)-dependent regulation of DNA repair by the chromatin remodeling enzyme ALC1. Science 325, 1240–1243 (2009)

    ADS  CAS  Article  Google Scholar 

  18. 18

    Gottschalk, A. J. et al. Poly(ADP-ribosyl)ation directs recruitment and activation of an ATP-dependent chromatin remodeler. Proc. Natl Acad. Sci. USA 106, 13770–13774 (2009)

    ADS  CAS  Article  Google Scholar 

  19. 19

    Timinszky, G. et al. A macrodomain-containing histone rearranges chromatin upon sensing PARP1 activation. Nature Struct. Mol. Biol. 16, 923–929 (2009)

    CAS  Article  Google Scholar 

  20. 20

    Mueller-Dieckmann, C. et al. The structure of human ADP-ribosylhydrolase 3 (ARH3) provides insights into the reversibility of protein ADP-ribosylation. Proc. Natl Acad. Sci. USA 103, 15026–15031 (2006)

    ADS  CAS  Article  Google Scholar 

  21. 21

    Oka, S., Kato, J. & Moss, J. Identification and characterization of a mammalian 39-kDa poly(ADP-ribose) glycohydrolase. J. Biol. Chem. 281, 705–713 (2006)

    CAS  Article  Google Scholar 

  22. 22

    Alberti, S., Gitler, A. D. & Lindquist, S. A suite of Gateway cloning vectors for high-throughput genetic analysis in Saccharomyces cerevisiae . Yeast 24, 913–919 (2007)

    CAS  Article  Google Scholar 

  23. 23

    Kabsch, W. Evaluation of single-crystal X-ray diffraction data from a position-sensitive detector. J. Appl. Cryst. 21, 916–924 (1988)

    CAS  Article  Google Scholar 

  24. 24

    Adams, P. D. et al. PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr. D 66, 213–221 (2010)

    CAS  Article  Google Scholar 

  25. 25

    Perrakis, A., Morris, R. & Lamzin, V. S. Automated protein model building combined with iterative structure refinement. Nature Struct. Biol. 6, 458–463 (1999)

    CAS  Article  Google Scholar 

  26. 26

    Emsley, P. & Cowtan, K. Coot: model-building tools for molecular graphics. Acta Crystallogr. D 60, 2126–2132 (2004)

    Article  Google Scholar 

  27. 27

    Phillips, J. C. et al. Scalable molecular dynamics with NAMD. J. Comput. Chem. 26, 1781–1802 (2005)

    CAS  Article  Google Scholar 

  28. 28

    Cornell, W. D. et al. A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. J. Am. Chem. Soc. 117, 5179–5197 (1995)

    CAS  Article  Google Scholar 

  29. 29

    Jakalian, A., Jack, D. B. & Bayly, C. I. Fast, efficient generation of high-quality atomic charges. AM1-BCC model: II. Parameterization and validation. J. Comput. Chem. 23, 1623–1641 (2002)

    CAS  Article  Google Scholar 

  30. 30

    Coulier, L. et al. Simultaneous quantitative analysis of metabolites using ion-pair liquid chromatography-electrospray ionization mass spectrometry. Anal. Chem. 78, 6573–6582 (2006)

    CAS  Article  Google Scholar 

Download references


We thank G. Clark for genomic DNA from E. dispar, G. Smith for the PARP inhibitor, M. Rossi for purified proteins and R. Thorough for editing English. We thank D. Ahel, A. Jordan, D. Ogilvie, S. Terzic, D. Neuhaus and S. Eustermann for helpful discussions. We are grateful to B. Lüscher for the gift of the PARP10 expression plasmid, and K. Labib and the members of his laboratory for advice with yeast work. This work was funded by Cancer Research UK. D.S. holds an AXA Research Fund post-doctoral fellowship. D.L. is a Royal Society University Research Fellow. Access to Diamond beamlines is gratefully acknowledged.

Author information




D.S. performed biochemical and in vivo experiments, prepared proteins for crystallization, analysed data and wrote the manuscript. M.S.D. performed structural/biophysical studies and analysed data. E.B. performed biochemical and in vivo experiments; R.W. performed supporting studies. M.A. and N.D. performed LC/MS analyses; P.L. performed molecular modelling studies. I.A. and D.L. wrote the manuscript, designed experiments and analysed data.

Corresponding author

Correspondence to Ivan Ahel.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Information

The file contains a Supplementary Discussion, Supplementary Table 1, Supplementary Figures 1-9 with legends and Supplementary References. (PDF 775 kb)

PowerPoint slides

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Slade, D., Dunstan, M., Barkauskaite, E. et al. The structure and catalytic mechanism of a poly(ADP-ribose) glycohydrolase. Nature 477, 616–620 (2011).

Download citation

Further reading


By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.


Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing