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

Nature

Volumn 477, Issue 7366, 2011, Pages 616-622

  Slade, Dea ^a,b   Dunstan, Mark S ^c   Barkauskaite, Eva ^a   Weston, Ria ^a   Lafite, Pierre ^d   Dixon, Neil ^c   Ahel, Marijan ^e   Leys, David ^c   Ahel, Ivan ^a  

^a UNIVERSITY OF MANCHESTER   (United Kingdom)

^b UNIVERSITÉ PARIS DESCARTES   (France)

^c UNIVERSITY OF MANCHESTER   (United Kingdom)

^d Université d'Orléans   (France)

^e RUDER BO KOVI INSTITUTE   (Croatia)

Author keywords

[No Author keywords available]

Indexed keywords

GLYCOSIDASE; NICOTINAMIDE ADENINE DINUCLEOTIDE; POLY(ADENOSINE DIPHOSPHATE RIBOSE); POLY(ADP RIBOSE) GLYCOHYDROLASE; UNCLASSIFIED DRUG;

APOPTOSIS; BACTERIUM; BIOCHEMISTRY; CATALYSIS; CHEMICAL BINDING; CHROMOSOME; CRYSTAL STRUCTURE; DISEASE; DIVERGENCE; ENZYME ACTIVITY; FUNGUS; MOLECULAR ANALYSIS; PROTEIN; PUBLIC HEALTH; SUGAR;

ARTICLE; BINDING AFFINITY; CATALYSIS; CRYSTAL STRUCTURE; DNA REPAIR; ENZYME ACTIVITY; ENZYME STRUCTURE; ESCHERICHIA COLI; HUMAN; MOLECULAR DYNAMICS; MUTAGENESIS; NONHUMAN; PHYLOGENY; PRIORITY JOURNAL; STRUCTURE ANALYSIS; THERMOMONOSPORA; THERMOMONOSPORA CURVATA;

ACTINOMYCETALES; ADENOSINE DIPHOSPHATE; ADENOSINE DIPHOSPHATE RIBOSE; AMINO ACID SEQUENCE; BIOCATALYSIS; CATALYTIC DOMAIN; CRYSTALLOGRAPHY, X-RAY; EVOLUTION, MOLECULAR; GLYCOSIDE HYDROLASES; HUMANS; HYDROLYSIS; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PHYLOGENY; POLY ADENOSINE DIPHOSPHATE RIBOSE; POLY(ADP-RIBOSE) POLYMERASES; PROTEIN CONFORMATION; PROTEINS; PYRROLIDINES;

BACTERIA (MICROORGANISMS); FUNGI; THERMOMONOSPORA CURVATA;

EID: 80053375417     PISSN: 00280836     EISSN: 14764687     Source Type: Journal    
DOI: 10.1038/nature10404     Document Type: Article

References (30)

1. Hakmé, A.,Wong, H. K., Dantzer, F.&Schreiber, V. The expanding field of poly(ADPribosyl) ation reactions. EMBO Rep. 9, 1094-1100 (2008).
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). (Pubitemid 29425344)
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). (Pubitemid 40051949)
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). (Pubitemid 38084207)
5. Karras, G. I. et al. Themacro domain is an ADP-ribose bindingmodule. EMBO J. 24, 1911-1920 (2005).
6. Till, S. & Ladurner, A. G. Sensing NAD metabolites through macro domains. Front. Biosci. 14, 3246-3258 (2009).
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). (Pubitemid 40839926)
8. Panda, S., Poirier, G. G. & Kay, S. A. tej defines a role for poly(ADP-ribosyl)ation in establishingperiod length of the Arabidopsis circadian oscillator.Dev. Cell 3,51-61 (2002). (Pubitemid 34778395)
9. Koh, D. W. et al. Identification of an inhibitor binding site of poly(ADP-ribose) glycohydrolase. Biochemistry 42, 4855-4863 (2003). (Pubitemid 36532037)
10. Ahel, I. et al. Poly(ADP-ribose)-binding zinc fingermotifs inDNA repair/checkpoint proteins. Nature 451, 81-85 (2008).
11. Kothe, G. O., Kitamura, M.,Masutani, M., Selker, E. U.& Inoue, H. PARPis involved in replicative aging in Neurospora crassa. Fungal Genet. Biol. 47, 297-309 (2010).
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). (Pubitemid 43800186)
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). (Pubitemid 351589219)
14. Tao, Z., Gao, P. & Liu, H. W. Studies of the expression of human poly(ADPribose) polymerase-1 in Saccharomyces cerevisiae and identification of PARP-1 substrates by yeast proteome microarray screening. Biochemistry 48, 11745-11754 (2009).
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). (Pubitemid 27202761)
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). (Pubitemid 40980814)
17. Ahel, D. et al. Poly(ADP-ribose)-dependent regulation of DNA repair by the chromatin remodeling enzyme ALC1. Science 325, 1240-1243 (2009).
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).
19. Timinszky, G. et al. A macrodomain-containing histone rearranges chromatin upon sensing PARP1 activation. Nature Struct. Mol. Biol. 16, 923-929 (2009).
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). (Pubitemid 44583158)
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).
22. Alberti, S., Gitler, A. D. & Lindquist, S. A suite of Gateway cloning vectors for highthroughput genetic analysis in Saccharomyces cerevisiae. Yeast 24, 913-919 (2007). (Pubitemid 47611130)
23. Kabsch, W. Evaluation of single-crystal X-ray diffraction data from a positionsensitive detector. J. Appl. Cryst. 21, 916-924 (1988).
24. Adams, P. D. et al. PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr. D 66, 213-221 (2010).
25. Perrakis, A.,Morris, R.&Lamzin, V. S. Automated proteinmodel buildingcombined with iterative structure refinement. Nature Struct. Biol. 6, 458-463 (1999). (Pubitemid 29218016)
26. Emsley, P. & Cowtan, K. Coot: model-building tools for molecular graphics. Acta Crystallogr. D 60, 2126-2132 (2004). (Pubitemid 41742764)
27. Phillips, J. C. et al. Scalable molecular dynamics with NAMD. J. Comput. Chem. 26, 1781-1802 (2005). (Pubitemid 43078511)
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).
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). (Pubitemid 35330860)
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). (Pubitemid 44413611)