The mechanism of the elongation and branching reaction of Poly(ADP-ribose) polymerase as derived from crystal structures and mutagenesis

Journal of Molecular Biology

Volumn 278, Issue 1, 1998, Pages 57-65

  Ruf, Armin ^a   Rolli, Véronique ^b   De Murcia, Gilbert ^b   Schulz, Georg E ^a  

^a UNIVERSITY OF FREIBURG   (Germany)

^b Ecl Natl Sup Phys de Strasbourg   (France)

Author keywords

ADP ribose acceptor; ADP ribosylation; DNA repair; Polymer branching; X ray structure analysis

Indexed keywords

NICOTINAMIDE ADENINE DINUCLEOTIDE; NICOTINAMIDE ADENINE DINUCLEOTIDE ADENOSINE DIPHOSPHATE RIBOSYLTRANSFERASE;

ARTICLE; BINDING SITE; CONTROLLED STUDY; CRYSTAL STRUCTURE; CRYSTALLIZATION; ENZYME BINDING; ENZYME MECHANISM; GEOMETRY; MUTAGENESIS; PRIORITY JOURNAL;

EID: 0032562650     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1998.1673     Document Type: Article

References (35)

1. Althaus F.R., Richter C.R. ADP-ribosylation of proteins. Enzymology and biological significance. Mol. Biol. Biochem. Biophys. 37:1987;1-125
2. Alvarez-Gonzalez R. 3′-deoxy-NAD as substrate for poly-(ADP-ribose) polymerase and the reaction mechanism of poly(ADP-ribose) elongation. J. Biol. Chem. 263:1988;17690-17696
3. Alvarez-Gonzalez R., Jacobson M.K. Characterization of polymers of adenosine diphosphate ribose generated in vitro and in vivo. Biochemistry. 26:1987;3218-3224
4. Banasik M., Ueda K. Inhibitors and activators of ADP-ribosylation reactions. Mol. Cell. Biochem. 138:1994;185-197
5. Bell C.E., Eisenberg D. Crystal structure of diphtheria toxin bound to nicotinamide adenine dinucleotide. Biochemistry. 35:1996;1137-1149
6. Brünger A.T. X-PLOR Version 3. 1, A System for X-ray Crystallography and NMR. 1992;New Haven
7. Courtney M., Buchwalder A., Tessier L.H., Jaye M., Benavente A., Balland A., Kohli V., Lathe R., Tolstoshev P., Lecocq J.P. High-level production of biologically active human alpha 1-antitrypsin in Escherichia coli. Proc. Natl Acad. Sci. USA. 81:1984;669-673
8. Evans P.R. Data reduction. Sawyer L., Isaacs N., Bailey S. Data Collection and Processing Proceedings of the CCP4 Study Weekend. 1993;114-122 SERC, Daresbury Laboratory, Warrington, U.K
9. Jiang J.-S., Brünger A.T. Protein hydration observed by X-ray diffraction solvation properties of penicillopepsin and neuraminidase crystal structures. J. Mol. Biol. 243:1994;100-115
10. Jung S., Alves Miranda E., Ménissier-de Murcia J., Niedergang C., Delarue M., Schulz G.E., de Murcia G. Crystallization and X-ray crystallographic analysis of recombinant chicken poly(ADP-ribose) polymerase catalytic domain produced in Sf9 insect cells. J. Mol. Biol. 244:1994;114-116
11. Kabsch W. Evaluation of single crystal X-ray diffraction data from a position sensitive detector. J. Appl. Crystallog. 21:1988;916-924
12. Keith G., Desgrès J., de Murcia G. Use of two-dimensional thin-layer chromatography for components study of poly(adenosine diphosphate ribose). Anal. Biochem. 191:1990;309-313
13. Kleywegt G.J. Dictionaries for heteros. ESF/CCP4 Newsletter, no. 31. 1995;45-50 Daresbury Laboratory, Warrington, WA4 4AD
14. Kleywegt G.J., Brünger A.T. Checking your imagination applications of the free R value. Structure. 4:1996;897-904
15. Kraulis P.J. MOLSCRIPT a program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallog. 24:1991;946-950
16. Kunkel T.A., Roberts J.D., Zakour R.A. Rapid and efficient site-specific mutagenesis without phenotypic selection. Methods Enzymol. 154:1987;367-382
17. Laskowski R.A., MacArthur M.W., Moss D.S., Thornton J.M. PROCHECK a program to check the stereochemical quality of protein structures. J. Appl. Crystallog. 26:1993;283-291
18. Lautier D., Lagueux J., Thibodeau J., Ménard L., Poirier G.G. Molecular and biochemical features of poly(ADP-ribose) metabolism. Mol. Cell. Biochem. 122:1993;171-193
19. Li M., Dyda F., Benhar I., Pastan I., Davies D.R. Crystal structure of the catalytic domain of Pseudomonas exotoxin A complexed with a nicotinamide adenine dinucleotide analogue implications for activation process and for ADP-ribosylation. Proc. Natl Acad. Sci. USA. 93:1996;6902-6906
20. Marsischky G.T., Wilson B.A., Collier R.J. Role of glutamic acid 988 of human poly-ADP-ribose polymerase in polymer formation. J. Biol. Chem. 270:1995;3247-3255
21. Miwa M., Ishihara M., Takishima S., Takasuka N., Maeda M., Yamaizumi Z., Sugimura T., Yokoyama S., Miyazawa T. The branching and linear portions of poly(adenosine diphosphate ribose) have the same α (1→2) ribose-ribose linkage. J. Biol. Chem. 256:1980;2916-2921
22. Moodie S.L., Mitchell J.B.O., Thornton J.M. Protein recognition of adenylate an example of a fuzzy recognition template. J. Mol. Biol. 263:1996;486-500
23. de Murcia G., Ménissier-de Murcia J. Poly(ADP-ribose) polymerase a molecular nick sensor. Trends Biochem. Sci. 19:1994;172-176
24. Niedergang C., Okazaki H., Mandel P. Properties of purified calf thymus poly(adenosine diphosphate ribose) polymerase. Eur. J. Biochem. 102:1979;43-57
25. Oei S.L., Griesenbeck J., Schweiger M. The rôle of poly(ADP-ribosyl)ation. Rev. Physiol. Biochem. Pharmacol. 131:1997;127-173
26. Okazaki I.J., Moss J. Common structure of the catalytic sites of mammalian and bacterial toxin ADP-ribosyltransferases. Mol. Cell. Biochem. 138:1994;177-181
27. Read R.J. Improved Fourier coefficients for maps using phases from partial structures with errors. Acta Crystallog. sect. A. 42:1986;140-149
28. Rolli V., O'Farrel M., Ménissier-de Murcia J., de Murcia G. Random mutagenesis of the poly(ADP-ribose) polymerase catalytic domain reveals amino acids involved in polymer branching. Biochemistry. 36:1997;12147-12154
29. Ruf A., Ménissier-de Murcia J., de Murcia G., Schulz G.E. Structure of the catalytic fragment of poly(ADP-ribose) polymerase from chicken. Proc. Natl Acad. Sci. USA. 93:1996;7481-7485
30. i3C20. Biochemistry. 36:1997;8215-8223
31. Simonin F., Ménissier-de Murcia J., Poch O., Muller S., Gradwohl G., Molinete M., Penning C., Keith G., de Murcia G. Expression and site-directed mutagenesis of the catalytic domain of human poly(ADP-ribose) polymerase in Escherichia coli. J. Biol. Chem. 265:1990;19249-19256
32. Simonin F., Briand J.P., Muller S., de Murcia G. Detection of poly(ADP-ribose) polymerase in crude extracts by activity-blot. Anal. Biochem. 195:1991;226-231
33. Simonin F., Höfferer L., Panzeter P.L., Muller S., de Murcia G., Althaus F.R. The carboxyl-terminal domain of human poly(ADP-ribose) polymerase. J. Biol. Chem. 268:1993;13454-13461
34. Slama J.T., Simmons A.M. Carba-nicotinamide adenine dinucleotide synthesis and enzymological properties of carbocyclic analogue of oxidized nicotinamide adenine dinucleotide. Biochemistry. 27:1988;183-193
35. Slama J.T., Simmons A.M. Inhibition of NAD glycohydrolase and ADP-ribosyl transferases by carbocyclic analogues of oxidized nicotinamide adenine dinucleotide. Biochemistry. 28:1989;7688-7694