Crystal structure of calf spleen purine nucleoside phosphorylase in a complex with hypoxanthine at 2.15 Å resolution

Journal of Molecular Biology

Volumn 265, Issue 2, 1997, Pages 202-216

  Koellner, Gertraud ^a   Luić, Marija ^b   Shugar, David ^c   Saenger, Wolfram ^a   Bzowska, Agnieszka ^c  

^a FREIE UNIVERSITÄT BERLIN   (Germany)

^b RUDER BO KOVI INSTITUTE   (Croatia)

^c UNIVERSITY OF WARSAW   (Poland)

Author keywords

Calf spleen; Crystallization; Hypoxanthine; Purine nucleoside phosphorylase; X ray crystallography

Indexed keywords

ASPARAGINE; GLUTAMIC ACID; HYPOXANTHINE; INOSINE; LYSINE; PURINE NUCLEOSIDE PHOSPHORYLASE; WATER;

ARTICLE; BINDING SITE; CATTLE; CHEMICAL BOND; CHEMICAL MODIFICATION; CRYSTAL STRUCTURE; ENZYME BINDING; ENZYME ISOLATION; HYDROGEN BOND; MICHAELIS MENTEN KINETICS; NONHUMAN; PHYSICAL CHEMISTRY; PRIORITY JOURNAL; SYNCHROTRON; X RAY DIFFRACTION;

BOS TAURUS;

EID: 0031575420     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1996.0730     Document Type: Article

References (62)

1. Agarwal R. P., Parks R. E. Jr. Purine nucleoside phosphorylase from human erythrocytes. Crystallization and some properties. J. Biol. Chem. 244:1969;644-647.
2. Agarwal K. C., Agarwal R. P., Stoeckler J. D., Parks R. E. Jr. Purine nucleoside phosphorylase. Microheterogeneity and comparison of kinetic behaviour of the enzyme from several tissues and species. Biochemistry. 14:1975;79-84.
3. Brünger A. T. XPLOR Version 3.1: 1992;Yale University Press, New Haven.
4. Bzowska A., Kulikowska E., Darzynkiewicz E., Shugar D. Purine nucleoside phosphorylase: structure-acitivity relationships for substrate and inhhibitor properties of N (1)-, N (7)- and C (8)-substituted analogues; differentiation of mammalian and bacterial enzymes with N (1)-methylinosine and guanosine. J. Biol. Chem. 263:1988;9212-9217.
5. Bzowska A., Kulikowska E., Shugar D. Properties of purine nucleoside phosphorylase (PNP) of mammalian and bacterial origin. Z. Naturforsch. 45c:1990;59-70.
6. Bzowska A., Kulikowska E., Shugar D., Bing-yi C., Lindborg B., Johansson N. G. Acyclonucleoside analogue inhibitors of mammalian purine nucleoside phosphorylase. Biochem. Pharmacol. 41:1991;1791-1803.
7. Bzowska A., Kulikowska E., Shugar D. Linear free energy relationship for N (7)-substituted guanosines as substrates of calf spleen purine nucleoside phosphorylase. Possible role of N (7)-protonation as an intermediary in phosphorolysis. Z. Naturforsch. 48c:1993;803-811.
8. Bzowska A., Ananiev A. V., Ramzaeva N., Alksins E., Maurins J. A., Kulikowska E., Shugar D. Purine nucleoside phosphorylase: inhibition by purine N (7)- and N (9)-acyclonucleosides; and substrates properties of 7-β- D -ribofuranosylguanine and 7-β- D -ribofuranosylhypoxanthine. Biochem. Pharmacol. 48:1994;937-947.
9. Bzowska A., Luić M., Schröder W., Shugar D., Saenger W., Koellner G. Calf spleen purine nucleoside phosphorylase: purification, sequence and crystal structure of its complex with an N (7)-acycloguanosine inhibitor. FEBS Letters. 367:1995;214-218.
10. Collaborative Computational Project Number 4 CCP4. Acta Crystallog. sect. D. 50:1994;760-763.
11. Cook W. J., Ealick S. E., Stoeckler J. D., Parks R. E. Jr. Crystallization and preliminary X-ray investigation of human erythrocytic purine nucleoside phosphorylase. J. Biol. Chem. 256:1981;4079-4080.
12. Ealick S. E., Babu Y. S., Narayana S. V. L., Cook W. J., Bugg C. Design of purine nucleoside phosphorylase inhibitors using X-ray crystallography. Crystallographic and Modeling Methods in Molecular Design. 1990a;Springer Verlag, New York.
13. Ealick S. E., Rule S. A., Carter D. C., Greenhough T. J., Babu Y. S., Cook W. J., Habash J., Helliwell J. R., Stoeckler J. D., Parks R. E. Jr, Chen S. F., Bugg C. E. Three-dimensional structure of human purine nucleoside phosphorylase at 3.2 Å resolution. J. Biol. Chem. 265:1990b;1812-1820.
14. Ealick S. E., Babu Y. S., Bugg C. E., Erion M. D., Guida W. C., Montgomery J. A., Secrist J. A. III. Application of crystallographic and modeling methods in the design of purine nucleoside phophorylase inhibitors. Proc. Natl Acad. Sci. USA. 88:1991;11540-11544.
15. Edwards Y. H., Hopkinson D. A., Harris H. Inherited variant of human purine nucleoside phosphorylase. Ann. Hum. Genet. 34:1971;395-408.
16. Erion M. D., Niwas S., Rose J. D., Subramanian A., Allen M., Secrist J. A. III, Babu Y. S., Bugg C. E., Guida W. C., Ealick S. E., Montgomery J. A. Structure-based drug design of purine nucleoside phosphorylase. 3. 9-Arylmethyl derivatives of 9-deazaguanine substituted on the methylene group. J. Med. Chem. 36:1993;3771-3783.
17. Giblett E. R., Ammann A. J., Wara D. W., Sandman R., Diamond L. K. Nucleoside phosphorylase deficiency in a child with severely defective T-cell immunity and normal B-cell immunity. Lancet. i:1975;1010-1013.
18. Gilbertsen R. B., Ammann A. J., Kossarek L. M., Sircar J. C., Kostlan R. K., Conroy M. C. Selective in vitro inhibition of human Molt-4 lymphoblasts by the novel purine nucleoside phosphorylase inhibitor, CI-972. Biochem. Biophys. Res. Commun. 178:1991;1351-1358.
19. Halazy S., Erhard A., Danzin C. 9-(Difluorophosphonoalkyl)-guanines as a new class of multisubstrate analogue inhibitors of purine nucleoside phosphorylase. J. Am. Chem. Soc. 113:1991;315-317.
20. Herzberg O., Moult J. Analysis of the steric strain in the polypeptide backbone of protein molecules. Proteins: Struct. Funct. Genet. 11:1991;223-229.
21. Hodel A., Kim S.-H., Brünger A. T. Model bias in macromolecular crystal structures. Acta Crystallog. sect. A. 48:1992;851-858.
22. Hutchinson E. G., Thornton J. M. Promotif - a program to identify and analyze structural motifs in proteins. Protein Sci. 5:1996;212-220.
23. Johnson, C. K. 1976, ORTEP II. Report ORNL-5158, Oak Ridge National Laboratory, Tennessee, USA.
24. Jones T. A. A graphics model building and refinement system for macromolecules. J. Appl. Crystallog. 11:1978;268-272.
25. Kazmers I. S., Mitchell B. S., Dadonna P. E., Wotring L. B., Townsend L. B., Kelly W. N. Inhibition of purine nucleoside phosphorylase by 8-aminoguanosine; selective toxicity for T-lymphoplasts. Science. 214:1981;1137-1139.
26. Keller, E. 1988, SCHAKAL, a FORTRAN program for the graphic representation of molecular and crystallographic models, Universität Freiburg, Germany.
27. Kelley J. L., McLean E. W., Crouch R. C., Averett D. R., Tuttle J. V. [[(Guaninylalkyl)phos-phinico]methyl]phosphonic acids. Multisubstrate analogue inhibitors of human erythrocyte purine nucleoside phosphorylase. J. Med. Chem. 38:1995;1005-1014.
28. Kline P. C., Schramm V. L. Purine nucleoside phosphorylase. Inosine hydrolysis, tight binding of the hypoxanthine intermediate, and third-the-sites reactivity. Biochemistry. 31:1992;5964-5973.
29. Kline P. C., Schramm V. L. Purine nucleoside phosphorylase. Catalytic mechanism and transition-state analysis of the arsenolysis reaction. Biochemistry. 32:1993;13212-13219.
30. Kraulis P. J. MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallog. 24:1991;946-950.
31. Krenitsky Th. A. Purine nucleoside phosphorylase: kinetics, mechanism and specificity. Mol. Pharmacol. 3:1967;526-536.
32. Krenitsky Th. A., Elion J. B., Henderson A. M., Hitchings G. H. Inhibition of human purine nucleoside phosphorylase: studies with intact erythrocytes and the purified enzyme. J. Biol. Chem. 243:1968;2876-2881.
33. Kulikowska E., Bzowska A., Wierzchowski J., Shugar D. Properties of two unusual and fluorescent substrates of purine nucleosides phosphorylase: 7-methylguanosine and 7-methylinosine. Biochim. Biophys. Acta. 874:1986;355-363.
34. Luzzati V. Traitement statistique des erreurs dans la détermination des structures cristallines. Acta Crystallog. 5:1952;802-810.
35. Matthews B. W. Solvent content of protein crystals. J. Mol. Biol. 33:1968;491-497.
36. Minor, W. 1993, XDISPLAYF Program, Purdue University, IN.
37. Montgomery J. A., Niwas S., Rose J. D., Secrist J. A. III, Babu Y. S., Bugg C. E., Erion M. D., Guida W. C., Ealick S. E. Structure-based drug design of purine nucleoside phosphorylase. 1. 9-(Arylmethyl) derivatives of 9-deazaguanine. J. Med. Chem. 36:1993;55-69.
38. Murray R. K., Granner D. K., Mayes P. A., Rodwell V. W. Harper's Biochemistry. 1990;Appleton and Lang, Norwalk, CT and San Mateo.
39. Navazza J. AMoRe: an automated package for molecular replacement. Acta. Crystallog. sect. B. 50:1994;157-163.
40. Osborne W. R. A. Human red cell purine nucleoside phosphorylase. J. Biol. Chem. 255:1980;7089-7092.
41. Otwinowski, Z. 1993, Oscillation data reduction program, Proceedings of the CCP4 Study Weekend: Data Collection and Processing 29-30 January 1993 compiled by, Sawyer, L.Isaacs, N.Bailey, S. SERC Daresbury Laboratory, England.
42. Parks R. E. Jr, Crabtree G. W., Kong C. M., Agarwal R. P., Agarwal K. C., Scholar E. M. Incorporation of analog purine nucleosides into the formed elements of human blood: erythrocytes, platelets and lymphocytes. Ann. N.Y. Acad. Sci. 255:1975;412-434.
43. Parks R. E. Jr, Stoeckler J. D., Cambor C., Savarese T. M., Crabtree G. W., Chu S. H. Purine nucleoside phosphorylase and 5′-methylthioadenosine phosphorylase: targets of chemotherapy. Sartorelli A., Lazo J. S., Bertino J. Molecular Actions and Targets for Cancer Chemotherapeutic Agents. 1981;Academic Press, New York.
44. Ropp P. A., Traut Th. W. Purine nucleoside phosphorylase: allosteric regulation of a dissociating enzyme. J. Biol. Chem. 266:1991;7682-7687.
45. Secrist J. A. III, Niwas S., Rose J. D., Babu Y. S., Bugg C. E., Erion M. D., Guida W. C., Ealick S. E. Structure-based drug design of purine nucleoside phosphorylase. 2. 9-Alicyclic and 9-heteroalicyclic derivatives of 9-deazaguanine. J. Med. Chem. 36:1993;1847-1854.
46. Shewach D. S., Chern J.-W., Pillote K. E., Townsend L. B., Daddona P. E. Potentiation of 2′-deoxyguanosine cytotoxity by a novel inhibitor of purine nucleoside phosphorylase, 8-amino-9-benzyl-guanine. Cancer Res. 46:1986;519-523.
47. Sircar J. C., Kostlan C. R., Pinter G. W., Suto J. M., Bobovski T. P., Capiris T., Schwender C. F., Dong M. K., Scott M. E., Bennett M. K., Kossarek L. M., Gilbertsen R. B. 8-Amino-9-substitited guanines: potent purine nucleoside phosphorylase (PNP) inhibitors. Agents Actions. 21:1987;253-256.
48. Sircar J. C., Kostlan C. R., Gilbertsen R. B., Bennett M. K., Dong M. K., Cetenko W. J. Inhibi-tion of human purine nucleoside phosphorylase. Synthesis of pyrrolo[3,2-d]pyrimidines, a new class of purine nucleoside phosphorylase inhibitors as potentialy T-cell selective immunosuppressive agents. Description of 2,6-diamino-3,5-dihydro-7-(3-thienylmethyl)-4H-pyrrolo[3,2-d]pyrimidin-4-one. J. Med. Chem. 35:1992;1605-1609.
49. Stein J. M., Stoeckler J. D., Li S.-Y., Tolman R. L., MacCoss M., Chen A., Karkas J. D., Ashton W. T., Parks R. E. Jr. Inhibition of human purine nucleoside phosphorylase by acyclic nucleo-sides and nucleotides. Biochem. Pharmacol. 36:1987;1237-1244.
50. Stoeckler J. D. Purine nucleoside phosphorylase: a target for chemotherapy. Glazer R. I. Developments in Cancer Chemotherapy. 1984;CRC Press Inc. Boca Raton.
51. Stoeckler J. D., Agarwal R. P., Agarwal K. C., Schmid K., Parks R. E. Jr. Purine nucleoside phosphorylase from human erythrocytes: physicochemical properties of the crystalline enzyme. Biochemistry. 17:1978a;278-283.
52. Stoeckler J. D., Agarwal R. P., Agarwal K. C., Parks R. E. Jr. Purine nucleoside phosphorylase from human erythrocytes. Methods Enzymol. 51:1978b;530-538.
53. Stoeckler J. D., Cambor C., Burgess F. W., Erban S. B., Parks R. E. Jr. Purine nucleoside phosphorylase inhibitors as potential chemotherapeutic and immunosuppressive agents. Pharmacologist. 22:1980a;99-105.
54. Stoeckler J. D., Cambor C., Parks R. E. Jr. Human erythrocytic purine nucleoside phosphorylase; reaction with sugar-modified nucleoside substrates. Biochem. 19:1980b;102-107.
55. Stoeckler J. D., Ealick S. E., Bugg C. E., Parks R. E. Jr. Design of purine nucleoside phos-phorylase inhibitors. Fed. Am. Soc. Exp. Biol. 45:1986a;2773-2778.
56. Stoeckler J. D., Ryden J. B., Parks R. E. Jr, Chu M.-Y., Lim M.-I., Ren W.-I., Klein R. S. Inhibition of purine nucleoside phosphorylase: effects of 9-deazapurine ribonucleosides and synthesis of 5′-deoxy-5-iodo-9-deazainosine. Cancer Res. 46:1986b;1774-1778.
57. Traut Th. W. Physiological concentrations of purines and pyrimidines. Mol. Cell. Biochem. 140:1994;1-22.
58. Tronrud D. E., Ten Eyck L. F., Matthews B. W. An efficient general-purpose least-squares refinement program for macromolecular structures. Acta Crystallog. sect. A. 43:1987;489-501.
59. Tuttle J. V., Krenitsky T. A. Effects of acyclovir and its metabolites on purine nucleoside phosphorylase. J. Mol. Chem. 259:1984;4065-4069.
60. Van der Weyden M. B., Bailey M. B. A micromethod for determining adenosine deaminase and purine nucleoside phosphorylase activity in cells from peripheral blood. Clin. Chim. Acta. 82:1982;179-185.
61. Zannis V., Doyle D., Martin D. W. Jr. Purification and characterization of purine nucleoside phosphorylase and its subunits. J. Biol. Chem. 253:1978;504-510.
62. Zoltewicz J. A., Clark D. F., Sharpless T. W., Grahe G. Kinetics and mechanism of the acid catalyzed hydrolysis of some purine nucleosides. J. Am. Chem. Soc. 92:1970;1741-1750.