Crystal structure of calf spleen purine nucleoside phosphorylase with two full trimers in the asymmetric unit: Important implications for the mechanism of catalysis

Journal of Molecular Biology

Volumn 342, Issue 3, 2004, Pages 1015-1032

  Bzowska, Agnieszka ^a   Koellner, Gertraud ^b   Wielgus Kutrowska, Beata ^a   Stroh, Albrecht ^b   Raszewski, Grzegorz ^a,b   Holý, Antonin ^c   Steiner, Thomas ^b   Frank, Joachim ^d  

^a UNIVERSITY OF WARSAW   (Poland)

^b FREIE UNIVERSITÄT BERLIN   (Germany)

^c INSTITUTE OF MATHEMATICS   (Czech Republic)

^d FRITZ HABER INSTITUT DER MAX PLANCK GESELLSCHAFT   (Germany)

Author keywords

conformational change; fluorescence titration; isothermal titration calorimetry; purine nucleoside phosphorylase; X ray crystallography

Indexed keywords

2,6 DIAMINO 9 [2 (PHOSPHONOMETHOXY)PROPYL]PURINE; ACYCLIC NUCLEOSIDE; ALANINE; ARGININE; CALCIUM; ENZYME INHIBITOR; GLUTAMIC ACID; HYPOXANTHINE; MONOMER; OXYGEN; PHOSPHATE; PHOSPHONIC ACID DERIVATIVE; PURINE DERIVATIVE; PURINE NUCLEOSIDE PHOSPHORYLASE; THREONINE; UNCLASSIFIED DRUG;

AMINO ACID SEQUENCE; ARTICLE; ASYMMETRIC CATALYSIS; BINDING SITE; CALORIMETRY; CATTLE; CHEMICAL STRUCTURE; CONFORMATION; CRYSTAL STRUCTURE; CRYSTALLIZATION; DRUG PROTEIN BINDING; HYDROGEN BOND; PRIORITY JOURNAL; SPECTROFLUOROMETRY; SPLEEN; STOICHIOMETRY; TITRIMETRY;

EID: 4444273108     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2004.07.017     Document Type: Article

References (48)

1. J.D. Stoeckler Purine nucleoside phosphorylase: a target for chemotherapy R.J. Glazer Developments in Cancer Chemotherapy 1984 CRC Press Boca Raton, FL 35 60
2. J.A. Montgomery Purine nucleoside phosphorylase: a target for drug design Med. Res. Rev. 13 1993 209 228
3. A. Bzowska, E. Kulikowska, and D. Shugar Purine nucleoside phosphorylase: properties, functions and clinical aspects Pharmacol. Ther. 88 2000 349 425
4. E.J. Sorscher, S. Peng, Z. Bebok, P.A. Allan, L.L. Bennett Jr, and W.B. Parker Tumour bystander killing in colonic carcinoma utilizing the Escherichia coli DeoD gene to generate toxic purines Gene Ther. 1 1994 233 238
5. B. Kierdaszuk, A. Modrak-Wojcik, and D. Shugar Binding of phosphate and sulphate anions by purine nucleoside phosphorylase from E. coli: ligand-dependent quenching of enzyme intrinsic fluorescence Biophys. Chem. 63 1997 107 118
6. G. Koellner, A. Bzowska, B. Wielgus-Kutrowska, M. Luić, T. Steiner, W. Saenger, and J. Stepiński 'Open' and 'closed' conformation of the E. coli purine nucleoside phosphorylase active center and implications for the catalytic mechanism J. Mol. Biol. 315 2002 351 371
7. P.C. Kline, and V.L. Schramm Purine nucleoside phosphorylase. Inosine hydrolysis, tight binding of the hypoxanthine intermediate, and third-the-sites reactivity Biochemistry 31 1992 5964 5973
8. F. Wang, R.W. Miles, G. Kicska, E. Nieves, V.L. Schramm, and R.H. Angeletti Immucillin-H binding to purine nucleoside phosphorylase reduces dynamic solvent exchange Protein Sci. 9 2000 1660 1668
9. A. Bzowska Calf spleen purine nucleoside phosphorylase: complex kinetic mechanism, hydrolysis of 7-methylguanosine, and oligomeric state in solution Biochim. Biophys. Acta 1596 2002 293 317
10. K. Šedivá, A.V. Ananiev, I. Votruba, A. Holý, and I. Rosenberg Inhibition of purine nucleoside phosphorylase by phosphonylmethylalkyl analogues of nucleotides Int. J. Purine Pyrimid. Res. 2 1991 35 39
11. A. Holý, H. Dvoráková, and M. Masojí dková Synthesis of enantiomeric N-(2-phosphonomethoxypropyl) derivatives of purine and pyrimidine bases. II. The synthon approach Collect. Czech. Chem. Commun. 60 1995 1390 1409
12. E. Kulikowska, A. Bzowska, A. Holý, L. Magnowska, and D. Shugar Antiviral acyclic nucleoside phosphonate analogues as inhibitors of purine nucleoside phosphorylase Advan. Expt. Med. Biol. 431 1998 747 752
13. A. Bzowska, M. Luić, W. Schröder, D. Shugar, W. Saenger, and G. Koellner 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
14. G. Koellner, M. Luić, D. Shugar, W. Saenger, and A. Bzowska Crystal structure of the calf spleen purine nucleoside phosphorylase in a complex with hypoxanthine at 2.15 Å resolution J. Mol. Biol. 265 1997 202 216
15. C. Mao, W.J. Cook, M. Zhou, A.A. Fedorov, S.C. Almo, and S.E. Ealick Calf spleen purine nucleoside phosphorylase complexed with substrates and substrate analogues Biochemistry 37 1998 7135 7146
16. M. Luić, G. Koellner, D. Shugar, W. Saenger, and A. Bzowska Calf spleen purine nucleoside phosphorylase: structure of its ternary complex with an N(7)-acycloguanosine inhibitor and a phosphate anion Acta Crystallog. sect. D 57 2001 30 36
17. A. Fedorov, W. Shi, G. Kicska, E. Fedorov, P.C. Tyler, and R.H. Furneaux Transition state structure of purine nucleoside phosphorylase and principles of atomic motion in enzymatic catalysis Biochemistry 40 2001 853 860
18. S.E. Ealick, S.A. Rule, D.C. Carter, T.J. Greenhough, Y.S. Babu, and W.J. Cook Three-dimensional structure of human erythrocytic purine nucleoside phosphorylase at 3.2 Å resolution J. Biol. Chem. 265 1990 1812 1820
19. M.D. Erion, J.D. Stoeckler, W.C. Guida, R.L. Walter, and S.E. Ealick Purine nucleoside phosphorylase. 2. Catalytic mechanism Biochemistry 36 1997 11735 11748
20. J. Wierzchowski, E. Kulikowska, A. Bzowska, A. Holý, L. Magnowska, and D. Shugar Interactions of the calf spleen purine nucleoside phosphorylase with antiviral acyclic nucleoside phosphonate inhibitors: kinetic and emission studies Nucleosides Nucleotides 18 1999 875 876
21. E.G. Hutchinson, and J.M. Thornton PROMOTIF-a program to identify and analyze structural motifs in proteins Protein Sci. 5 1996 212 220
22. 2+ binding site J. Biol. Chem. 266 1991 20666 20671
23. W. Yang, H.W. Lee, H. Hellinga, and J.J. Yang Structural analysis, identification, and design of calcium-binding sites in proteins Proteins: Struct. Funct. Genet. 47 2002 344 356
24. F.H. Allen, and W.D. Motherwell Applications of the Cambridge Structural Database in organic chemistry and crystal chemistry Acta Crystallog. sect. B 58 2002 407 422
25. M. Luić, G. Koellner, T. Yokomatsu, S. Shibuya, and A. Bzowska Calf spleen purine nucleoside phosphorylase: crystal structure of its binary complex with a potent multisubstrate analogue inhibitor Acta Crystallog. sect. D 60 2004 1417 1424
26. S. Halazy, A. Ehrhard, and C. Danzin 9-(Difluorophosphonooalkyl)guanines as a new class of multisubstrate analogue inhibitors of purine nucleoside phosphorylase J. Am. Chem. Soc. 113 1991 315 317
27. G.M. Blackburn, and D.E. Kent Synthesis of α- and γ-fluoroalkylphosphonates J. Chem. Perkin Trans. 1 1986 913 917
28. R.M.C. Dawson D. Elliott W.H. Elliott K.M. Jones Spectral data and pK values for purines, pyrimidines, nucleosides, and nucleotides Data for Biochemical Research 1969 Oxford University Press Oxford 169 179
29. J. Tebbe, A. Bzowska, B. Wielgus-Kutrowska, W. Schröder, D. Shugar, W. Saenger, and G. Koellner Crystal structures of purine nucleoside phosphorylase (PNP) from Cellulomonas sp. and its implications of the molecular mechanism of trimeric PNPs J. Mol. Biol. 294 1999 1239 1255
30. E. Kulikowska, A. Bzowska, J. Wierzchowski, and D. Shugar Properties of two unusual, and fluorescent substrates of purine nucleoside phosphorylase: 7-methylguanosine and 7-methylinosine Biochim. Biophys. Acta 874 1986 355 363
31. A. Bzowska, E. Kulikowska, and D. Shugar Properties of purine nucleoside phosphorylase (PNP) of mammalian and bacterial origin Z. Naturforsch. 45c 1990 59 70
32. A. Bzowska, E. Kulikowska, E. Darzynkiewicz, and D. Shugar Purine nucleoside phosphorylase. Structure-activity relationships for substrate and inhibitor 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
33. D. Shugar, and A. Psoda Tautomerism of purines and pyrimidines, their nucleosides and various analogues Landolt-Börnstein Encyklopedie vol. 7/1d 1990 Springer-Verlag Heidelberg
34. R.W. Miles, P.C. Tyler, R.H. Furneaux, C.K. Bagdassarian, and V.L. Schramm One third-the-sites transition-state inhibitors for purine nucleoside phosphorylase Biochemistry 37 1998 8615 8621
35. G.A. Kicska, P.C. Tyler, G.B. Evans, R.H. Furneaux, W. Shi, and A. Fedorov Atomic dissection of the hydrogen bond network for transition-state analogue binding to purine nucleoside phosphorylase Biochemistry 10 2002 14489 14498
36. J.D. Stoeckler, R.P. Agarwal, K.C. Agarwal, and R.E. Parks Jr Purine nucleoside phosphorylase from human erythrocytes Methods Enzymol. 51 1978 530 538
37. M. Muraoka Synthesis and properties of 2,6-diamino-8,2′-anhydro-8- mercapto-9-β-d-arabinofuranosylpurine Chem. Pharm. Bull. 29 1981 3449 3454
38. B. Ames Assay for inorganic phosphate, total phosphate and phosphonates Methods Enzymol. 8 1966 115 116
39. B. Wielgus-Kutrowska, A. Bzowska, J. Tebbe, G. Koellner, and D. Shugar Purine nucleoside phosphorylase (PNP) from Cellulomonas sp.: physico-chemical properties, and binding of substrates determined by ligand-dependent enhancement of enzyme intrinsic fluorescence, and by protective effects of ligands on thermal inactivation of the enzyme Biochim. Biophys. Acta 1597 2002 320 334
40. T. Wiseman, S. Williston, J.F. Brandts, and L.-N. Lin Rapid measurement of binding constants and heats of binding using a new titration calorimeter Anal. Biochem. 179 1989 131 137
41. M.R. Eftink Fluorescence methods for studying equilibrium macromolecule-ligand interactions Methods Enzymol. 278 1997 221 257
42. Z. Otwinowski Oscillation data reduction program L. Sawyer N. Isaacs S. Bailey Data Collection and Processing. CCP4 Daresbury Study Weekend, nos DL/SCI/R34, ISSN 0144-5677 1993 Daresbury Laboratory Warrington, UK 56 62
43. Collaborative Computational Project, Number 4 The CCP4 suite: programs for protein crystallography Acta Crystallog. sect. D 50 1994 760 763
44. A.T. Brünger, P.D. Adams, G.M. Clore, W.L. DeLano, P. Gros, and R.W. Grosse-Kunstleve Crystallography & NMR systems: a new suite for macromolecular structure determination Acta Crystallog. sect. D 54 1998 905 921
45. T.A. Jones, J.-Y. Zou, S.W. Cowan, and M. Kjeldgaard Improved methods for building protein models in electron density maps and the location of errors of these models Acta Crystallog. sect. A 47 1991 110 119
46. R.J. Read Improved Fourier coefficients for maps using phases from partial structures with errors Acta Crystallog. sect. A 42 1986 140 149
47. M.F. Sanner, A.J. Olson, and J.-C. Spehner Reduced surface: an efficient way to compute molecular surfaces Biopolymers 38 1996 305 320
48. V. Luzzati Traitement statistique des erreurs dans la determination des structures cristallines Acta Crystallog. 5 1952 802 810