The crystal structure of pyrimidine nucleoside phosphorylase in a closed conformation

Structure

Volumn 6, Issue 11, 1998, Pages 1467-1479

  Pugmire, Matthew J ^a   Ealick, Steven E ^a  

^a Department of Obstetrics Gynecology   (United States)

Author keywords

Domain movement; Gliostatin; Platelet derived endothelial cell growth factor; Thymidine phosphorylase

Indexed keywords

EID: 0032533446     PISSN: 09692126     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0969-2126(98)00145-2     Document Type: Article

References (39)

1. Hamamoto, T., Noguchi, T. & Midorikawa, Y. (1996). Purification and characterization of purine nucleoside phosphorylase and pyrimidine nucleoside phosphorylase from Bacillus stearothermophilus TH 6-2. Biosci. Biotech. Biochem. 60 (7), 1179-1180.
2. Schwartz, M. (1971). Thymidine phosphorylase from Escherichia coli: properties and kinetics. Eur. J. Biochem. 21, 191-198.
3. Blank, J.G. & Hoffee, P.A. (1975). Purification and properties of thymidine phosphorylase from Salmonella typhimurium. Arch. Biochem. Biophys. 168, 259-265.
4. Iltzch, M.H., el Kouni, M.H. & Cha, S. (1985). Kinetic studies of thymidine phosphorylase from mouse liver. Biochemistry 24, 6799-6807.
5. Avraham, Y., Grossowicz, N. & Yashphe, J. (1990). Purification and characterization of uridine and thymidine phosphorylase from Lactobacillus casei. Biochim. Biophys. Acta 1040, 287-293.
6. Walter, M.R. et al., & Ealick, S.E. (1990). Three-dimensional structure of thymidine phosphorylase from Escherichia coli at 2.8 Å resolution. J. Biol. Chem. 265 (23), 14016-14022.
7. Pugmire, M.J., Cook, W.J., Jasanoff, A., Walter, M.R. & Ealick, S.E. (1998). Structural and theoretical studies suggest domain movement produces an active conformation of thymidine phosphorylase. J. Mol. Biol. 281, 285-299.
8. Gerstein, M. & Chothia, C. (1991). Analysis of protein loop closure: two types of hinges produce one motion in lactate dehydrogenase. J. Mol. Biol. 220, 133-149.
9. Gerstein, M., Anderson, B.F., Norris, G.E., Baker, E.N., Lesk, A.M. & Chothia, C. (1993). Domain closure in lactoferin: two hinges produce a see-saw motion between alternative close-packed interfaces. J. Mol. Biol. 234, 357-372.
10. Zhou, M., Pugmire, M. J., Vuong, B.Q. & Ealick, S.E. (1998). Cloning, expression, and crystallization of pyrimidine nucleoside phosphorylase from Bacillus stearothermophilus. Acta Cryst. D, in press.
11. Wriggers, W. & Schulten, K. (1997). Protein domain movements: detection of rigid domains and visualization of hinges in comparison of atomic coordinates. Proteins 29, 1-14.
12. Humphrey, W., Dalke, A. & Schulten, K. (1996). VMD - Visual molecular dynamics. J. Mol. Graphics 14.1, 33-38.
13. Jernigan, R., Raghunathan, G. & Bahar, I. (1994). Characterization of interactions and metal ion binding sites in proteins. Curr. Opin. Struct. Biol. 4, 256-263.
14. Mao, C., Cook, W.J., Zhou, M., Federov, A., Almo, S.C. & Ealick, S.E. (1998). Calf spleen purine nucleoside phosphorylase complexed with substrtaes and substrate analogues. Biochemistry 37, 7135-7146.
15. Erion, M.D., et al., & Ealick, S.E. (1997). Purine nucleoside phosphorylase 2. Catalytic mechanism. Biochemistry 36, 11725-11734.
16. Saenger, W. (1984). Structure and conformational properties of bases, furanose sugars and phosphate groups. In Principles of Nucleic Acid Structure. (Cantor, C.R., ed.) pp. 51-104. Springer-Verlag, New York.
17. Miyadera, K., et al., & Akiyama, S. (1995). Structural characterization of thymidine phosphorylase from human placenta. Biochem. Biophys. Res. Commun. 212 (3), 1040-1045.
18. Asai, K., et al., & Kato, T. (1992). A novel glial growth inhibitory factor, gliostatin, derived from neurofibroma. J. Neurochem. 59, 307-317.
19. Schwartz, E.L., Hoffman, M., O'Connor, C.J. & Wadler, S. (1992). Stimulation of 5-fluorouracil metabolic activation by interferon-α in human colon carcinoma cells. Biochem. Biophys. Res. Commun. 182, 1232-1239.
20. Takebayashi, Y., et al., & Aikou, T. (1995). The correlation of thymidine phosphorylase activity with the expression of interleukin 1α, interferon α and interferon γ in human colorectal carcinoma. Cancer Lett. 95, 57-62.
21. Takebayashi, Y., et al., & Aikou, T. (1995). The expression of thymidine phosphorylase and thrombomodulin in human colorectal carcinomas. Cancer Lett. 92, 1-7.
22. Toi, M., Hoshina, S., Taniguchi, T., Yamamoto, Y., Ishitsuka, H. & Tominaga, T. (1995). Expression of platelet-derived endothelial cell growth factor/thymidine phosphorylase in human breast cancer, Intl J. Cancer 64, 79-82.
23. Fox, S., et al., & Dickinson, A. (1995). Platelet derived endothelial cell growth factor/thymidine phosphorylase is elevated in bladder cancer. Proc. Am. Urological Assoc. J. Urol. 153, Supplement, p. 521 A.
24. Giatromanolaki, A., et al., & Gatter, K.C. (1997). Platelet-derived endothelial cell growth factor (thymidine phosphorylase) expression in lung cancer. J. Pathol. 181, 196-199.
25. Niedzwicki, J.G., Chu, S.H., el Kouni, M.H., Rowe, E.G. & Sungman, C. (1982). 5-Benzylacyclouridine and 5-benzyloxybenzylacyclouridine, potent inhibitors of uridine phosphorylase. Biochem. Pharmacol. 31, 1857-1861.
26. Woodman, P.W., Sarrif, A.M. & Heidelberger, C. (1980). Specificity of pyrimidine nucleoside phosphorylase and the phosphorolysis of 5-fluoro-2′-deoxyuridine. Cancer Res. 50, 507-511.
27. Patterson, A.V., et al., & Harris, A.L. (1995). Increased sensitivity to the prodrug 5′-deoxy-5-fluorouridine and modulation of 5-fluoro-2′-deoxyuridine sensitivity in MCF-7 cells transfected with thymidine phosphorylase. Brit. J. Cancer 72, 669-675.
28. Kirkwood, J.M., Ensminger, W., Rosowsky, A., Papathanasopoulos, N. & Frei, E. (1980). Comparison of pharmacokinetics of 5-fluorouracil with concurrent thymidine infusions in a phase I trial. Cancer Res. 40, 107-113.
29. Walter, R.L., et al., & Ealick, S.E. (1995). High-resolution macromolecular structure determination using CCD detectors and synchrotron radiation. Structure 3, 835-844.
30. Otwinowski, Z. (1988). DENZO. A program for automatic evaluation of film densities. Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT.
31. Brünger, A.T. (1990). Extension of molecular replacement: a new search strategy based on patterson correlation refinement. Acta Cryst. A 46, 46-57.
32. Brünger, A.T. (1992). X-PLOR Version 3.1: A System for X-ray Crystallography and NMR. Yale University Press, New Haven, CT, USA.
33. DeLano, W.L. & Brünger, A.T. (1995). The direct rotation function: rotational patterson correlation search applied to molecular replacement. Acta Cryst. D 51, 740-748.
34. Jones, T.A. & Kjeldgaard, M.O. (1995). O - The Manual. Uppsala, Sweden, Uppsala University.
35. McMartin, C. & Bohacek, R.S. (1997). QXP: powerful, rapid computer algorithms for structure-based drug design. J. Comput. Aided Mol. Des. 11, 333-344.
36. Mohamadi, F., et al., & Still, W.C. (1990). Macromodel - an integrated software system for modeling organic and bioorganic molecules using molecular mechanics. J. Comput. Chem. 11, 440-467.
37. Weiner, S.J., et al., & Weiner, P. (1984). A new force field for molecular mechanical simulation of nucleic acids and proteins. J. Am. Chem. Soc. 106, 765-784.
38. Weiner, S.J., Kollman, P.A., Nguyen, D.T. & Case, D.A. (1986). An all atom force field for simulations of proteins and nucleic acids. J. Comp. Chem. 7, 230-252.
39. Kraulis, P.J. (1991). MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures. J. Appl. Cryst. 24, 946-950.