Journal of Biomedicine and Biotechnology
Volume 2008 (2008), Article ID 841312, 6 pages
doi:10.1155/2008/841312
Research Article

Structure-Based Inhibitors Exhibit Differential Activities against Helicobacter pylori and Escherichia coli Undecaprenyl Pyrophosphate Synthases

Chih-Jung Kuo,1,2 Rey-Ting Guo,1,2 I-Lin Lu,3 Hun-Ge Liu,4 Su-Ying Wu,3 Tzu-Ping Ko,4 Andrew H.-J. Wang,1,2,4 and Po-Huang Liang1,2,4

1Taiwan International Graduate Program, Academia Sinica, Taipei 115, Taiwan
2Institute of Biochemical Sciences, National Taiwan University, Taipei 106, Taiwan
3Division of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Chu-Nan, Miaw-Li 350, Taiwan
4Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan

Received 21 September 2007; Accepted 27 December 2007

Academic Editor: Daniel Howard

Copyright © 2008 Chih-Jung Kuo et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Linked References

  1. C. M. Allen, “Purification and characterization of undecaprenyl pyrophosphate synthetase,” Methods in Enzymology, vol. 110, pp. 281–299, 1985.
  2. J. Robyt, Essential of Carbohydrate Chemistry, Springer, New York, NY, USA, 1998, chapter 10.
  3. K. Ogura and T. Koyama, “Enzymatic aspects of isoprenoid chain elongation,” Chemical Reviews, vol. 98, no. 4, pp. 1263–1276, 1998. View at Publisher · View at Google Scholar
  4. P.-H. Liang, T.-P. Ko, and A. H.-J. Wang, “Structure, mechanism and function of prenyltransferases,” European Journal of Biochemistry, vol. 269, no. 14, pp. 3339–3354, 2002. View at Publisher · View at Google Scholar
  5. A. Chen, P. A. Kroon, and C. D. Poulter, “Isoprenyl diphosphate synthases: protein sequence comparisons, a phylogenetic tree, and predictions of secondary structure,” Protein Science, vol. 3, no. 4, pp. 600–607, 1994.
  6. N. Shimizu, T. Koyama, and K. Ogura, “Molecular cloning, expression, and purification of undecaprenyl diphosphate synthase. No sequence similarity between E- and Z-prenyl diphosphate synthases,” Journal of Biological Chemistry, vol. 273, no. 31, pp. 19476–19481, 1998. View at Publisher · View at Google Scholar
  7. C. M. Apfel, B. Takács, M. Fountoulakis, M. Stieger, and W. Keck, “Use of genomics to identify bacterial undecaprenyl pyrophosphate synthetase: cloning, expression, and characterization of the essential UPPS gene,” Journal of Bacteriology, vol. 181, no. 2, pp. 483–492, 1999.
  8. H. Fujii, T. Koyama, and K. Ogura, “Efficient enzymatic hydrolysis of polyprenyl pyrophosphates,” Biochimica et Biophysica Acta, vol. 712, no. 3, pp. 716–718, 1982.
  9. R.-T. Guo, T.-P. Ko, A. P.-C. Chen, C.-J. Kuo, A. H.-J. Wang, and P.-H. Liang, “Crystal structures of undecaprenyl pyrophosphate synthase in complex with magnesium, isopentenyl pyrophosphate, and farnesyl thiopyrophosphate: roles of the metal ion and conserved residues in catalysis,” Journal of Biological Chemistry, vol. 280, no. 21, pp. 20762–20774, 2005. View at Publisher · View at Google Scholar · View at PubMed
  10. A. Nomura, G. N. Stemmermann, P. H. Chyou, G. J. Perez-Perez, and M. J. Blaser, “Helicobacter pylori infection and the risk for duodenal and gastric ulceration,” Annals of Internal Medicine, vol. 120, pp. 977–981, 1994.
  11. F. Mauch, G. Bode, and P. Malfertheiner, “Identification and characterization of an ATPase system of Helicobacter pylori and the effect of proton pump inhibitors,” American Journal of Gastroenterology, vol. 88, no. 10, pp. 1801–1802, 1993.
  12. P. Bytzer and C. O'Morain, “Treatment of Helicobacter pylori,” Helicobacter, vol. 10, no. S1, pp. 40–46, 2005. View at Publisher · View at Google Scholar · View at PubMed
  13. S.-Y. Chang, T.-P. Ko, A. P.-C. Chen, A. H.-J. Wang, and P.-H. Liang, “Substrate binding mode and reaction mechanism of undecaprenyl pyrophosphate synthase deduced from crystallographic studies,” Protein Science, vol. 13, no. 4, pp. 971–978, 2004. View at Publisher · View at Google Scholar · View at PubMed
  14. J.-J. Pan, L.-W. Yang, and P.-H. Liang, “Effect of site-directed mutagenesis of the conserved aspartate and glutamate on E. coli undecaprenyl pyrophosphate synthase catalysis,” Biochemistry, vol. 39, no. 45, pp. 13856–13861, 2000. View at Publisher · View at Google Scholar
  15. A. P.-C. Chen, S.-Y. Chang, Y.-C. Lin, et al., “Substrate and product specificities of cis-type undecaprenyl pyrophosphate synthase,” Biochemical Journal, vol. 386, no. 1, pp. 169–176, 2005. View at Publisher · View at Google Scholar · View at PubMed
  16. Z. Otwinowski and W. Minor, “Processing of X-ray diffraction data collected in oscillation mode,” Methods in Enzymology, vol. 276, pp. 307–326, 1997. View at Publisher · View at Google Scholar
  17. A. T. Brunger, “Assessment of phase accuracy by cross validation: the free R value. Methods and applications,” Acta Crystallographica Section D, vol. 49, no. 1, pp. 24–36, 1998. View at Publisher · View at Google Scholar · View at PubMed
  18. A. T. Brünger, P. D. Adams, G. M. Clore, et al., “Crystallography & NMR system: a new software suite for macromolecular structure determination,” Acta Crystallographica Section D, vol. 54, no. 5, pp. 905–921, 1998.
  19. 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 in these models,” Acta Crystallographica Section A, vol. 47, no. 2, pp. 110–119, 1991. View at Publisher · View at Google Scholar
  20. P. J. Kraulis, “MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures,” Journal of Applied Crystallography, vol. 24, no. 5, pp. 947–950, 1991.
  21. E. A. Merritt and M. E. P. Murphy, “Raster3D version 2.0 A program for photorealistic molecular graphics,” Acta Crystallographica Section D, vol. 50, no. 6, pp. 869–873, 1994. View at Publisher · View at Google Scholar · View at PubMed
  22. T.-P. Ko, Y.-K. Chen, H. Robinson, et al., “Mechanism of product chain length determination and the role of a flexible loop in Escherichia coli undecaprenyl-pyrophosphate synthase catalysis,” Journal of Biological Chemistry, vol. 276, no. 50, pp. 47474–47482, 2001. View at Publisher · View at Google Scholar · View at PubMed
  23. S.-Y. Chang, T.-P. Ko, P.-H. Liang, and A. H.-J. Wang, “Catalytic mechanism revealed by the crystal structure of undecaprenyl pyrophosphate synthase in complex with sulfate, magnesium, and triton,” Journal of Biological Chemistry, vol. 278, no. 31, pp. 29298–29307, 2003. View at Publisher · View at Google Scholar · View at PubMed
  24. H. Li, J. Huang, X. Jiang, M. Seefeld, M. McQueney, and R. Macarron, “The effect of triton concentration on the activity of undecaprenyl pyrophosphate synthase inhibitors,” Journal of Biomolecular Screening, vol. 8, no. 6, pp. 712–715, 2003. View at Publisher · View at Google Scholar · View at PubMed
  25. A. A. Scholte, L. M. Eubanks, C. D. Poulter, and J. C. Vederas, “Synthesis and biological activity of isopentenyl diphosphate analogues,” Bioorganic and Medicinal Chemistry, vol. 12, no. 4, pp. 763–770, 2004. View at Publisher · View at Google Scholar · View at PubMed
  26. R.-T. Guo, R. Cao, P.-H. Liang, et al., “Bisphosphonates target multiple sites in both cis- and trans- prenyltransferases,” Proceedings of the National Academy of Sciences of the United States of America, vol. 104, no. 24, pp. 10022–10027, 2007. View at Publisher · View at Google Scholar · View at PubMed