Journal of Biophysics
Volume 2009 (2009), Article ID 434038, 12 pages
doi:10.1155/2009/434038
Research Article

Crystal Structural and Functional Analysis of the Putative Dipeptidase from Pyrococcus horikoshii OT3

1Experimental Facility Division, SPring-8 Group, National Synchrotron Radiation Research Center, 101 Hsin-Ann Road, Hsinchu 30076, Hsinchu Science Park, Taiwan
2Peptide Institute, Inc., Ina Mino-shi, Osaka 562-8686, Japan
3RIKEN SPring-8 Center, Harima Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
4RIKEN Systems and Structural Biology Center, Yokohama Institute, RIKEN, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
5Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan

Received 3 February 2009; Accepted 30 April 2009

Academic Editor: Eaton Edward Lattman

Copyright © 2009 Jeyaraman Jeyakanthan 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. M. Booth, P. V. Jennings, I. N. Fhaolain, and G. O'Cuinn, “Prolidase activity of Lactobacillus lactis subsp. cremoris AM2: partial purification and characterization,” Journal of Dairy Research, vol. 57, pp. 245–254, 1990.
  2. P. Browne and G. O'Cuinn, “The purification and characterization of a proline dipeptidase from guinea pig brain,” The Journal of Biological Chemistry, vol. 258, no. 10, pp. 6147–6154, 1983.
  3. F. Endo, A. Tanoue, H. Nakai, et al., “Primary structure and gene localization of human prolidase,” The Journal of Biological Chemistry, vol. 264, no. 8, pp. 4476–4481, 1989.
  4. H. Sjöström, O. Norén, and L. Josefsson, “Purification and specificity of pig intestinal prolidase,” Biochimica et Biophysica Acta, vol. 327, no. 2, pp. 457–470, 1973.
  5. M. D. Fernández-Esplá, M. C. Martín-Hernández, and P. F. Fox, “Purification and characterization of a prolidase from Lactobacillus casei subsp. casei IFPL 731,” Applied and Environmental Microbiology, vol. 63, no. 1, pp. 314–316, 1997.
  6. K. T. Suga, T. Kabashima, K. Ito, et al., “Prolidase from Xanthomonas maltophilia: purification and characterization of the enzyme,” Bioscience, Biotechnology and Biochemistry, vol. 59, no. 11, pp. 2087–2090, 1995.
  7. R. C. Scriver, R. J. Smith, and J. M. Phang, “Disorders of proline and hydroxyproline metabolism,” in The Metabolic Basis of Inherited Diseases, J. B. Stanbury, D. S. Wyngaarden, J. L. Fredrickson, M. S. Goldstein, and Brown, Eds., McGraw Hill, New York, NY, USA, 1983.
  8. W. Bockelmann, “The proteolytic system of starter and non-starter bacteria: components and their importance for cheese ripening,” International Dairy Journal, vol. 5, no. 8, pp. 977–994, 1995.
  9. T.-C. Cheng, L. Liu, B. Wang, et al., “Nucleotide sequence of a gene encoding an organophosphorus nerve agent degrading enzyme from Alteromonas haloplanktis,” Journal of Industrial Microbiology and Biotechnology, vol. 18, no. 1, pp. 49–55, 1997.
  10. M. J. Maher, M. Ghosh, A. M. Grunden, et al., “Structure of the prolidase from Pyrococcus furiosus,” Biochemistry, vol. 43, no. 10, pp. 2771–2783, 2004. View at Publisher · View at Google Scholar · View at PubMed
  11. S. C. Graham, M. Lee, H. C. Freeman, and J. M. Guss, “An orthorhombic form of Escherichia coli aminopeptidase P at 2.4 Å resolution,” Acta Crystallographica D, vol. 59, no. 5, pp. 897–902, 2003. View at Publisher · View at Google Scholar
  12. T. H. Tahirov, H. Oki, T. Tsukihara, et al., “Crystal structure of methionine aminopeptidase from hyperthermophile, Pyrococcus furiosus,” Journal of Molecular Biology, vol. 284, no. 1, pp. 101–124, 1998. View at Publisher · View at Google Scholar · View at PubMed
  13. M. Ghosh, A. M. Grunden, D. M. Dunn, R. Weiss, and M. W. Adams, “Characterization of native and recombinant forms of an unusual cobalt-dependenct proline dipeptidase (prolidase) from the hyperthermophilic archaeon Pyrococcus furiosus,” Journal of Bacteriology, vol. 180, pp. 4781–4789, 1998.
  14. 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
  15. W. A. Hendrickson, J. R. Horton, and D. M. LeMaster, “Selenomethionyl proteins produced for analysis by multiwavelength anomalous diffraction (MAD): a vehicle for direct determination of three dimensional structure,” The EMBO Journal, vol. 9, no. 5, pp. 1665–1672, 1990.
  16. T. C. Terwilliger and J. Berendzen, “Automated MAD and MIR structure solution,” Acta Crystallographica D, vol. 55, no. 4, pp. 849–861, 1999. View at Publisher · View at Google Scholar
  17. A. Perrakis, R. Morris, and V. S. Lamzin, “Automated protein model building combined with iterative structure refinement,” Nature Structural Biology, vol. 6, no. 5, pp. 458–463, 1999. View at Publisher · View at Google Scholar · View at PubMed
  18. A.T. Brünger, J. Kuriyan, and M. Karplus, “Crystallographic R factor refinement by molecular dynamics,” Science, vol. 235, no. 4787, pp. 458–460, 1987.
  19. A. T. Brünger, P. D. Adams, G. M. Clore, et al., “Crystallography & NMR system: a new software suite for macromolecular structure determination,” Acta Crystallographica D, vol. 54, no. 5, pp. 905–921, 1998.
  20. P. J. Kraulis, “A program to produce both detailed and schematic plots of protein structures,” Journal of Applied Crystallography, vol. 24, part 5, pp. 947–950, 1991.
  21. E. A. Merritt and D. J. Bacon, “Raster3D: photorealistic molecular graphic,” Methods in Enzymology, vol. 277, pp. 505–524, 1997.
  22. H. Durchschlag, in Thermodynamic Data for Biochemistry and Biotechnology, H.-J. Hinz, Ed., chapter 3, p. 45, Springer, Berlin, Germany, 1986.
  23. R. A. Laskowski, M. W. McArthur, D. S. Moss, and J. M. Thornton, “PROCHECK: a program to check the stereochemical quality of protein structures,” Journal of Applied Crystallography, vol. 26, pp. 283–291, 1993.
  24. A. Yaron and D. Mlynar, “Aminopeptidase-P,” Biophys Res Commun, vol. 32, pp. 658–663, 1968.
  25. G. Yang, R. B. Kirkpatrick, T. Ho, et al., “Steady-state kinetic characterization of substrates and metal-ion specificities of the full-length and N-terminally truncated recombinant human methionine aminopeptidases (type 2),” Biochemistry, vol. 40, no. 35, pp. 10645–10654, 2001. View at Publisher · View at Google Scholar
  26. S. Tanskul, K. Oda, H. Oyama, N. Noparatnaraporn, M. Tsunemi, and K. Takada, “Substrate specificity of alkaline serine proteinase isolated from photosynthetic bacterium, Rubrivivax gelatinosus KDDS1,” Biochemical and Biophysical Research Communications, vol. 309, no. 3, pp. 547–551, 2003. View at Publisher · View at Google Scholar
  27. W. A. Kabsch, “Solution for the best rotation to relate two sets of vectors,” Acta Crystallographica A, vol. 32, pp. 922–923, 1976.
  28. B. Padmanabhan, A. Paehler, and M. Horikoshi, “Structure of creatine amidinohydrolase from Actinobacillus,” Acta Crystallographica D, vol. 58, no. 8, pp. 1322–1328, 2002. View at Publisher · View at Google Scholar
  29. J. F. Bazan, L. H. Weaver, S. L. Roderick, R. Huber, and B. W. Matthews, “Sequence and structure comparison suggest that methionine aminopeptidase, prolidase, aminopeptidase P, and creatinase share a common fold,” Proceedings of the National Academy of Sciences of the United States of America, vol. 91, no. 7, pp. 2473–2477, 1994.
  30. S. Liu, J. Widom, C. W. Kemp, C. M. Crews, and J. Clardy, “Structure of human methionine aminopeptidase-2 complexed with fumagillin,” Science, vol. 282, no. 5392, pp. 1324–1327, 1998.
  31. M. C. J. Wilce, C. S. Bond, N. E. Dixon, et al., “Structure and mechanism of a proline-specific aminopeptidase from Escherichia coli,” Proceedings of the National Academy of Sciences of the United States of America, vol. 95, no. 7, pp. 3472–3477, 1998. View at Publisher · View at Google Scholar
  32. S. L. Roderick and B. W. Matthews, “Structure of the cobalt-dependent methionine aminopeptidase from Escherichia coli: a new type of proteolytic enzyme,” Biochemistry, vol. 32, no. 15, pp. 3907–3912, 1993.
  33. H. W. Hoeffken, S. H. Knof, P. A. Bartlett, R. Huber, H. Moellering, and G. Schumacher, “Crystal structure determination, refinement and molecular model of creatine amidinohydrolase from Pseudomonas putida,” Journal of Molecular Biology, vol. 204, no. 2, pp. 417–433, 1988.
  34. W. T. Lowther and B. W. Mathews, “Metalloamonopeptidases: common functional themes in disparate structural surrounding,” Chemical Reviews, vol. 102, pp. 4581–4607, 2002.
  35. V. Plotnikov, A. Rochalski, M. Brandts, et al., “An autosampling differential scanning calorimeter instrument for studying molecular interactions.,” Assay Drug Dev Technol, vol. 1, no. 1, part 1, pp. 83–90, 2002.
  36. V. M. D'souza, B. Bennett, A. J. Copik, and R. C. Holz, “Divalent metal binding properties of the methionyl aminopeptidase from Escherichia coli,” Biochemistry, vol. 39, no. 13, pp. 3817–3826, 2000. View at Publisher · View at Google Scholar
  37. J. D. Thompson, D. G. Higgins, and T. J. Gibson, “ClustalW: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice,” Nucleic Acids Research, vol. 22, pp. 4673–4680, 1994.
  38. P. Gouet, X. Robert, and E. Courcelle, “ESPript/ENDscript: extracting and rendering sequence and 3D information from atomic structures of proteins,” Nucleic Acids Research, vol. 31, no. 13, pp. 3320–3323, 2003. View at Publisher · View at Google Scholar
  39. E. C. Griffith, Z. Su, S. Niwayama, C. A. Ramsay, Y.-H. Chang, and J. O. Liu, “Molecular recognition of angiogenesis inhibitors fumagillin and ovalicin by methionine aminopeptidase 2,” Proceedings of the National Academy of Sciences of the United States of America, vol. 95, no. 26, pp. 15183–15188, 1998. View at Publisher · View at Google Scholar
  40. W. T. Lowther, A. M. Orville, D. T. Madden, S. Lim, D. H. Rich, and B. W. Matthews, “Escherichia coli methionine aminopeptidase: implications of crystallographic analyses of the native, mutant, and inhibited enzymes for the mechanism of catalysis,” Biochemistry, vol. 38, no. 24, pp. 7678–7688, 1999. View at Publisher · View at Google Scholar · View at PubMed
  41. J. Funahashi, K. Takano, and K. Yutani, “Are the parameters of various stabilization factors estimated from mutant human lysozymes compatible with other proteins?” Protein Engineering, vol. 14, no. 2, pp. 127–134, 2001.
  42. S. F. Altschul, T. L. Madden, A. A. Schäffer, et al., “Gapped BLAST and PSI-BLAST: a new generation of protein database search programs,” Nucleic Acids Research, vol. 25, no. 17, pp. 3389–3402, 1997. View at Publisher · View at Google Scholar