Crystal Structures of Substrate and Inhibitor Complexes of Ribose 5-Phosphate Isomerase A from Vibrio vulnificus YJ016

  • Kim, Tae Gyun (Department of Chemistry, Pohang University of Science and Technology) ;
  • Kwon, Taek Hun (School of Life Sciences and Biotechnology, Korea University) ;
  • Min, Kyoungin (Department of Chemistry, Pohang University of Science and Technology) ;
  • Dong, Mi-Sook (School of Life Sciences and Biotechnology, Korea University) ;
  • Park, Young In (School of Life Sciences and Biotechnology, Korea University) ;
  • Ban, Changill (Department of Chemistry, Pohang University of Science and Technology)
  • Received : 2008.10.21
  • Accepted : 2008.10.28
  • Published : 2009.01.31


Ribose-5-phosphate isomerase A (RpiA) plays an important role in interconverting between ribose-5-phosphate (R5P) and ribulose-5-phosphate in the pentose phosphate pathway and the Calvin cycle. We have determined the crystal structures of the open form RpiA from Vibrio vulnificus YJ106 (VvRpiA) in complex with the R5P and the closed form with arabinose-5-phosphate (A5P) in parallel with the apo VvRpiA at $2.0{\AA}$ resolution. VvRpiA is highly similar to Escherichia coli RpiA, and the VvRpiA-R5P complex strongly resembles the E. coli RpiA-A5P complex. Interestingly, unlike the E. coli RpiA-A5P complex, the position of A5P in the VvRpiA-A5P complex reveals a different position than the R5P binding mode. VvRpiA-A5P has a sugar ring inside the binding pocket and a phosphate group outside the binding pocket: By contrast, the sugar ring of A5P interacts with the Asp4, Lys7, Ser30, Asp118, and Lys121 residues; the phosphate group of A5P interacts with two water molecules, W51 and W82.


Arabinose-5-phosphate;crystal structure;E. coli RpiA;Ribose-5 phosphate isomerase A (RpiA);Vibrio vulnificus YJ016


Supported by : Pohang University of Science and Technology, Korea Health Industry Development Institute, Korea Health Industry Development Institute, Korea Research Foundation


  1. DeLano, W.L. (2002). The PyMOL Molecular Graphics System, DeLano Scientific, San Carlos, CA
  2. Essenbeg, M.K., and Cooper, R.A. (1975). Two ribose-5-phosphate isomerases from Escherichia coli K-12: partial characterization of the enzymes and consideration of their possible physiological roles. Eur. J. Biochem. 55, 323-332
  3. Heo, S.D., Cho, M., Ku, J.K., and Ban, C. (2007). Steady-state ATPase activity of E. coli MutS modulated by its dissociation from heteroduplex DNA. Biochem. Biophys. Res. Commun. 364, 264-269
  4. Huck, J.H., Verhoeven, N.M., Struys, E.A., Salomons, G.S., Jakobs, C., and van der Knaap, M.S. (2004). Ribose-5-phosphate isomerase deficiency: new inborn error in the pentose phosphate pathway associated with a slowly progrssive leukoencephalopathy. Am. J. Hum. Genet. 74, 745-751
  5. Shin, D.H., Roberts, A., Jancarik, J., Yokota, H., Kim, R., Wemmer, D.E., and Kim, S.H. (2003). Crystal structure of a phosphatase with a unique substrate binding domain from Thermotoga maritime. Protein Sci. 12, 1464-1472
  6. Ishikawa, K., Matsui, I., Payan, F., Cambillau, C., Ishida, H., Kawarabayasi, Y., Kikuchi, H., and Roussel, A. (2002). A hyperthermostable D-ribose-5-phosphate isomerase from Pyrococcus horikoshii characterization and three-dimensional structure. Structure 10, 877-886
  7. Melendez-Hevia, E., Waddell, T.G., Heinrich, R., and Montero, F. (1997). Theoretical approaches to the evolutionary optimization of glycolysis-chemical analysis. Eur. J. Biochem. 244, 527-543
  8. Rault, M., Giudici-Orticoni, M.T., Gontero, B., and Ricard, J. (1993). Structural and functional properties of a multi-enzyme complexfrom spinach chloroplast. 1. Stoichiometry of the polypeptide chains. Eur. J. Biochem. 217, 1065-1073
  9. Holmes, M.A., Buckner, F.S., Van Voorhis, W.C., Verlinde, C.L.M.J., Mehlin, C., Boni, E., DeTitta, G., Luft, J., Lauricella, A., Anderson, L., et al. (2006). Structure of ribose 5-phosphate isomerase from Plasmodium falciparum. Acta Crystallogr. F62, 427-431
  10. Park, S.-Y., Heo, Y.-J., Kim, K.-S., and Cho, Y.-H. (2005). Drosophila melanogaster Is Susceptible to Vibrio cholerae Infection. Mol. Cells 20, 409-415
  11. Rangarajan, E.S., Sivaraman, J., Matte, A., and Cygler, M. (2002). Crystal structure of D-ribose-5-phosphate isomerase (RpiA) from Escherichia coli. PROTEINS: Structure, Functions, and Genetics 48, 737-740
  12. Thompson, J.D., Higgins, D.G., and Gibson, T.J. (1994). CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22, 4673-4680
  13. Grochowski, L.L., Xu, H., and White, R.H. (2005). Ribose-5- phosphate biosynthesis in Methanocaldococcus jannaschii Occurs in the absence of pentose-phosphate pathway. J. Bacteriol. 187, 7382-7389
  14. Zhang, R., Andersson, C.E., Savchenko, A., Skarina, T., Evdokimova, E., Beasley, S., Arrowsmith, C.H., Edwards, A.M., Joachimiak, A., and Mowbray, S.L. (2003). Structure of Escherichia coli ribose-5-phosphate isomerase: a ubiquitous enzyme of the pentose phosphate pathway and the Calvin cycle. Structure 11, 31-42
  15. Roos, A.K. (2007). Structural and Functional Studies of Ribose-5- phosphate isomerase B. Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology 332, 1-5
  16. Ryu, E.K., Kim, T.G., Kwon, T.H., Jung, I.D., Ryu, D., Park, Y.M., Kim, J., Ahn, K.H., and Ban, C. (2007). Crystal structure of recombinant human stromal cell-derived factor-1$\alpha$. PROTEINS: Structure, Function, and Bioinformatics 67, 1193-1197
  17. Adams, P.D., Grosse-Kunstleve, R.W., Hung, L.W., Ioerger, T.R., McCoy, A.J., Moriarty, N.W., Read, R.J., Sacchettini, J.C., Sauter, N.K., and Terwilliger, T.C. (2002). PHENIX: building new software for automated crystallographic structure determination. Acta Crystallogr. D58, 1948-1954
  18. Hove-Jensen, B., and Maigaard, M. (1993). Escherichia coli rpiA gene encoding ribose phosphate isomerase A. J. Bacteriol. 175, 5628-5635
  19. Kleywegt, G.J., and Jones, T.A. (1996). Phi/psi-chology: Ramachandran revisited. Structure 4, 1395-1400
  20. Otwinowski, Z. and Minor, W. (1997). Processing of x-ray diffraction data collected in oscillation mode. Methods Enzymol. 276, 307-326
  21. Lee, J.H., Kim, S.Y., Rho, S.-H., Im, Y.J., Kim, Y.R., Kim, M.-K., Kang, G.B., Rhee, J.H., and Eom, S.H. (2005). Crystallization and preliminary X-ray crystallographic analysis of PAS factor from Vibrio vulnificus. Mol. Cells 20, 361-363
  22. Choquet, C.G., Richards, J.C., Patel, G.B., and Sprott, G.D. (1994). Ribose biosynthesis in methanogenic bacteria. Arch. Microbiol. 161, 481-488
  23. Graile, M., Meyer, P., Leulloit, N., Sorel, I., Janin, J., Van Tilbeurgh, H., and Quevillon-Cheruel, S. (2005). Crystal structure of the S. cerevisiae D-ribose-5-phosphate isomerase: comparison with the archaeal and bacterial enzymes. Biochimie 87, 763-769
  24. Lim, H., Kim, K., Han, D., Oh, J., and Kim, Y. (2008). Crystal Structure of TTC0263, a Thermophilic TPR Protein from Thermus thermophilus HB27. Mol. Cells 24, 27-36
  25. Brunger, A.T., Adams, P.D., Clore, G.M., Delano, W.L., Gros, P., Grosse-Kunsteve, R.W., Jiang, J.S., Kuszwewski, J., Nilges, M., and Pannu, N.S. (1998). Crystallography & NMR system: a new software suite for macromolecular structure determination. Acta Crystallogr. D54, 905-921
  26. Eisenreich, W., and Bacher, A. (1991). Biosynthesis of 5 hydroxybenzimidazolycobamid (factor III) in Methanobacterium thermoautotrophicum. J. Biol. Chem. 266, 23840-23849
  27. Gouet, P., Robert, X., and Courcelle, E. (2003). ESPript/ENDscript: extracting and rendering sequence and 3D information from atomic structures of proteins. Nucleic Acids Res. 31, 3320-3323
  28. Dandekar, T., Schuster, S., Snel, B., Huyen, M., and Bork, P. (1999). Pathway alignment: application to the comparative analysis of glycolytic enzymes. Biochem. J. 343, 115-124
  29. Decker, P., Schweer, H., and Pohlmann, R. (1982). Identification of formose sugars, presumable prebiotic metabolites, using capillary gas chromatography/gas chromatography-mass spectrometry of n-butoximine trifluoroactatcs on OV-225. J. Chromatogr. 244, 281-291
  30. Laskowski, R.A., Macarthur, M.W., Moss, D.S., and Thornton, J.M. (1993). PROCHECK: a program to check the stereochemical quality of the protein structure. J. Appl. Crystallogr. 26, 283-291
  31. Leslie, A.G. (1999). Integration of macromolecular diffraction data. Acta Crystallogr. D. Biol. Crystallogr. 55, 1696-1702