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BioMed Research International
Volume 2013 (2013), Article ID 458571, 13 pages
http://dx.doi.org/10.1155/2013/458571
Research Article

Structure-Based Mechanism for Early PLP-Mediated Steps of Rabbit Cytosolic Serine Hydroxymethyltransferase Reaction

1Dipartimento di Scienze Biochimiche, Sapienza Università di Roma, 00185 Roma, Italy
2Center for the Study of Biological Complexity and Institute for Structural Biology and Drug Discovery, Richmond, VA 23284-2030, USA
3Department of Biochemistry and Institute of Structural Biology and Drug Discovery, Virginia Commonwealth University, Richmond, VA 23219, USA

Received 6 June 2013; Accepted 26 June 2013

Academic Editor: Alessandro Paiardini

Copyright © 2013 Martino L. Di Salvo 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. V. Schirch, Mechanism of Folate-Requiring Enzymes in One-Carbon Metabolism, vol. 1, Academic Press, San Diego, Calif, USA, 1998.
  2. R. Florio, M. L. Di Salvo, M. Vivoli, and R. Contestabile, “Serine hydroxymethyltransferase: a model enzyme for mechanistic, structural, and evolutionary studies,” Biochimica et Biophysica Acta, vol. 1814, no. 11, pp. 1489–1495, 2011. View at Publisher · View at Google Scholar · View at Scopus
  3. A. Amadasi, M. Bertoldi, R. Contestabile et al., “Pyridoxal 5′-phosphate enzymes as targets for therapeutic agents,” Current Medicinal Chemistry, vol. 14, no. 12, pp. 1291–1324, 2007. View at Publisher · View at Google Scholar · View at Scopus
  4. F. Daidone, R. Florio, S. Rinaldo et al., “In silico and in vitro validation of serine hydroxymethyltransferase as a chemotherapeutic target of the antifolate drug pemetrexed,” European Journal of Medicinal Chemistry, vol. 46, no. 5, pp. 1616–1621, 2011. View at Publisher · View at Google Scholar · View at Scopus
  5. M. L. di Salvo, R. Contestabile, A. Paiardini, and B. Maras, “Glycine consumption and mitochondrial serine hydroxymethyltransferase in cancer cells: the heme connection,” Medical Hypotheses, vol. 80, pp. 633–636, 2013. View at Publisher · View at Google Scholar
  6. P. Stover and V. Schirch, “Enzymatic mechanism for the hydrolysis of 5,10-methenyltetrahydropteroylglutamate to 5-formyltetrahydropteroylglutamate by serine hydroxymethyltransferase,” Biochemistry, vol. 31, no. 7, pp. 2155–2164, 1992. View at Publisher · View at Google Scholar · View at Scopus
  7. M. L. di Salvo, R. Florio, A. Paiardini, M. Vivoli, S. D'Aguanno, and R. Contestabile, “Alanine racemase from Tolypocladium inflatum: a key PLP-dependent enzyme in cyclosporin biosynthesis and a model of catalytic promiscuity,” Archives of Biochemistry and Biophysics, vol. 529, pp. 55–65, 2013. View at Publisher · View at Google Scholar
  8. R. Contestabile, A. Paiardini, S. Pascarella, M. L. Di Salvo, S. D'Aguanno, and F. Bossa, “L-Threonine aldolase, serine hydroxymethyltransferase and fungal alanine racemase: a subgroup of strictly related enzymes specialized for different functions,” European Journal of Biochemistry, vol. 268, no. 24, pp. 6508–6525, 2001. View at Publisher · View at Google Scholar · View at Scopus
  9. V. Schirch and D. M. E. Szebenyi, “Serine hydroxymethyltransferase revisited,” Current Opinion in Chemical Biology, vol. 9, no. 5, pp. 482–487, 2005. View at Publisher · View at Google Scholar · View at Scopus
  10. G. Giardina, R. Montioli, S. Gianni et al., “Open conformation of human DOPA decarboxylase reveals the mechanism of PLP addition to Group II decarboxylases,” Proceedings of the National Academy of Sciences of the United States of America, vol. 108, no. 51, pp. 20514–20519, 2011. View at Publisher · View at Google Scholar · View at Scopus
  11. F. Malerba, A. Bellelli, A. Giorgi, F. Bossa, and R. Contestabile, “The mechanism of addition of pyridoxal 5′-phosphate to Escherichia coli apo-serine hydroxymethyltransferase,” Biochemical Journal, vol. 404, no. 3, pp. 477–485, 2007. View at Publisher · View at Google Scholar · View at Scopus
  12. L. Schirch, “Serine transhydroxymethylase: relaxation and transient kinetic study of the formation and interconversion of the enzyme glycine complexes,” Journal of Biological Chemistry, vol. 250, no. 5, pp. 1939–1945, 1975. View at Scopus
  13. C.-F. Cheng and J. L. Haslam, “A kinetic investigation of the interaction of serine transhydroxymethylase with glycine,” Biochemistry, vol. 11, no. 19, pp. 3512–3518, 1972. View at Scopus
  14. H. C. Dunathan, “Conformation and reaction specificity in pyridoxal phosphate enzymes,” Proceedings of the National Academy of Sciences of the United States of America, vol. 55, no. 4, pp. 712–716, 1966. View at Scopus
  15. L. Schirch, “Serine hydroxymethyltransferase,” Advances in Enzymology and Related Areas of Molecular Biology, vol. 53, pp. 83–112, 1982. View at Scopus
  16. S. Pascarella, S. Angelaccio, R. Contestabile, S. Delle Fratte, M. Di Salvo, and F. Bossa, “The structure of serine hydroxymethyltransferase as modeled by homology and validated by site-directed mutagenesis,” Protein Science, vol. 7, no. 9, pp. 1976–1982, 1998. View at Scopus
  17. S. Angelaccio, S. Pascarella, E. Fattori, F. Bossa, W. Strong, and V. Schirch, “Serine hydroxymethyltransferase: origin of substrate specificity,” Biochemistry, vol. 31, no. 1, pp. 155–162, 1992. View at Scopus
  18. M. Vivoli, F. Angelucci, A. Ilari et al., “Role of a conserved active site cation-π interaction in Escherichia coli serine hydroxymethyltransferase,” Biochemistry, vol. 48, no. 50, pp. 12034–12046, 2009. View at Publisher · View at Google Scholar · View at Scopus
  19. P. Baiocco, L. J. Gourlay, F. Angelucci et al., “Probing the Mechanism of GSH Activation in Schistosoma haematobium Glutathione-S-transferase by Site-directed Mutagenesis and X-ray Crystallography,” Journal of Molecular Biology, vol. 360, no. 3, pp. 678–689, 2006. View at Publisher · View at Google Scholar · View at Scopus
  20. J. N. Scarsdale, G. Kazanina, S. Radaev, V. Schirch, and H. T. Wright, “Crystal structure of rabbit cytosolic serine hydroxymethyltransferase at 2.8 Å resolution: mechanistic implications,” Biochemistry, vol. 38, no. 26, pp. 8347–8358, 1999. View at Publisher · View at Google Scholar · View at Scopus
  21. J. M. Goldberg, J. Zheng, H. Deng, Y. Q. Chen, R. Callender, and J. F. Kirsch, “Structure of the complex between pyridoxal 5′-phosphate and the tyrosine 225 to phenylalanine mutant of Escherichia coli aspartate aminotransferase determined by isotope-edited classical Raman difference spectroscopy,” Biochemistry, vol. 32, no. 32, pp. 8092–8097, 1993. View at Scopus
  22. V. Trivedi, A. Gupta, V. R. Jala et al., “Crystal structure of binary and ternary complexes of serine hydroxymethyltransferase from Bacillus stearothermophilus. Insights into the catalytic mechanism,” Journal of Biological Chemistry, vol. 277, no. 19, pp. 17161–17169, 2002. View at Publisher · View at Google Scholar · View at Scopus
  23. D. M. E. Szebenyi, F. N. Musayev, M. L. Di Salvo, M. K. Safo, and V. Schirch, “Serine hydroxymethyltransferase: role of Glu75 and evidence that serine is cleaved by a retroaldol mechanism,” Biochemistry, vol. 43, no. 22, pp. 6865–6876, 2004. View at Publisher · View at Google Scholar · View at Scopus
  24. T.-F. Fu, J. N. Scarsdale, G. Kazanina, V. Schirch, and H. T. Wright, “Location of the pteroylpolyglutamate-binding site on rabbit cytosolic serine hydroxymethyltransferase,” Journal of Biological Chemistry, vol. 278, no. 4, pp. 2645–2653, 2003. View at Publisher · View at Google Scholar · View at Scopus
  25. D. M. E. Szebenyi, X. Liu, I. A. Kriksunov, P. J. Stover, and D. J. Thiel, “Structure of a murine cytoplasmic serine hydroxymethyltransferase quinonoid ternary complex: evidence for asymmetric obligate dimers,” Biochemistry, vol. 39, no. 44, pp. 13313–13323, 2000. View at Publisher · View at Google Scholar · View at Scopus
  26. R. Contestabile, S. Angelaccio, F. Bossa et al., “Role of tyrosine 65 in the mechanism of serine hydroxymethyltransferase,” Biochemistry, vol. 39, no. 25, pp. 7492–7500, 2000. View at Publisher · View at Google Scholar · View at Scopus
  27. B. S. Bhavani, V. Rajaram, S. Bisht et al., “Importance of tyrosine residues of Bacillus stearothermophilus serine hydroxymethyltransferase in cofactor binding and l-allo-Thr cleavage: crystal structure and biochemical studies,” FEBS Journal, vol. 275, no. 18, pp. 4606–4619, 2008. View at Publisher · View at Google Scholar · View at Scopus
  28. M. L. Di Salvo, S. D. Fratte, D. De Biase, F. Bossa, and V. Schirch, “Purification and characterization of recombinant rabbit cytosolic serine hydroxymethyltransferase,” Protein Expression and Purification, vol. 13, no. 2, pp. 177–183, 1998. View at Publisher · View at Google Scholar · View at Scopus
  29. M. Otwinowski, “Processing of X-ray diffraction data collected in oscillation mode,” in Methods in Enzymology, W. Charles and J. Carter, Eds., Macromolecular Crystallography Part A, pp. 307–326, Elsevier, 1997.
  30. “The CCP4 suite: programs for protein crystallography,” Acta Crystallographica D, vol. 50, pp. 760–763, 1994. View at Publisher · View at Google Scholar
  31. P. Emsley and K. Cowtan, “Coot: model-building tools for molecular graphics,” Acta Crystallographica D, vol. 60, no. 12, pp. 2126–2132, 2004. View at Publisher · View at Google Scholar · View at Scopus
  32. 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. View at Scopus