The mechanism of addition of pyridoxal 5′-phosphate to Escherichia coli apo-serine hydroxymethyltransferase

Biochemical Journal

Volumn 404, Issue 3, 2007, Pages 477-485

  Malerba, Francesca ^a   Bellelli, Andrea ^a   Giorgi, Alessandra ^a   Bossa, Francesco ^a   Contestabile, Roberto ^a  

^a SAPIENZA UNIVERSITY OF ROME   (Italy)

Author keywords

Cofactor addition; Escherichia coli; Fold type i enzyme; Folding pathway; Pyridoxal 5 phosphate; Serine hydroxymethyltransferase

Indexed keywords

COFACTOR ADDITION; FOLD-TYPE I ENZYME; FOLDING PATHWAY;

CONFORMATIONS; ENZYMES; ESCHERICHIA COLI; PHOSPHATES; POLYMERS;

AROMATIC HYDROCARBONS;

ALDEHYDE; APO SERINE HYDROXYMETHYLTRANSFERASE; APOENZYME; GLYCINE HYDROXYMETHYLTRANSFERASE; HOLOENZYME; PYRIDOXAL 5 PHOSPHATE; UNCLASSIFIED DRUG;

ARTICLE; BINDING SITE; CONTROLLED STUDY; ENZYME ASSAY; ENZYME CONFORMATION; ENZYME KINETICS; ESCHERICHIA COLI; FLOW KINETICS; NONHUMAN; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN FOLDING; PROTEIN STRUCTURE;

APOENZYMES; BINDING SITES; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; GLYCINE HYDROXYMETHYLTRANSFERASE; PROTEIN BINDING; PROTEIN FOLDING; PYRIDOXAL PHOSPHATE; VITAMIN B COMPLEX;

ESCHERICHIA COLI;

EID: 34250789658     PISSN: 02646021     EISSN: None     Source Type: Journal    
DOI: 10.1042/BJ20061681     Document Type: Article

References (43)

1. Higgins, C. L., Muralidhara, B. K. and Wittung-Stafshede, P. (2005) How do cofactors modulate protein folding? Protein Pept. Lett. 12, 165-170
2. Wittung-Stafshede, P. (2002) Role of cofactors in protein folding. Acc. Chem. Res. 35, 201-208
3. Wittung-Stafshede, P. (2004) Role of cofactors in folding of the blue-copper protein azurin. Inorg. Chem. 43, 7926-7933
4. Bettati, S., Benci, S., Campanini, B., Raboni, S., Chirico, G., Beretta, S., Schnackerz, K. D., Hazlett, T. L., Gratton, E. and Mozzarelli, A. (2000) Role of pyridoxal 5′-phosphate in the structural stabilization of O-acetylserine sulfhydrylase. J. Biol. Chem. 275, 40244-40251
5. Groha, C., Bartholmes, P. and Jaenicke, R. (1978) Refolding and reactivation of Escherichia coli tryptophan synthase β2 subunit after inactivation and dissociation in guanidine hydrochloride at acidic pH. Eur. J. Biochem. 92, 437-441
6. Herold, M. and Leistler, B. (1992) Coenzyme binding of a folding intermediate of aspartate aminotransferase detected by HPLC fluorescence measurements. FEBS Lett. 308, 26-29
7. Bertoldi, M., Cellini, B., Laurents, D. V. and Borri Voltattorni, C. (2005) Folding pathway of the pyridoxal 5′-phosphate C-S lyase MalY from Escherichia coli. Biochem. J. 389, 885-898
8. Cai, K., Schirch, D. and Schirch, V. (1995) The affinity of pyridoxal 5′-phosphate for folding intermediates of Escherichia coli serine hydroxymethyltransferase. J. Biol. Chem. 270, 19294-19299
9. Grishin, N. V., Phillips, M. A. and Goldsmith, E. J. (1995) Modeling of the spatial structure of eukaryotic ornithine decarboxylases. Protein Sci. 4, 1291-1304
10. Fu, T. F., di Salvo, M. and Schirch, V. (2001) Distribution of B6 vitamers in Escherichia coli as determined by enzymatic assay. Anal. Biochem. 298, 314-321
11. Cai, K. and Schirch, V. (1996) Structural studies on folding intermediates of serine hydroxymethyltransferase using fluorescence resonance energy transfer. J. Biol. Chem. 271, 27311-27320
12. Cai, K. and Schirch, V. (1996) Structural studies on folding intermediates of serine hydroxymethyltransferase using single tryptophan mutants. J. Biol. Chem. 271, 2987-2994
13. Fu, T. F., Boja, E. S., Safo, M. K. and Schirch, V. (2003) Role of proline residues in the folding of serine hydroxymethyltransferase. J. Biol. Chem. 278, 31088-31094
14. Scarsdale, J. N., Radaev, S., Kazanina, G., Schirch, V. and Wright, H. T. (2000) Crystal structure at 2.4 Å resolution of E. coli serine hydroxymethyltransferase in complex with glycine substrate and 5-formyl tetrahydrofolate. J. Mol. Biol. 296, 155-168
15. Churchich, J. E. and Farrelly, J. G. (1968) Reconstitution of aspartate aminotransferase from pig heart. Biochem. Biophys. Res. Commun. 31, 316-321
16. Verge, D. and Arrio-Dupont, M. (1981) Interactions between apoaspartate aminotransferase and pyridoxal 5′-phosphate: a stopped-flow study. Biochemistry 20, 1210-1216
17. Toney, M. D. and Kirsch, J. F. (1991) Kinetics and equilibria for the reactions of coenzymes with wild type and the Y70F mutant of Escherichia coli aspartate aminotransferase. Biochemistry 30, 7461-7466
18. O'Leary, M. H. and Malik, J. M. (1972) Kinetics and mechanism of the binding of pyridoxal 5′-phosphate to apoglutamate decarboxylase: evidence for a rate-determining conformation change. J. Biol. Chem. 247, 7097-7105
19. Erez, T., Phillips, R. S. and Parola, A. H. (1998) Pyridoxal phosphate binding to wild type, W330F, and C298S mutants of Escherichia coli apotryptophanase: unraveling the cold inactivation. FEBS Lett. 433, 279-282
20. Iurescia, S., Condo, I., Angelaccio, S., Delle Fratte, S. and Bossa, F. (1996) Site-directed mutagenesis techniques in the study of Escherichia coli serine hydroxymethyltransferase. Protein Expression Purif. 7, 323-328
21. Schirch, V. (1997) Purification of folate-dependent enzymes from rabbit liver. Methods Enzymol. 281, 146-161
22. Fischer, E. H., Kent, A. B., Snyder, E. R. and Krebs, E. G. (1958) The reaction of sodium borohydrate with muscle phosphorylase. J. Am. Chem. Soc. 80, 2906-2907
23. Schirch, V., Hopkins, S., Villar, E. and Angelaccio, S. (1985) Serine hydroxymethyltransferase from Escherichia coli: purification and properties. J. Bacteriol. 163, 1-7
24. Schirch, L. and Peterson, D. (1980) Purification and properties of mitochondrial serine hydroxymethyltransferase. J. Biol. Chem. 255, 7801-7806
25. Cornish-Bowden, A. (1995) Fundamentals of Enzyme Kinetics, pp. 1-6, 216, 289, Portland Press, London
26. Hajós, A. (1979) Complex Hydrides and Related Reducing Agents in Organic Synthesis, Elsevier, New York
27. Hughes, R. C., Jenkins, W. T. and Fischer, E. H. (1962) The site of binding of pyridoxal-5′-phosphate to heart glutamic-aspartic transaminase. Proc. Natl. Acad. Sci. U.S.A. 48, 1615-1618
28. Motulsky, H. (1995) Intuitive Biostatistics, Oxford University Press, Oxford
29. Henry, E. R. and Hofrichter, J. (1992) Singular value decomposition: application to analysis of experimental data. Methods Enzymol. 210, 129-193
30. Bevington, P. R. (1969) Data Reduction and Error Analysis for the Physical Sciences, p. 206, McGraw-Hill, New York
31. Harris, C. M., Johnson, R. J. and Metzler, D. E. (1976) Band-shape analysis and resolution of electronic spectra of pyridoxal phosphate and other 3-hydroxypyridine-4-aldehydes. Biochim. Biophys. Acta 421, 181-194
32. Metzler, D. E., Harris, C. M., Johnson, R. J., Saino, D. B. and Thomson, J. A. (1973) Spectra of 3-hydroxypyridines: band-shape analysis and evaluation of tautomeric equilibria. Biochemistry 12, 5377-5392
33. Johnson, R. J. and Metzler, D. E. (1970) Analyzing spectra of vitamin B6 derivatives. Methods Enzymol. 18A, 433-471
34. Metzler, C. M. and Metzler, D. E. (1987) Quantitative description of absorption spectra of a pyridoxal phosphate-dependent enzyme using lognormal distribution curves. Anal. Biochem. 166, 313-327
35. Fu, T. F., Scarsdale, J. N., Kazanina, G., Schirch, V. and Wright, H. T. (2003) Location of the pteroylpolyglutamate-binding site on rabbit cytosolic serine hydroxymethyltransferase. J. Biol. Chem. 278, 2645-2653
36. Webb, H. K. and Matthews, R. G. (1995) 4-Chlorothreonine is substrate, mechanistic probe, and mechanism-based inactivator of serine hydroxymethyltransferase. J. Biol. Chem. 270, 17204-17209
37. Ahrens, M. L., Maass, G., Schuster, P. and Winkler, H. (1970) Kinetic study of the hydration mechanism of vitamin B6 and related compounds. J. Am. Chem. Soc. 92, 6134-6139
38. Minelli, A., Charteris, A. T., Voltattorni, C. B. and John, R. A. (1979) Reactions of DOPA (3,4-dihydroxyphenylalanine) decarboxylase with DOPA. Biochem. J. 183, 361-368
39. Hayashi, H., Mizuguchi, H. and Kagamiyama, H. (1993) Rat liver aromatic L-amino acid decarboxylase: spectroscopic and kinetic analysis of the coenzyme and reaction intermediates. Biochemistry 32, 812-818
40. Hayashi, H., Tsukiyama, F., Ishii, S., Mizuguchi, H. and Kagamiyama, H. (1999) Acid-base chemistry of the reaction of aromatic L-amino acid decarboxylase and dopa analyzed by transient and steady-state kinetics: preferential binding of the substrate with its amino group unprotonated. Biochemistry 38, 15615-15622
41. Goldberg, J. M., Zheng, J., Deng, H., Chen, Y. Q., Callender, R. and Kirsch, J. F. (1993) 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 32, 8092-8097
42. m. Biochemistry 30, 305-312
43. Kallen, R. G., Korpela, T., Martell, A. E., Matsushima, Y., Metzler, C. M., Metzler, D. E., Morozov, Y. V., Ralston, I. M., Savin, F. A., Torchinsky, Y. M. and Ueno, I. (1985) Chemical and spectroscopic properties of pyridoxal and pyridoxamine phosphates. In Transaminases (Christen, P. and Metzler, D. E., eds), Wiley Interscience, New York