Refined structure of transketolase from Saccharomyces cerevisiae at 2.0 Å resolution

Journal of Molecular Biology

Volumn 238, Issue 3, 1994, Pages 387-404

  Nikkola, Matti ^a   Lindqvist, Ylva ^a   Schneider, Gunter ^a  

^a SWEDISH UNIVERSITY OF AGRICULTURAL SCIENCES   (Sweden)

Author keywords

Crystal structure; Pyruvate dehydrogenase; Thiamine diphosphate; Transketolase; Yeast

Indexed keywords

SACCHAROMYCES CEREVISIAE;

COCARBOXYLASE; TRANSKETOLASE;

ARTICLE; CRYSTAL STRUCTURE; ENZYME STRUCTURE; NONHUMAN; PRIORITY JOURNAL; SACCHAROMYCES CEREVISIAE; X RAY ANALYSIS;

EID: 0028305456     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1994.1299     Document Type: Article

References (48)

1. Abedinia, M., Layfield, R., Jones, S. M., Nixon, P. S. & Mattick, J. S. (1992). Nucleotide and predicted amino acid sequence of a cDNA clone encoding part of human transketolase. Biochem. Biophys. Res. Commun. 183, 1159-1166.
2. Baker, E. N. & Hubbard, R. E. (1984). Hydrogen bonding in globular proteins. Progr. Biophys. Mol. Biol. 44, 97-179.
3. Blass, J. P. & Gibson, G. E. (1977). Abnormality of a thiamine-requiring enzyme in patients with Wernicke-Korsakoff syndrome. New Engl. J. Med. 197, 1367-1370.
4. Breslow, R. (1958). On the mechanism of thiamine action. IV. Evidence from studies on model systems. J. Amer. Chem. Soc. 80, 3719-3726.
5. Brünger, A. T. (1989). Crystallographic refinement by simulated annealing: application to crambin. Acta Crystallogr. sect. A. 45, 50-61.
6. Cavalieri, S. W., Neet, K. E. & Sable, H. Z. (1975). Enzymes of pentose biosynthesis. The quaternary structure and reacting form of transketolase from baker's yeast. Arch. Biochem. Biophys. 171, 527-532.
7. 2 fixation operon of Rhodobacter sphaeroides. J. Biol. Chem. 266, 20447-20452.
8. Datta, A. G. & Racker, E. (1961). Mechanism of action of transketolase. J. Biol. Chem. 236, 624-628.
9. De la Haba, G., Leder, I. G. & Racker, E. (1955). Crystalline transketolase from baker's yeast. Isolation and properties. J. Biol. Chem. 214, 409-426.
10. Dyda, F., Furey, W., Swaminathan, S., Sax, M., Farrenkopf, B. & Jordan, F. (1993). Catalytic centers in the thiamin diphosphate enzyme pyruvate decarboxylase at 2.4Å resolution. Biochemistry, 32, 6165-6170.
11. Egan, R. M. & Sable, H. Z. (1981). Transketolase kinetics. The slow reconstitution of the holoenzyme is due to rate-limiting dimerization of the subunits. J. Biol. Chem. 256, 4877-4883.
12. Heinrich, P. C., Steffen, H., Janser, P. & Wiss, O. (1972). Studies on the reconstitution of apotransketolase with thiamine pyrophosphate and analogs of the coenzyme. Eur. J. Biochem. 30, 533-541.
13. Horecker, B. L., Smyrniotis, P. Z. & Klenow, H. J. (1953). The formation of sedoheptulose phosphate from pentose phosphate. J. Biol. Chem. 205, 661-682.
14. Iida, A., Teshiba, S. & Mizobuchi, K. (1993). Identification and characterization of the tktB gene encoding a second transketolase in Escherichia coli K-12. J. Bacteriol. 175, 5375-5383.
15. Janin, J., Miller, S. & Chothia, C. (1988). Surface, subunit interfaces and interior of oligometric proteins. J. Mol. Biol. 204, 155-164.
16. Janowicz, Z. A., Eckart, M. R., Drewke, C., Roggenkamp, R. O., Hollenberg, C. P., Maat, J., Ledeboer, A. M., Visser, C. & Verrips, C. T. (1985). Cloning and characterization of the DAS gene encoding the major methanol assimilatory enzyme from the methylotrophic yeast Hansenula polymorpha. Nucl. Acids Res. 13, 3034-3061.
17. Jones, T. A., Zou, J.-Y., Cowan, S. W. & Kjeldgaard, M. (1991). Methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr, sect. A, 47, 110-119.
18. Jordan, F., Chen, G., Nishikawa, S. & Wu, B. S. (1982). Potential roles of the aminopyrimidine ring in thiamin catalyzed reactions. Ann. N. Y. Acad. Sci. 378, 14-29.
19. Kabsch, W. & Sander, C. (1983). Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers, 22, 2577-2637.
20. Kleywegt, G. J. & Jones, T. A. (1994). Detection, delineation, measurement and display of cavities in Macromolecular structures. Acta Crystallogr. sect. D, in the press.
21. Kobori, Y., Myles, D. C. & Whitesides, G. M. (1992). Substrate specificity and carbohydrate synthesis using transketolase. J. Org. Chem. 57, 5899-5907.
22. Kochetov, G. A. (1982). Transketolase from yeast, rat liver and pig liver. Methods Enzymol. 90, 209-223.
23. Konareva, N. V., Kuranova, J. P., Mikhailov, A. M., Usmanov, R. A. & Kochetov, G. A. (1983). A preliminary X-ray study of baker's yeast transketolase. Biochem. Int. 6, 799-803.
24. Kraulis, P. (1991). MOLSCRTPT: a program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallogr. 24, 946-950.
25. Lapsys, N. M., Layfield, R., Baker, E., Callen, D. F., Sutherland, G. R., Abedinia, M., Nixon, P. F. & Mattick, J. S. (1992). Chromosomal location of the human transketolase gene. Cytogenet. Cell Genet. 61, 274-275.
26. Laskowski, R. A., MacArthur, M. W., Moss, D. S. & Thornton, J. M. (1993). PROCHECK: a program to check the stereochemical quality of protein structures. J. Appl. Crystallogr. 26, 283-291.
27. Lindqvist, Y., Schneider, G., Ermler, U. & Sundström, M. (1992). Three-dimensional structure of transketolase, a thiamine disphosphate dependent enzyme, at 2.5Å resolution. EMBO J. 11, 2373-2379.
28. Luzzati, V. (1952). Traitement statistique des erreurs dans la détermination des structures cristallines. Acta Crystallogr. 5, 802-810.
29. McCool, B. A., Plonk, S. G., Martin, P. R. & Singleton, C. K. (1993). Cloning of the human transketolase cDNAs and comparison of the nucleotide sequence of the coding region in Wernicke-Korsakoff and non-Wernicke-Korsakoff individuals. J. Biol. Chem. 268, 1397-1404.
30. McDonald, I. K., Naylor, D., Jones, D. T. & Thornton, J. M. (1993). HBPLUS, Computer Programme, Department of Biochemistry and Molecular Biology, University College, London.
31. Meshalkina, L. E., Usmanov, R. A. & Kochetov, G. A. (1991). In Biochemistry and Physiology of Thiamin Disphosphate Dependent Enzymes (Bisswanger, H. & Ullrich, J., eds), pp. 343-352, Verlag Chemie, Weinheini.
32. Mukherjee, A. B., Svoronos, S., Ghazanfari, A., Martin, P. R., Fisher, A., Roechlein, R., Rodbard, D., Staton, R., Behar, D., Berg, C. J. & Manjunath, R. (1987). Transketolase abnormality in cultured fibroplasts from familial chronic alcoholic men and their male offspring. J. Clin. Invest. 79, 1039-1043.
33. Muller, Y. A. & Schulz, G. E. (1993). Structure of the thiamine- and flavin-dependent enzyme pyruvate oxidase. Science, 259, 965-967.
34. Muller, Y. A., Lindqvist, Y., Furey, W., Schulz, G. E., Jordan, F. & Sehneider, G. (1993). A thiamin diphosphate binding fold revealed by comparison of the crystal structures of transketolase, pyruvate oxidase and pyruvate decarboxylase. Structure, 1, 95-103.
35. Nilsson, U., Lindqvist, Y., Kluger, R. & Schneider, G. (1993). Crystal structure of transketolase in complex with thiamine thiazolone diphosphate, an analogue of the reaction intermediate, at 2.3Å resolution. FEBS Letters, 326, 145-148.
36. Pletcher, J. & Sax, M. (1972). Crystal and molecular structure of thiamine pyrophosphate hydrochloride. J. Amer. Chem. Soc. 94, 3998-4005.
37. Radnis, B. A., Rhee, D. K. & Morrison, D. A. (1990). Genetic transformation in Streptococcus pneumoniae: nucleotide sequence and predicted amino acid sequence of recP. J. Bacteriol. 172, 3669-3674.
38. Schellenberger, A. (1982). The amino group and steric factors in thiamin catalysis. Ann. N. Y. Acad. Sci. 378, 51-62.
39. 14 is a useful cluster compound for isomorphous replacement in protein crystallography. Acta Crystallogr, in the press.
40. Schneider, G. & Lindqvist, Y. (1993b). Enzymatic thiamine catalysis: mechanistic implications from the three-dimensional structure of transketolase. Bioorg. Chem. 21, 109-117.
41. Schneider, G., Sundström, M. & Lindqvist, Y. (1989). Preliminary crystallographic data for transketolase from yeast. J. Biol. Chem. 264, 21629-21620.
42. Shin, W., Pletcher, J., Sax, M. & Blank, G. (1979). Crystal and molecular structure of oxythiamin chloride hydrochloride monohydrate. A thiamin antagonist with a conformation that differs from thiamin. J. Amer. Chem. Soc. 99, 1396-1403.
43. Sprenger, G. A. (1992). EMBL Data Bank, rel. 33, X68025.
44. Srere, P., Cooper, J. R., Tabachnick, M. & Racker, E. (1958). The oxidative pentose phosphate cycle. I. Preparation of substrates and enzymes. Arch. Biochem. Biophys. 74, 295-305.
45. Stephens, P. E., Darlison, M. G., Lewis, H. M. & Guest, J. R. (1983). The pyruvate dehydrogenase complex of Escherichia coli K-12. Nucleotide sequence encoding the pyruvate dehydrogenase component. Eur. J. Biochem. 191, 337-346.
46. Sundström, M., Lindqvist, Y. & Schneider, G. (1992). Three-dimensional structure of apotransketolase. Flexible loops at the active site enable cofactor binding. FEBS Letters, 313, 229-231.
47. Sundström, M., Lindqvist, Y., Sehneider, G., Hellman, U. & Ronne, H. (1993). Yeast TKL1 encodes a transketolase that is required for efficient glycolysis and biosynthesis of aromatic amino acids. J. Biol. Chem. 268, 24346-24352.
48. Toone, E. J., Simon, E. S., Bednarski, M. D. & Whitesides, G. M. (1989). Enzyme-catalyzed synthesis of carbohydrates. Tetrahedron, 45, 5365-5420.