Effect of coenzyme modification on the structural and catalytic properties of wild-type transketolase and of the variant E418A from Saccharomyces cerevisiae: Contrasting protonation state requirements of thiamin diphosphate in decarboxylases and transketolases

FEBS Journal

Volumn 272, Issue 6, 2005, Pages 1326-1342

  Golbik, Ralph ^a   Meshalkina, Ludmilla E ^b   Sandalova, Tatjana ^c   Tittmann, Kai ^a   Fiedler, Erik ^a   Neef, Holger ^a   König, Stephan ^a   Kluger, Ronald ^d   Kochetov, German A ^b   Schneider, Gunter ^c   Hübner, Gerhard ^a  

^a MARTIN LUTHER UNIVERSITY HALLE WITTENBERG   (Germany)

^b MOSCOW STATE UNIVERSITY   (Russian Federation)

^c KAROLINSKA INSTITUTE   (Sweden)

^d UNIVERSITY OF TORONTO   (Canada)

Author keywords

Intermediates; Stopped flow kinetics; Thiamin diphosphate analogues; Transketolase; X ray crystallography

Indexed keywords

4' METHYLAMINOTHIAMINE DIPHOSPHATE; AMINOPYRIDINE; COCARBOXYLASE; METHYL GROUP; PYROPHOSPHORIC ACID DERIVATIVE; TRANSKETOLASE; UNCLASSIFIED DRUG;

ARTICLE; CIRCULAR DICHROISM; COENZYME; CONTROLLED STUDY; ELECTRON TRANSPORT; ENZYME ACTIVE SITE; ENZYME CONFORMATION; ENZYME MODIFICATION; ENZYME STABILITY; ENZYME STRUCTURE; NONHUMAN; PRIORITY JOURNAL; PROTEIN METABOLISM; PROTEIN METHYLATION; SACCHAROMYCES CEREVISIAE; ULTRAVIOLET SPECTROSCOPY;

AMINO ACID SUBSTITUTION; BINDING SITES; CRYSTALLOGRAPHY, X-RAY; KINETICS; MUTATION, MISSENSE; PROTEIN CONFORMATION; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS; SPECTROPHOTOMETRY, ULTRAVIOLET; SUBSTRATE SPECIFICITY; TRANSKETOLASE;

SACCHAROMYCES CEREVISIAE;

EID: 20144389887     PISSN: 1742464X     EISSN: None     Source Type: Journal    
DOI: 10.1111/j.1742-4658.2005.04562.x     Document Type: Article

References (66)

1. Breslow R (1957) Rapid deuterium exchange in thiazolium salts. J Am Chem Soc 79, 1762-1763.
2. Sundstrøm M, Lindqvist Y & Schneider G (1992) Three-dimensional structure of apotransketolase. Flexible loops at the active site enable cofactor binding. FEBS Lett 313, 229-231.
3. Lindqvist Y, Schneider G, Ermler U & Sundstrøm M (1992) Three-dimensional structure of transketolase, a thiamine diphosphate dependent enzyme, at 2.5 A resolution. EMBO J 11, 2373-2379.
4. Nikkola M, Lindqvist Y & Schneider G (1994) Refined structure of transketolase from Saccharomyces cerevisiae at 2.0 Å resolution. J Mol Biol 238, 387-404.
5. Schneider G & Lindqvist Y (1998) Crystallography and mutagenesis of transketolase: mechanistic implications for enzymatic thiamin catalysis. Biochim Biophys Acta 1385, 387-398.
6. Horecker BL, Smyrniotis PZ & Klenow HJ (1953) The formation of sedoheptulose phosphate from pentose phosphate. J Biol Chem 205, 661-682.
7. Racker E (1961) Transketolase. In The Enzymes (Boyer PD, Lardy H & Myrbäck K, eds), Vol 5, pp. 397-406. Academic Press, New York.
8. Racker E, de la Haba G & Leder IG (1953) Thiamine pyrophosphate, a coenzyme of transketolase. J Am Chem Soc 75, 1010-1011.
9. Jordan F, Liu M, Sergienko E, Zhang Z, Brunskill A, Arjunan P & Furey W (2004) Yeast pyruvate decarboxylase: new features of the structure and mechanism. In Thiamine: Catalytic Mechanisms in Normal and Disease States (Jordan F & Patel, MS, eds), pp. 173-215. Marcel Dekker, Inc., New York, Basel.
10. König S, Schellenberger A, Neef H & Schneider G (1994) Specificity of coenzyme binding in thiamin diphosphate-dependent enzymes. Crystal structures of yeast transketolase in complex with analogs of thiamin diphosphate. J Biol Chem 269, 10879-10882.
11. Wikner C, Meshalkina L, Nilsson U, Nikkola M, Lindqvist Y, Sundstrøm M & Schneider G (1994) Analysis of an invariant cofactor-protein interaction in thiamin diphosphate-dependent enzymes by site-directed mutagenesis. Glutamic acid 418 in transketolase is essential for catalysis. J Biol Chem 269, 32144-32150.
12. Kochetov GA, Meshalkina LE & Usmanov RA (1976) The number of active sites in a molecule of transketolase. Biochem Biophys Res Commun 69, 839-843.
13. Kern D, Kern G, Neef H, Tittmann K, Killenberg-Jabs M, Wikner C, Schneider G & Hübner G (1997) How thiamine diphosphate is activated in enzymes. Science 275, 67-70.
14. Kochetov GA (1982) Transketolase from yeast, rat liver and pig liver. Methods Enzymol 90, 209-223.
15. Kochetov GA, Usmanov RA & Mevkh AT (1978) A new method of determination of transketolase activity by asymmetric synthesis reaction. Anal Biochem 88, 296-301.
16. Bykova IA, Solovjeva ON, Meshalkina LE, Kovina MV & Kochetov GA (2001) One-substrate transketolase-catalyzed reaction. Biochem Biophys Res Commun 280, 845-847.
17. Solovjeva ON, Bykova IA, Meshalkina LE, Kovina MV & Kochetov GA (2001) Cleaving of ketosubstrates by transketolase and the nature of the products formed. Biochemistry (Moscow) 66, 1144-1149.
18. Usmanov RA & Kochetov GA (1981) Determination of the activity of transketolase by the rate of reduction of hexacyanoferrate (III). A new method of quantitative determination of fructose-6-phosphate and some other keto compounds. Biochem Int 3, 33-39.
19. Tittmann K, Golbik R, Uhlemann K, Khailova L, Schneider G, Patel M, Jordan F, Chipman DM, Duggleby RG & Hübner G (2003) NMR analysis of covalent intermediates in thiamin diphosphate enzymes. Biochemistry 42, 7885-7891.
20. Schellenberger A, Hübner G & Neef H (1997) Cofactor designing in functional analysis of thiamin diphosphate enzymes. Methods Enzymol 279, 131-146.
21. Lindqvist Y, Meshalkina LE, Nilsson U, Schneider G & Wikner C (1996) Insights into enzymatic thiamin catalysis: structure and function of transketolase. In Biochemistry and Physiology of Thiamin Diphosphate Enzymes (Proceedings of the 4th International Meeting on the Function of Thiamin Diphosphate Enzymes held at the Heinrich-Fabri-Institut Blaubeuren, Germany, March 27-30). (Bisswanger H & Schellenberger A, eds), pp. 505-515. AuC Intemann, Wissenschaftlicher Verlag, Prien.
22. Heinrich CP, Noack K & Wiss O (1971) A circular dichroism study of transketolase from baker's yeast. Biochem Biophys Res Commun 44, 275-279.
23. Kochetov GA, Usmanov RA & Merzlov VP (1970) Thiamine pyrophosphate induced changes in the optical activity of baker's yeast transketolase. FEBS Lett 9, 265-266.
24. Meshalkina LE, Wikner C & Nilsson U (1996) CD spectra of recombinant wild-type and mutant transketolase. In Biochemistry and Physiology of Thiamin Diphosphate Enzymes (Proceedings of the 4th International Meeting on the Function of Thiamin Diphosphate Enzymes held at the Heinrich-Fabri-Institut Blaubeuren, Germany, March 27-30). (Bisswanger H & Schellenberger A, eds), pp. 532-542. AuC Intemann, Wissenschaftlicher Verlag, Prien.
25. Jordan F, Zhang Z & Sergienko E (2002) Spectroscopic evidence for participation of the 1′,4′-imino tautomer of thiamin diphosphate in catalysis by yeast decarboxylase. Bioorg Chem 30, 188-198.
26. Jordan F (2003) Current mechanistic understanding of thiamin diphosphate-dependent enzymatic reactions. Nat Prod Report 20, 184-201.
27. Kovina MV, Bykova IA, Solovjeva ON, Meshalkina LE & Kochetov GA (2002) The origin of the absorption band induced through the interaction between apotransketolase and thiamin diphosphate. Biochem Biophys Res Commun 294, 155-160.
28. Hübner G, Tittmann K, Killenberg-Jabs M, Schaffner J, Spinka M, Neef H, Kern D, Kern G, Schneider G, Wikner C et al. (1998) Activation of thiamin diphosphate in enzymes. Biochim Biophys Acta 1385, 221-228.
29. Pustynnikov MG, Neef H, Usmanov RA, Schellenberger A & Kochetov GA (1986) Functional groups of thiamine pyrophosphate in holotransketolase. Biokhimiya (Russia) 51, 1003-1016.
30. Fiedler E, Thorell S, Sandalova T, Golbik R, König S & Schneider G (2002) Snapshot of a key intermediate in enzymatic thiamin catalysis: crystal structure of the α-carbanion of (α,β-dihydroxyethyl)-thiamin diphosphate in the active site of transketolase from Saccharomyces cerevisiae. Proc Natl Acad Sci USA 99, 591-595.
31. Fiedler E (2002) Kinetische und strukturelle Untersuchungen zur Donorsubstrat- und Ligandenbindung an Transketolase aus Saccharomyces cerevisiae. PhD Thesis, Martin-Luther-Universität Halle-Wittenberg, Halle/Saale.
32. Chabriere E, Charon MH, Volbeda A, Pieulle L, Hatchikian EC & Fontecilla-Camps JC (1999) Crystal structures of the key anaerobic enzyme pyruvate: ferredoxin oxidoreductase, free and in complex with pyruvate. Nat Struct Biol 6, 182-190.
33. Hasson MS, Muscate A, McLeish MJ, Polovnikova LS, Gerlt JA, Kenyon GL, Petsko GA & Ringe D (1998) The crystal structure of benzoylformate decarboxylase at 1.6 Ångstrem resolution - diversity of catalytic residues in thiamin diphosphate-dependent enzymes. Biochemistry 37, 9918-9930.
34. Aevarsson A, Chuang JL, Wynn RM, Turley S, Chuang DT & Hol WGJ (2000) Crystal structure, of human branched-chain alpha-ketoacid dehydrogenase and the molecular basis of multienzyme complex deficiency in marple syrup urine disease. Struct Fold Des 8, 277-291.
35. Pang SS, Duggleby RG & Guddat LW (2002) Crystal structure of yeast acetohydroxyacid synthase: a target for herbicidal inhibitors. J Mol Biol 317, 249-262.
36. Arjunan P, Nemeria NS, Brunskill A, Chandrasekhar K, Sax M, Van Y, Jordan F, Guest JR & Furey W (2002) Structure of the pyruvate dehydrogenase multienzyme complex E1 component from Escherichia coli at 1.85 Å resolution. Biochemistry 41, 5213-5221.
37. Schütz A, Sandalova T, Ricagno S, Hübner G, König S & Schneider G (2003) Crystal structure of thiamindi-phosphate-dependent indolepyruvate decarboxylase from Enterobacter cloacae, an enzyme involved in the biosynthesis of plant hormone indole-3-acetic acid. Eur J Biochem 270, 2312-2321.
38. Muller YA, Schumacher G, Rudolph R & Schulz GE (1994) The refined structures of a stabilized mutant and of wild-type pyruvate oxidase from Lactobacillus plantarum. J Mol Biol 237, 315-335.
39. Arjunan P, Umland T, Dyda F, Swaminathan S, Furey W, Sax M, Farrenkopf B, Gao Y, Zhang D & Jordan F (1996) Crystal structure of the thiamin diphosphate-dependent enzyme pyruvate decarboxylase from the yeast Saccharomyces cerevisiae at 2.3 Å resolution. J Mol Biol 256, 590-600.
40. Aevarsson A, Seger K, Turley S, Sokatch JR & Hol WG (1999) Crystal structure of 2-oxoisovalerate and dehydrogenase and the architecture of 2-oxo acid dehydrogenase multienzyme complexes. Nat Struct Biol 6, 785-792.
41. Dobritzsch D, König S, Schneider G & Lu GG (1998) High resolution crystal structure of pyruvate decarboxylase from Zymomonas mobilis - implications for substrate activation in pyruvate decarboxylases. J Biol Chem 273, 20196-20204.
42. Ciszak EM, Korotchkina LG, Dominiak PM, Sidhu S & Patel MS (2003) Structural basis for flip-flop action of thiamin pyrophosphate-dependent enzymes revealed by human pyruvate dehydrogenase. J Biol Chem 278, 21240-21246.
43. Jordan F & Mariam YH (1978) N′-methylthiaminium diiodide. Model study on the effect of a coenzyme bound positive charge on reaction mechanisms requiring thiamin pyrophosphate. J Am Chem Soc 100, 2534-2541.
44. Eppendorfer S, König S, Golbik R, Neef H, Lehle K, Jaenicke R, Schellenberger A & Hübner G (1993) Effects of metal ions, thiamine diphosphate analogues and subunit interactions on the reconstitution behaviour of pyruvate decarboxylase from brewer's yeast. Biol Chem Hoppe-Seyler 374, 1129-1134.
45. Kobori Y, Myles DC & Whitesides GM (1992) Substrate specificity and carbohydrate synthesis using transketolase. J Org Chem 57, 5899-5907.
46. Sandalova T, Thorell S, Schneider G, Fiedler E, Golbik R & König S (2004) Structure of the α-carbanion/enamine reaction intermediate in the active site of transketolase, determined by kinetic crystallography. In Thiamine: Catalytic Mechanisms in Normal and Disease States (Jordan F & Patel MS, eds), pp. 159-171. Marcel Dekker, Inc., New York, Basel.
47. Kluger R, Lam JF, Pezacki JP & Yang CM (1995) Diverting thiamin from catalysis to destruction - mechanism of fragmentation of N(1′)-methyl-2- (1-hydroxybenzyl) thiamin. J Am Chem Soc 117, 11383-11389.
48. Kluger R & Moore IF (2000) Destruction of vitamin B1 by benzaldehyde. Reactivity of intermediates in the fragmentation of N1′-benzyl-2-(1- hydroxybenzyl) thiamin. J Am Chem Soc 122, 6145-6150.
49. Kluger R, Hu Q & Moore IF (2004) Benzoylformate decarboxylase: intermediates, transition states, and diversions. In Thiamine: Catalytic Mechanisms in Normal and Disease States (Jordan, F & Patel, MS, eds), pp. 291-308. Marcel Dekker, Inc., New York, Basel.
50. Schellenberger A (1967) Structure and mechanism of action of the active center of yeast pyruvate decarboxylase. Angew Chem (Intern, ed.) 6, 1024-1035.
51. Schellenberger A (1982) The amino group and steric factors in thiamin catalysis. Ann N Y Acad Sci 378, 51-62.
52. Schellenberger A (1998) Sixty years of thiamin diphosphate biochemistry. Biochim Biophys Acta 1385, 177-186.
53. Zoltewicz JA & Baugh TD (1980) An improved synthesis of 1′-methyl-thiaminium salts. Synthesis 3, 217-218.
54. Schellenberger A & Winter K (1966) Research on the function of the amino group in thiaminepyrophosphate (Cocarboxylase). 3. Synthesis and biochemical features of a 4′ varied analogue of thiaminepyrophosphate. Hoppe-Seylers Z Phys Chem 344, 16-24.
55. Schellenberger A, Müller V, Winter K & Hübner G (1966) On the theory of cocarboxylase action. II. Origin and fundamentals of a two-center mechanism of thiamine pyrophosphate action from research on models and enzymatic measurements, Hoppe-Seylers Z Phys Chem 344, 244-260.
56. Eppendorfer S (1991) Beiträge zur Affinität definierter Strukturelemente des Thiaminpyrophosphats und der Metallionen zum aktiven Zentrum der Hefe-Pyruvatde-carboxylase. PhD Thesis, Martin-Luther-University Halle-Wittenberg, Halle/Saale.
57. Sundstrøm M, Lindqvist Y, Schneider G, Hellmann U & Ronne H (1993) Yeast TKL1 gene encodes a transketolase that is required for efficient glycolysis and biosynthesis of aromatic amino acids. J Biol Chem 268, 24346-24352.
58. Erhardt E & Hollenberg CP (1983) The presence of a defensive LEU2 gene on 2 μ DNA recombinant plasmid of Saccharomyces cerevisiae is responsible for curing and high copy number. J Bacteriol 156, 625-635.
59. Fiedler E, Golbik R, Schneider G, Tittmann K, Neef H, König S & Hübner G (2001) Examination of donor substrate conversion in yeast transketolase. J Biol Chem 276, 16051-16058.
60. Gill SC & von Hippel PH (1989) Calculation of protein extinction coefficients from amino acid sequence data. Anal Biochem 182, 319-326.
61. Usmanov RA & Kochetov GA (1983) Binding of substrates to baker's yeast transketolase. Biokhimiya (Russia) 48, 478-484.
62. Kochetov GA, Usmanov RA & Mevkh AT (1973) The role of the charge transfer complex in the transketolase catalyzed reaction. Biochem Biophys Res Commun 54, 1619-1626.
63. Schneider G, Sundstrøm M & Lindqvist Y (1989) Preliminary crystallographic data for transketolase from yeast. J Biol Chem 264, 21619-21620.
64. Otwinowski Z (1993) In Proceedings of the CCP4 Study Weekend (Lawyer L, Isaacs N & Bailey S, eds), pp. 56-62. Daresbury Laboratory, Warrington, UK.
65. Jones TA, Zou J-Y & Cowan SW (1991) Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr A47, 110-119.
66. Brünger AT, Adams PD, Clore GM, DeLano WL, Gros P, Grosse-Kunstleve RW, Jiang J-S, Kuszewski J, Nilges M, Pannu NS et al. (1998) Crystallography & NMR system: a new software suite for macromolecular structure determination. Acta Crystallogr D54, 905-921.