Theoretical studies on the common catalytic mechanism of transketolase by using simplified models

Journal of Molecular Graphics and Modelling

Volumn 39, Issue , 2013, Pages 23-28

  Sheng, Xiang ^a   Liu, Yongjun ^a,b   Liu, Chengbu ^a  

^a SHANDONG UNIVERSITY   (China)

^b NORTHWEST INSTITUTE OF PLATEAU BIOLOGY   (China)

Author keywords

2 Carbon fragment transfer; Density functional theory (DFT) method; Reaction mechanism; ThDP dependent enzyme; Transketolase

Indexed keywords

AMINO ACIDS; CATALYSIS; CHEMICAL BONDS; PROTON TRANSFER; QUANTUM CHEMISTRY; THORIUM COMPOUNDS;

2-CARBON FRAGMENT TRANSFER; CALCULATION RESULTS; CATALYTIC MECHANISMS; DENSITY FUNCTIONAL THEORY METHODS; PROTON TRANSFER PROCESS; REACTION MECHANISM; TRANSFER MECHANISMS; TRANSKETOLASE;

DENSITY FUNCTIONAL THEORY;

CARBON; HISTIDINE; PROTON; TRANSKETOLASE;

ARTICLE; CATALYSIS; CHEMICAL BOND; COMPUTATIONAL FLUID DYNAMICS; CONTROLLED STUDY; DENSITY FUNCTIONAL THEORY; ENZYME ACTIVE SITE; MOLECULAR MECHANICS; PRIORITY JOURNAL; PROTEIN CLEAVAGE; PROTON TRANSPORT; THEORETICAL STUDY;

EID: 84870307937     PISSN: 10933263     EISSN: 18734243     Source Type: Journal    
DOI: 10.1016/j.jmgm.2012.11.001     Document Type: Article

References (52)

1. R. Kluger Thiamin diphosphate: a mechanistic update on enzymic and nonenzymic catalysis of decarboxylation Chemical Reviews 87 1987 863 876
2. A. Schellenberger Sixty years of thiamin diphosphate biochemistry Biochimica et Biophysica Acta 1385 1998 177 186
3. R.A.W. Frank, F.J. Leeper, and B.F. Luisi Structure, mechanism and catalytic duality of thiamine-dependent enzymes Cellular and Molecular Life Sciences 64 2007 892 905
4. F. Jordan Current mechanistic understanding of thiamin diphosphate-dependent enzymatic reactions Natural Products Reports 20 2003 184 201
5. Y. Lindqvist, G. Schneider, U. Ermler, and M. Sundström Three-dimensional structure of transketolase, a thiamine diphosphate dependent enzyme, at 2.5 resolution EMBO Journal 11 1992 2373 2379
6. M. Nikkola, Y. Lindqvist, and G. Schneider Refined structure of transketolase from Saccharomyces cerevisiae at 2.0 resolution Journal of Molecular Biology 238 1994 387 404
7. G. Schneider, and Y. Lindqvist Crystallography and mutagenesis of transketolase: mechanistic implications for enzymatic thiamin catalysis Biochimica et Biophysica Acta 1385 1998 387
8. M.V. Kovina, and G.A. Kochetov Cooperativity and flexibility of active sites in homodimeric transketolase FEBS Letters 440 1998 81 84
9. G. Schenk, R.G. Duggleby, and P.F. Nixon Properties and functions of the thiamin diphosphate dependent enzyme transketolase International Journal of Biochemistry and Cell Biology 30 1998 1297 1318
10. C.M. Sax, C. Salamon, W.T. Kays, J. Guo, F.X. Yu, R.A. Cuthbertson, and J. Piatigorsky Transketolase is a major protein in the mouse cornea Journal of Biological Chemistry 271 1996 33568 33574
11. L.G. Boros, J. Puigjaner, M. Cascante, W.N. Paul Lee, J.L. Brandes, S. Bassilian, F.I. Yusuf, R.D. Williams, P. Muscarella, W.S. Melvin, and W.J. Schirmer Oxythiamine and dehydroepiandrosterone inhibit the nonoxidative synthesis of ribose and tumor cell proliferation Cancer Research 57 1997 4242 4248
12. K. Alexander-Kaufman, and C. Harper Transketolase: observations in alcohol-related brain damage research International Journal of Biochemistry and Cell Biology 41 2009 717 720
13. S. Gerhardt, S. Echt, M. Busch, J. Freigang, G. Auerbach, G. Bader, W.F. Martin, A. Bacher, R. Huber, and M. Fischer Structure and properties of an engineered transketolase from maize Plant Physiology 132 2003 1941 1949
14. P. Asztalos, C. Parthier, R. Golbik, M. Kleinschmidt, G. Hübner, M.S. Weiss, R. Friedemann, G. Wille, and K. Tittmann Strain and near attack conformers in enzymic thiamin catalysis: X-ray crystallographic snapshots of bacterial transketolase in covalent complex with donor ketoses cylulose 5-phosphate and fructose 6-phosphate, and in noncovalent complex with acceptor aldose ribose 5-phosphate Biochemistry 46 2007 12037 12052
15. N.J. Veitch, D.A. Maugeri, J.J. Cazzulo, Y. Lindqvist, and M.P. Barrett Transketolase from Leishmania mexicana has a dual subcellular localization Biochemical Journal 382 2004 759 767
16. L. Mitschke, C. Parthier, K. Schröeder-Tittmann, J. Coy, S. Lüdtke, and K. Tittmann The crystal structure of human transketolase and new insights into its mode of action Journal of Biological Chemistry 285 2010 31559 31570
17. M. Sundström, Y. Lindqvist, G. Schneider, U. Hellman, and H. Ronne Yeast TKL1 gene encodes a transketolase that is required for efficient glycolysis and biosynthesis of aromatic amino acids Journal of Biological Chemistry 268 1993 24346 24352
18. G.A. Sprenger, U. Schörken, G. Sprenger, and H. Sahm Transketolase a of Escherichia coli K12 European Journal of Biochemistry 230 1995 525 532
19. B.A. McCool, S.G. Plonk, P.R. Martin, and C.K. Singleton Cloning of human transketolase cDNAs and comparison of the nucleotide sequence of the coding region in Wernicke-Korsakoff and non-Wernicke-Korsakoff individuals Journal of Biological Chemistry 268 1993 1397 1404
20. E. Fullam, F. Pojer, T. Bergfors, T.A. Jones, and S.T. Cole Structure and function of the transketolase from Mycobacterium tuberculosis and comparison with the human enzyme Open Biology 2 2012 110026
21. K. Tittmann, R. Golbik, K. Uhlemann, L. Khailova, G. Schneider, M. Patel, F. Jordan, D.M. Chipman, R.G. Duggleby, and G. Hübner NMR analysis of covalent intermediates in thiamin diphosphate enzymes Biochemistry 42 2003 7885 7891
22. C. Wikner, U. Nilsson, L. Meshalkina, C. Udekwu, Y. Lindqvist, and G. Schneider Identification of catalytically important residues in yeast transketolase Biochemistry 36 1997 15643 15649
23. O.A. Esakova, L.E. Meshalkina, R. Golbik, G. Hübner, and G.A. Kochetov Donor substrate regulation of transketolase European Journal of Biochemistry 271 2004 4189 4194
24. M. Killenberg-Jabs, S. Köenig, I. Eberhardt, S. Hohmann, and G. Hübner Role of Glu51 for cofactor binding and catalytic activity in pyruvate decarboxylase from yeast studied by site-directed mutagenesis Biochemistry 36 1997 1900 1905
25. G.A. Kochetov, and I.A. Sevostyanova Binding of the coenzyme and formation of the transketolase active center IUBMB Life 57 2005 491 497
26. I.A. Sevostyanova, V.A. Selivanov, V.A. Yurshev, O.N. Solovjeva, S.V. Zabrodskaya, and G.A. Kochetov Cooperative binding of substrates to transketolase from Saccharomyces cerevisiae Biochemistry (Moscow) 74 2009 789 792
27. V.A. Selivanov, M.V. Kovina, N.V. Kochevova, L.E. Meshalkina, and G.A. Kochetov Kinetic study of the H103A mutant yeast transketolase FEBS Letters 567 2004 270 274
28. C. Wikner, L. Meshalkina, U. Nilsson, S. Bäckström, Y. Lindqvist, and G. Schneider His103 in yeast transketolase is required for substrate recognition and catalysis European Journal of Biochemistry 233 1995 750 755
29. J.Y. Wang, H. Dong, S.H. Li, and H.W. He Theoretical study toward understanding the catalytic mechanism of pyruvate decarboxylase Journal of Physical Chemistry B 109 2005 18664 18672
30. Q.Q. Hou, J. Gao, Y.J. Liu, and C.B. Liu A QM/MM study on the catalytic mechanism of pyruvate decarboxylase Theoretical Chemistry Accounts 131 2012 1280
31. 2α bond cleavage in thiamin catalysis Journal of Molecular Catalysis B 61 2009 36 38
32. R.S. Assary, and L.J. Broadbelt Computatinal screening of novel thiamine-catalyzed decarboxylation reactions of 2-keto acids Bioprocess and Biosystems Engineering 34 2011 375 388
33. J. Gonzalo, J. Verónica, V. Jordi, P. Xavier, D. Eduardo, and B.A. Joel A QM/MM study on the last steps of the catalytic cycle of acetohydroxyacid synthase Computational and Theoretical Chemistry 966 2011 159 166
34. - intermediate Proteins 78 2010 1774 1788
35. Y. Xiong, J.J. Liu, G.F. Yang, and C.G. Zhan Computational determination of fundamental pathway and activation barriers for acetohydroxyacid synthase-catalyzed condensation reactions of α-keto acids Journal of Computational Chemistry 31 2010 1592 1602
36. A.D. Becke Density-functional exchange-energy approximation with correct asymptotic behavior Physical Review A 38 1988 3098 3100
37. A.D. Becke Density-functional thermochemistry. I. The effect of the exchange-only gradient correction Journal of Chemical Physics 96 1992 2155 2160
38. A.D. Becke Density-functional thermochemistry. II. The effect of the Perdew-Wang generalized-gradient correlation correction Journal of Chemical Physics 97 1992 9173 9177
39. A.D. Becke Density-functional thermochemistry. III. The role of exact exchange Journal of Chemical Physics 98 1993 5648 5652
40. C. Lee, W. Yang, and R.G. Parr Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density Physical Review B 37 1998 785 789
41. B. Miehlich, A. Savin, H. Stoll, and H. Preuss Results obtained with the correlation energy density functionals of Becke and Lee, Yang and Parr Chemical Physics Letters 157 1989 200 206
42. M.A. Khan, R. Lo, T. Bandyopadhyay, and B. Ganguly Probing the reactivation process of sarin-inhibited acetylcholinesterase with α-nucleophiles: hydroxylamine anion is predicted to be a better antidote with DFT calculations Journal of Molecular Graphics and Modelling 29 2011 1039 1046
43. M. Frisch Gaussian 03, Revision D.01 2004 Gaussian Inc. Wallingford, CT
44. G.M. Morris, D.S. Goodsell, R.S. Halliday, R. Huey, W.E. Hart, R.K. Belew, and A.J. Olson Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function Journal of Computational Chemistry 19 1998 1639 1662
45. V. Barone, M. Cossi, and J. Tomasi Geometry optimization of molecular structures in solution by the polarizable continuum model Journal of Computational Chemistry 19 1998 404 417
46. J. Tomasi, and M. Persico Molecular interactions in solution: an overview of methods based on continuous distributions of the solvent Chemical Reviews 94 1994 2027 2094
47. D. Kern, G. Kern, H. Neef, K. Tittmann, M. Killenberg-Jabs, C. Wikner, G. Schneider, and G. Hübner How thiamine diphosphate is activated in enzymes Science 275 1997 67 70
48. G. Hübner, K. Tittmann, M. Killenberg-Jabs, J. Schäffner, M. Spinka, H. Neef, D. Kern, G. Kern, G. Schneider, C. Wikner, and S. Ghisla Activation of thiamin diphosphate in enzymes Biochimica et Biophysica Acta 1385 1998 221 228
49. K. Tittmann, K. Mesch, M. Pohl, G. Hübner, K. Tittmann, K. Mesch, M. Pohl, and G. Hübner Activation of thiamine diphosphate in pyruvate decarboxylase from Zymomonas mobilis FEBS Letters 441 1998 404 406
50. A. Bar-Ilan, V. Balan, K. Tittmann, R. Golbik, M. Vyazmensky, G. Hübner, Z. Barak, and D.M. Chipman Binding and activation of thiamin diphosphate in acetohydroxyacid synthase Biochemitry 40 2001 11946 11954
51. Y.A. Muller, Y. Lindqvist, W. Furey, G.E. Schuza, F. Jordan, and G. Schneider A thiamin diphosphate binding fold revealed by comparison of the crystal structures of transketolase pyruvate oxidase and pyruvate decarboxylase Structure 1 1992 93 103
52. Y.A. Muller, and G.E. Schulz Structure of the thiamine- and flavin-dependent enzyme pyruvate oxidase Science 259 1993 965 967