Tetrahedral intermediates in thiamin diphosphate-dependent decarboxylations exist as a 1′,4′-imino tautomeric form of the coenzyme, unlike the Michaelis complex or the free coenzyme

Biochemistry

Volumn 43, Issue 21, 2004, Pages 6565-6575

  Nemeria, Natalia ^a   Baykal, Ahmet ^a   Joseph, Ebenezer ^a   Zhang, Sheng ^a   Yan, Yan ^a   Furey, William ^b,c   Jordan, Frank ^a  

^a State University   (United States)

^b VETERANS AFFAIRS MEDICAL CENTER   (United States)

^c UNIVERSITY OF PITTSBURGH SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CATALYSIS; CHARGE TRANSFER; ENZYMES; ESCHERICHIA COLI; ISOMERS; YEAST;

CIRCULAR DICHROISM; DECARBOXYLATION;

BIOCHEMICAL ENGINEERING;

1',4' IMINOPYRIMIDINE TAUTOMER; 2 AMINOPYRIMIDINE; 2ALPHA HYDROXYETHYLTHIAMINE DIPHOSPHATE; 2ALPHA LACTYLTHIAMINE DIPHOSPHATE; ACETALDEHYDE; COCARBOXYLASE; PYRIMIDINE; PYRUVATE DECARBOXYLASE; PYRUVIC ACID; THIAZOLE DERIVATIVE; THIAZOLIUM; UNCLASSIFIED DRUG;

ACID BASE BALANCE; ARTICLE; CATALYSIS; CIRCULAR DICHROISM; COENZYME; DECARBOXYLATION; ESCHERICHIA COLI; ISOMERISM; MICHAELIS CONSTANT; NONHUMAN; PRIORITY JOURNAL; TAUTOMER; TAUTOMERIC SHIFT;

BINDING SITES; CATALYSIS; CIRCULAR DICHROISM; COENZYMES; DECARBOXYLATION; FUNGAL PROTEINS; MODELS, CHEMICAL; MODELS, MOLECULAR; PHOSPHONOACETIC ACID; POINT MUTATION; PROTEIN CONFORMATION; PYRUVATE DECARBOXYLASE; PYRUVATE DEHYDROGENASE COMPLEX; THIAMINE PYROPHOSPHATE; TITRIMETRY;

ESCHERICHIA COLI;

EID: 2542557579     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi049549r     Document Type: Article

References (30)

1. Jordan, F. (2003) Current Mechanistic Understanding of Thiamin Diphosphate-Dependent Enzymatic Reactions, Nat. Prod. Rep. 20, 184-201.
2. Jordan, F., Liu, M., Sergienko, E., Zhang, Z., Brunskill, A., Arjunan, P., and Furey, W. (2004) Yeast Pyruvate Decarboxylase: New Features of the Structure and Mechanism, in Thiamine: Catalytic Mechanisms and Role in Normal and Disease States (Jordan, F. and Patel, M., Eds.) pp 173-215, Marcel Dekker, New York.
3. Furey, W., Arjunan, P., Brunskill, A., Chandrasekhar, K., Nemeria, N., Wei, W., Yan, Y., Zhang, Z., and Jordan, F. (2004) Structure and Intersubunit Information Transfer in the Escherichia coli Pyruvate Dehydrogenase Multienzyme Complex, in Thiamine: Catalytic Mechanisms and Role in Normal and Disease States (Jordan, F. and Patel, M., Eds.) pp 407 -432, Marcel Dekker, New York.
4. Jordan, F., Nemeria, N. S., Zhang, S., Yan, Y., Arjunan, P., and Furey, W. (2003) Dual Catalytic Apparatus of the Thiamin Diphosphate Coenzyme: Acid-base via the 1′,4′-Imino-pyrimidine Tautomer along with its Electrophilic Role, J. Am. Chem. Soc. 125, 12732-12738.
5. Nemeria, N., Yan, Y., Zhang, Z., Brown, A. M., Arjunan, P., Furey, W., Guest, J. R.and Jordan, F. (2001) Inhibition of the E. coli Pyruvate Dehydrogenase Complex-E1 Subunit and its Tyrosine 177 Variant by Thiamin 2-Thiazolone and Thiamin 2-Thiothiazolone Diphosphates: Evidence for Reversible Tight-binding Inhibition, J. Biol. Chem. 276, 45969-45978.
6. Dyda, F., Furey, W., Swaminathan, S., Sax, M., Farrenkopf, B., and Jordan, F. (1993) Catalytic Centers in the Thiamin Diphosphate Dependent Enzyme Pyruvate Decarboxylase at 2.4 Å Resolution, Biochemistry 32, 6165-6170.
7. Arjunan, P., Umland, T., Dyda, F., Swaminathan, S., Furey, W., Sax, M., Farrenkopf, B., Gao, Y., Zhang, D., and 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.
8. Arjunan, P., Nemeria, N., Brunskill, A., Chandrasekhar, K., Sax, M., Yan, Y., Jordan, F., Guest, J. R., and Furey, W. (2002) Structure of the Pyruvate Dehydrogenase Multienzyme Complex E1 Component from E. coli at 1.85 Å Resolution, Biochemistry 41, 5213-5221.
9. Arjunan, P., Chandrasekhar, K., Sax, M., Brunskill, A., Nemeria, N., Jordan, F., and Furey, W. (2004) Structural Features Determining Enzyme-Inhibitor Affinity: The E1 Component of Pyruvate Dehydrogenase from Escherichia coli in Complex with the Inhibitor Thiamin 2-Thiazolone Diphosphate, Biochemistry 43, 2405-2411.
10. Guo, F., Zhang, D., Kahyaoglou, A., Farid, R. S., and Jordan, F. (1998) Is a Hydrophobic Amino Acid Required to Maintain the Reactive V Conformation at the Active Center of Thiamin Diphosphate-Requiring Enzymes? Experimental and Computational Studies of Isoleucine 415 of Yeast Pyruvate Decarboxylase, Biochemistry 37, 13379-13391.
11. Sergienko, E. A., and Jordan, F. (2001) Catalytic Acid-Base Groups in Yeast Pyruvate Decarboxylase II. Insights to the Specific Roles of D28 and E477 From the Rates and Stereo-specificity of Formation of Carboligase Side Products, Biochemistry 40, 7369-7381.
12. Jordan, F., Zhang, Z., and Sergienko, E. (2002) Spectroscopic Evidence for Participation of the 1′,4′-Imino Tautomer of Thiamin Diphosphate in Catalysis by Yeast Pyruvate Decarboxylase, Bioorg. Chem. 30, 188-198.
13. Wikner, C., Nilsson, U., Meshalkina, L., Udekwu, C., Lindqvist, Y., and Schneider, G. (1997) Identification of Catalytically Important Residues in Yeast Transketolase, Biochemistry 36, 15643-15649.
14. Khailova, L. S., Korochkina, L. G., and Severin, S. E. (1989) Organization and Functioning of Muscle Pyruvate Dehydrogenase Active Centers, Ann. N. Y. Acad. Sci. 573, 36-54.
15. Kluger, R., and Wasserstein, P. (1973) Mechanism of Metal Ion Promoted Hydrogen Exchange Reactions. Magnesium(II) and Acetonyl Phosphonate, J. Am. Chem. Soc. 95, 1071-1044.
16. Gruys, K. J., Halkides, C. J., and Frey, P. A. (1987) Synthesis and Properties of 2-Acetylthiamin Pyrophosphate; An Enzymatic Reaction Intermediate, Biochemistry 26, 7575-7585.
17. Barletta, G. L., Huskey, W. P., and Jordan, F. (1997) Ionization Kinetics at the C2α Position of 2-Benzylthiazolium Salts Leading to Enamines Relevant to Thiamin Catalyzed Enzymatic Reactions, J. Am. Chem. Soc. 119, 2356-2362.
18. Yan, Y. (2003) Ph.D. Dissertation, Rutgers University Graduate Faculty at Newark, NJ.
19. Nemeria, N., Arjunan, P., Brunskill, A. Sheibani, F. Wei, W., Yan, Y., Zhang, S. Jordan, F., and Furey, W. (2002) Histidine 407, a Phantom Residue in the E1 Subunit of the Escherichia coli Pyruvate Dehydrogenase Complex, Activates Reductive Acetylation of Lipoamide on the E2 Subunit. An Explanation for Conservation of Active Sites between the E1 Subunit and Transketolase, Biochemistry 41, 15459-15467.
20. Li, H., Furey, W., and Jordan, F. (1999) Role of Glutamate 91 in Information Transfer during Substrate Activation of Yeast Pyruvate Decarboxylase, Biochemistry 38, 9992-10003.
21. Gao, Y. (2000) Ph.D. Dissertation, Rutgers University Graduate Faculty at Newark, NJ.
22. Liu, M. (2002) Ph.D. Dissertation, Rutgers University Graduate Faculty at Newark, NJ.
23. Nemeria, N., Volkov, A., Brown, A., Yi, J. Zipper, L., Guest, J. R., and Jordan, F. (1998) Systematic Study of all Six Cysteines of the E1 Subunit of the Pyruvate Dehydrogenase Multienzyme Complex from Escherichia coli: None is Essential for Activity, Biochemistry 37, 911-922.
24. Yi, J., Nemeria, N., McNally, A., Jordan, F., Guest, J. R., and Machado, R. (1996) Effect of Mutations in the Thiamin Diphosphate-Mg Fold on the Activation and Inhibition of the Pyruvate Dehydrogenase Complex from E. coli, J. Biol. Chem. 271, 33192-33200.
25. Nemeria, N., Joseph, E., Zhou, L., Tittmann, K., Hübner, G., and Jordan, F. in preparation.
26. Lindqvist, Y., Schneider, G., Ermler, V., and Sundstrom, M. (1992) Three-Dimensional Structure of Transketolase, a Thiamine Diphosphate Dependent Enzyme, at 2.5 Å Resolution, EMBO J. 11, 2373-2379.
27. Kluger, R., and Pike, D. C. (1977) Active Site Generated Analogues of Reactive Intermediates in Enzymic Reactions. Potent Inhibition of Pyruvate Dehydrogenase by a Phosphonate Analogue of Pyruvate, J. Am. Chem. Soc. 99, 4504-4506.
28. Usmanov, R. A., Meshalkina, L. E., Neef, H., Schellenberger, A., and Kochetov, G. A. (1996) Interaction of the Transketolase with Thiamine Pyrophosphate Analogs, in Biochemistry and Physiology of Thiamin Diphosphate Enzymes (Bisswanger, H. and Schellenberger, A., Eds.) pp 516-531, A. u. C. Intemann Verlag, Prien, Germany.
29. Farzami, B., Mariam, Y. H., and Jordan, F. (1977) Solvent Effects on Thiamin-Enzyme Model Interactions I. Interaction with Tryptophan, Biochemistry 16, 1105-1110.
30. Sergienko, E. A., and Jordan, F. (2001) Catalytic Acid-Base Groups in Yeast Pyruvate Decarboxylase III. A Steady-State Kinetic Model Consistent with the Behavior of Both Wild-Type and Variant Enzymes at all Relevant pH Values, Biochemistry 40, 7382-7403.