Function of a conserved loop of the β-domain, not involved in thiamin diphosphate binding, in catalysis and substrate activation in yeast pyruvate decarboxylase

Biochemistry

Volumn 45, Issue 45, 2006, Pages 13517-13527

  Joseph, Ebenezer ^a   Wei, Wen ^a   Tittmann, Kai ^b   Jordan, Frank ^a  

^a RUTGERS UNIVERSITY   (United States)

^b MARTIN LUTHER UNIVERSITY HALLE WITTENBERG   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ACTIVATION ANALYSIS; CATALYSIS; CHEMICAL ACTIVATION; CRYSTAL STRUCTURE; X RAY ANALYSIS; YEAST;

ACTIVATION BEHAVIOR; CONFORMATIONAL EQUILIBRIUM; ENZYME CONFORMATIONS; THIAMIN DIPHOSPHATE (THDP);

ENZYMES;

AMIDE; AMINO ACID; ASPARAGINE; ASPARTIC ACID; COCARBOXYLASE; GLUTAMINE; LEUCINE; PYRUVAMIDE; PYRUVATE DECARBOXYLASE; PYRUVIC ACID DERIVATIVE; SERINE; THREONINE; UNCLASSIFIED DRUG;

AMINO ACID SEQUENCE; ARTICLE; CATALYSIS; CATALYST; CONFORMATIONAL TRANSITION; CRYSTAL STRUCTURE; ENZYME ACTIVATION; ENZYME ACTIVITY; ENZYME CONFORMATION; ENZYME SUBSTRATE COMPLEX; NONHUMAN; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTON NUCLEAR MAGNETIC RESONANCE; SEQUENCE ANALYSIS; SITE DIRECTED MUTAGENESIS; STEADY STATE; STRUCTURE ANALYSIS; X RAY CRYSTALLOGRAPHY; YEAST;

AMINO ACID SEQUENCE; AMINO ACID SUBSTITUTION; CATALYSIS; ENZYME ACTIVATION; KINETICS; MUTAGENESIS, SITE-DIRECTED; PROTEIN STRUCTURE, TERTIARY; PYRUVATE DECARBOXYLASE; SACCHAROMYCES CEREVISIAE; THIAMINE PYROPHOSPHATE;

EID: 33751021391     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi0615588     Document Type: Article

References (32)

1. 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 2.4Å Resolution, Biochemistry 32, 6165-6170.
2. 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 thiamin diphosphate-dependent enzyme pyruvate decarboxylase from the Yeast Saccharomyces cerevisiae at 2.3 Å resolution, J. Mol. Biol. 256, 590-600.
3. Lu, G., Dobritzsch, D., Baumann, S., Schneider, G., and König, S. (2000) The structural basis of substrate activation in yeast pyruvate decarboxylase, Eur. J. Biochem. 267, 861-868.
4. Boiteux, A., and Hess, B. (1970) Allosteric properties of yeast pyruvate decarboxylase, FEBS Lett. 9, 293-296.
5. Ullrich, J., and Donner, I. (1970) Kinetic evidence for two active sites in cytoplasmic yeast pyruvate decarboxylase, Hoppe-Seyler's Z. Physiol. Chem. 351, 1026-1029.
6. Baburina, I., Gao, Y., Hu, Z., Jordan, F., Hohmann, S., and Furey, W. (1994) Substrate Activation of Brewers' Yeast Pyruvate Decarboxylase Is Abolished by Mutation of Cysteine 221 to Serine, Biochemistry 33, 5630-5635.
7. 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.
8. Li, H., and Jordan, F. (1999) Effects of Substitution of Tryptophan 412 in the Substrate Activation Pathway of Yeast Pyruvate Decarboxylase, Biochemistry 38, 10004-10012.
9. Jordan, F. (2003) Current mechanistic understanding of thiamin diphosphate-dependent enzymatic reactions, Nat. Prod. Rep. 20, 184-201.
10. Eberhardt, I., and Hohmann, S. (1995) Strategy for deletion of complete open reading frames in Saccharomyces cerevisiae, Curr. Genet. 27, 306-308.
11. Eberhardt, I., Cederberg, H., Li, H., König, S., Jordan, F., and Hohmann, S. (1999) Autoregulation of yeast pyruvate decarboxylase gene expression requires the enzyme but not its catalytic activity, Eur. J. Biochem. 262, 191-201.
12. Li, H. (1999) Ph.D. Thesis, Rutgers University.
13. Liu, M., Sergienko, E. A., Guo, F., Wang, J., Tittmann, K., Hübner, G., Furey, W., and Jordan, F. (2001) (2001) Catalytic Acid-Base Groups in Yeast Pyruvate Decarboxylase. 1. Site-Directed Mutagenesis and Steady-State Kinetic Studies on the Enzyme with the D28A, H114F, H115F, and E477Q Substitutions, Biochemistry 40, 7355-7368.
14. Holzer, H., Schultz, G., Villar-Palasi, C., and Jutgen-Sell, J. (1956) Isolierung der hefecarboxylase and untersuchunger uber die activitat des enzymes in lebenden zellen, Biochem. Z. 327, 331-344.
15. Sergienko, E. A., and Jordan, F. (2002) A New Model for Activation of Yeast Pyruvate Decarboxylase by Substrate Consistent with the Alternating Sites Mechanism: Demonstration of the Existence of Two Active Forms of the Enzyme, Biochemistry 41, 3952-3967.
16. Krieger, F., Spinka, M., Golbik, R., Hübner, G., and König, S. (2002) Pyruvate decarboxylase from Kluyveromyces lactis. An enzyme with an extraordinary substrate activation behavior, Eur. J. Biochem. 269, 3256-3263.
17. Tittmann, K., Golbik, R., Uhlemann, K., Khailova, L., Schneider, G., Patel, M., Jordan, F., Chipman, D. M., Duggleby, R. G., and Hübner, G. (2003) NMR Analysis of Covalent Intermediates in Thiamin Diphosphate Enzymes, Biochemistry 42, 7885-7891.
18. Wei, W. (2003) Ph.D. Thesis Rutgers University.
19. Alvarez, F. J., Ermer, J., Hübner, G., Schellenberger, A., and Schowen, R. L. (1995) The linkage of catalysis and regulation in enzyme action. Solvent isotope effects as probes of protonic sites in the yeast pyruvate decarboxylase mechanism, J. Am. Chem. Soc. 117, 1678-1683.
20. Hübner, G., Weidhase, R., and Schellenberger, A. (1978) The mechanism of substrate activation of pyruvate decarboxylase: a first approach, Eur. J. Biochem. 92, 175-181.
21. Green, J. B. (1989) Pyruvate decarboxylase is like acetolactate synthase (ILV2) and not like the pyruvate dehydrogenase E1 subunit, FEBS Lett. 246, 1-5.
22. Hawkins, C. F., Borges, A., and Perham, R. N. (1989) A common structural motif in thiamin pyrophosphate-binding enzymes, FEBS Lett. 255, 77-82.
23. Candy, J. M., and Duggleby, R. G. (1998) Structure and properties of pyruvate decarboxylase and site-directed mutagenesis of the Zymomonas mobilis enzyme, Biochim. Biophys. Acta 1385, 323-338.
24. Gao, Y. (2000) Ph.D. Thesis, Rutgers University.
25. Baburina, I., Li, H., Bennion, B., Furey, W., and Jordan, F. (1998) Interdomain information transfer during substrate activation of yeast pyruvate decarboxylase: the interaction between cysteine 221 and histidine 92, Biochemistry 37, 1235-1244.
26. Zeng, X., Farrenkopf, B., Hohmann, S., Dyda, F., Furey, W., and Jordan, F. (1993) Role of cysteines in the activation and inactivation of brewers' yeast pyruvate decarboxylase investigated with a PDC1-PDC6 fusion protein, Biochemistry 32, 2704-2709.
27. Baburina, I., Moore, D. J., Volkov, A., Kahyaoglu, A., Jordan, F., and Mendelsohn, R. (1996) Three of Four Cysteines, Including That Responsible for Substrate Activation, Are Ionized at pH 6.0 in Yeast Pyruvate Decarboxylase: Evidence from Fourier Transform Infrared and Isoelectric Focusing Studies, Biochemistry 35, 10249-10255.
28. Baburina, I., Dikdan, G., Guo, F., Tous, G. I., Root, B., and Jordan, F. (1998) Reactivity at the substrate activation site of yeast pyruvate decarboxylase: inhibition by distortion of domain interactions. Biochemistry 37, 1245-1255.
29. Wang, J., Golbik, R., Seliger, B., Spinka, M., Tittmann, K., Hübner, G., and Jordan, F. (2001) Consequences of a Modified Putative Substrate-Activation Site on Catalysis by Yeast Pyruvate Decarboxylase, Biochemistry 40, 1755-1763.
30. Wei, W., Liu, M., and Jordan, F. (2002) Solvent kinetic isotope effects monitor changes in hydrogen bonding at the active center of yeast pyruvate decarboxylase concomitant with substrate activation: the substituent at position 221 can control the state of activation, Biochemistry 41, 451-461.
31. König, S., Hübner, G., and Schellenberger, A. (1990) Cross-linking of pyruvate decarboxylase. Characterization of the native and substrate-activated enzyme states, Biomed. Biochim. Acta 49, 465-471.
32. Hübner, G., König, S., Schellenberger, A., and Koch, M. H. (1990) An X-ray solution scattering study of the cofactor and activator induced structural changes in yeast pyruvate decarboxylase (PDC), FEBS Lett. 266, 17-20.