Kinetic mechanism of glutaryl-CoA dehydrogenase

Biochemistry

Volumn 45, Issue 51, 2006, Pages 15853-15861

  Rao, K Sudhindra ^a   Albro, Mark ^a   Dwyer, Timothy M ^c   Frerman, Frank E ^a,b  

^a Children's Hospital Colorado   (United States)

^b UNIVERSITY OF COLORADO   (United States)

^c TOWSON UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BINDING ENERGY; CARBOXYLATION; ENZYMES; MONOMERS; OXIDATION;

GLUTARYL-COA DEHYDROGENASE (GCD); RATE-DETERMINING STEPS; TRANSIT TIMES;

ENZYME KINETICS;

ACYL COENZYME A DEHYDROGENASE; FLAVINE ADENINE NUCLEOTIDE; GLUTARYL COENZYME A DEHYDROGENASE;

ARTICLE; COVALENT BOND; DECARBOXYLATION; ENZYME ACTIVE SITE; ENZYME ASSAY; ENZYME KINETICS; NUCLEOTIDE SEQUENCE; OXIDATION; PRIORITY JOURNAL; SEQUENCE ANALYSIS; STEADY STATE; WILD TYPE;

ACYL COENZYME A; BINDING SITES; CATALYSIS; DECARBOXYLATION; DEUTERIUM EXCHANGE MEASUREMENT; ELECTRON TRANSPORT; ENERGY TRANSFER; FLAVIN-ADENINE DINUCLEOTIDE; GLUTARYL-COA DEHYDROGENASE; HUMANS; KINETICS; OXIDATION-REDUCTION; PROTONS; SUBSTRATE SPECIFICITY;

EID: 33845945737     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi0609016     Document Type: Article

References (33)

1. Lenich, A. C., and Goodman, S. I. (1986) The purification and characterization of glutaryl-coenzyme A dehydrogenase from porcine and human liver, J. Biol. Chem. 261, 4090-4096.
2. Westover, J. B., Goodman, S. I., and Frerman, F. E. (2001) Binding, Hydration, and Decarboxylation of the Reaction Intermediate Glutaconyl-Coenzyme A by Human Glutaryl-CoA Dehydrogenase, Biochemistry 40, 14106-14114.
3. Dwyer, T. M., Rao, K. S., Goodman, S. I., and Frerman, F. E. (2000) Proton Abstraction Reaction, Steady-State Kinetics, and Oxidation-Reduction Potential of Human Glutaryl-CoA Dehydrogenase, Biochemistry 39, 11488-11499.
4. Dwyer, T. M., Rao, K. S., Westover, J. B., Kim, J. J., and Frerman, F. E. (2001) The function of Arg-94 in the oxidation and decarboxylation of glutaryl-CoA by human glutaryl-CoA dehydrogenase, J. Biol. Chem. 276, 133-138.
5. Fu, Z., Wang, M., Paschke, R., Rao, K. S., Frerman, F. E., and Kim, J. J. (2004) Crystal Structures of Human Glutaryl-CoA Dehydrogenase with and without an Alternate Substrate: Structural Bases of Dehydrogenation and Decarboxylation Reactions, Biochemistry 43, 9674-9684.
6. Rao, K. S., Albro, M., Zirrolli, J. A., Vander Velde, D., Jones, D. N., and Frerman, F. E. (2005) Protonation of Crotonyl-CoA Dienolate by Human Glutaryl-CoA Dehydrogenase Occurs by Solvent-Derived Protons, Biochemistry 44, 13932-13940.
7. Cleland, W. W. (1975) Partition Analysis and the Concept of Net Rate Constants as Tools in Enzyme Kinetics, Biochemistry 14, 3220-3224.
8. Fisher, H. F. (2005) Transient-State Kinetic Approach to Mechanisms of Enzymatic Catalysis, Acc. Chem. Res. 38, 157-166.
9. Ghisla, S., and Thorpe, C. (2004) Acyl-CoA dehydrogenases. A mechanistic overview, Eur. J. Biochem. 271, 494-508.
10. Fersht, A. (1999) Structure and Mechanism in Protein Science: A Guide to Catalysis and Protein Folding, W. H. Freeman and Co., New York.
11. Waterson, R. M., and Hill, R. L. (1972) Enoyl coenzyme A hydratase (crotonase). Catalytic properties of crotonase and its possible regulatory role in fatty acid oxidation, J. Biol. Chem. 247, 5258-5265.
12. Buckel, W., Dorn, U., and Semmler, R. (1981) Glutaconate CoA-transferase from Acidaminococcus fermentans, Eur. J. Biochem. 118, 315-321.
13. Klees, A. G., and Buckel, W. (1991) Synthesis and properties of (R)-2-hydroxyglutaryl-1-CoA: (R)-2-hydroxyglutaryl-5-CoA, an erroneous product of glutaconate CoA-transferase, Biol. Chem. Hoppe-Seyler 372, 319-324.
14. Corkey, B. E. (1988) Analysis of acyl-coenzyme A esters in biological samples, Methods Enzymol. 166, 55-70.
15. Goodman, S. I., Kratz, L. E., DiGiulio, K. A., Biery, B. J., Goodman, K. E., Isaya, G., and Frerman, F. E. (1995) Cloning of glutaryl-CoA dehydrogenase cDNA, and expression of wild type and mutant enzymes in Escherichia coli, Hum. Mol. Genet. 4, 1493-1498.
16. Mack, M., Bendrat, K., Zelder, O., Eckel, E., Linder, D., and Buckel, W. (1994) Location of the two genes encoding glutaconate coenzyme A-transferase at the beginning of the hydroxyglutarate operon in Acidaminococcus fermentans, Eur. J. Biochem. 226, 41-51.
17. Rao, K. S., Albro, M., Vockley, J., and Frerman, F. E. (2003) Mechanism-based inactivation of human glutaryl-CoA dehydrogenase by 2-pentynoyl-CoA: rationale for enhanced reactivity, J. Biol. Chem. 278, 26342-26350.
18. Paul, P. V., and Ballou, D. P. (2000) The use of protocatechuate dioxygenase for maintaining anaerobic conditions in biochemical experiments, Anal. Blochem. 286, 187-192.
19. Massey, V., and Hemmerich, P. (1978) Photoreduction of Flavoproteins and Other Biological Compounds Catalyzed by Deazaflavins, Biochemistry 17, 9-16.
20. Glickman, M. H., Wiseman, J. S., and Klinman, J. P. (1994) Extremely Large Isotope Effects in the Soybean Lipoxygenase-Linoleic Acid Reaction, J. Am. Chem. Soc. 116, 793-794.
21. Rose, I. A. (1970) Enzymology of proton abstraction and transfer reactions in The Enzymes (Boyer, P. D., Ed.) 3rd ed., Vol. 2, pp 281-320, Academic Press, New York.
22. Maniscalco, S. J., Tally, J. F., and Fisher, H. F. (2004) The interpretation of multiple-step transient-state kinetic isotope effects, Arch. Biochem. Biophys. 425, 165-172.
23. Pohl, B., Raichle, T., and Ghisla, S. (1986) Studies on the reaction mechanism of general acyl-CoA dehydrogenase. Determination of selective isotope effects in the dehydrogenation of butyryl-CoA, Eur. J. Biochem. 160, 109-115.
24. Lehman, T. C., and Thorpe, C. (1990) Alternate Electron Acceptors for Medium-Chain Acyl-CoA Dehydrogenase: Use of Ferricenium Salts, Biochemistry 29, 10594-10602.
25. Saenger, A. K., Nguyen, T. V., Vockley, J., and Stankovich, M. T. (2005) Thermodynamic Regulation of Human Short-Chain Acyl-CoA Dehydrogenase by Substrate and Product Binding, Biochemistry 44, 16043-16053.
26. Bhattacharyya, S., Ma, S., Stankovich, M. T., Truhlar, D. G., and Gao, J. (2005) Potential of Mean Force Calculation for the Proton and Hydride Transfer Reactions Catalyzed by Medium-Chain Acyl-CoA Dehydrogenase: Effect of Mutations on Enzyme Catalysis, Biochemistry 44, 16549-16562.
27. Poulsen, T. D., Garcia-Viloca, M., Gao, J. L., and Truhlar, D. G. (2003) Free Energy Surface, Reaction Paths, and Kinetic Isotope Effect of Short-Chain Acyl-CoA Dehydrogenase, J. Phys. Chem. B 107, 9567-9578.
28. Bordwell, F. G., Vanderpuy, M., and Vanier, N. R. (1976) Carbon Acids. 9. Effects of Divalent Sulfur and Divalent Oxygen on Carbanion Stabilities, J. Org. Chem. 41, 1885-1886.
29. Lau, S. M., Brantley, R. K., and Thorpe, C. (1988) The Reductive Half-Reaction in Acyl-CoA Dehydrogenase from Pig Kidney: Studies with Thiaoctanoyl-CoA and Oxaoctanoyl-CoA Analogues, Biochemistry 27, 5089-5095.
30. Kyte, J. (1995) Mechanism in Protein Chemistry, Garland Publishing, New York.
31. Rao, K. S., Vander Velde, D., Dwyer, T. M., Goodman, S. I., and Frerman, F. E. (2002) Alternate Substrates of Human Glutaryl-CoA Dehydrogenase: Structure and Reactivity of Substrates, and Identification of a Novel 2-Enoyl-CoA Product, Biochemistry 41, 1274-1284.
32. Smith, M. B., and March, J. (2001) March's Advanced Organic Chemistry: Reactions, Mechanisms, and Structure, 5th ed., Wiley-Interscience, New York.
33. Cleland, W. W., and Northrop, D. B. (1999) Energetics of substrate binding, catalysis, and product release, Methods Enzymol. 308, 3-27.