The effect of a Glu370Asp mutation in glutaryl-CoA dehydrogenase on proton transfer to the dienolate intermediate

Biochemistry

Volumn 46, Issue 50, 2007, Pages 14468-14477

  Rao, K Sudhindra ^a   Fu, Zhuji ^c   Albro, Mark ^a   Narayanan, Beena ^c   Baddam, Saritha ^a   Lee, Hyun Joo K ^c,d   Kim, Jung Ja P ^c   Frerman, Frank E ^a,b  

^a Children's Hospital Colorado   (United States)

^b UNIVERSITY OF COLORADO   (United States)

^c MEDICAL COLLEGE OF WISCONSIN   (United States)

^d Chungju National University   (South Korea)

Author keywords

[No Author keywords available]

Indexed keywords

DEHYDROGENASE; DIENOLATE INTERMEDIATES; MUTANT COCRYSTALLIZATION; MUTATION; NITROBUTYRIC ACID;

MOLECULAR MODELING; MUTAGENESIS; PROTON TRANSFER; RATE CONSTANTS; SUBSTRATES;

ENZYMES;

ASPARTIC ACID; BUTYRIC ACID DERIVATIVE; CARBON; COENZYME A; CROTONYL COENZYME A; FLAVINE ADENINE NUCLEOTIDE; GLUTAMIC ACID; GLUTARYL COENZYME A DEHYDROGENASE; QUERCETIN; UNCLASSIFIED DRUG; VINYLACETYL COENZYME A;

AMINO ACID SUBSTITUTION; ARTICLE; CATALYSIS; CRYSTAL STRUCTURE; DECARBOXYLATION; ENZYME ACTIVE SITE; ENZYME METABOLISM; GEOMETRY; ISOMERIZATION; MUTATION; OXIDATION KINETICS; PRIORITY JOURNAL; PROTON TRANSPORT; REDUCTION KINETICS; THERMODYNAMICS;

ACYL COENZYME A; AMINO ACID SUBSTITUTION; ASPARTIC ACID; CHROMATOGRAPHY, HIGH PRESSURE LIQUID; CRYSTALLOGRAPHY; GLUTAMIC ACID; GLUTARYL-COA DEHYDROGENASE; KINETICS; MASS SPECTROMETRY; MUTAGENESIS, SITE-DIRECTED; MUTATION; PROTONS; SUBSTRATE SPECIFICITY;

EID: 37249001773     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi7009597     Document Type: Article

References (30)

1. Goodman, S. I., and Frerman, F. E. (2001) Organic acidemias due to defects in lysine oxidation: 2-Ketoadipic acidemia and glutaric acidemia, in The Metabolic and Molecular Bases of Inherited Disease (Scriver, C. R., Beaudet, A. L., Valle, D., Sly, W., Childs, B., Kinzler, K. W., and Vogelstein, B., Eds.) 8th ed., pp 2195-2205, McGraw-Hill, New York.
2. 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.
3. 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.
4. 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.
5. 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.
6. Rao, K. S., Albro, M., Dwyer, T. M., and Frerman, F. E. (2006) Kinetic mechanism of glutaryl-CoA dehydrogenase, Biochemistry 45, 15853-15861.
7. Buckel, W., Dorn, U., and Semmler, R. (1981) Glutaconate CoA-transferase from Acidaminococcus fermentans, Eur. J. Biochem. 118, 315-321.
8. 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.
9. Fong, J. C., and Schulz, H. (1981) Short-chain and long-chain enoyl-CoA hydratases from pig heart muscle, Methods Enzymol. 71, 390-398.
10. 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.
11. Buckel, W. (1986) Biotin-dependent decarboxylases as bacterial sodium pumps - Purification and reconstitution of glutaconyl-CoA decarboxylase from Acidaminococcus fermentons, Methods Enzymol. 125, 547-558.
12. Hubbard, P. A., Yu, W., Schulz, H., and Kim, J. J. (2005) Domain swapping in the low-similarity isomerase/hydratase superfamily: the crystal structure of rat mitochondrial Delta3, Delta2-enoyl-CoA isomerase, Protein Sci. 14, 1545-1555.
13. Steinman, H. M., and Hill, R. L. (1975) Bovine liver crotonase (enoyl coenzyme A hydratase). EC 4.2.1.17 L-3-hydroxyacyl-CoA hydrolyase, Methods Enzymol. 35, 136-151.
14. Massey, V., and Hemmerich, P. (1978) Photoreduction of flavoproteins and other biological compounds catalyzed by deazaflavins, Biochemistry 17, 9-16.
15. Stoffel, W., and Grol, M. (1978) Purification and properties of 3-cis-2-trans-enoyl-CoA isomerase (dodecenoyl-CoA delta-isomerase) from rat liver mitochondria, Hoppe-Seyler's Z. Physiol. Chem. 359, 1777-1782.
16. Otwinowski, Z., and Minor, W. (1997) Processing of X-ray diffraction data collected in oscillation mode, Methods Enzymol. 276, 307-326.
17. Brunger, A. T., Adams, P. D., Clore, G. M., DeLano, W. L., Gros, P., Grosse-Kunstleve, R. W., Jiang, J. S., Kuszewski, J., Nilges, M., Pannu, N. S., Read, R. J., Rice, L. M., Simonson, T., and Warren, G. L. (1998) Crystallography & NMR system: A new software suite for macromolecular structure determination, Acta Crystallogr. D 54, 905-921.
18. Roussel, A., Inisan, A. G., Knoop-Mouthuy, A., and Cambillau, C., Eds. (1999) Turbo-Frodo, Version OpenGL.1, CNRS/Universitite, Marseille, France.
19. Gustafson, W. G., Feinberg, B. A., and McFarland, J. T. (1986) Energetics of beta-oxidation. Reduction potentials of general fatty acyl-CoA dehydrogenase, electron transfer flavoprotein, and fatty acyl-CoA substrates, J. Biol. Chem. 261, 7733-7741.
20. Schmidt, J., Reinsch, J., and McFarland, J. T. (1981) Mechanistic studies on fatty acyl-CoA dehydrogenase, J. Biol. Chem. 256, 11667-11670.
21. 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.
22. Ghisla, S., and Thorpe, C. (2004) Acyl-CoA dehydrogenases. A mechanistic overview, Eur. J. Biochem. 271, 494-508.
23. Tokuoka, K., Nakajima, Y., Hirotsu, K., Miyahara, I., Nishina, Y., Shiga, K., Tamaoki, H., Setoyama, C., Tojo, H., and Miura, R. (2006) Three-dimensional structure of rat-liver acyl-CoA oxidase in complex with a fatty acid: insights into substrate-recognition and reactivity toward molecular oxygen, J. Biochem. (Tokyo) 139, 789-795.
24. Satoh, A., Nakajima, Y., Miyahara, I., Hirotsu, K., Tanaka, T., Nishina, Y., Shiga, K., Tamaoki, H., Setoyama, C., and Miura, R. (2003) Structure of the transition state analog of medium-chain acyl-CoA dehydrogenase. Crystallographic and molecular orbital studies on the charge-transfer complex of medium-chain acyl-CoA dehydrogenase with 3-thiaoctanoyl-CoA, J. Biochem. (Tokyo) 134, 297-304.
25. Tanaka, T., Tamaoki, H., Nishina, Y., Shiga, K., Ohno, T., and Miura, R. (2006) Theoretical study on charge-transfer interaction between acyl-CoA dehydrogenase and 3-thiaacyl-CoA using density functional method, J. Biochem. (Tokyo) 139, 847-855.
26. Frost, A. A., and Pearson, R. G. (1953) Kinetics and Mechanism, John Wiley & Sons, Inc., New York.
27. Benson, S. W., and Bose, A. N. (1963) The iodine-catalyzed, positional isomerization of olefins. A new tool for the precise measurement of thermodynamic data, J. Am. Chem. Soc. 85, 1385-1387.
28. Smith, M. B., and March, J. (2001) March's Advanced Organic Chemistry: Reactions, Mechanisms, and Structure, 5th ed., Wiley-Interscience, New York.
29. Efimov, I., and McIntire, W. S. (2005) Relationship between charge-transfer interactions, redox potentials, and catalysis for different forms of the flavoprotein component of p-cresol methylhydroxylase, J. Am. Chem. Soc. 127, 732-741.
30. Dmitrenko, O., Thorpe, C., and Bach, R. D. (2003) Effect of a charge-transfer interaction on the catalytic activity of Acyl-CoA dehydrogenase: A theoretical study of the role of oxidized flavin, J. Phys. Chem. B 107, 13229-13236.