Structural basis for promoting and preventing decarboxylation in glutaryl-coenzyme a dehydrogenases

Biochemistry

Volumn 49, Issue 25, 2010, Pages 5350-5357

  Wischgoll, Simon ^a   Demmer, Ulrike ^b   Warkentin, Eberhard ^b   Günther, Robert ^a   Boll, Matthias ^a   Ermler, Ulrich ^b  

^a UNIVERSITY OF LEIPZIG   (Germany)

^b MAX PLANCK INSTITUTE OF BIOPHYSICS   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ANAEROBIC BACTERIUM; CARBOXYLATE GROUPS; CATALYTIC BEHAVIOR; COENZYME A; DECARBOXYLASES; GLUTAMIC ACID; GUANIDINIUM; KEY FACTORS; LEAVING GROUPS; MONODENTATE HYDROGEN BOND; STRUCTURAL BASIS; STRUCTURAL CHANGE; TRANSITION STATE;

AMINO ACIDS; BACTERIA; CARBOXYLATION; HYDROGEN; HYDROGEN BONDS; MOLECULAR DYNAMICS; ORGANIC ACIDS; SODIUM;

CRYSTAL ATOMIC STRUCTURE;

ARGININE; GLUTACONYL CARBOXYLATE; GLUTARYL COENZYME A DEHYDROGENASE; GUANIDINE; TYROSINE; UNCLASSIFIED DRUG; VALINE;

ANAEROBIC BACTERIUM; ARTICLE; ATOM; CATALYSIS; CRYSTAL STRUCTURE; DECARBOXYLATION; DEHYDROGENATION; DESULFOCOCCUS MULTIVORANS; HUMAN; HYDROGEN BOND; MOLECULAR DYNAMICS; MOLECULAR INTERACTION; NONHUMAN; PRIORITY JOURNAL;

BACTERIA, ANAEROBIC; CARBOXYLIC ACIDS; CRYSTALLOGRAPHY, X-RAY; FLAVIN-ADENINE DINUCLEOTIDE; GLUTARYL-COA DEHYDROGENASE; HYDROGEN BONDING; MODELS, MOLECULAR; MUTAGENESIS, SITE-DIRECTED; PROTEIN CONFORMATION; SUBSTRATE SPECIFICITY;

DESULFOCOCCUS MULTIVORANS;

EID: 77953882830     PISSN: 00062960     EISSN: 15204995     Source Type: Journal    
DOI: 10.1021/bi100317m     Document Type: Article

References (35)

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. Goodman, S. I., Stein, D. E., Schlesinger, S., Christensen, E., Schwartz, M., Greenberg, C. R., and Elpeleg, O. N. (1998) Glutaryl-CoA dehydrogenase mutations in glutaric acidemia (type I): Review and report of thirty novel mutations Hum. Mutat. 12, 141-144
4. Westover, J. B., Goodman, S. I., and Frerman, F. E. (2003) Pathogenic mutations in the carboxyl-terminal domain of glutaryl-CoA dehydrogenase: Effects on catalytic activity and the stability of the tetramer Mol. Genet. Metab. 79, 245-256
5. Boll, M., Fuchs, G., and Heider, J. (2002) Anaerobic oxidation of aromatic compounds and hydrocarbons Curr. Opin. Chem. Biol. 6, 604-611
6. Carmona, M., Zamarro, M. T., Blazquez, B., Durante-Rodriguez, G., Juarez, J. F., Valderrama, J. A., Barragan, M. J., Garcia, J. L., and Diaz, E. (2009) Anaerobic catabolism of aromatic compounds: A genetic and genomic view Microbiol. Mol. Biol. Rev. 73, 71-133
7. Fuchs, G. (2008) Anaerobic metabolism of aromatic compounds Ann. N.Y. Acad. Sci. 1125, 82-99
8. Blazquez, B., Carmona, M., Garcia, J. L., and Diaz, E. (2008) Identification and analysis of a glutaryl-CoA dehydrogenase-encoding gene and its cognate transcriptional regulator from Azoarcus sp. CIB Environ. Microbiol. 10, 474-482
9. Härtel, U., Eckel, E., Koch, J., Fuchs, G., Linder, D., and Buckel, W. (1993) Purification of glutaryl-CoA dehydrogenase from Pseudomonas sp., an enzyme involved in the anaerobic degradation of benzoate Arch. Microbiol. 159, 174-181
10. Wischgoll, S., Heintz, D., Peters, F., Erxleben, A., Sarnighausen, E., Reski, R., Van Dorsselaer, A., and Boll, M. (2005) Gene clusters involved in anaerobic benzoate degradation of Geobacter metallireducens Mol. Microbiol. 58, 1238-1252
11. Wischgoll, S., Taubert, M., Peters, F., Jehmlich, N., von Bergen, M., and Boll, M. (2009) Decarboxylating and nondecarboxylating glutaryl-coenzyme A dehydrogenases in the aromatic metabolism of obligately anaerobic bacteria J. Bacteriol. 191, 4401-4409
12. 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
13. 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
14. 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
15. Gomes, B., Fendrich, G., and Abeles, R. H. (1981) Mechanism of action of glutaryl-CoA and butyryl-CoA dehydrogenases. Purification of glutaryl-CoA dehydrogenase Biochemistry 20, 1481-1490
16. Rao, K. S., Albro, M., Dwyer, T. M., and Frerman, F. E. (2006) Kinetic mechanism of glutaryl-CoA dehydrogenase Biochemistry 45, 15853-15861
17. Rao, K. S., Fu, Z., Albro, M., Narayanan, B., Baddam, S., Lee, H. J., Kim, J. J., and Frerman, F. E. (2007) The effect of a Glu370Asp mutation in glutaryl-CoA dehydrogenase on proton transfer to the dienolate intermediate Biochemistry 46, 14468-14477
18. 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 s lvent-derived protons Biochemistry 44, 13932-13940
19. Peters, F., Rother, M., and Boll, M. (2004) Selenocysteine-containing proteins in anaerobic benzoate metabolism of Desulfococcus multivorans J. Bacteriol. 186, 2156-2163
20. Beatrix, B., Bendrat, K., Rospert, S., and Buckel, W. (1990) The biotin-dependent sodium ion pump glutaconyl-CoA decarboxylase from Fusobacterium nucleatum (subsp. nucleatum). Comparison with the glutaconyl-CoA decarboxylases from Gram-positive bacteria Arch. Microbiol. 154, 362-369
21. Boiangiu, C. D., Jayamani, E., Brugel, D., Herrmann, G., Kim, J., Forzi, L., Hedderich, R., Vgenopoulou, I., Pierik, A. J., Steuber, J., and Buckel, W. (2005) Sodium ion pumps and hydrogen production in glutamate fermenting anaerobic bacteria J. Mol. Microbiol. Biotechnol. 10, 105-119
22. Buckel, W. (2001) Sodium ion-translocating decarboxylases Biochim. Biophys. Acta 1505, 15-27
23. Otwinowski, Z. and Minor, W. (1997) Processing of X-ray diffraction data collected in oscillation mode Methods Enzymol. 276, 307-326
24. Kabsch, W. (1993) Automatic processing of rotation diffraction data from crystals of initially unknown symmetry and cell constants J. Appl. Crystallogr. 26, 795-800
25. McCoy, A. J., Grosse-Kunstleve, R. W., Adams, P. D., Winn, M. D., Storoni, L. C., and Read, R. J. (2007) Phaser crystallographic software J. Appl. Crystallogr. 40, 658-674
26. Murshudov, G. N., Vagin, A. A., and Dodson, E. J. (1997) Refinement of macromolecular structures by the maximum-likelihood method Acta Crystallogr. D53, 240-255
27. Emsley, P. and Cowtan, K. (2004) Coot: Model-building tools for molecular graphics Acta Crystallogr. D60, 2126-2132
28. Laskowski, R. A., Moss, D. S., and Thornton, J. M. (1993) Main-chain bond lengths and bond angles in protein structures J. Mol. Biol. 231, 1049-1067
29. Makarova, O., Kamberov, E., and Margolis, B. (2000) Generation of deletion and point mutations with one primer in a single cloning step BioTechniques 29, 970-972
30. Johnson, M., Zaretskaya, I., Raytselis, Y., Merezhuk, Y., McGinnis, S., and Madden, T. L. (2008) NCBI BLAST: A better web interface Nucleic Acids Res. 36, W5-W9
31. Larkin, M. A., Blackshields, G., Brown, N. P., Chenna, R., McGettigan, P. A., McWilliam, H., Valentin, F., Wallace, I. M., Wilm, A., Lopez, R., Thompson, J. D., Gibson, T. J., and Higgins, D. G. (2007) Clustal W and Clustal X version 2.0 Bioinformatics 23, 2947-2948
32. Waterhouse, A. M., Procter, J. B., Martin, D. M., Clamp, M., and Barton, G. J. (2009) Jalview Version 2: A multiple sequence alignment editor and analysis workbench Bioinformatics 25, 1189-1191
33. Battaile, K. P., Nguyen, T. V., Vockley, J., and Kim, J. J. (2004) Structures of isobutyryl-CoA dehydrogenase and enzyme-product complex: Comparison with isovaleryl- and short-chain acyl-CoA dehydrogenases J. Biol. Chem. 279, 16526-16534
34. Ghisla, S. and Thorpe, C. (2004) Acyl-CoA dehydrogenases. A mechanistic overview Eur. J. Biochem. 271, 494-508
35. 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