Insights into the mechanism of pseudomonas dacunhae aspartate β-decarboxylase from rapid-scanning stopped-flow kinetics

Biochemistry

Volumn 49, Issue 24, 2010, Pages 5066-5073

  Phillips, Robert S ^a,b   Lima, Santiago ^b   Khristoforov, Roman ^a   Sudararaju, Bakthavatsalam ^a  

^a UNIVERSITY OF GEORGIA   (United States)

^b NONE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ABSORPTION PEAKS; ACTIVE SITE RESIDUES; APPARENT RATE CONSTANT; ASPARTATES; BINDING EQUILIBRIA; COFACTORS; CONFORMATIONAL CHANGE; DEAD TIME; DECARBOXYLASES; DISODIUM SALT; ERYTHRO; KETIMINES; PHOSPHATE COMPLEXES; PROTONATED; PYRUVATES; SCHIFF-BASE; STOPPED FLOW; STOPPED-FLOW KINETICS; STOPPED-FLOW SPECTROPHOTOMETRY; WILD TYPES;

FUNCTIONAL GROUPS; HYDROSTATIC PRESSURE; PROTONATION; SPECTROPHOTOMETRY;

RATE CONSTANTS;

ASPARTATE BETA DECARBOXYLASE; BACTERIAL ENZYME; SCHIFF BASE; UNCLASSIFIED DRUG;

ARTICLE; FLOW KINETICS; HYDROSTATIC PRESSURE; NONHUMAN; PRIORITY JOURNAL; PSEUDOMONAS; PSEUDOMONAS DACUNHAE;

ASPARTIC ACID; BACTERIAL PROTEINS; CARBOXY-LYASES; HYDROSTATIC PRESSURE; KINETICS; MUTATION; PROTEIN CONFORMATION; PSEUDOMONAS; PYRIDOXAL PHOSPHATE; SPECTROPHOTOMETRY; STEREOISOMERISM; SUCCINIC ACID;

PSEUDOMONAS DACUNHAE;

EID: 77953661074     PISSN: 00062960     EISSN: 15204995     Source Type: Journal    
DOI: 10.1021/bi100272g     Document Type: Article

References (29)

1. Tate, S. S. and Meister, A. (1971) l -Aspartate-β-decarboxylase: Structure, catalytic activities, and allosteric regulation Adv. Enzymol. Relat. Areas Mol. Biol. 35, 503-543
2. Rathod, P. K. and Fellman, J. H. (1985) Identification of mammalian aspartate-4-decarboxylase Arch. Biochem. Biophys. 238, 435-446
3. Abe, K., Ohnishi, F., Yagi, K., Nakajima, T., Higuchi, T., Sano, M., Machida, M., Sarker, R. I., and Maloney, P. C. (2002) Plasmid-encoded asp operon confers a proton motive metabolic cycle catalyzed by an aspartate-alanine exchange reaction J. Bacteriol. 184, 2906-2913
4. Lima, S., Sundararaju, B., Huang, C., Khristoforov, R., Momany, C., and Phillips, R. S. (2009) The crystal structure of the Pseudomonas dacunhae aspartate-β-decarboxylase dodecamer reveals an unknown oligomeric assembly for a pyridoxal-5′-phosphate-dependent enzyme J. Mol. Biol. 388, 98-108
5. Chen, H. J., Ko, T. P., Lee, C. Y., Wang, N. C., and Wang, A. H. (2009) Structure, assembly, and mechanism of a PLP-dependent dodecameric l -aspartate β-decarboxylase Structure 17, 517-529
6. Jones, C. W., III, Leyden, D. E., and Stammer, C. H. (1969) threo and erythro β-hydroxy- dl -aspartic acids Can. J. Chem. 47, 4363-4366
7. Matheson, I. B. C. (1990) A critical comparison of least absolute deviation fitting (robust) and least-squares fitting: The importance of error distributions Comput. Chem. 14, 49-57
8. Strickland, S., Palmer, G., and Massey, V. (1975) Determination of dissociation constants and specific rate constants of enzyme-substrate (or protein-ligand) interactions from rapid reaction kinetic data J. Biol. Chem. 250, 4048-4052
9. Kitamura, Y. and Itoh, T. (1987) Reaction of protonic ionization for buffering agents J. Solution Chem. 16, 715-725
10. Li, Y.-H. (1967) Equation of state of water and sea water J. Geophys. Res. 72, 2665-2678
11. Soda, K. and Tanizawa, K. (1979) Kynureninases: Enzymological properties and regulation mechanism Adv. Enzymol. Relat. Areas Mol. Biol. 49, 1-40
12. Zheng, L., White, R. H., Cash, V. L., and Dean, D. R. (1994) Mechanism for the desulfurization of l -cysteine catalyzed by the nif S gene product Biochemistry 33, 4714-4720
13. Esaki, N., Karai, N., Nakamura, T., Tanaka, H., and Soda, K. (1985) Mechanism of reactions catalyzed by selenocysteine β-lyase Arch. Biochem. Biophys. 238, 418-423
14. Metzler, C. M. and Metzler, D. E. (1987) Quantitative description of absorption spectra of a pyridoxal phosphate-dependent enzyme using lognormal distribution curves Anal. Biochem. 166, 313-327
15. Novogrodsky, A. and Meister, A. (1964) Control of aspartate β-decarboxylase activity by transamination J. Biol. Chem. 239, 879-888
16. Rosenberg, R. M. and O'Leary, M. H. (1985) Aspartate β-decarboxylase from Alcaligenes faecalis: Carbon-13 kinetic isotope effect and deuterium exchange experiments Biochemistry 24, 1598-1603
17. Miles, E. W. and Meister, A. (1967) The mechanism of the reaction of β-hydroxyaspartate with l -aspartate β-decarboxylase. A new type of pyridoxal 5′-phosphate-enzyme inhibition Biochemistry 6, 1734-1743
18. Jenkins, T. (1969) Glutamic-Aspartic Transaminase VI. The Reaction with Certain β-Substituted Aspartic Acid Analogues J. Biol. Chem. 236, 1121-1125
19. von Stosch, A. G. (1996) Aspartate aminotransferase complexed with erythro -β-hydroxyaspartate: Crystallographic and spectroscopic identification of the carbinolamine intermediate Biochemistry 35, 15260-15268
20. Hayashi, H. and Kagamiyama, H. (1995) Reaction of aspartate aminotransferase with l-erythro -3-hydroxyaspartate: Involvement of Tyr70 in stabilization of the catalytic intermediates Biochemistry 34, 9413-9423
21. a during catalysis Biochemistry 37, 15076-15085
22. Jager, J., Moser, M., Sauder, U., and Jansonius, J. N. (1994) Crystal structures of Escherichia coli aspartate aminotransferase in two conformations. Comparison of an unliganded open and two liganded closed forms J. Mol. Biol. 239, 285-305
23. Phillips, R. S., Miles, E. W., Holtermann, G., and Goody, R. S. (2005) Hydrostatic Pressure Stabilizes the Open Conformation of Salmonella typhimurium Tryptophan Synthase Biochemistry 44, 7921-7928
24. Phillips, R. S., McPhie, P., Miles, E. W., Marchal, S., and Lange, R. (2008) Quantitative Effects of Allosteric Ligands and Mutations on Conformational Equilibria in Salmonella typhimurium Tryptophan Synthase Arch. Biochem. Biophys. 470, 8-19
25. Phillips, R. S., Miles, E. W., Marchal, S., and Lange, R. (2008) Pressure and Temperature Jump Relaxation Kinetics of Salmonella typhimurium Tryptophan Synthase l -Serine Complex Reveal Large Transition State Compressibility and Heat Capacity Changes J. Am. Chem. Soc. 130, 13580-13588
26. Seifert, T., Bartholmes, P., and Jaenicke, R. (1982) Reconstitution of the isolated β2-subunit of tryptophan synthase from Escherichia coli after dissociation induced by high hydrostatic pressure. Equilibrium and kinetic studies Biophys. Chem. 15, 1-8
27. Kogan, A., Gdalevsky, G. Y., Cohen-Luria, R., Goldgur, Y., Phillips, R. S., Parola, A. H., and Almog, O. (2009) Conformational changes and loose packing promote E. coli tryptophanase cold lability BMC Struct. Biol. 9, 65
28. Kallen, R. G., Korpela, T., Martell, A. E., Matsushima, Y., Metzler, C. M., Metzler, D. E., Morozov, Yu. V., Ralston, I. M., Savin, F. A., Torchinsky, Yu. M., and Ueno, H. (1985) in Transaminases (Christen, P. and Metzler, D. E., Eds.) pp 37 - 108, John Wiley & Sons, New York.
29. Guex, N. and Peitsch, M. C. (1997) SWISS-MODEL and the Swiss-PdbViewer: An environment for comparative protein modeling Electrophoresis 18, 2714-2723