Differential inhibition of cytosolic PEPCK by substrate analogues. Kinetic and structural characterization of inhibitor recognition

Biochemistry

Volumn 47, Issue 7, 2008, Pages 2099-2109

  Stiffin, Rose Mary ^b,c   Sullivan, Sarah M ^a   Carlson, Gerald M ^a,b   Holyoak, Todd ^a  

^a UNIVERSITY OF KANSAS SCHOOL OF MEDICINE   (United States)

^b UNIVERSITY OF TENNESSEE HEALTH SCIENCE CENTER   (United States)

^c University Counseling Support Services   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CHEMICAL BONDS; ELECTRONS; ENZYMES; MOLECULAR RECOGNITION;

BINDING GEOMETRY; CYTOSOLIC PHOSPHOENOLPYRUVATE CARBOXYKINASE (CPEPCK); PHOSPHOENOLPYRUVATE (PEP);

CYTOLOGY;

ACETIC ACID DERIVATIVE; CARBENE; CARBONYL DERIVATIVE; CARBOXYLIC ACID; FOSCARNET; GLYCOLIC ACID DERIVATIVE; MANGANESE; OXALOACETIC ACID; PHOSPHOENOLPYRUVATE; PHOSPHOENOLPYRUVATE CARBOXYKINASE (GTP); PROPIONIC ACID DERIVATIVE; SULFONIC ACID DERIVATIVE;

ARTICLE; BINDING AFFINITY; ELECTRON; ENZYME INHIBITION; GEOMETRY; KINETICS; MOLECULAR INTERACTION; PRIORITY JOURNAL; STRUCTURE ANALYSIS;

BINDING SITES; CRYSTALLIZATION; CYTOSOL; ENZYME INHIBITORS; KINETICS; MODELS, MOLECULAR; MOLECULAR STRUCTURE; PHOSPHOENOLPYRUVATE CARBOXYKINASE (GTP);

EID: 39649124209     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi7020662     Document Type: Article

References (36)

1. Beale, E. G., Chrapkiewicz, N. B., Scoble, H. A., Metz, R. J., Quick, D. P., Noble, R. L., Donelson, J. E., Biemann, K., and Granner, D. K. (1985) Rat hepatic cytosolic phosphoenolpyruvate carboxykinase (GTP). Structures of the protein, messenger RNA, and gene, J. Biol. Chem. 260, 10748-10760.
2. Utter, M. F., and Kolenbrander, H. M. (1972) in The Enzymes (Boyer, P. D., Ed.) pp 117-168, Academic Press, New York.
3. Weldon, S. L., Rando, A., Matathias, A. S., Hod, Y., Kalonick, P. A., Savon, S., Cook, J. S., and Hanson, R. W. (1990) Mitochondrial phosphoenolpyruvate carboxykinase from the chicken. Comparison of the cDNA and protein sequences with the cytosolic isozyme, J. Biol. Chem. 265, 7308-7317.
4. Dunten, P., Belunis, C., Crowther, R., Hollfelder, K., Kammlott, U., Levin, W., Michel, H., Ramsey, G. B., Swain, A., Weber, D., and Wertheimer, S. J. (2002) Crystal structure of human cytosolic phosphoenolpyruvate carboxykinase reveals a new GTP-binding site, J. Mol. Biol. 316, 257-264.
5. Holyoak, T., Sullivan, S. M., and Nowak, T. (2006) Structural Insights into the Mechanism of PEPCK Catalysis, Biochemistry 45, 8254-8263.
6. Sullivan, S. M., and Holyoak, T. (2007) Structures of rat cytosolic PEPCK: Insight into the mechanism of phosphorylation and decarboxylation of oxaloacetic acid, Biochemistry 46, 10078-10088.
7. Ash, D. E., Emig, F. A., Chowdhury, S. A., Satoh, Y., and Schramm, V. L. (1990) Mammalian and Avian Liver Phosphoenolpyruvate Carboxykinase - Alternate Substrates and Inhibition by Analogs of Oxaloacetate, J. Biol. Chem. 265, 7377-7384.
8. Guidinger, P. F., and Nowak, T. (1990) Analogs of oxalacetate as potential substrates for phosphoenolpyruvate carboxykinase, Arch. Biochem. Biophys. 278, 131-141.
9. Stubbe, J. A., and Kenyon, G. L. (1972) Analogs of phosphoenolpyruvate. Substrate specificities of enolase and pyruvate kinase from rabbit muscle, Biochemistry 11, 338-345.
10. Duffy, T. H., and Nowak, T. (1985) 1H and 31P relaxation rate studies of the interaction of phosphoenolpyruvate and its analogues with avian phosphoenolpyruvate carboxykinase, Biochemistry 24, 1152-1160.
11. Fitch, C. D., Chevli, R., and Jellinek, M. (1979) Phosphocreatine does not inhibit rabbit muscle phosphofructokinase or pyruvate kinase, J. Biol. Chem. 254, 11357-11359.
12. Izui, K., Matsuda, Y., Kameshita, I., Katsuki, H., and Woods, A. E. (1983) Phosphoenolpyruvate carboxylase of Escherichia coli. Inhibition by various analogs and homologs of phosphoenolpyruvate, J. Biochem. (Tokyo) 94, 1789-1795.
13. Janc, J. W., Cleland, W. W., and O'Leary, M. H. (1992) Mechanistic studies of phosphoenolpyruvate carboxylase from Zea mays utilizing formate as an alternate substrate for bicarbonate, Biochemistry 31, 6441-6446.
14. Janc, J. W., O'Leary, M. H., and Cleland, W. W. (1992) A kinetic investigation of phosphoenolpyruvate carboxylase from Zea mays, Biochemistry 31, 6421-6426.
15. Meyer, C. R., Rustin, P., and Wedding, R. T. (1989) A kinetic study of the effects of phosphate and organic phosphates on the activity of phosphoenolpyruvate carboxylase from Crassula argentea, Arch. Biochem. Biophys. 271, 84-97.
16. Colombo, G., Carlson, G. M., and Lardy, H. A. (1978) Phosphoenolpyruvate carboxykinase (guanosine triphosphate) from rat liver cytosol. Separation of homogeneous forms of the enzyme with high and low activity by chromatography on agarose-hexane-guanosine triphosphate, Biochemistry 17, 5321-5329.
17. Lewis, C. T., Seyer, J. M., and Carlson, G. M. (1989) Cysteine 288: an essential hyperreactive thiol of cytosolic phosphoenolpyruvate carboxykinase (GTP), J. Biol. Chem. 264, 27-33.
18. Nowak, T., and Mildvan, A. S. (1970) Stereoselective interactions of phosphoenolpyruvate analogues with phosphoenolpyruvate-utilizing enzymes, J. Biol. Chem. 245, 6057-6064.
19. Cleland, W. W. (1979) Statistical analysis of enzyme kinetic data, Methods Enzymol. 63, 103-138.
20. Segal, I. H. (1976) in Biochemical Calculations pp 246-273, John Wiley & Sons, New York.
21. Otwinowski, Z., and Minor, W. (1997) Processing of X-ray Diffraction Data Collected in Oscillation Mode, Methods Enzymol. 276, 307-326.
22. Vagin, A., and Teplyakov, A. (1997) MOLREP: an automated program for molecular replacement, J. Appl. Crystallogr. 30, 1022-1025.
23. Bailey, S. (1994) The Ccp4 Suite - Programs for Protein Crystallography, Acta Crystallogr. D50, 760-763.
24. Emsley, P., and Cowtan, K. (2004) Coot: model-building tools for molecular graphics, Acta Crystallogr. D60, 2126-2132.
25. Painter, J., and Merritt, E. A. (2005) A molecular viewer for the analysis of TLS rigid-body motion in macromolecules, Acta Crystallogr. D61, 465-471.
26. Laskowski, R. A., Macarthur, M. W., Moss, D. S., and Thornton, J. M. (1993) Procheck - a Program to Check the Stereochemical Quality of Protein Structures, J. Appl. Crystallogr. 26, 283-291.
27. Reed, G. H., and Morgan, S. D. (1974) Kinetic and magnetic resonance studies of the interaction of oxalate with pyruvate kinase, Biochemistry 13, 3537-3541.
28. Cotelesage, J. J. H., Prasad, L., Zeikus, J. G., Laivenieks, M., and Delbaere, L. T. J. (2005) Crystal structure of Anaerobiospirillum succiniciproducens PEP carboxykinase reveals an important active site loop, Int. J. Biochem. Cell Biol. 37, 1829.
29. Hebda, C. A., and Nowak, T. (1982) The purification, characterization, and activation of phosphoenolpyruvate carboxykinase from chicken liver mitochondria, J. Biol. Chem. 257, 5503-5514.
30. Hebda, C. A., and Nowak, T. (1982) Phosphoenolpyruvate carboxykinase. Mn2+ and Mn2+ substrate complexes, J. Biol. Chem. 257, 5515-5522.
31. Reed, A. E., and Schleyer, P. V. (1990) Chemical Bonding in Hypervalent Molecules - the Dominance of Ionic Bonding and Negative Hyperconjugation over D-Orbital Participation, J. Am. Chem. Soc. 112, 1434-1445.
32. Kanyo, Z. F., and Christianson, D. W. (1991) Biological recognition of phosphate and sulfate, J. Biol. Chem. 266, 4264-4208.
33. Radzicka, A., and Wolfenden, R. (1991) Analogues of intermediates in the action of pig kidney prolidase, Biochemistry 30, 4160-4164.
34. Peng, Z. Y., Mansour, J. M., Araujo, F., Ju, J. Y., McKenna, C. E., and Mansour, T. E. (1995) Some phosphonic acid analogs as inhibitors of pyrophosphate-dependent phosphofructokinase, a novel target in Toxoplasma gondii, Biochem. Pharmacol. 49, 105-113.
35. Harris, W. R., and Nesset-Tollefson, D. (1991) Binding of phosphonate chelating agents and pyrophosphate to apotransferrin, Biochemistry 30, 6930-6936.
36. Brunger, A. T. (1992) Free R-Value - a Novel Statistical Quantity for Assessing the Accuracy of Crystal-Structures, Nature 355, 472-475.