Structural insights into the mechanism of PEPCK catalysis

Biochemistry

Volumn 45, Issue 27, 2006, Pages 8254-8263

  Holyoak, Todd ^a   Sullivan, Sarah M ^a   Nowak, Thomas ^b  

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

^b UNIVERSITY OF NOTRE DAME   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOCHEMISTRY; CARBOXYLATION; CATALYSIS; PHOSPHATES; STABILIZATION;

GLYCERONEOGENESIS; OXALOACETIC ACID; PHOSPHORYL TRANSFER; SERINE RESIDUE;

ENZYMES;

CYSTEINE; GUANOSINE DIPHOSPHATE; GUANOSINE TRIPHOSPHATE; MALONIC ACID; MANGANESE; MERCAPTOETHANOL; METAL COMPLEX; OXALOACETIC ACID; PHOSPHOENOLPYRUVATE CARBOXYKINASE (GTP); SERINE;

ARTICLE; CARBOXYLATION; CATALYSIS; COMPLEX FORMATION; CRYSTAL STRUCTURE; DECARBOXYLATION; ENZYME ACTIVE SITE; ENZYME MECHANISM; ENZYME STRUCTURE; GLUCONEOGENESIS; HYDROGEN BOND; PH; PRIORITY JOURNAL; PROTON TRANSPORT; SACCHAROMYCES CEREVISIAE; STEREOCHEMISTRY;

ANIMALS; CATALYSIS; CHICKENS; CRYSTALLOGRAPHY, X-RAY; CYSTEINE; DIMERIZATION; ISOENZYMES; MANGANESE; MITOCHONDRIA; PROTEIN CONFORMATION; PROTEIN-SERINE-THREONINE KINASES;

EID: 33745814413     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi060269g     Document Type: Article

References (50)

1. Guidinger, P. F., and Nowak, T. (1990) Analogs of oxalacetate as potential substrates for phosphoenolpyruvate carboxykinase, Arch. Biochem. Biophys. 278, 131-41.
2. Lee, M. H., Hebda, C. A., and Nowak, T. (1981) The role of cations in avian liver phosphoenolpyruvate carboxykinase catalysis. Activation and regulation, J. Biol. Chem. 256, 12793-801.
3. Croniger, C. M., Chakravarty, K., Olswang, Y., Cassuto, H., Reshef, L., and Hanson, R. W. (2002) Phosphoenolpyruvate carboxykinase revisited II. Control of PEPCK-C gene expression, Biochem. Mol. Biol. Educ. 30, 353-62.
4. Croniger, C. M., Olswang, Y., Reshef, L., Kalhan, S. C., Tilghman, S. M., and Hanson, R. W. (2002) Phosphoenolpyruvate carboxykinase revisited: Insights into its metabolic role. Biochem. Mol. Biol. Educ. 30, 14-20.
5. Delbaere, L. T. J., Sudom, A. M., Prasad, L., Leduc, Y., and Goldie, H. (2004) Structure/function studies of phosphoryl transfer by phosphoenolpyruvate carboxykinase, Biochim. Biophys. Acta 1697, 271-8.
6. Matte, A., Tari, L. W., Goldie, H., and Delbaere, L. T. (1997) Structure and mechanism of phosphoenolpyruvate carboxykinase, J. Biol. Chem. 272, 8105-8.
7. Sudom, A. M., Prasad, L., Goldie, H., and Delbaere, L. T. J. (2001) The phosphoryl-transfer mechanism of Escherichia coli phosphoenolpyruvate carboxykinase from the use of AlF3, J. Mol. Biol. 314, 83-92.
8. 2+ clusters in enzyme-catalyzed phosphoryl-transfer reactions, Nat. Struct. Biol. 4, 990-4.
9. Chen, C. Y., Sato, Y., and Schramm, V. L. (1991) Isotope trapping and positional isotope exchange with rat and chicken liver phosphoenolpyruvate carboxykinases. Biochemistry 30, 4143-51.
10. Konopka, J. M., Lardy, H. A., and Frey, P. A. (1986) Stereochemical course of thiophosphoryl transfer catalyzed by cytosolic phosphoenolpyruvate carboxykinase, Biochemistry 25, 5571-5.
11. Sheu, K. F., Ho, H. T., Nolan, L. D., Markovitz, P., Richard, J. P., Utter, M. F., and Frey, P. A. (1984) Stereochemical course of thiophosphoryl group transfer catalyzed by mitochondrial phosphoenolpyruvate carboxykinase, Biochemistry 23, 1779-83.
12. Consoli, A., Nurjhan, N., Capani, F., and Gerich, J. (1989) Predominant Role of Gluconeogenesis in Increased Hepatic Glucose-Production in Niddm, Diabetes 38, 550-7.
13. Magnusson, I., Rothman, D. L., Katz, L. D., Shulman, R. G., and Shulman, G. I. (1992) Increased Rate of Gluconeogenesis in Type-Ii Diabetes-Mellitus: A C-13 Nuclear-Magnetic-Resonance Study, J. Clin. Invest. 90, 1323-7.
14. Gomez-Valades, A. G., Vidal-Alabro, A., Molas, M., Boada, J., Bermudez, J., Bartrons, R., and Perales, J. C. (2006) Overcoming Diabetes-Induced Hyperglycemia through Inhibition of Hepatic Phosphoenolpyruvate Carboxykinase (GTP) with RNAi, Mol. Ther. 13, 401.
15. 2+ substrate complexes, J. Biol. Chem. 257, 5515-22.
16. Hwang, S. H., and Nowak, T. (1986) Stereochemistry of phosphoenolpyruvate carboxylation catalyzed by phosphoenolpyruvate carboxykinase, Biochemistry 25, 5590-5.
17. Holyoak, T., and Nowak, T. (2004) pH dependence of the reaction catalyzed by avian mitochondrial phosphoenolpyruvate carboxykinase, Biochemistry 43, 7054-65.
18. 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, 257-64.
19. Holyoak, T., Fenn, T. D., Wilson, M. A., Moulin, A. G., Ringe, D., and Petsko, G. A. (2003) Malonate: A versatile cryoprotectant and stabilizing solution for salt-grown macromolecular crystals, Acta Crystallogr. D59, 2356-8.
20. Lee, M. H., and Nowak, T. (1984) Phosphorus-31 nuclear relaxation rate studies of the nucleotides on phosphoenolpyruvate carboxykinase, Biochemistry 23, 6506-13.
21. Hebda, C. A., and Nowak, T. (1982) The purification, characterization, and activation of phosphoenolpyruvate carboxykinase from chicken liver mitochondria, J. Biol. Chem. 257, 5503-14.
22. Otwinowski, Z., and Minor, W. (1997) Processing of X-ray Diffraction Data Collected in Oscillation Mode, in Methods in Enzymology (Carter, C. W., Jr., and Sweet, R. M., Eds.) pp 307-26, Academic Press, New York.
23. Schwede, T., Kopp, J., Guex, N., and Peitsch, M. C. (2003) SWISS-MODEL: An automated protein homology-modeling server, Nucleic Acids Res. 31, 3381-5.
24. Vagin, A., and Teplyakov, A. (1997) MOLREP: An automated program for molecular replacement, J. Appl. Crystallogr. 30, 1022-5.
25. Bailey, S. (1994) The Ccp4 Suite: Programs for Protein Crystallography, Acta Crystallogr. D50, 760-3.
26. Murshudov, G. N., Vagin, A. A., and Dodson, E. J. (1997) Refinement of macromolecular structures by the maximum-likelihood method, Acta Crystallogr. D53, 240-55.
27. Emsley, P., and Cowtan, K. (2004) Coot: Model-building tools for molecular graphics, Acta Crystallogr. D60, 2126-32.
28. Painter, J., and Merritt, E. A. (2005) A molecular viewer for the analysis of TLS rigid-body motion in macromolecules, Acta Crystallogr. D61, 465-71.
29. 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. D54 (Part 5), 905-21.
30. 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, 283-91.
31. 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, 7308-17.
32. Holyoak, T. (2000) Kinetic, structural and genetic characterization of phosphoenolpyruvate carboxykinase, Ph.D. Thesis, University of Notre Dame, Notre Dame, IN.
33. Foley, L. H., Wang, P., Dunten, P., Ramsey, G., Gubler, M.-L., and Wertheimer, S. J. (2003) X-ray structures of two xanthine inhibitors bound to PEPCK and N-3 modifications of substituted 1,8-dibenzylxanthines, Bioorg. Med. Chem. Lett. 13, 3871.
34. Matte, A., Goldie, H., Sweet, R. M., and Delbaere, L. T. (1996) Crystal structure of Escherichia coli phosphoenolpyruvate carboxykinase: A new structural family with the P-loop nucleoside triphosphate hydrolase fold, J. Mol. Biol. 256, 126-43.
35. Encinas, M. V., Gonzalez-Nilo, F. D., Goldie, H., and Cardemil, E. (2002) Ligand interactions and protein conformational changes of phosphopyridoxyl- labeled Escherichia coli phosphoenolpyruvate carboxykinase determined by fluorescence spectroscopy, Eur. J. Biochem. 269, 4960-8.
36. 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.
37. Lewis, C. T., Haley, B. E., and Carlson, G. M. (1989) Formation of an intramolecular cystine disulfide during the reaction of 8-azidoguanosine 5′-triphosphate with cytosolic phosphoenolpyruvate carboxykinase (GTP) causes inactivation without photolabeling, Biochemistry 28, 9248-55.
38. Lewis, C. T., Seyer, J. M., and Carlson, G. M. (1992) Photochemical cross-linking of guanosine 5′-triphosphate to phosphoenolpyruvate carboxykinase (GTP), Bioconjugate Chem. 3, 160-6.
39. Makinen, A. L., and Nowak, T. (1989) A reactive cysteine in avian liver phosphoenolpyruvate carboxykinase, J. Biol. Chem. 264, 12148-57.
40. Lewis, C. T., Seyer, I. M., and Carlson, G. M. (1989) Cysteine 288: An essential hyperreactive thiol of cytosolic phosphoenolpyruvate carboxykinase (GTP), J. Biol. Chem. 264, 27-33.
41. Alvear, M., Encinas, M. V., Kemp, R. G., Latshaw, S. P., and Cardemil, E. (1992) ATP-dependent Saccharomyces cerevisiae phosphoenolpyruvate carboxykinase: Isolation and sequence of a peptide containing a highly reactive cysteine, Biochim. Biophys. Acta 1119, 35-8.
42. Encinas, M. V., Quinones, V., and Cardemil, E. (1990) Saccharomyces cerevisiae phosphoenolpyruvate carboxykinase: Physicochemical characteristics of the nucleotide binding site, as deduced from fluorescent spectroscopy measurements, Biochemistry 29, 4548-53.
43. Hlavaty, J. J., and Nowak, T. (1997) Formation and characterization of an active phosphoenolpyruvate carboxykinase-cobalt(III) complex, Biochemistry 36, 3389-403.
44. Arinze, I. J., Garber, A. J., and Hanson, R. W. (1973) The regulation of gluconeogenesis in mammalian liver. The role of mitochondrial phosphoenolpyruvate carboxykinase, J. Biol. Chem. 248, 2266-74.
45. Hopgood, M. F., Ballard, F. J., Reshef, L., and Hanson, R. W. (1973) Synthesis and degradation of phospoenolpyruvate carboxykinase in rat liver and adipose tissue, Biochem. J. 134, 445-53.
46. Felicioli, R. A., Barsacchi, R., and Ipata, P. L. (1970) Chicken liver mitochondrial phosphoenolpyruvate carboxykinase. Kinetic studies, Eur. J. Biochem. 13, 403-9.
47. Jomain-Baum, M., and Schramm, V. L. (1978) Kinetic mechanism of phosphoenolpyruvate carboxykinase (GTP) from rat liver cytosol. Product inhibition, isotope exchange at equilibrium, and partial reactions, J. Biol. Chem. 253, 3648-59.
48. Metchkarova, M. (2001) Kinetic mechanism of avian mitochondrial phosphoenolpyruvate carboxykinase, M.S. Thesis, University of Notre Dame, Notre Dame, IN.
49. Holmes, R. R. (2004) Phosphoryl transfer enzymes and hypervalent phosphorus chemistry, Acc. Chem. Res. 37, 746-53.
50. Brunger, A. T. (1992) Free R-Value: A Novel Statistical Quantity for Assessing the Accuracy of Crystal-Structures, Nature 355, 472-5.