Snapshot of an enzyme reaction intermediate in the structure of the ATP-Mg2+-oxalate ternary complex of Escherichia coli PEP carboxykinase

Nature Structural Biology

Volumn 3, Issue 4, 1996, Pages 355-363

  Tari, Leslie W ^a   Matte, Allan ^a   Pugazhenthi, Umarani ^a   Goldie, Hughes ^a   Delbaere, Louis T J ^a  

^a UNIVERSITY OF SASKATCHEWAN   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

ADENOSINE TRIPHOSPHATE; BACTERIAL ENZYME; MAGNESIUM ION; OXALIC ACID; OXALOACETIC ACID; PHOSPHOENOLPYRUVATE; PHOSPHOPYRUVATE CARBOXYLASE;

ARTICLE; CHEMICAL REACTION; CITRIC ACID CYCLE; CRYSTAL STRUCTURE; ENZYME ACTIVE SITE; ENZYME MECHANISM; ENZYME SUBSTRATE; ESCHERICHIA COLI; GLUCONEOGENESIS; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN DOMAIN; SEQUENCE ANALYSIS;

ADENOSINE TRIPHOSPHATE; AMINO ACID SEQUENCE; BINDING SITES; CRYSTALLOGRAPHY, X-RAY; ESCHERICHIA COLI; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; OXALATES; PHOSPHOENOLPYRUVATE CARBOXYKINASE (GTP); PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEIN STRUCTURE, TERTIARY;

BACTERIA (MICROORGANISMS); ESCHERICHIA COLI;

EID: 0029989464     PISSN: 10728368     EISSN: None     Source Type: Journal    
DOI: 10.1038/nsb0496-355     Document Type: Article

References (56)

1. 2 fixation on phosphoenolpyruvate. In The Enzymes (Boyer, P. D. ed.), 6, 117-168 (1972).
2. Williamson, J.R. Effects of fatty acids, glucagon, and anti-insulin serum on the control of gluconeogenesis and ketogenesis in rat liver. Adv. Enzyme Regul. 5, 229-254 (1967).
3. Valera, A., Pujol, A., Pelegrin, M. & Bosch, F. Transgenic mice overexpressing phosphoenolpyruvate carboxykinase develop noninsulin-dependent diabetes mellitus. Proc. Natl. Acad. Sci. USA 91, 9151-9154 (1994).
4. Hanson, R.W. & Patel, Y.M. Phosphoenolpyruvate carboxykinase (GTP): the gene and the enzyme. Adv. Enzymol. 68, 203-281 (1994).
5. Jomain-Baum, M. & Schramm, V.L. Kinetic mechanism of phosphoenolpyruvate carboxykinase (GTP) from rat liver cytosol. J. Biol. Chem. 253, 3648-3659 (1978).
6. Krebs, A. & Bridger, W.A. The kinetic properties of phosphoenolpyruvate carboxykinase of Escherichia coli. Can. J. Biochem. 58, 309-318 (1980).
7. Chen, C., Sato, Y. & Schramm, V.L. Isotope trapping and positional isotope exchange with rat and chicken liver phosphoenolpyruvate carboxykinases. Biochemistry 30, 4143-4151 (1991).
8. Malebrán, L.P. & Cardemil, E. The presence of functional arginine residues in phosphoenolpyruvate carboxykinase from Saccharomyces cerevisiae. Biochim. Biophys. Acta 915, 385-392 (1987).
9. Makinen, A.L. & Nowak, T. A reactive cysteine in avian liver phosphoenolpyruvate carboxykinase. J. Biol. Chem. 264, 12148-12157 (1989).
10. Cheng, K. & Nowak, T. A histidine residue at the active site of avian liver phosphoenolpyruvate carboxykinase. J. Biol. Chem. 264, 19666-19676 (1989).
11. Guidinger, P.F. & Nowak, T. An active site lysine in avain liver phosphoenolpyruvate carboxykinase. Biochemistry 30, 8851-8861 (1991).
12. Bazeaes, S., Silva, R., Goldie, H., Cardemil, E. & Jabalquinto, A. M. Reactivity of cysteinyl, arginyl and lysyl residues of Escherichia coli phosphoenolpyruvate carboxykinase against group-specific chemical reagents. J. Protein Chem. 12, 571-577 (1993).
13. Rojas, M.C., Encinas, M.V., Kemp, R.G., Latshaw, S.P. & Cardemil, E. Identification of reactive vicinal cysteines in Saccharomyces cerevisiae (ATP) and cytosolic rat liver (GTP) phosphoenolpyruvate carboxykinases. Biochim. Biophys. Acta 1164, 143-151 (1993).
14. Bazaes, S., Goldie, H., Cardemil, E. & Jabalquinto, A.M. Identification of reactive lysines in phosphoenolpyruvate carboxykinases from Escherichia coli and Saccharomyces cerevisiae. FEBS Letters 360, 207-210 (1995).
15. Krautwurst, H. et al. Saccharomyces cerevisiae phosphoenolpyruvate carboxykinase: revised amino acid sequence, site-directed mutagenesis, and microenvironment characteristics of cysteines 365 and 458. Biochemistry 34, 6382-6388 (1995).
16. Lee, M.H., Hebda, C.A. & Nowak, T. The role of cations in avian liver phosphoenolpyruvate carboxykinase catalysis. J. Biol. Chem. 256, 12793-12801 (1981).
17. 2+ substrate complexes. J. Biol. Chem. 257, 5515-5522 (1982).
18. 2+ in the regulation of cytosolic phosphoenolpyruvate carboxykinase from rat liver is unlikely. Biochem. J. 292, 365-370 (1993).
19. Miller, R.S. & Lane, M.D. The enzymatic carboxylation of phosphoenolpyruvate. J. Biol. Chem., 243, 6041-6049 (1968).
20. Sheu, K. et al. Stereochemical course of thiophosphoryl group transfer catalyzed by mitochondrial phosphoenolpyruvate carboxykinase. Biochemistry 23, 1779-1783 (1984).
21. Ash, D.E. et al. Mammalian and avian liver phosphoenolpyruvate carboxykinase: alternate substrates and inhibition by analogues of oxaloacetate. J. Biol. Chem. 265, 7377-7384 (1990).
22. Matte, A., Goldie, H., Sweet, R.M. & Delbaere, L.T.J. Crystal structure of Escherichia coli phosphoenolpyruvate carboxykinase - a new structural family with the P-loop nucleoside triphosphate hydrolase fold. J. Mol. Biol. 256, 126-143 (1996).
23. Ramakrishnan, C. & Ramachandran, G.N. Stereochemical criteria for polypeptide and protein chain conformations II. Allowed conformations for a pair of peptide units. Biophys. J. 5, 909-933 (1965).
24. Rose, G.D., Gierasch, L.M. & Smith, J.A. Turns in peptides and proteins. Adv. Protein Chem. 37, 1-109 (1985).
25. Murzin, A.G., Brenner, S.E., Hubbard, T. & Chothia, C. SCOP: A structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol., 247, 536-540 (1995).
26. Saraste, M., Sibbald, P.R. & Wittinghofer, A. The P-loop - a common motif in ATP- and GTP-binding proteins. Trends Biochem. Sci. 15, 430-434 (1990).
27. Holm, L. & Sander, C. Protein structure comparison by alignment of distance matrices. J. Mol. Biol. 233, 123-138 (1993).
28. Schulz, G.E., Müller, C.W. and Diederichs, K. Induced-fit movements in adenylate kinases. J. Mol. Biol. 213, 627-630 (1990).
29. Bennett, W.S. & Steitz, T.A. Structure of a complex between yeast hexokinase A and glucose. J. Mol. Biol. 140, 211-230 (1980).
30. Gerstein, M., Lesk, A.M. & Chothia, C. Structural mechanisms for domain movements in proteins. Biochemistry 33, 6739-6749 (1994).
31. Traut, T.W. The functions and consensus motifs of nine types of peptide segments that form different types of nucleotide-binding sites. Eur. J. Biochem. 222, 9-19 (1994).
32. 5A refined at 1.9 Å resolution. J. Mol. Biol. 224, 159-177 (1992).
33. Story, R.M. & Steitz, T.A. Structure of the recA protein-ADP complex. Nature 355, 374-376 (1992).
34. Milner-White, E.J., Coggins, J.R. and Anton, I.A. Evidence for an ancestral core structure in nucleotide-binding proteins with the type A motif. J. Mol. Biol. 221, 751-754 (1991).
35. Altona, C. & Sundaralingam, M. Conformational analysis of the sugar ring in nucleosides and nucleotides. A new description using the concept of pseudorotation. J. Amer. Chem. Soc. 94, 8205-8212 (1972).
36. Saran, A., Perahia, D. & Pullman, B. Molecular orbital calculations on the conformation of nucleic acids and their constituents. VII. Conformation of the sugar ring in β-nucleosides: The pseudorotational representation. Theor. Chim. Acta 30, 31-44 (1973).
37. Rhodes, L.M. & Schimmel, P.R. Nanosecond relaxation processes in aqueous mononucleoside solution. Biochemistry 10, 4426-4433 (1971).
38. Encinas, M.V., Rojas, M.C., Goldie, H. & Cardemil, E. Comparative steady-state fluorescence studies of cytosolic rat liver (GTP), Saccharomyces cerevisiae (ATP) and Escherichia coli (ATP) phosphoenolpyruvate carboxykinases. Biochim. Biophys. Acta 1162, 195-202 (1993).
39. Alvear, M. et al. Identification of reactive vicinal cysteines in Saccharomyces cerevisiae (ATP) and cytosolic rat liver (GTP) phosphoenolpyruvate carboxykinases. Biochim. Biophys. Acta 1119, 35-38 (1992).
40. Lewis, C.T., Seyer, J.M. & Carlson, G.M. Cysteine 288: An essential hyperreactive thiol of cytosolic phosphoenolpyruvate carboxykinase (GTP). J. Biol. Cnem. 264, 27-33 (1989).
41. Wigley, D.B. et al. Crystal structure of an N-terminal fragment of the DNA gyrase B protein. Nature, 351, 624-629 (1991).
42. Berchtold, H. et al. Crystal structure of active elongation factor Tu reveals major domain rearrangements. Nature 365, 126-132 (1993).
43. Pai, E.F. et al. Structure of the guanine-nucleotide-binding domain of the Ha-ras oncogene product p21 in the triphosphate conformation. Nature 341, 209-214 (1989).
44. Jabalquinto, A.M. & Cardemil, E. The kinetic mechanism of yeast phosphoenolpyruvate carboxykinase. Biochim. Biophys. Acta 1161, 85-90 (1993).
45. Konopka, J.M., Lardy, H.A. & Frey, P.A. Stereochemical course of thiophosphoryl transfer catalyzed by cytosolic phosphoenolpyruvate carboxykinase. Biochemistry, 25, 5571-5575 (1986).
46. Sakabe, N. A focusing Weissenberg camera with multi-layer-line screens for macromolecular crystallography. J. Appl. Crystallogr. 16, 542-547 (1983).
47. Higashi, T. The processing of diffraction data taken on a screenless Weissenberg camera for macromolecular crystallography. J. Appl. Crystallgr. 22, 9-18 (1989).
48. Collaborative Computational Project #4. The CCP4 suite: Programs for protein crystallography. Acta Crystallogr. D50, 760-763 (1994).
49. French, S. & Wilson, K. On the treatment of negative intensity observations. Acta Crystallogr. A34, 517-525 (1978).
50. Delbaere, L.T.J. et al. Crystallization of calcium-activated phosphoenolpyruvate carboxykinase from Escherichia coli K12. J. Mol. Biol. 219, 593-594 (1991).
51. Matthews, B.W. Solvent content of protein crystals. J. Mol. Biol. 33, 491-497 (1968).
52. Brünger, A.T. X-PLOR Manual, Version 3.1, (Yale University Press, New Haven, USA 1993).
53. Roussel, A. & Cambillau, C. TURBO FRODO. in Silicon Graphics Geometry Partner Directory, 77-88, (Silicon Graphics, Mountain View, CA1989).
54. Engh, R.A. & Huber, R. Accurate bond and angle parameters for x-ray protein structure refinement. Acta Crystallogr. A47, 392-400 (1991).
55. Evans, S.V. SETOR: Hardware-lighted three-dimensional solid model representations of macromolecules. J. Mol. Graphics 11, 134-138 (1993).
56. Nicholls, A., Sharp, K. & Honig. B. GRASP Manual, (Columbia University, New York, NY 1992).