Aspartate transcarbamylase (ATCase) of Escherichia coli: A new crystalline R-state bound to PALA, or to product analogues citrate and phosphate

Biochemistry

Volumn 43, Issue 21, 2004, Pages 6415-6421

  Huang, Jingwei ^a   Lipscomb, William N ^a  

^a HARVARD UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACIDS; CRYSTALLINE MATERIALS; CRYSTALLOGRAPHY; ESCHERICHIA COLI; MOLECULAR STRUCTURE;

HOLOENZYMES;

ENZYMES;

ASPARTATE CARBAMOYLTRANSFERASE; BACTERIAL ENZYME; CARBAMOYL PHOSPHATE; CARBAMYL SUCCINATE; CITRIC ACID; HOLOENZYME; MALONIC ACID; PHOSPHATE; PHOSPHONOACETAMIDE; PHOSPHONOACETIC ACID; SPARFOSIC ACID; UNCLASSIFIED DRUG;

ARTICLE; CRYSTAL STRUCTURE; CRYSTALLOGRAPHY; ENZYME STRUCTURE; ESCHERICHIA COLI; NONHUMAN; PRIORITY JOURNAL; PROTEIN STRUCTURE; X RAY CRYSTALLOGRAPHY;

ASPARTATE CARBAMOYLTRANSFERASE; ASPARTIC ACID; BINDING SITES; CITRATES; CRYSTALLOGRAPHY, X-RAY; ESCHERICHIA COLI PROTEINS; HOLOENZYMES; MODELS, MOLECULAR; PHOSPHATES; PHOSPHONOACETIC ACID; PROTEIN CONFORMATION;

BACTERIA (MICROORGANISMS); ESCHERICHIA COLI; GENETTA;

EID: 2542569639     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi030213b     Document Type: Article

References (37)

1. Gerhart, J. C., and Pardee, A. B. (1962) Enzymology of control by feedback inhibition, J. Biol. Chem. 237, 891-896.
2. Wild, J. R., Loughrey-Chen, S. J., and Corder, T. S. (1989) In the presence of CTP, UTP becomes an allosteric inhibitor of aspartate transcarbamylase, Proc. Natl. Acad. Sci. U.S.A. 86, 46-50.
3. Collins, K. D., and Stark, G. R. (1971) Aspartate transcarbamylase: interaction with the transition state analogue N-(phosphonacetyl)-L-aspartate, J. Biol. Chem. 246, 6599-6605.
4. Swyryd, E. A., Seaver, S. S., and Stark, G. R. (1974) N-(phosphonacetyl)-L-aspartate, a potent transition state analogue of aspartate transcarbamylase, blocks proliferation of mammalian cells in culture, J. Biol. Chem. 249, 6945-6950.
5. Weber, K. (1968) New structural model of E. coli aspartate transcarbamylase and the amino acid sequence of the regulatory polypeptide chain, Nature 218, 1116-1119.
6. Wiley, D. C., and Lipscomb, W. N. (1968) Crystallographic determination of symmetry of aspartate transcarbamylase: studies of trigonal and tetragonal crystalline forms of aspartate transcarbamylase show that the molecule has a three-fold and a two-fold symmetry axis, Nature 218, 1119-1121.
7. Honzatko, R. B., Crawford, J. L., Monaco, H. L., Ladner, J. E., Edwards, B. F. P., Evans, D. R., Warren, S. G., Wiley, D. C., and Ladner, R. C., Lipscomb, W. N. (1982) Crystal and molecular structures of native and CTP-liganded aspartate carbamoyltransferase from Escherichia coli, J. Mol. Biol. 160, 219-263.
8. Stevens, R. C., Gouaux, J. E., and Lipscomb, W. N. (1990) Structural consequences of effector binding to the T state of aspartate carbamoyltransferase: crystal structures of the unligated and ATP- and CTP-complexed enzymes at 2.6 Å resolution, Biochemistry 29, 7691-7701.
9. Ke, H. M., Lipscomb, W. N., Cho, Y., and Honzatko R. B. (1988) Complex of N-(phosphonacetyl)-L-aspartate with aspartate carbamoyltransferase: X-ray refinement, analysis of conformational changes and catalytic and allosteric mechanisms, J. Mol. Biol. 204, 725-747.
10. Jin, L., Stec, B., Lipscomb, W. N., and Kantrowitz, E. R. (1999) Proteins: Struct., Funct. Genet. 37, 727-742.
11. Svergun, D. I., Barberato, C., Koch, M. H. J., Fetler, L., and Vachette, P.(1997) Large differences are observed between the crystal and solution quaternary structures of allosteric aspartate transcarbamylase in the R-state, Proteins 27, 110-117.
12. Fetler, L., and Vachette, P. (2001) The allosteric activator Mg-ATP modifies the quaternary structure of the R-state of Escherichia coli aspartate transcarbamylase without altering the T↔R equilibrium, J. Mol. Biol. 309, 817-831.
13. Nowlan, S. F., and Kantrowitz, E. R.(1985) Superproduction and rapid purification of E. coli aspartate transcarbamoylase and its catalytic subunit under extreme derepression of the pyrimidine pathway, J. Biol. Chem. 260, 14712-14716.
14. Xu, W., Pitts, M. A., Middleton, S. A., Kelleher, K. S., and Kantrowitz, E. R. (1988) Propagation of allosteric changes through the catalytic-regulatory interface of Escherichia coli aspartate transcarbamylase, Biochemistry 27, 5507-5515.
15. Porter, R. W., Modebe, M. O., and Stark, G. R. (1969) Aspartate Transcarbamylase: kinetic studies of the catalytic subunit, J. Biol. Chem. 244, 1846-1850.
16. Masood, R., and Venkitasubramanian, T. A. (1987) Role of various carbon and nitrogen sources in the regulation of enzymes of pyrimidine biosynthesis in Mycobacterium smegmatis TMC 1546, Ann. Inst. Pasteur/Microbiol. 138, 501-507.
17. Navaza, J. (1994) AMoRe: an automated package for molecular replacement, Acta Crystallogr., Sect. A: Found. Crystallogr. 50, 157-163.
18. Kleywegt, G. J., and Jones, T. A.(1998) Databases in protein crystallography, Acta Crystallogr., Sect. D: Biol. Crystallogr. 54, 1119-1131.
19. Brunger, A. T., Adams, P. D., Clore, G. M., DeLano, W. L., Gros, P., Grosse-Kunstleve, R. W., Jiang, J.-S., Kuszewski, J., Nilges, N., Pannu, N. S., Read, R. J., Rice, L. M., Simonson, T., and Warren, G. L. (1998) Crystallography and NMR system (CNS): A new software system for macromolecular structure determination, Acta Crystallogr., Sect. D: Biol. Crystallogr. 54, 905-921.
20. Jones, T. A., Zou, J.-Y., Cowan, S. W., and Kjeldgaard, M. (1991) Improved Methods for Building Protein Models in Electron Density Maps and the Location of Errors in these Models, Acta Crystallogr., Sect. A: Found. Crystallogr. 47, 110-119.
21. 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. App. Crystallogr. 26, 283-291.
22. Jones, S., and Thornton, J. M. (1996) Principles of Protein-Protein Interactions Derived From Structural Studies, Proc. Natl. Acad. U.S.A. 93, 13-20.
23. Luzzati, V. (1952) Traitement statistique des erreurs dans la determination des structures cristallines, Acta Crystallogr. 5, 802-810.
24. Delano, W. L. (2002) The PyMOL molecular graphic system, San Carlos, CA, Delano Scientific.
25. Kraulis, P. J. (1991) MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures, J. Appl. Crystallogr. 24, 946-950.
26. Esnouf, R. M. (1999) Further additions to MolScript version 1.4, including reading and contouring of electron-density maps, Acta Crystallogr., Sect. D: Biol. Crystallogr. 55, 938-940.
27. Gouaux, J. E., and Lipscomb, W. N.(1988) Three-dimensional structure of carbamoyl phosphate and succinate bound to aspartate carbamoyltransferase, Proc. Natl. Acad. U.S.A. 85, 4205-4208.
28. Gouaux, J. E., and Lipscomb, W. N. (1990) Crystal structure of phosphonoacetamide ligated T and phosphonoacetamide and malonate ligated R states of aspartate carbamoyltransferase at 2.8 Å resolution and neutral pH, Biochemistry 29, 389-402.
29. Gouaux, J. E., Krause, K. L., and Lipscomb, W. N. (1987) The catalytic mechanism of Escherichia coli aspartate carbamoyltransferase: a molecular modeling study, Biochem. Biophys. Res. Commun. 142, 893-897.
30. Robey, E. A., Wente, S. R., Markby, D. W., Flint, A., Yang, Y. R., and Schachman, H. K. (1986) Effect of amino acid substitutions on the catalytic and regulatory properties of aspartate transcarbamoylase, Proc. Natl. Acad. Sci. U.S.A. 83, 5934-5938.
31. Waldrop, G. L., Urbauer, J. L., and Cleland, W. W. (1992) Nitrogen-15 isotope effects on nonenzymic and aspartate transcarbamylase catalyzed reactions of carbamyl phosphate, J. Am. Chem. Soc. 114, 5941-5945.
32. Bürgi, H. B., and Dunitz, J. D. (1983) From crystal statics to chemical dynamics, Acc. Chem. Res. 16, 153-161.
33. Christianson, D. W., and Lipscomb, W. N. (1988) Comparison of carboxypeptidase A and thermolysin: inhibition by phosphonamidates, J. Am. Chem. Soc. 110, 5560-5565.
34. Christianson, D. W., and Lipscomb, W. N. (1989) Carboxypeptidase A, Acc. Chem. Res. 22, 62-69.
35. Hur, S., and Bruice, T. C. (2002) The mechanism of catalysis of the chorismate to prephenate reaction by the Escherichia coli mutase enzyme, Proc. Natl. Acad. U.S.A. 99, 1176-1181.
36. Lightstone, F. C., and Bruice, T. C. (1996) Ground State Conformations and Entropic and Enthalpic Factors in the Efficiency of Intramolecular and Enzymic Reactions. 1. Cyclic Anhydride Formation by Substituted Glutarates, Succinate, and 3,6-Endoxo-Δ4-tetrahydrophthalate Monophenyl Esters, J. Am. Chem. Soc. 118, 2595-2605.
37. Bruice, T. C., and Lightstone, F. C. (1999) Ground State and Transition State Contributions to the Rate of Intramolecular and Enzymic Reactions, Acc. Chem. Res. 32, 127-136.