Intersubunit hydrogen bond acts as a global molecular switch in Escherichia coli aspartate transcarbamoylase

Proteins: Structure, Function and Genetics

Volumn 33, Issue 3, 1998, Pages 430-443

  Ha, Ya ^a   Allewell, Norma M ^a  

^a UNIVERSITY OF MINNESOTA   (United States)

Author keywords

Allostery; Long range interactions; Protein crystallography; Pyrimidine biosynthesis; Site directed mutagenesis

Indexed keywords

ASPARTATE CARBAMOYLTRANSFERASE;

ALLOSTERISM; AMINO ACID SUBSTITUTION; ARTICLE; BINDING AFFINITY; CONFORMATIONAL TRANSITION; CRYSTAL STRUCTURE; ENZYME ACTIVE SITE; ENZYME MECHANISM; ENZYME STRUCTURE; ESCHERICHIA COLI; HYDROGEN BOND; MOLECULAR DYNAMICS; MOLECULAR INTERACTION; NONHUMAN; PH; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN QUATERNARY STRUCTURE; PROTEIN TERTIARY STRUCTURE; STRUCTURE ACTIVITY RELATION;

AMINO ACID SEQUENCE; ASPARTATE CARBAMOYLTRANSFERASE; ESCHERICHIA COLI; HYDROGEN BONDING; MOLECULAR SEQUENCE DATA; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEIN STRUCTURE, TERTIARY;

BACTERIA (MICROORGANISMS); ESCHERICHIA COLI; NEGIBACTERIA;

EID: 0032533412     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1097-0134(19981115)33:3<430::AID-PROT11>3.0.CO;2-O     Document Type: Article

References (42)

1. Schachman, H.K. From allostery to mutagenesis: 20 years with aspartate transcarbamoylase. Biochem. Soc. Trans. 15:772-775, 1987.
2. Allewell, N.M. Escherichia coli aspartate transcarbamoylase: Structure, energetics, and catalytic and regulatory mechanisms. Annu. Rev. Biophys. Biophys. Chem. 18:71-92, 1989.
3. Hervé, G. Aspartate transcarbamoylase from Escherichia coli. In: "Allosteric Enzymes." Hervé, G. (ed.). Boca Raton, FL: CRC Press, 1989;61-79.
4. Kantrowitz, E.R., Lipsomb, W.N. Escherichia coli aspartate transcarbamoylase: The molecular basis for a concerted allosteric transition. Trends Biochem. Sci. 15:53-59, 1990.
5. Wild, J.R., Wales, M.E. Molecular evolution and genetic engineering of protein domains involving aspartate transcarbamoylase. Annu. Rev. Microbiol. 44:193-218, 1990.
6. Lipscomb, W.N. Aspartate transcarbamylase from Escherichia coli: Activity and regulation. Adv. Enzymol. Relat. Areas Mol. Biol. 68:67-151, 1994.
7. Weber, K. New structural model of E. coli aspartate transcarbamoylase and the amino-acid sequence of the regulatory polypeptide chain. Nature 218:1116-1118, 1968.
8. Wiley, D.C., Lipscomb, W.N. Crystallographic determination of symmetry of aspartate transcarbamoylase. Nature 218:1119-1121, 1968.
9. Honzatko, R.B., Crawford, J.L., Monaco, H.L., et al. Crystal and molecular structures of native and CTP-liganded aspartate carbamoyltransferase from Escherichia coli. J. Mol. Biol. 160:219-263, 1982.
10. Krause, K.L., Volz, K.W., Lipscomb, W.N. Structure at 2.9 Å resolution of aspartate carbamoyltransferase complexed with the bisubstrate analogue N-(phosphonacetyl)-L-aspartate. Proc. Natl. Acad. Sci. USA 82:1643-1647, 1985.
11. Gerhart, J.C., Schachman, H.K. Allosteric interactions in aspartate transcarbamoylase. II. Evidence for different conformational states of the protein in the presence and absence of specific ligands. Biochemistry 7:538-552, 1968.
12. Krause, K.L., Votz, K.W., Lipscomb, W.N. 2.5 Å structure of aspartate carbamoyltransferase complexed with the bisubstrate analog N-(phosphonacetyl)-L-aspartate. J. Mol. Biol. 193:527-553, 1987.
13. Ke, H., Lipscomb, W.N., Cho, Y., Honzatko, R.B. 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, 1988.
14. Svergun, D.I., Barberato, C., Koch, M.H., Fetler, L., Vachette, P. Large differences are observed between the crystal and solution quaternary structures of allosteric aspartate transcarbamylase in the R state. Proteins 27:110-117, 1997.
15. Burz, D.S. Quaternary structure, energetics and function of single-site mutants of E. coli aspartate transcarbamoylase. Ph.D. Thesis, Wesleyan University, Middletown, 1990.
16. Licata, V.J., Burz, D.S., Moerke, N.J., Allewell, N.M. Variability of the magnitude of the allosteric conformational transition of aspartate transcarbamylase. Biochemistry, in press.
17. Gouaux, J.E., Stevens, R.C., Lipscomb, W.N. Crystal structures of aspartate carbamoyltransferase ligated with phosphonoacetamide, malonate, and CTP or ATP at 2.8 Å resolution and neutral pH. Biochem. 29:7702-7715, 1990.
18. Stevens, R.C., Gouaux, J.E., Lipscomb, W.N. 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. Bichem. 29:7691-7701, 1990.
19. Stevens, R.C., Lipscomb, W.N. A molecular mechanism for pyrimidine and purine nucleotide control of aspartate transcarbamoylase. Proc. Natl. Acad. Sci. USA 89:5281-5285, 1992.
20. Robey, E.A., Schachman, H.K. Site-specific mutagenesis of aspartate transcarbamoylase. Replacement of tyrosine 165 in the catalytic chain by serine reduces enzymatic activity. J. Biochemistry 259:11180-11183, 1984.
21. Wales, M.E., Hoover, T.A., Wild, J.R. Site-specific substitutions of the Tyr-165 residue in the catalytic chain of aspartate transcarbamoylase promotes a T-state preference in the holoenzyme. J. Biochemistry 263:6109-6114, 1988.
22. Ladjimi, M.M., Kantrowitz, E.R. A possible model for the concerted allosteric transition in Escherichia coli aspartate transcarbamylase as deduced from site-directed mutagenesis studies. Biochem. 27:276-283, 1988.
23. Middleton, S.A., Kantrowitz, E.R. Function of arginine-234 and aspartic acid-271 in domain closure, cooperativity, and catalysis in Escherichia coli aspartate transcarbamylase. Biochemistry 27:8653-8660, 1988.
24. Middleton, S.A., Stebbins, J.W., Kantrowitz, E.R. A loop involving catalytic chain residues 230-245 is essential for the stabilization of both allosteric forms of Escherichia coli aspartate transcarbamylase. Biochem. 28:1617-1626, 1989.
25. Yuan, X., LiCata, V.J., Allewell, N.M. Effects of assembly and mutations outside the active site on the functional pH dependence of Escherichia coli aspartate transcarbamylase. J. Biochemistry 271:1285-1294, 1996.
26. Gouaux, J.E., Stevens, R.C., Ke, H., Lipscomb, W.N. Crystal structure of the Glu-239/Gln mutant of aspartate carbamoyltransferase at 3.1 Å resolution: An intermediate quaternary structure. Proc. Natl. Acad. Sci. USA 86:8212-8216, 1989.
27. Siemens Energy & Automation, Inc. XENGEN manual, 1990.
28. Brünger, A.T. X-PLOR manual, version 3.0. New Haven: Yale University, 1992.
29. Kosman, R.P., Gouaux, E.J., Lipscomb, W.N. Crystal structure of CTP-ligated T state aspartate transcarbamoylase at 2.5 Å resolution: Implications for ATCase mutants and the mechanism of negative cooperativity. Proteins 15:147-176, 1993.
30. Jones, T.A., Zou, J.Y., Cowan, S.W., Kjeldgaard, M. Improved methods for binding protein models in electron density maps and the location of errors in these models. Acta Crystallogr. A 47:110-119, 1991.
31. Gouaux, J.E., Lipscomb, W.N. Crystal structures 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, 1990.
32. Stebbins, J.W., Zhang, Y., Kantrowitz, E.R. Importance of residues Arg-167 and Gin-231 in both the allosteric and catalytic mechanisms of Escherichia coli aspartate transcarbamoylase. Biochemistry 29:3821-3827, 1990.
33. Eisenstein, E., Markby, D.W., Schachman, H.K. Changes in stability and allosteric properties of aspartate transcarbamoylase resulting from amino acid substitutions in the zinc-binding domain of the regulatory chains. Proc. Natl. Acad. Sci. USA 86:3094-3098, 1989.
34. Newton, C.J., Kantrowitz, E.R. The regulatory subunit of Escherichia coli aspartate carbamoyltransferase may influence homotropic cooperativity and heterotropic interactions by a direct interaction with the loop containing residues 230-245 of the catalytic chain. Proc. Natl. Acad. Sci. USA 87:2309-2313, 1990.
35. Kraulis, P.J. MOLSCRIPT: A program to produce both detailed and schematic plots of protein structures. J. Appl. Cryst. 24:946-950, 1991.
36. Bacon, D.J., Anderson, W.F. A fast algorithm for rendering space-filling molecule pictures. J. Mol. Graph. 6:219-220, 1988.
37. Merritt, E.A., Murphy, M.E.P. Raster3D version 2.0: A program for photorealistic molecular graphics. Acta Crystallogr. D 50:869-873, 1994.
38. Ackers, G.K. Deciphering the molecular code of hemoglobin allostery. Adv. Prot. Chem. 51:185-253, 1998.
39. Gouaux, J.E., Lipscomb, W.N. Structural transitions in crystals of native aspartate carbamoyltransferase. Proc. Natl. Acad. Sci. U.S.A. 86:845-848, 1989.
40. Jin, L., Seaton, B.A., Head, J.F. Crystal structure at 2.8 Å resolution of anabolic ornithine transcarbamylase from E. coli. Nat. Struct. Biol. 4:622-625, 1997.
41. Ha, Y., McCann, M.T., Tuchman, M., Allewell, N.M. Substrate-induced conformational change in a trimeric ornithine transcarbamoylase. Proc. Natl. Acad. Sci. USA 94: 9550-9555, 1997.
42. Shi, D., Morizono, H., Ha, Y., Aoyagi, M., Tuchman, M., Allewell, N.M. 1.85 Å resolution crystal structure of human ornithine transcarbamoylase complexed with N-phosphonacetyl-L-ornithine: Catalytic mechanism and correlation with inhberited deficiency. J. Biol. Chem., in press.