Structure and control of pyridoxal phosphate dependent allosteric threonine deaminase

Structure

Volumn 6, Issue 4, 1998, Pages 465-475

  Gallagher, D Travis ^a   Gilliland, Gary L ^a   Xiao, Gaoyi ^a   Zondlo, James ^a   Fisher, Kathryn E ^a   Chinchilla, Diana ^a   Eisenstein, Edward ^a,b  

^a UNIVERSITY OF MARYLAND BIOTECHNOLOGY INSTITUTE   (United States)

^b UNIVERSITY OF MARYLAND BALTIMORE COUNTY   (United States)

Author keywords

Allostery; Cooperativity; Crystal structure; Pyridoxal phosphate; Threonine deaminase

Indexed keywords

EID: 0032522653     PISSN: 09692126     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0969-2126(98)00048-3     Document Type: Article

References (57)

1. Stryer, L. (1988). Biochemistry. p. 1089, W.H. Freeman.
2. Umbarger, H.E. (1992). The origin of a useful concept - feedback inhibition. Protein Sci. 1, 1392-1395.
3. Changeux, J.-P. (1993). Allosteric proteins: from regulatory enzymes to receptors - personal recollections. BioEssays 15, 625-634.
4. Umbarger, H.E. (1956). Evidence for a negative-feedback mechanism in the biosynthesis of isoleucine. Science 123, 848.
5. Umbarger, H.E. & Brown, B. (1956). Threonine deamination in Escherichia coli. I. D- and L-threonine deaminase activities of cell free extracts. J. Bacteriol. 71, 443-449.
6. Umbarger, H.E. & Brown, B. (1957). Threonine deamination in Escherichia coli. II. Evidence for two L-threonine deaminases. J. Bacteriol. 73, 105-112.
7. Umbarger, H.E. & Brown, B. (1957). Isoleucine and valine metabolism in Escherichia coli. VII. A negative feedback mechanism controlling isoleucine biosynthesis. J. Biol. Chem. 233, 415-420.
8. Changeux, J.-P. (1961). The feedback control mechanism of biosynthetic L-threonine deaminase by L-isoleucine. Cold Spring Harbor Symp. Quant. Biol. 26, 313-318.
9. Changeux, J.-P. (1962). Effet des analogues de la L-threonine et de la L-isoleucine sur la L-threonine deaminase. J. Mol. Biol. 4, 220-225.
10. Changeux, J.-P. (1963). Allosteric interactions on biosynthetic L-threonine deaminase from E. coli K-12. Cold Spring Harbor Symp. Quant. Biol. 28, 497-504.
11. Freundlich, M. & Umbarger, H.E. (1963). The effects of analogues of threonine and of isoleucine on the properties of threonine deaminase. Cold Spring Harbor Symp. Quant. Biol. 28, 505-511.
12. Monod, J., Wyman, J. & Changeux, J.-P. (1965). On the nature of allosteric transitions: a plausible model. J. Mol. Biol. 12, 88-118.
13. Eisenstein, E. (1991). Cloning, expression, purification and characterization of biosynthetic threonine deaminase from Escherichia coli. J. Biol. Chem. 266, 5801-5807.
14. Eisenstein, E., Yu, H.D. & Schwarz, F.P. (1994). Cooperative binding of the feedback modifiers isoleucine and valine to biosynthetic threonine deaminase from Escherichia coli. J. Biol. Chem. 269, 29423-29429.
15. Eisenstein, E. (1994). Energetics of cooperative ligand binding to the active sites of biosynthetic threonine deaminase from Escherichia coli. J. Biol. Chem. 269, 29416-29422.
16. Eisenstein, E., Yu, H.D., Fisher, K.E., Iacuzio, D.A., Ducote, K.R. & Schwarz, F.P. (1995). An expanded two-state model accounts for homotropic cooperativity in biosynthetic threonine deaminase from Escherichia coli. Biochemistry 34, 9403-9412.
17. Lipscomb, W.N. (1991). Structure and function of allosteric enzymes. Chemtracts-Biochemistry Mol. Biol. 2, 1-15.
18. Mattevi, A., Rizzi, M. & Bolognesi, M. (1996). New structures of allosteric proteins revealing remarkable conformational changes. Curr. Opin. Struct. Biol. 6, 824-829.
19. Gallagher, D.T., et al., & Gilliland, G.L. (1997). Polymorphous crystallization and diffraction of threonine deaminase from E. coli. Acta Cryst. D 54, 467-469.
20. Rossmann, M.G., et al., & Webb, L. (1973). Molecular symmetry axes and subunit interfaces in certain dehydrogenases. J. Mol. Biol. 76, 533-537.
21. Taillon, B.E., Little, R. & Lawther, R.P. (1988). Analysis of the functional domains of biosynthetic threonine deaminase by comparison of the amino acid sequences of three wild-type alleles to the amino acid sequence of biodegradative threonine deaminase. Gene 63, 245-252.
22. Fisher, K.E. & Eisenstein, E. (1993). An efficient approach to identify ilvA mutations reveals an amino-terminal catalytic domain in biosynthetic threonine deaminase from Escherichia coli. J. Bacteriol. 175, 6605-6613.
23. Mockel, B., Eggling, L. & Sahm, H. (1994). Threonine dehydratases of Corynebacterium glutamicum with altered allosteric control: their generation and biochemical and structural analysis. Mol. Microbiol. 13, 833-842.
24. Kabsch, W. & Sander, S. (1983). Secondary structure definition by the program DSSP. Biopolymers 22, 2577-2637.
25. Needleman, S.B. & Wunsch, C.D. (1970). A general method applicable to the search for similarities in the amino acid sequence of two proteins. J. Mol. Biol. 48, 443-453.
26. Hyde, C.C., Ahmed, S.A., Padlan, E.A., Miles, E.W. & Davies, D.R. (1988). Three dimensional structure of tryptophan synthase α2β2 multienzyme complex from Salmonella typhimurium. J. Biol. Chem. 269, 17857-17871.
27. Orengo, C.A. & Thornton, J.M. (1994). Alpha plus beta folds revisited: some favoured motifs. Structure 1, 105-120.
28. Connolly, M.L. (1993). The molecular surface package. J. Mol. Graph. 11, 139-141.
29. Parsot, C. (1986). Evolution of biosynthetic pathways: a common ancestor for threonine synthase, threonine dehydratase and D-serine dehydratase. EMBO J. 5, 3013-3019.
30. Bork, P. & Rhode, K. (1990). Sequence similarities between tryptophan synthase b subunit and other pyridoxal-phosphate-dependent enzymes. Biochem. Biophys. Res. Commun. 171, 1319-1325.
31. Grishin, N.V., Phillips, M.A. & Goldsmith, E.J. (1995). Modeling of the spatial structure of eukaryotic ornithine decarboxylases. Protein Sci. 4, 1291-1304.
32. Satow, Y., Cohen, G., Padlan, E.A. & Davies, D.P. (1986). Phosphocholine binding immunoglobin FabMcPC603: an X-ray diffraction study at 2.7 A resolution. J. Mol. Biol. 190, 593-604.
33. Ji, X., Zhang, P., Armstrong, R.N. & Gilliland, G.L. (1992). The three-dimensional structure of a glutathione S-transferase from the mu gene class: structural analysis of the binary complex of isozyme 3-3 and glutathione at 2.2 Å resolution. Biochemistry 31, 10169-10194.
34. Miles, E.W. (1979). Tryptophan synthase: structure, function and subunit interaction. Adv. Enzymology 49, 127-186.
35. Andersen, K.S., Miles, E.W. & Johnson, K.A. (1991). Serine modulates substrate channeling in tryptophan synthase. J. Biol. Chem. 266, 8020-8033.
36. Pan, P., Woehl, E. & Dunn, M.F. (1997). Protein architecture, dynamics and allostery in tryptophan synthase channeling. Trends Biochem. Sci. 22, 22-27.
37. Hayashi, H., Wada, H., Yoshimura, Y., Esaki, N. & Soda, K. (1990). Recent topics in pyridoxal 5′-phosphate enzyme studies. Annu. Rev. Biochem. 59, 87-110.
38. Alexander, F.W., Sandmeier, E., Mehta, P.K. & Christen, P. (1994). Evolutionary relationships among pyridoxal-5′-phosphate-dependent enzymes. Eur. J. Biochem. 219, 953-960.
39. Eisenstein, E. (1995). Allosteric regulation of biosynthetic threonine deaminase from Escherichia coli: effects of isoleucine and valine on active-site ligand binding and catalysis. Arch. Biochem. Biophys. 316, 311-318.
40. Schuller, D.J., Grant, G.A. & Banaszak, L.J. (1995). Crystal structure reveals the allosteric ligand site in the Vmax-type cooperative enzyme: D-3-phosphoglycerate dehydrogenase. Nat. Struct. Biol. 2, 69-76.
41. Grant, G.A., Schuller, D.J. & Banaszak, L.J. (1996). A model for the regulation of D-3-phosphoglycerate dehydrogenase, a Vmax-type allosteric enzyme. Protein Sci. 5, 34-41.
42. Mockel, B., Eggeling, L. & Sahm, H. (1992). Functional and structural analyses of threonine dehydratase from Corynebacterium glutamicum. J. Bacteriol. 174, 8065-8072.
43. Kirsch, J.F., Eichele, G., Ford, G.C., Vincent, M.G. & Jansonius, J.N. (1984). Mechanism of action of aspartate aminotransferase proposed on the basis of its spatial structure. J. Mol. Biol. 174, 497-525.
44. Jager, J., Moser, M., Saunder, U. & Jansonius, J.N. (1994). Crystal structures of E. coli aspartate aminotransferase in two conformations: comparison of an unliganded open and two liganded closed forms. J. Mol. Biol. 239, 285-305.
45. Ahmed, S.A., Ruvinov, S.B., Kayastha, A.M. & Miles, E.W. (1991). Mechanism of mutual activation of the tryptophan synthase alpha and beta subunits. J. Biol. Chem. 266, 21540-21557.
46. Rhee, S., Parris, K.D., Hyde, C., Ahmed, S.A., Miles, E.W. & Davies, D.R. (1997). Crystal structures of a mutant (βK87T) tryptophan synthase α2β2 complex with ligands to the active sites of the α- and β-subunits reveal ligands-induced conformational changes. Biochemistry 36, 7664-7680.
47. 2 complex. Biochemistry 35, 4211-4221.
48. Furey, W. & Swaminathan, S. (1997). PHASES-95: a program package for the processing and analysis of diffraction data from macromolecules. In Methods in Enzymology. (Carter, C. & Sweet, R.), 277, pp. 590-620, Academic Press, Orlando, FL.
49. Wang, B.C. (1985). Resolution of phase ambiguity in macromolecular crystallography. Methods in Enzymology 115, 90-112.
50. Brünger, AT. (1992). X-PLOR (Version 3.1) Manual. Yale University Press, New Haven, CT.
51. Tronrud, D.E., Ten Eyck, L.F. & Matthews, B.W. (1987). An efficient general-purpose least-squares refinement program for macromolecular structures. Acta Cryst. A 43, 489-501.
52. Jones, T.A., Zou, J.Y., Cowan, S.W. & Kjeldgaard, M. (1991). Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Cryst. A 47, 110-119.
53. Laskowski, R.A., MacArthur, M.W., Moss, D.S. & Thornton, J.M. (1993). PROCHECK - a program to check the stereochemical quality of protein structures. J. App/. Cryst. 26, 283-291.
54. Bernstein, F.C., et al., & Shimanouchi, T. (1977). The protein data bank: a computer-based archival file for macromolecular structures. J. Mol. Biol. 112, 535-542.
55. Bacon, D.J. & Andersen, W.F. (1988). A fast algorithm for rendering space-filling molecule pictures. J. Mol. Graph. 6, 219-220.
56. Merrit, E.A. & Murphy, M.E.P. (1994). Raster3D version 2.0 - a program for photorealistic molecular graphics. Acta Cryst. D 50, 869-873.
57. Kraulis, P.J. (1991). MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures. J. Appl. Cryst. 24, 946-950.