Enzyme flexibility: A new concept in recognition of hydrophobic substrates

Journal of Biochemistry

Volumn 122, Issue 1, 1997, Pages 55-63

  Kawaguchi, Shin Ichi ^a,c   Nobe, Yuko ^a   Yasuoka, Jun Ichi ^a   Wakamiya, Tateaki ^a,b   Kusumoto, Shoichi ^a   Kuramitsu, Seiki ^a  

^a OSAKA UNIVERSITY   (Japan)

^b KINKI UNIVERSITY   (Japan)

^c JAPAN SOCIETY FOR THE PROMOTION OF SCIENCE   (Japan)

Author keywords

Aromatic amino acid aminotransferase; Aspartate aminotransferase; Hydrophobic interaction; Protein dynamics; Substrate specificity

Indexed keywords

AROMATIC AMINO ACID; ASPARTATE AMINOTRANSFERASE; CHIMERIC PROTEIN;

ARTICLE; CATALYSIS; ENZYME SPECIFICITY; ENZYME STABILITY; ENZYME SUBSTRATE COMPLEX; ESCHERICHIA COLI; HYDROPHOBICITY; MOLECULAR DYNAMICS; MOLECULAR RECOGNITION; NONHUMAN;

ESCHERICHIA COLI;

EID: 0030871363     PISSN: 0021924X     EISSN: None     Source Type: Journal    
DOI: 10.1093/oxfordjournals.jbchem.a021740     Document Type: Article

References (64)

1. Mehta, P.K., Hale, T.I., and Christen, P. (1989) Evolutionary relationships among aminotransferases. Tyrosine aminotransferase, histidinol-phosphate aminotransferase, and aspartate aminotransferase are homologous proteins. Eur. J. Biochem. 186, 249-253
2. Creighton, T.E. (1993) Proteins (2nd ed.) pp. 385-461, W.H. Freeman and Company, New York
3. Fersht, A. (1985) Enzyme Structure and Mechanism (2nd ed.) pp. 293-310, W.H. Freeman and Company, New York
4. Xu, Z., Bernlohr, D.A., and Banaszak, L.J. (1993) The adipocyte lipid-binding protein at 1.6-Å resolution. J. Biol. Chem. 268, 7874-7884
5. Kim, J.-J.P., Wang, M., and Paschke, R. (1993) Crystal structures of medium-chain acyl-CoA dehydrogenase from pig liver mitochondria with and without substrate. Proc. Natl. Acad. Sci. USA 90, 7523-7527
6. Winter, N.S., Bratt, J.M., and Banaszak, L.J. (1993) Crystal structures of holo and apo-cellular retinol-binding protein II. J. Mol. Biol. 230, 1247-1259
7. Bone, R., Silen, J.L., and Agard, D.A. (1989) Structural plasticity broadens the specificity of an engineered protease. Nature 339, 191-195
8. Hedstrom, L., Szilagyi, L., and Rutter, W.J. (1992) Converting trypsin to chymotrypsin: The role of surface loops. Science 255, 1249-1253
9. Morton, A., Baase, W.A., and Matthews, B.W. (1995) Energetic origins of specificity of ligand binding in an interior nonpolar cavity of T4 lysozyme. Biochemistry 34, 8564-8575
10. Jackson, S.E., Moracci, M., elMasry, N., Johnson, C.M., and Fersht, A.R. (1993) Effect of cavity-creating mutations in the hydrophobic core of chymotrypsin inhibitor. Biochemistry 32, 11259-11269
11. Serrano, L., Kellis Jr, J.T., Cann, P., Matouschek, A., and Fersht, A.R. (1992) The folding of an enzyme II. Substructure of barnase and the contribution of different interactions to protein stability. J. Mol. Biol. 224, 783-804
12. Eriksson, A.E., Baase, W.A., and Matthews, B.W. (1993) Similar hydrophobic replacements of Leu99 and Phe153 within the core of T4 lysozyme have different structural and thermodynamic consequences. J. Mol. Biol. 229, 747-769
13. Denisov, V.P., Halle, B., Peters, J., and Hörlein, H.D. (1995) Residence times of the buried water molecules in bovine pancreatic trypsin inhibitor and its G36S mutant. Biochemistry 34, 9046-9051
14. Denisov, V.P., Peters, J., Hörlein, H.D., and Halle, B. (1996) Using buried water molecules to explore the energy landscape of proteins. Nature Struct. Biol. 3, 505-509
15. Feher, V.A., Baldwin, E.P., and Dahlquist, F.W. (1996) Access of ligands to cavities within the core of a protein is rapid. Nature Struct. Biol. 3, 516-521
16. Velick, S.F. and Vavra, J. (1962) A kinetic and equilibrium analysis of the glutamic oxaloacetate transaminase mechanism. J. Biol. Chem. 237, 2109-2122
17. Kiick, D.M. and Cook, P.F. (1983) pH studies toward the elucidation of the auxiliary catalyst for pig heart aspartate aminotransferase. Biochemistry 22, 375-382
18. Jenkins, W.T. and Fonda, M.L. (1985) Kinetics, equilibria, and affinity for coenzymes and substrates in Transaminases (Christen, P. and Metzler, D.E., eds.) pp. 216-234, John Wiley and Sons, New York
19. Kuramitsu, S., Hiromi, K., Hayashi, H., Morino, Y., and Kagamiyama, H. (1990) Pre-steady-state kinetics of Escherichia coli aspartate aminotransferase catalyzed reactions and thermodynamic aspects of its substrate specificity. Biochemistry 29, 5469-5476
20. Hayashi, H., Inoue, K., Nagata, T., Kuramitsu, S., and Kagamiyama, H. (1993) Escherichia coli aromatic amino acid aminotransferase: characterization and comparison with aspartate aminotransferase. Biochemistry 32, 12229-12239
21. Kuramitsu, S., Inoue, K., Ogawa, T., Ogawa, H., and Kagamiyama, H. (1985) Aromatic amino acid aminotransferase of Escherichia coli: nucleotide sequence of the tyrB gene. Biochem. Biophys. Res. Commun. 133, 134-139
22. Kuramitsu, S., Okuno, S., Ogawa, T., Ogawa, H., and Kagamiyama, H. (1985) Aspartate aminotransferase of Escherichia coli: nucleotide sequence of the aspC gene. J. Biochem. 97, 1259-1262
23. Kamitori, S., Okamoto, A., Hirotsu, K., Higuchi, T., Kuramitsu, S., Kagamiyama, H., Matsuura, Y., and Katsube, Y. (1990) Three-dimensional structures of aspartate aminotransferase from Escherichia coli and its mutant enzyme at 2.5 Å resolution. J. Biochem. 108, 175-184
24. Okamoto, A., Higuchi, T., Hirotsu, K., Kuramitsu, S., and Kagamiyama, H. (1994) X-ray crystallographic study of pyridoxal 5′-phosphate-type aspartate aminotransferases from Escherichia coli in open and closed form. J. Biochem. 116, 95-107
25. Smith, D., Almo, S., Toney, M., and Ringe, D. (1989) 2.8-Å-resolution crystal structure of an active-site mutant of aspartate aminotransferase from Escherichia coli. Biochemistry 28, 8161-8167
26. Danishefsky, A., Onnufer, J., Petsko, G., and Ringe, D. (1991) Activity and structure of the active-site mutants R386Y and R386F of Escherichia coli aspartate aminotransferase. Biochemistry 30, 1980-1985
27. Malashkevich, V.N., Onuffer, J.J., Kirsch, J.F., and Jansonius, J.N. (1995) Alternating arginine-modulated substrate specificity in an engineered tyrosine aminotransferase. Nature Struct. Biol. 2, 548-553
28. Miyazawa, K., Kawaguchi, S., Okamoto, A., Kato, R., Ogawa, T., and Kuramitsu, S. (1994) Construction of aminotransferase chimeras and analysis of their substrate specificity. J. Biochem. 115, 568-577
29. Onuffer, J.J., Ton, B.T., Klement, I., and Kirsch, J.F. (1995) The use of natural and unnatural amino acid substrates to define the substrate specificity differences of Escherichia coli aspartate and tyrosine aminotransferases. Protein Sci. 4, 1743-1749
30. Barrett, G.C. (1985) Chemistry and Biochemistry of the Amino Acid, pp. 246-296, Chapman and Hall, London
31. 143 in the catalytic mechanism of Escherichia coli aspartate aminotransferase. J. Biol. Chem. 266, 6079-6085
32. Kamitori, S., Hirotsu, K., Higuchi, T., Kondo, K., Inoue, K., Kuramitsu, S., Kagamiyama, H., Higuchi, Y., Yasuoka, N., Kusunoki, M., and Matsuura, Y. (1987) Overproduction and preliminary X-ray characterization of aspartate aminotransferase from Escherichia coli. J. Biochem. 101, 813-816
33. Kawaguchi, S. and Kuramitsu, S. (1994) Homologous ligation. Trends Genet. 10, 420
34. Fersht, A. (1985) Enzyme Structure and Mechanism (2nd ed.), pp. 311-346, W.H. Freeman and Company, New York
35. Kuramitsu, S., Hamaguchi, K., Ogawa, T., and Ogawa, H. (1981) A large-scale preparation and some physicochemical properties of RecA protein. J. Biochem. 90, 1033-1045
36. Riddles, P.W., Blakeley, R.L., and Zerner, B. (1979) Ellman's reagent: 5,5′-dithiobis(2-nitrobenzoic acid) - a reexamination. Anal. Biochem. 94, 75-81
37. Blout, E.R., De Lozé, C., and Asadourian, A. (1961) The deuterium exchange of water-soluble polypeptides and proteins as measured by infrared spectroscopy. J. Am. Chem. Soc. 83, 1895-1900
38. Pfister, K., Kägi, J.H.R., and Christen, P. (1978) Syncatalytic conformational changes in aspartate aminotransferase determined by hydrogen-deuterium exchange. Proc. Natl. Acad. Sci. USA 75, 145-148
39. McAuliffe, C. (1966) Solubility in water of paraffin, cycloparaffin, olefin, acetylene, cycloolefin, and aromatic hydrocarbons. J. Phys. Chem. 70, 1267-1275
40. Mehta, P.K., Hale, T.I., and Christen, P. (1993) Aminotransferases: demonstration of homology and division into evolutionary subgroups. Eur. J. Biochem. 214, 549-561
41. Ovchinnikov, Y.A., Egorov, C.A., Aldanova, N.A., Feigina, M.Y., Lipkin, V.M., Abdulaev, N.G., Grishin, E.V., Kiselev, A.P., Modyanov, N.N., Braunstein, A.E., Polyanovsky, O.L., and Nosikov, V.V. (1973) The complete amino acid sequence of cytoplasmic aspartate aminotransferase. FEBS Lett. 29, 31-34
42. Bousquet-Lemercier, B., Pol, S., Pave-Preux, M., Hanoune, J., and Barouki, R. (1990) Properties of human liver cytosolic aspartate aminotransferase mRNAs generated by alternative polyadenylation site selection. Biochemistry 29, 5293-5299
43. Schultz, C.J. and Coruzzi, G.M. (1995) The aspartate aminotransferase gene family of Arabidopsis encodes isoenzymes localized to three distinct subcellular compartments. Plant J. 7, 61-75
44. Cronin, V.B., Maras, B., Barra, D.K., and Doonan, S. (1991) The amino acid sequence of the aspartate aminotransferase from baker's yeast (Saccharomyces cerevisiae). Biochem. J. 277, 335-340
45. Kagamiyama, H., Sakakibara, R., Tanase, S., Morino, Y., and Wada, H. (1980) Complete amino acid sequence of mitochondrial aspartate aminotransferase from pig heart muscle. Peptide ordering procedures and the complete sequence. J. Biol. Chem. 255, 6153-6159
46. Martini, F., Angelaccio, S., Barra, D., Pascarella, S., Maras, B., Doonan, S., and Bossa, F. (1985) The primary structure of mitochondrial aspartate aminotransferase from human heart. Biochim. Biophys. Acta 832, 46-51
47. Cheret, G., Pallier, C., Valens, M., Daignan-Fornier, B., Fukuhara, H., Bolotin-Fukuhara, M., and Sor, F. (1993) The DNA sequence analysis of the HAP4-LAP4 region on chromosome XI of Saccharomyces cereuisiae suggests the presence of a second aspartate aminotransferase gene in yeast. Yeast 9, 1259-1265
48. Gregerson, R.G., Miller, S.S., Petrowski, M., Gantt, J.S., and Vance, C.P. (1994) Genomic structure, expression and evolution of the alfalfa aspartate aminotransferase genes. Plant Mol. Biol. 25, 387-399
49. Reynolds, P.H., Smith, L.A., Dickson, J.M., Jones, W.T., Jones, S.D., Rodber, K.A., Carne, A., and Liddane, C.P. (1992) Molecular cloning of a cDNA encoding aspartate aminotransferase-P2 from lupin root nodules. Plant Mol. Biol. 19, 465-472
50. Fleischmann, R.D., Adams, M.D., White, O., Clayton, R.A., Kirkness, E.F., Kerlavage, A.R., Bult, C.J., Tomb, J.F., Dougherty, B.A., Merrick, J.M., McKenney, K., Sutton, G., FitzHugh, W., Fields, C., Gocayne, J.D., Scott, J., Shirley, R., Liu, L.I., Glodek, A., Kelley, J.M., Weidman, J.F., Phillips, C.A., Spriggs, T., Hedblom, E., Cotton, M.D., Utterback, T.R., Hanna, M.C., Nguyen, D.T., Saudek, D.M., Brandon, R.C., Fine, L.D., Fritchman, J.L., Fuhrmann, J.L., Geoghagen, N.S.M., Gnehm, C.L., McDonald, L.A., Small, K.V., Fraser, C.M., Smith, H.O., and Venter, J.C. (1995) Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science 269, 496-512
51. O'Hara, B.P., Hemmings, A.M., Buttle, D.J., and Pearl, L.H. (1995) Crystal structure of glycyl endopeptidase from Carica papaya: A cysteine endopeptidase of unusual substrate specificity. Biochemistry 34, 13190-13195
52. Fersht, A. (1985) Enzyme Structure and Mechanism (2nd ed.), pp. 347-368, W.H. Freeman and Company, New York
53. Wangikar, P.P., Rich, J.O., Clark, D.S., and Dordick, J.S. (1995) Probing enzymatic transition state hydrophobicities. Biochemistry 34, 12302-12310
54. Ryu, K. and Dordick, J.S. (1992) How do organic solvents affect peroxidase structure and function? Biochemistry 31, 2588-2598
55. Dorovska, V.N., Varfolomeyev, S.D., Kazanskaya, N.F., Klyosov, A.A., and Martinek, K. (1972) The influence of the geometric properties of the active centre on the specificity of α-chymotrypsin catalysis. FEBS Lett. 23, 122-124
56. 13C NMR study of the effects of mutation on the tryptophan dynamics in chymotrypsin inhibitor 2: Correlations with structure and stability. Biochemistry 32, 657-662
57. Wüthrich, K., Wagner, G., Richarz, R., and Braun, W. (1980) Correlations between internal mobility and stability of globular proteins. Biophys. J. 32, 549-560
58. Mace, J.E. and Agard, D.A. (1995) Kinetic and structural characterization of mutations of glycine 216 in α-lytic protease: A new target for engineering substrate specificity. J. Mol. Biol. 254, 720-736
59. Mace, J.E., Wilk, B.J., and Agard, D.A. (1995) Functional linkage between the active site of α-lytic protease and distant regions of structure : Scanning alanine mutagenesis of a surface loop affects activity and substrate specificity. J. Mol. Biol. 251, 116-134
60. Lawson, C.L. (1996) An atomic view of the L-tryptophan binding site of trp repressor. Nature Struct. Biol. 3, 986-987
61. Loris, R., Maes, D., Poortmans, F., Wyns, L., and Bouckaert, J. (1996) A structure of the complex between concanavalin A and methyl-3,6-di-O-(α-D-mannopyranosyl)-α-D-mannopyranoside reveals two binding modes. J. Biol. Chem. 271, 30614-30618
62. Frauenfelder, H., Sugar, S.G., and Wolynes, P.G. (1991) The energy landscapes and motions of proteins. Science 254, 1598-1603
63. Karplus, M. and McCammon, J.A. (1983) Dynamics of proteins: Elements and function. Annu. Rev. Biochem. 52, 263-300
64. Anone, A., Christen, P., Jansonius, J.N., and Metzler, D.E. (1985) Hypothetical mechanism of action of aspartate aminotransferases in Transaminases (Christen, P. and Metzler, D.E., eds.) pp. 326-357, John Wiley and Sons, New York