Mechanism of Action of D-Xylose Isomerase

Current Protein and Peptide Science

Volumn 1, Issue 3, 2000, Pages 237-254

  Asboth B ^a   Naray Szabo G ^b  

^a SZENT ISTVÁN UNIVERSITY   (Hungary)

^b EÖTVÖS LORÁND UNIVERSITY   (Hungary)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL PROTEIN; DIVALENT CATION; ISOMERASE; LIGAND; PROTON; XYLOSE ISOMERASE;

BACILLUS; CATALYSIS; CHEMICAL MODEL; CHEMICAL STRUCTURE; CHEMISTRY; ELECTRON SPIN RESONANCE; ENZYMOLOGY; KINETICS; METABOLISM; NUCLEAR MAGNETIC RESONANCE; PROTEIN CONFORMATION; REVIEW; SITE DIRECTED MUTAGENESIS; STREPTOMYCES; STRUCTURE ACTIVITY RELATION; X RAY CRYSTALLOGRAPHY;

ALDOSE-KETOSE ISOMERASES; BACILLUS; BACTERIAL PROTEINS; CATALYSIS; CATIONS, DIVALENT; CRYSTALLOGRAPHY, X-RAY; ELECTRON SPIN RESONANCE SPECTROSCOPY; KINETICS; LIGANDS; MODELS, CHEMICAL; MODELS, MOLECULAR; MUTAGENESIS, SITE-DIRECTED; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; PROTEIN CONFORMATION; PROTONS; STREPTOMYCES; STRUCTURE-ACTIVITY RELATIONSHIP;

EID: 0034334554     PISSN: 13892037     EISSN: None     Source Type: Journal    
DOI: 10.2174/1389203003381333     Document Type: Article

References (114)

1. Marshall, R.O. and Kooi, E.R. (1957) Science 125, 648-649.
2. Schray, K.J. and Rose, I.A. (1971) Biochemistry 10, 1058-1062.
3. McKay, G.A. and Tavlarides, L.L. (1979) J. Mol. Catal. 6, 51-69.
4. Angyal, S.J. (1980) Chem. Soc. Rev. 9, 415-428.
5. Zheng, Y.-Z., Merz, K.M. and Farber, G.K. (1993) Protein Eng. 6, 479-484.
6. Blow, D.M., Collyer, C.A., Goldberg, J.D. and Smart, O.S. (1992) Faraday Discuss. 93, 67-73.
7. Bhosale, S.H., Rao, M.B. and Deshpande, V.V. (1996) Microbiol. Rev. 60, 280-300.
8. Asbóth, B., Böcskei, Z., Fuxreiter, M. and Náray-Szabó, G. (1997) in Molecular Modeling and Dynamics of Bioinorganic Systems, (Banci, L. and Comba, P., Eds.), NATO ASI Series 3. High Technology - Vol. 41, Kluwer, Dordrecht, pp. 419-439.
9. Fersht, A.R. (1985) Enzyme Structure and Mechanism, Freeman, New York.
10. Rangarajan, M. and Hartley, B.S. (1992) Biochem. J. 283, 223-233.
11. Otzen, D.E. and Fersht, A.R. (1999) Protein Eng. 12, 41-45.
12. Brändén, C.I. and Tooze, J. (1991) Introduction to Protein Structure, Garland, New York.
13. Creighton, T. (1993) Protein Structure and Molecular Properties, Freeman, New York.
14. Wütrich, K. (1986) NMR of Proteins and Nucleic Acids, Wiley, New York.
15. Torda, A.E. and van Gunsteren, W.F. (1992) Rev. Comput. Chem. 3, 143-172.
16. Slichter, C.P. (1990) Principles of Magnetic Resonance, 3 Ed., Springer, Berlin.
17. Thornton, J.M. and Swindells, M.B. (1993) in Molecular Structures in Biology (Diamond, R., Koetzle, T.F., Prout, K. and Richardson, J.S., Eds.), Oxford University Press, Oxford, pp. 82.
18. Cioslowski, J. (1993) Rev. Comput. Chem. 4, 1-33.
19. St-Amant, A. (1996) Rev. Comput. Chem. 7, 217-259.
20. Bakowies, D. and Thiel, W. (1991) J. Am. Chem. Soc. 113, 3704-3712.
21. Strain, M.C., Scuseria, G.E. and Frisch, M.J. (1996) Science 271, 51-54.
22. Paizs, B., Fogarasi, G. and Pulay, P. (1998) J. Chem. Phys. 109, 6571-6576.
23. Stewart, J.J.P. (1990) Rev. Comput. Chem. 1, 45-81.
24. Náray-Szabó, G. and Surján, P.R. (1983) Chem. Phys. Lett. 96, 499-501.
25. Ferenczy, G., Rivail, J.L., Surján, P.R. and Náray-Szabö, G. (1992) J. Comp. Chem. 13, 830-837.
26. Humbel, S., Sieber, S. and Morokuma, K. (1996) J. Chem. Phys. 105, 1959-1965.
27. Gao, J. (1996) Rev. Comput. Chem. 7, 119-185.
28. Car, R. and Parrinello, M. (1985) Phys. Rev. Lett. 55, 2471-2474.
29. Parrinello, M. (1997) Solid State Comm. 102, 63-95.
30. Stote, R.H., Dejaegere, A. and Karplus, M. (1997) in Computational Approaches to Biochemical Reactivity (Náray-Szabó, G. and Warshel., A., Eds.), Kluwer, Dordrecht, pp. 153-198.
31. Sharp, K.A. and Honig, B. (1990) Annu. Rev. Biophys. Chem. 19, 301-342.
32. DelPhi: Electrostatic Potential and Salvation Software (1995) Molecular Simulations, Inc., 9685 Scranton Rd., San Diego, CA 92121.
33. Rey, F., Jenkins, J., Janin, J., Lasters, I., Alard, P., Claesens, M., Matthyessens G. and Wodak, S. (1988) Proteins 4, 165-173.
34. Jenkins, J., Janin, J., Rey, F., Chiadmi, M., van Tilbeurgh, H., Lasters, I., Maeyer, M.D., Belle, D.V., Wodak, S., Lauwereys, M., Stanssens, P., Mrabet, N.T., Snauwaert, J. and Lambeir, A.M. (1992) Biochemistry 31, 5449-5458.
35. Carrell, H.L., Rubin, B.H., Hurley, T.J. and Glusker, J.P. (1984) J. Biol. Chem. 259, 3230-3236.
36. Carrell, H.L., Glusker, J.P., Burger, V., Manfre, F., Tritsch, D. and Biellmann, J.F. (1989) Proc. Natl. Acad. Sci. U.S.A. 86, 4440-4444.
37. Whitlow, M., Howard, A. J., Finzel, B. C., Poulos, T. L., Winborne, E. and Gilliland, G.L. (1991) Proteins 9, 153-173.
38. Glasfeld, A., Farber, G.K., Ringe, D., Marcel, T., Drocourt, D., Tiraby, G. and Petsko, G.A. (1988) J. Biol. Chem. 263, 14612-14613.
39. Henrick, K. Collyer, C.A. and Blow, D.M. (1989) J. Mol. Biol. 208, 129-157.
40. Collyer, C. A., Henrick, K. and Blow, D. M. (1990) J. Mol. Biol. 212, 211-235.
41. Loviny-Anderton, T., Shaw, P., Shin, M. and Hartley, B.S. (1991) Biochem. J. 277, 263-271.
42. Cha, J., Cho, Y., Whitaker, R. D., Carrell, H. L., Glusker, J. P., Karplus, P. A. and Batt, C. A. (1994) J. Biol. Chem. 269, 2687-2694.
43. Farber, G.K., Petsko, G.A. and Ringe, D. (1987) Protein Eng. 1, 459-466.
44. Farber, G.K., Machin, P., Almo, S.C., Petsko, G.A. and Hajdu, J. (1988) Proc. Natl. Acad. Sci. U.S.A. 85, 112-118.
45. Zhu, X.Y., Gong, W.M., Niu, L.W., Teng, M.K., Xu, Q.P., Wu, C.J., Cui, T., Wang, Y.Z., and Wang, C. (1996) Science in China, Ser C 39, 636-644.
46. Chayen, N.E., Conti, E., Vielle, C. and Zeikus, J.G. (1997) Acta Cryst. D53, 229-230.
47. Chang, C., Park, B.C., Lee, D.S. and Suh, S.W. (1998) J. Biochem. Mol. Biol. 31, 600-603.
48. Chang, C., Park, B. C., Lee, D-S. and Suh, S.W. (1999) J. Mol. Biol. 288, 623-634.
49. Gaikwad, S.M., Rao, M.B. and Desphande V.V. (1993) Enzyme Microb. Technol. 15, 155-158.
50. Whitaker, R.D., Cho, Y., Cha, J., Carrell, H.L., Glusker, J.P., Karplus, P.A. and Batt, C.A. (1995) J. Biol. Chem. 270, 22895-22906.
51. Fuxreiter, M., Böcskei, Z., Szeibert, A., Szabó, E., Dallmann, G., Náray-Szabó, G. and Asbóth, B. (1997) Proteins 28, 183-193.
52. Gérczei, T., Böcskei, Z., Szabó, E., Asbóth, B. and Náray-Szabó, G. (1999) Int. J. Biol. Macromol. 25, 329-336.
53. Collyer, C.A., Goldberg, J.D., Viehmann, H, Blow, D.M., Ramsden, N.G., Fleet, G.W., Montgomery, F.J. and Grice P. (1992) Biochemistry 31, 12211-12218.
54. Collyer, C. A. and Blow, D. M. (1990) Proc. Natl. Acad. Sci. USA 87, 1362-1366.
55. Allen, K. N., Lavie, A., Petsko, G. A. and Ringe, D. (1995) Biochemistry 34, 3742-3749.
56. Carrell, H.L., Hoeir, H. and Glusker, J.P. (1994) Acta Cryst. D50, 113-123.
57. Banerjee, S., Anderson, F. and Farber, G.K. (1995) Protein Eng. 8, 1189-1195.
58. Callens, M., Kersters-Hilderson, H., Vangrysperre, W., van Opstal, O. and de Bruyne, C.K. (1988) Arch. Int. Physiol. Biochim. 94, B9.
59. Vangrysperre, W., Callens, M., Kersters-Hilderson, H. and de Bruyne, C.K. (1988) Biochem. J. 250, 153-160.
60. Gaikwad, S.M., More, M.W., Vartak, H.G. and Desphande, V.V. (1988) Biochem. Biophys. Res. Commun. 155, 270-277.
61. Vangrysperre, W., Callens, M., Kersters-Hilderson, H. and de Bruyne, C.K. (1989) Biochem. J. 260, 163-169.
62. Batt, C.A., Jamieson, A.C. and Vandeyar, M.A. (1990) Proc.Natl.Acad.Sci. USA 87, 618-622.
63. Jamieson, A.C. and Batt, C.A. (1992) Protein Eng. 5, 235-240.
64. Ghatge, M.S. and Desphande, V.V. (1993) Biochem. Biophys. Res. Commun. 193, 979-984.
65. Callens, M., Tomme, P., Kersters-Hilderson, H., Cornelis, R., Vangrysperre, W. and de Bruyne, C.K. (1988) Biochem. J. 250, 285-290.
66. Bogumil, R., Kappl, R., Hintermann, J. and Witzel, H. (1997) Biochemistry 36, 2345-2352.
67. Lavie, A., Allen, K. N., Petsko, G. A. and Ringe, D. (1994) Biochemistry 33, 5469-5480.
68. Allen, K. N., Lavie, A., Glasfeld, A., Tanada, T. N., Gerrity, D. P., Carlson, S. C., Farber, G. K., Petsko, G. A. and Ringe, D. (1994) Biochemistry 33, 1488-1494.
69. Lee, C., Bagdasarian, M., Meng, M. and Zeikus, J. G. (1990) J. Biol. Chem. 265, 19082-19090.
70. Fuxreiter, M., Farkas, Ö. and Náray-Szabó, G. (1995) Protein Eng. 8, 925-933.
71. Fábián, P., Asbóth, B. and Náray-Szabó, G. (1994) J. Mol. Struct. THEOCHEM 307, 171-178.
72. Blow, D.M., Birktoft, J.J. and Hartley, B.S. (1969) Nature 221, 337-340.
73. Blake, C.C.F., Johnson, L.N., Mair, G.A., North, A.C.T., Phillips, D.C. and Sarma, V.R. (1967) Proc. Roy. Soc. Ser. B 167, 378-388.
74. Ángyán, J. and Náray-Szabó, G. (1983) J. theor. Biol. 103, 349-356.
75. Náray-Szabó, G. and Gérczei, T. (1996) Croat. Chem. Acta 69, 955-965.
76. Gérczei, T., Asbóth, B. and Náray-Szabó, G. (1999) J. Chem. Inf. Comput. Sci. 39, 310-315.
77. Náray-Szabó G. (1998) in The Encyclopedia of Computational Chemistry (Schleyer P.v.R., Allinger N.L., Clark T., Gasteiger J., Kollman P.A., Schaefer III H.F. and Schreiner, P.R., Eds.), Vol. 1, pp. 905-912. Wiley, Chichester.
78. Lambeir, A-M., Lauwereys, M., Stanssens, P., Mrabet, N. T., Snauwaert, J., van Tilbeurgh, H., Matthyssens, G., Lasters, I., De Maeyer, M., Wodak, S. J., Jenkins, J., Chiadmi, M. and Janin, J. (1992) Biochemistry 31, 5459-5466.
79. Smart, O. S., Akins, J. and Blow, D. M. (1992) Proteins 13, 100-111.
80. Hu, H., Shi, Y.Y. and Wang, C.X. (1997) Proteins 27, 545-555.
81. van Bastelaere, P.B.M., Kersters-Hilderson, H.L.M. and Lambeir, A.M. (1995) Biochem. J. 307, 135-142.
82. Rose, I.A., O'Connell, E.L. and Mortlock, R.P. (1969) Biochim. Biophys. Acta 178, 376-382.
83. Allen, K.N., Lavie, A., Farber, G.K., Glasfeld, A., Petsko, G.A. and Ringe, D. (1994) Biochemistry 33, 1481-1487.
84. Meng, M., Bagdasarian, M. and Zeikus J.G. (1993) Proc. Natl. Acad. Sci. U.S.A. 90, 8459-8463.
85. Náray-Szabó G., Fuxreiter M. and Warshel A. (1997) in Computational Approaches to Biochemical Reactivity (Náray-Szabó G. and Warshel A., Eds.), pp. 237-293, Kluwer, Dordrecht.
86. Craik, C.S., Roczniak, S., Largeman, C. and Rutter, W.J. (1987) Science 237, 909-912.
87. Carter, P. and Wells, J.A. (1988) Nature 332, 564-567.
88. van Bastelaere, P. B. M., Callens, M., Vangrysperre, W. A. E. and Kersters-Hilderson, H. L. M. (1986) Enzyme Microb. Technol. 8, 696-700.
89. van Bastelaere, P.B.M., Vangrysperre, W. and Kersters-Hilderson, H. (1991) Biochem. J. 278, 285-292.
90. van Bastelaere, P. B. M., Callens, M., Vangrysperre, W. A. E. and Kersters-Hilderson, H. L. M. (1992) Biochem. J. 286, 729-735.
91. Callens, M.H., Kersters-Hilderson, H., Van Opstal, O. and Debruyne, C.K. (1986) Enzyme Microb. Technol. 8, 696-700.
92. Callens, M.H., Kersters-Hilderson, H., Vangrysperre, V. and Debruyne, C.K. (1988) Enzyme Microb. Technol. 10, 695-700.
93. Gaikwad, S.M., Rao, M.B. and Desphande, V.V. (1992) Enzyme Microb. Technol. 14, 317-320.
94. Ferenczy, G.G., Náray-Szabó, G. and Várnai, P. Int. J. Quant. Chem., in press.
95. Sudfeldt, C., Schaffer, A., Kagi, J. H. R., Bogumil, R., Schulz, H. P., Wulff, S. and Witzel, H. (1990) Eur. J. Biochem. 193, 863-871.
96. Bogumil, R., Hintermann, J., Kappl, R., Stabler, R., Sudfeldt, C. and Witzel, H. (1991) Eur. J. Biochem. 196, 305-312.
97. Bogumil, R., Kappl, R., Hüttermann, J., Sudfeldt, C. and Witzel, H. (1993) Eur. J. Biochem. 213, 1185-1192.
98. Dikanov, S.A., Tyryshkin, A.M., Hütterman, J. Bogumil, R. and Witzel, H. (1995) J. Am. Chem. Soc. 117, 4976-4986.
99. Bogumil, R., Kappl, R., Hütterman, J. and Witzel, H (1997) Biochemistry 36, 2345-2352.
100. Náray-Szabó G. and Menyhárd D. (1998) Ann. Reports, Royal Society of Chemistry, Section C 94, 49-88.
101. Harris, T.K. and Mildvan, A.S. (1999) Proteins 35, 275-282.
102. Hu, H., Shi, Y.Y. and Wang, C.X. (1996) Proteins 26, 157-166.
103. Zeikus, J.G., Vieille, C. and Savchenko, A. (1998) Extremophiles 2, 179-183.
104. Rangarajan, M., Asbóth, B. and Hartley, B.S. (1992) Biochem. J. 285, 889-898.
105. Varsani, L., Cui, T., Rangarajan, M., Hartley, B.S., Goldberg, J., Collyer, C. and Blow, D.M. (1993) Biochem. J. 291, 575-583.
106. Mrabet, N. T., Van den Broeck, A., Van den Brande, I., Stanssens, P., Laroche, Y., Lambeir, A. M., Matthijssens, G., Jenkins, J., Chiadmi, M., van Tilbeurgh, H., Rey, F., Janin, J., Quax, W. J., Lasters, I., Maeyer, M. D. and Wodak, S. J. (1992) Biochemistry 31, 2239-2253.
107. Wu, C.J., Xiao, Y.Z., Long, FR., Teng, M.K., Wang, C. and Cui, T. (1996) Acta Biochim. Biophys. Sinica 28, 272-278.
108. Zhu, G.P., Xu, C., Teng, M.K., Tao, L.M., Zhu, X.Y., Wu, C.J., Hang, J., Niu, L.W. and Wang, Y.Z. (1999) Prot.Eng. 12, 635-638.
109. Hess, J.M. and Kelly, R.M. (1999) Biotechnol. Bioeng. 62, 509-517.
110. Siddiqui, K.S., Loviny-Anderton, T., Rangarajan, M. and Hartley, B.S. (1993) Biochem.J. 296, 685-691.
111. van Tilbeurgh, H., Jenkins, J., Chiadmi, M., Janin, J., Wodak, S. J., Mrabet, N. T. and Lambeir, A-M. (1992) Biochemistry 31, 5467-5471.
112. Cha, J. and Batt, C.A. (1998) Mol. Cells 8, 374-382.
113. Ge, Y. Wang, Y., Zhou, H., Wang, S., Tong, Y. and Li, W. (1999) J. Biotechnol. 67, 33-40.
114. Bialy, H. (1993) Bio/Technology 11, 278-279.