Investigation of the enzymatic mechanism of the yeast chorismate mutase by docking a transition state analog

Journal of Molecular Biology

Volumn 271, Issue 5, 1997, Pages 838-845

  Lin, Shuo Liang ^a   Xu, Dong ^a   Li, Aijun ^a   Rosen, Maria ^b   Wolfson, Haim J ^b   Nussinov, Ruth ^a,b  

^a SAIC FREDERICK INC   (United States)

^b TEL AVIV UNIVERSITY   (Israel)

Author keywords

Chorismate; Docking; Modeling; Mutase; Structure

Indexed keywords

CHORISMATE MUTASE;

AMINO ACID SEQUENCE; ARTICLE; CONTROLLED STUDY; CRYSTAL STRUCTURE; ENZYME ACTIVE SITE; ENZYME MECHANISM; ENZYME STABILITY; ENZYME STRUCTURE; HYDROGEN BOND; NONHUMAN; PRIORITY JOURNAL; SACCHAROMYCES CEREVISIAE; YEAST;

BACTERIA (MICROORGANISMS); SACCHAROMYCES CEREVISIAE;

EID: 0031554881     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1997.1168     Document Type: Article

References (20)

1. Bartlett, P. A. & Jackson, C. R. (1985). An inhibitor of chorismate mutase resembling the transition-state conformation. J. Am. Chem. Soc. 107, 7792-7793.
2. Brünger, A. T. (1992). X-PLOR (version 3.1) Manual, Yale University Press, New Haven, CT.
3. Brooks, B. R., Bruccoleri, R. E., Olafson, B. D., States, D. J., Swaminathan, S. & Karplus, M. (1983). CHARMM: A program for macromolecular energy, minimization, and dynamic calculations. J. comput. Chem, 4, 187-217.
4. Chook, Y. M., Ke, H. & Lipscomb, W. (1993). Crystal structures of the monofunctional chorismate mutase from Bacillus subtilis and its complex with a transition state analog. Proc. Natl Acad. Sci. USA, 90, 8600-8603.
5. Fischer, D., Lin, S. L., Wolfson, H. J. & Nussinov, R. (1995). A geometry-based suite of molecular docking processes. J. Mol. Biol. 248, 459-477.
6. Jackson, D. Y., Jacobs, J. W., Sugawara, R., Riech, S. H., Bartlett, P. A. & Schultz, P. G. (1988). J. Am. Chem. Soc. 119, 4841-4842.
7. Kraulis, P. J. (1991). MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallog. 24, 946-950.
8. Lee, A. Y., Karplus, A., Ganem, B. & Clardy, J. (1995). Atomic structure of the buries catalytic pocket of Escherichia coli chorismate mutase. J. Am. Chem Soc. 117, 3627-3628.
9. Lin, S. L. (1995). SPAGS: detecting similar protein architectures by the geometry of secondary structures. In Building a Man Machine: Computational Medicine, Public Health, and Biotechnology (Witten, M, ed.), pp. 91-100, World Scientific Pub., London.
10. Lin, S. L. & Nussinov, R. (1996). Molecular recognition via face centre representation of a molecular surface. J. Mol. Graphics, 14, 78-90.
11. Lin, S. L., Nussinov, R., Fischer, D. & Wolfson, H. J. (1994). Molecular surface representations by sparse critical points. Proteins: Struct. Funct. Genet. 18, 94-101.
12. Nicholls, A., Sharp, K. A. & Honig, B. (1991). Protein folding and association: insights from the interfacial and thermodynamic properties of hydrocarbons. Proteins: Struct. Funct. Genet. 11, 281-296.
13. Norel, R., Lin, S. L., Wolfson, H. J. & Nussinov, R. (1995). Molecular surface complementarity at protein-prtotein interfaces: the critical role played by surface normals at well placed, sparse, points in docking. J. Mol. Biol. 252, 263-273.
14. Schmidheini, T., Mösch, H-U., Evans, J. N. S. & Braus, G. (1990). Yeast allosteric chorismate mutase is locked in the activated state by a single amino acid substitution. Biochemistry, 29, 3660-3668.
15. Sogo, S. G., Widlanski, T. S., Hoare, J. H., Grimshaw, C. E., Berchtold, G. A. & Knowles, J. R. (1984). Stereochemistry of the rearrangement of chorismate to prephenate: chorismate mutase involves a chair transition state. J. Am. Chem. Soc. 106, 2710-2703.
16. Stewart, J. J. (1990). MOPAC: a semiempirical molecular orbital program. J. Comput. Aided Mol. Des. 4, 1-105.
17. Sträter, N., Håkansson, K., Schnappauf, G., Braus, G. & Lipscomb, W. N. (1996). Crystal structure of the T state of allosteric yeast chorismate mutase and comparison with the R state. Proc. Natl Acad. Sci. USA, 93, 3330-3334.
18. Wiess, U. & Edwards, J. M. (1980). The Biosynthesis of Aromatic Amino Compounds, Wiley, New York.
19. Xue, Y. & Lipscom, W. N. (1995). Location of the active site of allosteric chorismate mutase from Saccharomyces cerevisiae, and comments on the catalytic and regulatory mechanisms. Proc. Natl Acad. Sci. USA, 92, 10595-10598.
20. Xue, Y., Lipscom, W. N., Graf, R. & Braus, G. (1994). The crystal structure of allosteric chorismate mutase at 2.2-Å resolution. Proc. Natl Acad. Sci. 91, 19814-10818.