Directed evolution relieves product inhibition and confers in vivo function to a rationally designed tyrosine aminotransferase

Protein Science

Volumn 13, Issue 3, 2004, Pages 763-772

  Rothman, Steven C ^a   Voorhies, Mark ^a   Kirsch, Jack F ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Aminotransferase; Directed evolution; Protein engineering; Pyridoxal phosphate; Substrate specificity

Indexed keywords

2 OXOGLUTARIC ACID; ASPARTATE AMINOTRANSFERASE; ASPARTIC ACID; DICARBOXYLIC ACID; OXALOACETIC ACID; PHENYLALANINE; TYROSINE; TYROSINE AMINOTRANSFERASE;

AMINO ACID SUBSTITUTION; ARTICLE; AUXOTROPHY; CITRIC ACID CYCLE; CONTROLLED STUDY; ENZYME ACTIVITY; ENZYME SPECIFICITY; ENZYME SYNTHESIS; ESCHERICHIA COLI; MUTATION; NEGATIVE FEEDBACK; NONHUMAN; PRIORITY JOURNAL; PROTEIN ENGINEERING;

AMINO ACIDS; ASPARTATE AMINOTRANSFERASES; ASPARTIC ACID; CELL DIVISION; CLONING, MOLECULAR; DIRECTED MOLECULAR EVOLUTION; DNA SHUFFLING; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; GENE DELETION; KINETICS; MODELS, CHEMICAL; MOLECULAR STRUCTURE; MUTAGENESIS, SITE-DIRECTED; PHENYLALANINE; POINT MUTATION; PROTEIN ENGINEERING; RECOMBINANT PROTEINS; SUBSTRATE SPECIFICITY; SUCROSE; TRANSFORMATION, BACTERIAL; TYROSINE TRANSAMINASE; VISCOSITY;

ESCHERICHIA COLI; TRIXIS;

EID: 1342310509     PISSN: 09618368     EISSN: None     Source Type: Journal    
DOI: 10.1110/ps.03117204     Document Type: Article

References (26)

1. Bornscheuer, U.T. and Pohl, M. 2001. Improved biocatalysts by directed evolution and rational protein design. Curr. Opin. Chem. Biol. 5: 137-143.
2. Brouwer, A.C. and Kirsch, J.F. 1982. Investigation of diffusion-limited rates of chymotrypsin reactions by viscosity variation. Biochemistry 21: 1302-1307.
3. Chen, R. 2001. Enzyme engineering: Rational redesign versus directed evolution. Trends Biotechnol. 19: 13-14.
4. Chen, R., Greer, A.F., and Dean, A.M. 1997. Structural constraints in protein engineering - The coenzyme specificity of Escherichia coli isocitrate dehydrogenase. Eur. J. Biochem. 250: 578-582.
5. Cherry, J.R., Lamsa, M.H., Schneider, P., Vind, J., Svendsen, A., Jones, A., and Pedersen, A.H. 1999. Directed evolution of a fungal peroxidase. Nat. Biotechnol. 17: 379-384.
6. Gloss, L.M., Planas, A., and Kirsch, J.F. 1992. Contribution to catalysis and stability of the five cysteines in Escherichia coli aspartate aminotransferase. Preparation and properties of a cysteine-free enzyme. Biochemistry 31: 32-39.
7. Goldberg, J.M. and Kirsch, J.F. 1996. The reaction catalyzed by Escherichia coli aspartate aminotransferase has multiple partially rate-determining steps, while that catalyzed by the Y225F mutant is dominated by ketimine hydrolysis. Biochemistry 35: 5280-5291.
8. 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.
9. Jager, J., Moser, M., Sauder, U., and Jansonius, J.N. 1994. Crystal structures of Escherichia coli aspartate aminotransferase in two conformations. Comparison of an unliganded open and two liganded closed forms. J. Mol. Biol. 239: 285-305.
10. Kast, P., Asif-Ullah, M., Jiang, N., and Hilvert, D. 1996. Exploring the active site of chorismate mutase by combinatorial mutagenesis and selection: The importance of electrostatic catalysis. Proc. Natl. Acad. Sci. 93: 5043-5048.
11. Kohler, E., Seville, M., Jager, J., Fotheringham, I., Hunter, M., Edwards, M., Jansonius, J.N., and Kirschner, K. 1994. Significant improvement to the catalytic properties of aspartate aminotransferase: Role of hydrophobic and charged residues in the substrate binding pocket. Biochemistry 33: 90-97.
12. Lorimer, I.A. and Pastan, I. 1995. Random recombination of antibody single chain Fv sequences after fragmentation with DNasel in the presence of Mn2+. Nucleic Acids. Res. 23: 3067-3068.
13. Luong, T.N. and Kirsch, J.F. 1997. A continuous coupled spectrophotometric assay for tyrosine aminotransferase activity with aromatic and other nonpolar amino acids. Anal. Biochem. 253: 46-49.
14. -. 2001. A general method for the quantitative analysis of functional chimeras: Applications from site-directed mutagenesis and macromolecular association. Protein Sci. 10: 581-591.
15. Malashkevich, V.N., Toney, M.D., and Jansonius, J.N. 1993. Crystal structures of true enzymatic reaction intermediates: Aspartate and glutamate ketimines in aspartate aminotransferase. Biochemistry 32: 13451-13462.
16. Malashkevich, V.N., Onuffer, J.J., Kirsch, J.F., and Jansonius, J.N. 1995. Alternating arginine-modulated substrate specificity in an engineered tyrosine aminotransferase. Nat. Struct. Biol. 2: 548-553.
17. Matsumura, I. and Ellington, A.D. 2001. In vitro evolution of β-glucuronidase into β-galactosidase proceeds through non-specific intermediates. J. Mol. Biol. 305: 331-339.
18. McPhalen, C.A., Vincent, M.G., Picot, D., Jansonius, J.N., Lesk, A.M., and Chothia, C. 1992. Domain closure in mitochondrial aspartate aminotransferase. J. Mol. Biol. 227: 197-213.
19. Okamoto, A., Nakai, Y., Hayashi, H., Hirotsu, K., and Kagamiyama, H. 1998. Crystal structures of Paracoccus denitrificans aromatic amino acid aminotransferase: A substrate recognition site constructed by rearrangement of hydrogen bond network. J. Mol. Biol. 280: 443-461.
20. Onuffer, J.J. and Kirsch, J.F. 1994. Characterization of the apparent negative co-operativity induced in Escherichia coli aspartate aminotransferase by the replacement of Asp222 with alanine. Evidence for an extremely slow conformational change. Protein Eng. 7: 413-424.
21. -. 1995. Redesign of the substrate specificity of Escherichia coli aspartate aminotransferase to that of Escherichia coli tyrosine aminotransferase by homology modeling and site-directed mutagenesis. Protein Sci. 4: 1750-1757.
22. Rothman, S.C. and Kirsch, J.F. 2003. How does an enzyme evolved in vitro compare to naturally occurring homologs possessing the targeted function? Tyrosine aminotransferase from aspartate aminotransferase. J. Mol. Biol. 327: 593-608.
23. Seville, M., Vincent, M.G., and Hahn, K. 1988. Modeling the three-dimensional structures of bacterial aminotransferases. Biochemistry, 27: 8344-8349.
24. Shaffer, W.A., Luong, T.N., Rothman, S.C., and Kirsch, J.F. 2002. Quantitative chimeric analysis of six specificity determinants that differentiate Escherichia coli aspartate from tyrosine aminotransferase. Protein Sci. 11: 2848-2859.
25. Stemmer, W.P. 1994. DNA shuffling by random fragmentation and reassembly: In vitro recombination for molecular evolution. Proc. Natl. Acad. Sci. 91: 10747-10751.
26. Zhao, G. and Winkler, M.E. 1996. A novel α-ketoglutarate reductase activity of the serA-encoded 3-phosphoglycerate dehydrogenase of Escherichia coli K-12 and its possible implications for human 2-hydroxyglutaric aciduria. J. Bacteriol. 178: 232-239.