Exploring sequence space: Profile analysis and protein-ligand docking to screen ω-aminotransferases with expanded substrate specificity

Biotechnology Journal

Volumn 3, Issue 5, 2008, Pages 676-686

  Seo, Joo Hyun ^a   Park, Hyung Yeon ^b   Kim, Juhan ^c   Lee, Bon Su ^b   Kim, Byung Gee ^a  

^a Seoul National University   (South Korea)

^b Inha University   (South Korea)

^c UNIVERSITY OF COLORADO   (United States)

Author keywords

aminotransferase; Profile analysis; Protein ligand docking; Screening; Substrate specificity prediction

Indexed keywords

AMINOTRANSFERASE; PROFILE ANALYSIS; PROTEIN-LIGAND DOCKING; SUBSTRATE SPECIFICITY PREDICTION;

AMINES; BIOCATALYSTS; ENZYMES; LIGANDS; PROTEINS;

BIOTECHNOLOGY;

4 AMINOBUTYRATE AMINOTRANSFERASE; 7,8 DIAMINOPELARGONATE AMINOTRANSFERASE; AMINOTRANSFERASE; OMEGA AMINOTRANSFERASE; ORNITHINE OXOACID AMINOTRANSFERASE; TRANSFERASE;

ARTICLE; BACTERIAL GENE; ENZYME ASSAY; ENZYME BINDING; ENZYME SPECIFICITY; ESCHERICHIA COLI; GENE SEQUENCE; LIGAND BINDING; NONHUMAN; NUCLEOTIDE SEQUENCE; PREDICTION; PRIORITY JOURNAL; RHIZOBIUM RADIOBACTER; RHODOBACTER SPHAEROIDES; STATISTICAL MODEL; STREPTOMYCES; STREPTOMYCES AVERMITILIS;

ALGORITHMS; AMINO ACID SEQUENCE; BINDING SITES; ENZYME ACTIVATION; LIGANDS; MOLECULAR SEQUENCE DATA; PROTEIN BINDING; PROTEIN INTERACTION MAPPING; SEQUENCE ANALYSIS, PROTEIN; SUBSTRATE SPECIFICITY; TRANSAMINASES;

BACTERIA (MICROORGANISMS);

EID: 44949263090     PISSN: 18606768     EISSN: None     Source Type: Journal    
DOI: 10.1002/biot.200700264     Document Type: Article

References (28)

1. Iwasaki, A., Yamada, Y., Kizaki, N., Ikenaka, Y., Hasegawa, J., Microbial synthesis of chiral amines by (R)-specific transaminatjon with Arthrobacter sp. KNK168. Appl. Microbiol. Biotechnol. 2006, 69, 499-505.
2. Shin, J. S., Kim, B. G., Asymmetric synthesis of chiral amines with omega-transaminase. Biotechnol. Bioeng. 1999, 65, 206-211.
3. Robin, K., Bornscheuer, U., Höhne, M., Process for the preparation of optically active chiral amines, PCT patent WO2007/ 093372. 2007.
4. Shin, J. S., Yun, H., Jang, J. W., Park, I., Kim, B. G., Purification, characterization, and molecular cloning of a novel amine:pyruvate transaminase from Vibrio fluvialis JS17. Appl. Microbiol. Biotechnol. 2003, 61, 463-471.
5. Yun, H., Hwang, B. Y., Lee, J. H., Kim, B. G., Use of enrichment culture for directed evolution of the Vibrio fluvialis JS17 omega-transaminase, which is resistant to product inhibition by aliphatic ketones. Appl. Environ. Microbiol. 2005, 71, 4220-4224.
6. Cho, B. K., Park, H. Y., Seo, J. H., Kim, J. et al., Redesigning the substrate specificity of omega-aminotransferase for the kinetic resolution of aliphatic chiral amines. Biotechnol. Bioeng. 2008, 99, 275-284.
7. Datsenko, K. A., Wanner, B. L., One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. Proc. Natl. Acad. Sci. USA 2000, 97, 6640-6645.
8. Thompson, J. D., Higgins, D. G., Gibson, T. J., CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 1994, 22, 4673-4680.
9. Eddy, S. R., Profile hidden Markov models. Bioinformatics 1998, 14, 755-763.
10. Mehta, P. K., Hale, T. I., Christen, P., Aminotransferases: demonstration of homology and division into evolutionary subgroups. Eur. J. Biochem. 1993, 214, 549-561.
11. Shi, J., Blundell, T. L., Mizuguchi, K., FUGUE: Sequence-structure homology recognition using environment- specific substitution tables and structure-dependent gap penalties. J. Mol. Biol. 2001, 310, 243-257.
12. Mizuguchi, K., Deane, C. M., Blundell, T. L., Johnson, M. S., Overington, J. P., JOY: Protein sequence-structure representation and analysis. Bioinformatics 1998, 14, 617-623.
13. Stebbings, L. A., Mizuguchi, K., HOMSTRAD: Recent developments of the Homologous Protein Structure Alignment Database. Nucleic Acids Res. 2004, 32, D203-D207.
14. Mannhold, R., Rekker, R. F., Sonntag, C., ter Laak, A. M. et al., Comparative evaluation of the predictive power of calculation procedures for molecular lipophilicity. J. Pharm. Sci. 1995, 84, 1410-1419.
15. Durbin, R., Eddy, S. R., Krogh, A., Mitchison, G., Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids, Cambridge University Press, New York 1998.
16. Shin, J. S., Kim, B. G., Exploring the active site of amine:pyruvate aminotransferase on the basis of the substrate structure-reactivity relationship: How the enzyme controls substrate specificity and stereoselectivity. J. Org. Chem. 2002, 67, 2848-2853.
17. Yun, H., Lim, S., Cho, B. K., Kim, B. G., omega-Amino acid:pyruvate transaminase from Alcaligenes denitrificans Y2k-2: A new catalyst for kinetic resolution of beta-amino acids and amines. Appl. Environ. Microbiol. 2004, 70, 2529-2534.
18. Voellym, R., Leisinger, T., Role of 4-aminobutyrate amino-transferase in the arginine metabolism of Pseudomonas aeruginosa. J. Bacteriol. 1976, 128, 722-729.
19. Yasuda, M., Tanizawa, K., Misono, H., Toyama, S., Soda, K., Properties of crystalline L-ornithine: alpha-ketoglutarate delta-aminotransferase from Bacillus sphaericus. J. Bacteriol. 1981, 148, 43-50.
20. Cho, B. K., Seo, J. H., Kang, T. J., Kim, J. et al., Engineering aromatic L-amino acid transaminase for the asymmetric synthesis of constrained analogs of L-phenylalanine. Biotechnol. Bioeng. 2006, 94, 842-850.
21. Kim, Y. G., Shin, D. S., Kim, E. M., Park, H. Y. et al., High-throughput identification of substrate specificity for protein kinase by using an improved one-bead-one-compound library approach. Angew. Chem. Int. Ed. Engl. 2007, 46, 5408-5411.
22. Kohen, A., Klinman, J. P., Hydrogen tunneling in biology. Chem. Biol. 1999, 6, R191-R198.
23. Sterner, B., Singh, R., Berger, B., Predicting and annotating catalytic residues: An information theoretic approach. J. Comput. Biol. 2007, 14, 1058-1073.
24. Ye, K., Feenstra, K. A., Heringa, J., Ijzerman, A. P., Marchiori, E., Multi-RELIEF: A method to recognize specificity determining residues from multiple sequence alignments using a Machine Learning approach for feature weighting. Bioinformatics 2008, 24, 18-25.
25. Fetrow, J. S., Skolnick, J., Method for prediction of protein function from sequence using the sequence-to-structure-to-function paradigm with application to glutaredoxins/thioredoxins and T1 ribonucleases. J. Mol. Biol. 1998, 281, 949-968.
26. Porter, C. T., Bartlett, G. J., Thornton, J. M., The Catalytic Site Atlas: A resource of catalytic sites and residues identified in enzymes using structural data. Nucleic Acids Res. 2004, 32, D129-133.
27. Hollidaym G. L., Almonacid, D. E., Mitchell, J. B., Thornton, J. M., The chemistry of protein catalysis. J. Mol. Biol. 2007, 372, 1261-1277.
28. Zhou, H., Zhou, Y., SPEM: Improving multiple sequence alignment with sequence profiles and predicted secondary structures. Bioinformatics 2005, 21, 3615-3621.