Directed evolution of transketolase activity on non-phosphorylated substrates

Journal of Biotechnology

Volumn 131, Issue 4, 2007, Pages 425-432

  Hibbert, Edward G ^a   Senussi, Tarik ^a   Costelloe, Sean J ^a   Lei, Wenling ^a   Smith, Mark E B ^a   Ward, John M ^a   Hailes, Helen C ^a   Dalby, Paul A ^a  

^a UNIVERSITY COLLEGE LONDON   (United Kingdom)

Author keywords

Biocatalysis; Directed evolution; Phylogenetics; Protein engineering; Transketolase

Indexed keywords

MUTAGENESIS; PHOSPHATES; PHOSPHORYLATION; REACTION KINETICS; SATURATION (MATERIALS COMPOSITION); SUBSTITUTION REACTIONS;

DIRECTED EVOLUTION; PHYLOGENETICS; PROTEIN ENGINEERING; TRANSKETOLASE;

ENZYME ACTIVITY;

ALDEHYDE DERIVATIVE; BACTERIAL ENZYME; CARBOHYDRATE DERIVATIVE; PYRUVIC ACID DERIVATIVE; TRANSKETOLASE;

AMINO ACID SEQUENCE; ARTICLE; BIOCATALYST; CATALYSIS; ENTROPY; ENZYME ACTIVE SITE; ENZYME ACTIVITY; ENZYME SPECIFICITY; ENZYME STRUCTURE; ENZYME SUBSTRATE; ESCHERICHIA COLI; MOLECULAR PHYLOGENY; MUTAGENESIS; PHOSPHORYLATION; PRIORITY JOURNAL; PROTEIN INTERACTION; STRUCTURAL HOMOLOGY; STRUCTURE ANALYSIS;

AMINO ACIDS; ANIMALS; CHROMATOGRAPHY, HIGH PRESSURE LIQUID; DIRECTED MOLECULAR EVOLUTION; ENTROPY; ESCHERICHIA COLI; MUTANT PROTEINS; PHOSPHORYLATION; SEQUENCE ALIGNMENT; SUBSTRATE SPECIFICITY; TRANSKETOLASE;

EID: 34648843275     PISSN: 01681656     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jbiotec.2007.07.949     Document Type: Article

References (43)

1. Amin N., Liu A.D., Ramer S., Aehle W., Meijer D., Metin M., Wong S., Gualfetti P., and Schellenberger V. Construction of stabilized proteins by combinatorial consensus mutagenesis. Protein Eng. Des. Sel. 17 (2004) 787-793
2. Ashworth J., Havranek J.J., Duarte C.M., Sussman D., Monnat R.J., Stoddard B.L., and Baker D. Computational redesign of endonuclease DNA binding and cleavage specificity. Nature 441 (2006) 656-659
3. Chen K., and Arnold F.H. Tuning the activity of an enzyme for unusual environments: sequential random mutagenesis of subtilisin E for catalysis in dimethylformamide. Proc. Natl. Acad. Sci. U.S.A. 90 (1993) 5618-5622
4. Cochran J.R., Kim Y.S., Lippow S.M., Rao B., and Wittrup K.D. Improved mutants from directed evolution are biased to orthologous substitutions. Protein Eng. Des. Sel. 19 (2006) 245-253
5. Dalby P.A. Optimising enzyme function by directed evolution. Curr. Opin. Struct. Biol. 13 (2003) 500-505
6. DiTursi M.K., Kwon S.J., Reeder P.J., and Dordick J.S. Bioinformatics-driven, rational engineering of protein thermostability. Protein Eng. Des. Sel. 19 (2006) 517-524
7. Dwyer M.A., Looger L.L., and Hellinga H.W. Computational design of a biologically active enzyme. Science 304 (2004) 1967-1971
8. Felsenstein J. PHYLIP - Phylogeny Inference Package (Version 3.2). Cladistics 5 (1989) 164-166
9. Flores H., and Ellington A.D. A modified consensus approach to mutagenesis inverts the cofactor specificity of Bacillus stearothermophilus lactate dehydrogenase. Protein Eng. Des. Sel. 18 (2005) 369-377
10. French C., and Ward J.M. Improved production and stability of E. coli recombinants expressing transketolase for large scale biotransformation. Biotechnol. Lett. 17 (1995) 247-252
11. Goud G.N., Artsaenko O., Bols M., and Sierks M. Specific glycosidase activity isolated from a random phage display antibody library. Biotechnol. Prog. 17 (2001) 197-202
12. Gyamerah M., and Willetts A.J. Kinetics of overexpressed transketolase from Escherichia coli JM 107/pQR 700. Enzyme Microb. Technol. 20 (1997) 127-134
13. Hall, T.A., 1999. BioEdit: a user-friendly biological sequence alignment editor and analysis. http://www.mbio.ncsu.edu/BioEdit/bioedit.html.
14. Hayes R.J., Bentzien J., Ary M.L., Hwang M.Y., Jacinto J.M., Vielmetter J., Kundu A., and Dahiyat B.I. Combining computational and experimental screening for rapid optimization of protein properties. Proc. Natl. Acad. Sci. U.S.A. 99 (2002) 15926-15931
15. Ingram C.U., Bommer M., Smith M.E.B., Dalby P.A., Ward J.M., Hailes H.C., and Lye G.J. One-pot synthesis of amino-alcohols using a de-novo transketolase and β-alanine:pyruvate transaminase pathway in Escherichia coli. Biotechnol. Bioeng. 96 (2007) 559-569
16. Lehmann M., Pasamontes L., Lassen S.F., and Wyss M. The consensus concept for thermostability engineering of proteins. Biochemi. Biophys. Acta Protein Struct. Mol. Enzyme 1543 (2000) 408-415
17. Lindqvist Y., Schneider G., Ermler U., and Sundstrom M. 3-Dimensional structure of transketolase, a thiamine diphosphate dependent enzyme, at 2.5 Angstrom resolution. EMBO J. 11 (1992) 2373-2379
18. Littlechild J.A., Turner N.J., Hobbs G.R., Lilly M.D., Rawas A., and Watson H. Crystallization and preliminary-X-ray crystallographic data with Escherichia-coli transketolase. Acta Crystallogr. D 51 (1995) 1074-1076
19. Miyazaki K., and Arnold F.H. Exploring nonnatural evolutionary pathways by saturation mutagenesis: rapid improvement of protein function. J. Mol. Evol. 49 (1999) 716-720
20. Morley K.L., and Kazlauskas R.J. Improving enzyme properties: when are closer mutations better?. Trends Biotechnol. 23 (2005) 231-237
21. Morris K.G., Smith M.E.B., Turner N.J., Lilly M.D., Mitra R.K., and Woodley J.M. Transketolase from Escherichia coli: a practical procedure for using the biocatalyst for asymmetric carbon-carbon bond synthesis. Tetrahedron Asymm. 7 (1996) 2185-2188
22. Mullegger J., Jahn M., Chen H.M., Warren R.A.J., and Withers S.G. Engineering of a thioglycoligase: randomized mutagenesis of the acid-base residue leads to the identification of improved catalysts. Protein Eng. Des. Sel. 18 (2005) 33-40
23. Murase K., Morrison K.L., Tam P.Y., Stafford R.L., Jurnak F., and Weiss G.A. EF-Tu binding peptides identified, dissected, and affinity optimized by phage display. Chem. Biol. 10 (2003) 161-168
24. Ness J.E., Kim S., Gottman A., Pak R., Krebber A., Borchert T.V., Govindarajan S., Mundorff E.C., and Minshull J. Synthetic shuffling expands functional protein diversity by allowing amino acids to recombine independently. Nat. Biotechnol. 20 (2002) 1251-1255
25. Nikkola M., Lindqvist Y., and Schneider G. Refined structure of transketolase from Saccharomyces cerevisiae at 2.0 Å resolution. J. Mol. Biol. 238 (1994) 387-404
26. Nilsson U., Meshalkina L., Lindqvist Y., and Schneider G. Examination of substrate binding in thiamin diphosphate-dependent transketolase by protein crystallography and site-directed mutagenesis. J. Biol. Chem. 272 (1997) 1864-1869
27. Parikh M.R., and Matsumura I. Site-saturation mutagenesis is more efficient than DNA shuffling for the directed evolution of β-fucosidase from β-galactosidase. J. Mol. Biol. 352 (2005) 621-628
28. Park S., Morley K.L., Horsman G.P., Holmquist M., Hult K., and Kazlauskas R.J. Focusing mutations into the P. fluorescens esterase binding site increases enantioselectivity more effectively than distant mutations. Chem. Biol. 12 (2005) 45-54
29. Peimbert M., and Segovia L. Evolutionary engineering of a beta-lactamase activity on a d-Ala d-Ala transpeptidase fold. Protein Eng. 16 (2003) 27-35
30. Santoro S.W., and Schultz P.G. Directed evolution of the site specificity of Cre recombinase. Proc. Natl. Acad. Sci. U.S.A. 99 (2002) 4185-4190
31. Sato K., Simon M.D., Levin A.M., Shokat K.M., and Weiss G.A. Dissecting the engrailed homeodomain-DNA interaction by phage-displayed shotgun scanning. Chem. Biol. 11 (2004) 1017-1023
32. Schenk G., Duggleby R.G., and Nixon P.F. Properties and functions of the thiamin diphosphate dependent enzyme transketolase. Int. J. Biochem. Cell B 30 (1998) 1297-1318
33. Schmitzer A.R., Lepine F., and Pelletier J.N. Combinatorial exploration of the catalytic site of a drug- resistant dihydrofolate reductase: creating alternative functional configurations. Protein Eng. Des. Sel. 17 (2004) 809-819
34. Shaeri J., Wohlgemuth R., and Woodley J.M. Semiquantitative process screening for the biocatalytic synthesis of d-xylulose-5-phosphate. Org. Process. Res. Dev. 10 (2006) 605-610
35. Shinkai A., Patel P.H., and Loeb L.A. The conserved active site motif a of Escherichia coli DNA polymerase I is highly mutable. J. Biol. Chem. 276. (2001) 18836-18842
36. Sprenger G.A., and Pohl M. Synthetic potential of thiamin diphosphate-dependent enzymes. J. Mol. Catal. B: Enzyme 6 (1999) 145-159
37. Sprenger G.A., Schorken U., Sprenger G., and Sahm H. Transketolase A of Escherichia coli K12. Purification and properties of the enzyme from recombinant strains. Eur. J. Biochem. 230 (1995) 525-532
38. Stemmer W.P.C. Rapid evolution of a protein in vitro by DNA shuffling. Nature 370 (1994) 389-391
39. Ting A.Y., Witte K., Shah K., Kraybill B., Shokat K.M., and Schultz P.G. Phage-display evolution of tyrosine kinases with altered nucleotide specificity. Biopolymers 60 (2001) 220-228
40. Turner N.J. Applications of transketolases in organic synthesis. Curr. Opin. Biotechnol. 11 (2000) 527-531
41. Wang L., Brock A., Herberich B., and Schultz P.G. Expanding the genetic code of Escherichia coli. Science 292 (2001) 498-500
42. Weinreich D.M., Delaney N.F., DePristo M.A., and Hartl D.L. Darwinian evolution can follow only very few mutational paths to fitter proteins. Science 312 (2006) 111-114
43. Yang Z. PAML: a program package for phylogenetic analysis by maximum likelihood. Comput. Appl. Biosci. 13 (1997) 555-556