Switching from an esterase to a hydroxynitrile lyase mechanism requires only two amino acid substitutions

Chemistry and Biology

Volumn 17, Issue 8, 2010, Pages 863-871

  Padhi, Santosh Kumar ^a,b   Fujii, Ryota ^a,c   Legatt, Graig A ^a   Fossum, Sara L ^a   Berchtold, Reto ^a,d   Kazlauskas, Romas J ^a  

^a UNIVERSITY OF MINNESOTA   (United States)

^b UNIVERSITY OF GREIFSWALD   (Germany)

^c MITSUI CHEMICALS INC   (Japan)

^d Bachem Holding AG   (Switzerland)

Author keywords

CHEMBIO; PROTEINS

Indexed keywords

ESTERASE; LYASE;

AMINO ACID SUBSTITUTION; ARTICLE; BIOCATALYSIS; CHEMICAL STRUCTURE; CHEMISTRY; ENZYME ACTIVE SITE; ENZYME SPECIFICITY; ENZYMOLOGY; GENETICS; HEVEA; METABOLISM; SEQUENCE ALIGNMENT; STEREOISOMERISM;

ALDEHYDE-LYASES; AMINO ACID SUBSTITUTION; BIOCATALYSIS; CATALYTIC DOMAIN; ESTERASES; HEVEA; MODELS, MOLECULAR; SEQUENCE ALIGNMENT; STEREOISOMERISM; SUBSTRATE SPECIFICITY;

HEVEA BRASILIENSIS;

EID: 77956021391     PISSN: 10745521     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.chembiol.2010.06.013     Document Type: Article

References (41)

1. J. Andexer, J. von Langermann, A. Mell, M. Bocola, U. Kragl, T. Eggert, and M. Pohl An R-selective hydroxynitrile lyase from Arabidopsis thaliana with an α/β-hydrolase fold Angew. Chem. Int. Ed. Engl. 46 2007 8679 8681
2. P.C. Babbitt, and J.A. Gerlt Understanding enzyme superfamilies. Chemistry as the fundamental determinant in the evolution of new catalytic activities J. Biol. Chem. 272 1997 30591 30594
3. M. Bauer, H. Griengl, and W. Steiner Kinetic studies on the enzyme (S)-hydroxynitrile lyase from Hevea brasiliensis using initial rate methods and progress curve analysis Biotechnol. Bioeng. 62 1999 20 29
4. P. Bernhardt, K. Hult, and R.J. Kazlauskas Molecular basis of perhydrolase activity in serine hydrolases Angew. Chem. Int. Ed. Engl. 44 2005 2742 2746
5. S. Bershtein, K. Goldin, and D.S. Tawfik Intense neutral drifts yield robust and evolvable consensus proteins J. Mol. Biol. 379 2008 1029 1044
6. J.D. Bloom, P.A. Romero, Z. Lu, and F.H. Arnold Neutral genetic drift can alter promiscuous protein functions, potentially aiding functional evolution Biol. Direct 2 2007 17
7. C. Branneby, P. Carlqvist, A. Magnusson, K. Hult, T. Brinck, and P. Berglund Carbon-carbon bonds by hydrolytic enzymes J. Am. Chem. Soc. 125 2003 874 875
8. C. Branneby, P. Carlqvist, K. Hult, T. Brinck, and P. Berglund Aldol additions with mutant lipase: analysis by experiments and theoretical calculations J. Mol. Catal., B Enzym. 31 2004 123 128
9. P. Carlqvist, M. Svedendahl, C. Branneby, K. Hult, T. Brinck, and P. Berglund Exploring the active-site of a rationally redesigned lipase for catalysis of Michael-type additions ChemBioChem 6 2005 331 336
10. J.D. Cheeseman, A. Tocilj, S. Park, J.D. Schrag, and R.J. Kazlauskas Structure of an aryl esterase from Pseudomonas fluorescens Acta Crystallogr. D Biol. Crystallogr. 60 2004 1237 1243
11. P.D. Cook, R.L. Kubiak, D.P. Toomey, and H.M. Holden Two site-directed mutations are required for the conversion of a sugar dehydratase into an aminotransferase Biochemistry 48 2009 5246 5253
12. H. Du, and D.F. Klessig Identification of a soluble, high-affinity salicylic acid-binding protein in tobacco Plant Physiol. 113 1997 1319 1327
13. F. Forouhar, Y. Yang, D. Kumar, Y. Chen, E. Fridman, S.W. Park, Y. Chiang, T.B. Acton, G.T. Montelione, and E. Pichersky Structural and biochemical studies identify tobacco SABP2 as a methyl salicylate esterase and implicate it in plant innate immunity Proc. Natl. Acad. Sci. USA 102 2005 1773 1778
14. J.A. Gerlt, and P.C. Babbitt Divergent evolution of enzymatic function: mechanistically diverse superfamilies and functionally distinct superfamilies Annu. Rev. Biochem. 70 2001 209 246
15. J.-F. Gibrat, T. Madej, and S.H. Bryant Surprising similarities in structure comparison Curr. Opin. Struct. Biol. 6 1996 377 385
16. M.E. Glasner, J.A. Gerlt, and P.C. Babbitt Evolution of enzyme superfamilies Curr. Opin. Chem. Biol. 10 2006 492 497
17. K. Gruber, G. Gartler, B. Krammer, H. Schwab, and C. Kratky Reaction mechanism of hydroxynitrile lyase of the α/β-hydrolase superfamily: The three-dimensional structure of the transient enzyme-substrate complex certifies the crucial role of Lys236 J. Biol. Chem. 279 2004 20501 20510
18. R. Guerois, J.E. Neilsen, and L. Serrano Predicting changes in the stability of proteins and protein complexes: a study of more than 1000 mutations J. Mol. Biol. 320 2002 369 387
19. R.D. Gupta, and D.S. Tawfik Directed enzyme evolution via small and effective neutral drift libraries Nat. Methods 5 2008 939 942
20. Holm, L., and Park, J. (2000). DaliLite workbench for protein structure comparison. Bioinformatics 16, 566-567. http://ekhidna.biocenter.helsinki.fi/ dali
21. M. Holmquist Alpha/beta-hydrolase fold enzymes: structures, functions and mechanisms Curr. Protein Pept. Sci. 1 2000 209 235
22. L. Jiang, E.A. Althoff, F.R. Clemente, L. Doyle, D. Roethlisberger, A. Zanghellini, J.L. Gallaher, J.L. Betker, F. Tanaka, and C.F.I.I.I. Barbas De novo computational design of retro-aldol enzymes Science 319 2008 1387 1391
23. H. Jochens, K. Stiba, C. Savile, R. Fujii, J.-G. Yu, T. Gerassenkov, R.J. Kazlauskas, and U.T. Bornscheuer Converting an esterase into an epoxide hydrolase Angew. Chem. Int. Ed. Engl. 48 2009 3532 3535
24. T. Kitazume, T. Ikeya, and K. Murata Synthesis of optically active trifluorinated compounds: asymmetric Michael addition with hydrolytic enzymes J. Chem. Soc. Chem. Commun. 17 1986 1331 1333
25. H. Lauble, B. Miehlich, S. Forster, C. Kobler, H. Wajant, and F. Effenberger Structure determinants of substrate specificity of hydroxynitrile lyase from Manihot esculenta Protein Sci. 11 2002 65 71
26. C. Li, X.-W. Feng, N. Wang, Y.-J. Zhou, and X.-Q. Yu Biocatalytic promiscuity: the first lipase-catalysed asymmetric aldol reaction Green Chem. 10 2008 616 618
27. A.M.F. Liu, N.A. Somers, R.J. Kazlauskas, T.S. Brush, F. Zocher, M.M. Enzelberger, U.T. Bornscheuer, G.P. Horsman, A. Mezzetti, C. Schmidt-Dannert, and R.D. Schmid Mapping the substrate selectivity of new hydrolases using colorimetric screening: lipases from Bacillus thermocatenulatus and Ophiostoma piliferum, esterases from Pseudomonas fluorescens and Streptomyces diastatochromogenes Tetrahedron Asymmetry 12 2001 545 556
28. T. Madej, J.-F. Gibrat, and S.H. Bryant Threading a database of protein cores Proteins 23 1995 356 369
29. D.L. Ollis, E. Cheah, M. Cygler, B. Dijkstra, F. Frolow, S.M. Franken, M. Harel, S.J. Remington, and I. Silman The α/β hydrolase fold Protein Eng. 5 1992 197 211
30. H.-S. Park, S.-H. Nam, J.K. Lee, C.N. Yoon, B. Mannervik, S.J. Benkovic, and H.-S. Kim Design and evolution of new catalytic activity with an existing protein scaffold Science 311 2006 535 538
31. G.J. Poelarends, V.P. Veetil, and C.P. Whitman The chemical versatility of the beta-alpha-beta fold: catalytic promiscuity and divergent evolution in the tautomerase superfamily Cell. Mol. Life Sci. 65 2008 3606 3618
32. T. Purkarthofer, K. Gruber, M. Gruber-Khadjawi, K. Waich, W. Skranc, D. Mink, and H. Griengl A biocatalytic Henry reaction - the hydroxynitrile lyase from Hevea brasiliensis also catalyzes nitroaldol reactions Angew. Chem. Int. Ed. Engl. 45 2006 3454 3456
33. F.P. Seebeck, and D. Hilvert Conversion of a PLP-dependent racemase into an aldolase by a single active site mutation J. Am. Chem. Soc. 125 2003 10158 10159
34. M. Svedendahl, P. Carlqvist, C. Branneby, O. Allner, A. Frise, K. Hult, P. Berglund, and T. Brinck Direct epoxidation in Candida antarctica lipase B studied by experiment and theory ChemBioChem 9 2008 2443 2451
35. Y. Terao, K. Miyamoto, and H. Ohta Introduction of single mutation changes arylmalonate decarboxylase to racemase Chem. Commun. (Camb.) 34 2006 3600 3602
36. O. Torre, I. Alfonso, and V. Gotor Lipase catalysed Michael addition of secondary amines to acrylonitrile Chem. Commun. (Camb.) 15 2004 1724 1725
37. U.G. Wagner, M. Hasslacher, H. Griengl, H. Schwab, and C. Kratky Mechanism of cyanogenesis: the crystal structure of hydroxynitrile lyase from Hevea brasiliensis Structure 4 1996 811 822
38. W.F. Willeman, U. Hanefeld, A.J.J. Straathof, and J.J. Heijnen Estimation of kinetic parameters by progress curve analysis for the synthesis of (R)-mandelonitrile by Prunus amygdalus hydroxynitrile lyase Enzyme Microb. Technol. 27 2000 423 433
39. H. Xiang, L. Luo, K.L. Taylor, and D. Dunaway-Mariano Interchange of catalytic activity within the 2-enoyl-coenzyme A hydratase/isomerase superfamily based on a common active site template Biochemistry 38 1999 7638 7652
40. G. Yan, S. Cheng, G. Zhao, S. Wu, Y. Liu, and W. Sun A single residual replacement improves the folding and stability of recombinant cassava hydroxynitrile lyase in E. coli Biotechnol. Lett. 25 2003 1041 1047
41. Z.-R. Zhang, M. Bai, X.-Y. Wang, J.-M. Zhou, and S. Perrett "Restoration" of glutathione transferase activity by single-site mutation of the yeast prion protein Ure2 J. Mol. Biol. 384 2008 641 651