Structure-guided directed evolution of alkenyl and arylmalonate decarboxylases

Angewandte Chemie - International Edition

Volumn 48, Issue 41, 2009, Pages 7691-7694

  Okrasa, Krzysztof ^a   Levy, Colin ^a   Wilding, Matthew ^a   Goodall, Mark ^a   Baudendistel, Nina ^b   Hauer, Bernhard ^b   Leys, David ^a   Micklefield, Jason ^a  

^a UNIVERSITY OF MANCHESTER   (United Kingdom)

^b BASF SE   (Germany)

Author keywords

Decarboxylase; Directed evolution; Enedlolates; Enzyme mechanisms; Inhibitors

Indexed keywords

DECARBOXYLASE; DIRECTED EVOLUTION; ENEDLOLATES; ENZYME MECHANISMS; INHIBITORS;

ENZYMES;

CRYSTAL STRUCTURE;

ALKENE; CARBOXYLYASE; MALONATE DECARBOXYLASE; MALONIC ACID; MALONIC ACID DERIVATIVE;

ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; DIRECTED MOLECULAR EVOLUTION; ENZYME ACTIVE SITE; METABOLISM; METHODOLOGY;

ALKENES; CARBOXY-LYASES; CATALYTIC DOMAIN; DIRECTED MOLECULAR EVOLUTION; MALONATES; MOLECULAR STRUCTURE;

EID: 70349998462     PISSN: 14337851     EISSN: None     Source Type: Journal    
DOI: 10.1002/anie.200904112     Document Type: Article

References (32)

1. a) J. Blanchet, J. Baudoux, M. Amere, M.-C. Lasne, J. Rouden, Eur. J. Org. Chem. 2008, 5493-5506;
2. b) M. Amere, M.-C. Lasne, J. Rouden, Org. Lett. 2007, 9, 2621-2624;
3. c) J. T. Mohr, T. Nishimata, D. C. Behenna, B. M. Stoltz, J. Am Chem. Soc. 2006, 128, 11348-11349.
4. K. Miyamoto, H. Ohta, J. Am. Chem. Soc. 1990, 112, 4077-4078.
5. a) K. Miyamoto, H. Ohta, Biocatalysis 1991, 5, 49-60;
6. b) K. Miyamoto, H. Ohta, Appl. Microbiol. Biotechnol. 1992, 38, 234-238;
7. c) K. Miyamoto, H. Ohta, Eur. J. Biochem. 1992,210, 475-481;
8. d) K. Matoishi, M. Ueda, K. Miyamoto, H. Ohta, J. Mol. Catal. B 2004, 27, 161-168.
9. a) Y. Ijima, K. Matoishi, Y. Terao, N. Doi, H. Yanagawa, H. Ohta, Chem. Commun. 2005, 877-879;
10. b) Y. Terao, Y. Ijima, K. Miyamoto, H. Ohta, J. Mol. Catal. B 2007, 45, 15-20.
11. K. Okrasa, C. Levy, B. Hauer, N. Baudendistel, D. Leys, J. Micklefield, Chem. Eur. J. 2008, 14, 6609-6613.
12. a) K. Miyamoto, Y. Yatake, K. Tamura, Y. Terao, H. Ohta, J. Biosci. Bioeng. 2007, 104, 263-267;
13. b) Y. Yatake, K. Miyamoto, H. Ohta, Appl Microbiol Biotechnol. 2008, 78, 793-799.
14. Another B. bronchiseptica AMDase structure was also reported at around the same time: E. B. Kuettner, A. Keim, M. Kircher, S. Rosmus, N. Sträter, J. Mol. Biol. 2008, 377, 386-394. This structure is proposed to possess four independent subunits and differs considerably from our structure. Attempts to align the two structures proved problematic. Also, there is no ligand bound to any of the subunits, in the structure from Kuettner et al., and none of the key active-site residues, apart from Cys188 are identified. Moreover, the Cysl88 residue had been modified by mercaptoethanol, presumably an artefact of the crystallisation process employed by Kuettner et al. From our work, the conditions of crystallisation were shown to be very important. The use of mercaptoethanol, in addition to modifying Cysl88 which would completely abolish the ability of this residue to function as a general acid, may also have effected the internal stabilisation of the protein leading to the four misfolded subunits. As a result, no reasonable structural or mechanistic conclusions can be drawn from this.
15. T. Lundqvist, S. L. Fisher, G. Kern, R. H. Folmer, Y. Xue, D. T. Newton, T. A. Keating, R. A. Aim, B. L. de Jonge, Nature 2007, 447, 817-822.
16. S. Tsuboi, K. Muranaka, T. Sakai, A. Takeda, J. Org. Chem. 1986, 51, 4944-4946.
17. a) L. E. Janes, A. C. Lowendahl, R. J. Kazlauskas, Chem. Eur. J. 1998, 4, 2324-2331;
18. b) A. Banerjee, P.Kaul, R. Sharma, U. C. Banerjee, J. Biomol. Screening 2003, 8, 559-565.
19. a) D. Grée, L. Vallerie, R. Gre, L. Toupet, I. Washington, J. Org. Chem. 2001, 66, 2374-2381;
20. b) M. Calí, M. Begtrup, Synthesis 2002, 63-66.
21. K. Tamura, Y. Terao, K. Miyamoto, H. Ohta, Biocatal. Bioiransform. 2008,26, 253-257.
22. J. W. Thanassi, Biochemistry 1970, 9, 525-532.
23. a) M. T. Reetz, J. D. Carballeira, A. Vogel, Angew. Chem. 2006, 118, 7909-7915;
24. Angew. Chem. Int. Ed. 2006, 45, 7745-7751;
25. b) M. T. Reetz, J. D. Carballeira, Nat. Protoc. 2007, 2, 891-903.
26. a) E.L. Corey, T. Hase, Tetrahedron Lett. 1979, 20, 335-338;
27. b) J.-M. Gamier, S. Robin, R. Guillot, G Rousseau, Tetrahedron: Asymmetry 2007, 18, 1434-1442.
28. G. T. Crisp, P. T. Glink, Tetrahedron 1992, 48, 3541-3556.
29. G. T. Pearce, W. E. Gore, R. M. Silverstein, J. Org. Chem. 1976, 41, 2797-2803.
30. a) Y Zheng, X. Chen, Y. Shen, Chem. Rev. 2008, 108, 5253-5277;
31. b) R. Ciriminna, M. Pagliaro, Adv. Synth. Catal. 2003,345, 383-388.
32. The atomic coordinates for B. bronchiseptica AMDase with benzylphosphonate bound to the active site dioxyanion hole has been deposited in the Protein Data Bank (accession number 3IP8).