ment, Relaxation, and Reversal of the Stereoselectivity for Phosphotriesterase by Rational Evolution of Active Site Residues), Biochemistry 40, 1332–1339. 38 Schoneboom, J.C., Lin, H., Reuter, N., Thiel, W., Cohen, S., Ogliaro, F., Shaik, S. 2002, (The Elusive Oxidant Species of Cytochrome P450 Enzymes: Characterization by Combined Quantum Mechanical/Molecular Mechanical (QM/MM) Calculations), J. Am. Chem. Soc. 124, 8142–8151. 39 Zhang, Y.X., Perry, K., Vinci, V.A., Powell, K., Stemmer, W.P.C., del Cardayre, S.B. 2002, (Genome Shuffling Leads to Rapid Phenotypic Improvement in Bacteria), Nature 415, 644–646. 40 Patnaik, R., Louie, S., Gavrilovic, V., Perry, K., Stemmer, W.P.C., Ryan, C.M., del Cardayre, S. 2002, (Genome Shuffling of Lactobacillus for Improved Acid Tolerance), Nat. Biotechnol. 20, 707–712. 41 Eckert, K.A., Kunkel, T.A. 1990, (High Fidelity DNA-synthesis by the Thermus aquaticus DNA-polymerase), Nucleic Acids Res. 18, 3739–3744. 42 Tindall, K.R., Kunkel, T.A. 1988, (Fidelity of DNA-synthesis by the Thermus aquaticus DNA-polymerase), Biochemistry 27, 6008–6013. 43 Cadwell, R.C., Joyce, G.F. 1992, Randomization of Genes by PCR Mutagenesis), PCR Methods Appl. 2, 28–33. 44 Cadwell, R.C., Joyce, G.F. 1995, (Mutagenic PCR), in PCR Primer: a Laboratory Manual, eds. Dieffenbach, C.H., Dveksler, G.S., CSHL Press, Cold Spring Harbor, (p.) 583. 45 Zaccolo, M., Williams, D.M., Brown, D.M., Gherardi, E. 1996, (An Approach to Random Mutagenesis of DNA Using Mixtures of Triphosphate Derivatives of Nucleoside Analogues), J. Mol. Biol. 255, 589–603. 46 Zhou, Y.H., Zhang, X.P., Ebright, R.H. 1991, (Random Mutagenesis of Gene-sized DNA-molecules by use of PCR with Taq DNA-polymerase), Nucleic Acids Res. 19, 6052–6052. 47 Jaeger, K.E., Eggert, T., Eipper, A., Reetz, M.T. 2001, (Directed Evolution and the Creation of Enantioselective Biocatalysts), Appl. Microbiol. Biotechnol. 55, 519–530. 48 Eggert, T., Reetz, M.T., Jaeger, K.E. 2004, (Directed Evolution by Random Mutagen- References 111 esis: a Critical Evaluation), in Enzyme Functionality: Design, Engineering, and Screening, ed. Svendsen, A., Marcel Dekker, New York, 375–390. 49 Bessler, C., Schmitt, J., Maurer, K.H., Schmid, R.D. 2003, (Directed Evolution of a Bacterial Alpha-amylase: Toward Enhanced pH-performance and Higher Specific Activity), Protein Sci. 12, 2141–2149. 50 Chen, K., Arnold, F.H. 1993, (Tuning the Activity of an Enzyme for Unusual Environments: Sequential Random Mutagenesis of Subtilisin E for Catalysis in Dimethylformamide), Proc. Natl. Acad. Sci. USA 90, 5618–5622. 51 Giver, L., Gershenson, A., Freskgard, P.O., Arnold, F.H. 1998, (Directed Evolution of a Thermostable Esterase), Proc. Natl. Acad. Sci. USA 95, 12809–12813. 52 Meyer, A., Schmid, A., Held, M., Westphal, A.H., Rothlisberger, M., Kohler, H.P., van Berkel, W.J., Witholt, B. 2002,(Changing the Substrate Reactivity of 2-Hydroxybiphenyl 3-Monooxygenase from Pseudomonas azelaica HBP1 by Directed Evolution), J. Biol. Chem. 277, 5575–5582. 53 Liebeton, K., Zonta, A., Schimossek, K., Nardini, M., Lang, D., Dijkstra, B.W., Reetz, M.T., Jaeger, K.E. 2000, (Directed Evolution of an Enantioselective Lipase), Chem. Biol. 7, 709–718. 54 Funke, S.A., Eipper, A., Reetz, M.T., Otte, N., Thiel, W., Van Pouderoyen, G., Dijkstra, B.W., Jaeger, K.E., Eggert, T. 2003, (Directed Evolution of an Enantioselective Bacillus subtilis Lipase), Biocatal. Biotrans. 21, 67–73. 55 Barettino, D., Feigenbutz, M., Valcarcel, R., Stunnenberg, H.G. 1994, (Improved Method for PCR-mediated Site-directed Mutagenesis), Nucleic Acids Res. 22, 541–542. 56 Urban, A., Neukirchen, S., Jaeger, K.E. 1997, (A Rapid and Efficient Method for Site-directed Mutagenesis Using One-step Overlap Extension PCR), Nucleic Acids Res. 25, 2227–2228. 57 Gray, K.A., Richardson, T.H., Kretz, K., Short, J.M., Bartnek, F., Knowles, R., Kan, L., Swanson, P.E., Robertson, D.E. 2001, (Rapid Evolution of Reversible Denaturation and Elevated Melting Temperature in a Microbial Haloalkane Dehalogenase), Adv. Synth. Catal. 343, 607–617.
112 4 Optimization of <strong>Industrial</strong> Enzymes by Molecular Engineering 58 DeSantis, G., Wong, K., Farwell, B., Chatman, K., Zhu, Z.L., Tomlinson, G., Huang, H.J., Tan, X.Q., Bibbs, L., Chen, P., Kretz, K., Burk, M.J. 2003, (Creation of a Productive, Highly Enantioselective Nitrilase Through Gene Site Saturation Mutagenesis (GSSM)), J. Am. Chem. Soc. 125, 11476–11477. 59 Stemmer, W.P.C. 1994, (DNA Shuffling by Random Fragmentation and Reassembly – In Vitro Recombination for Molecular Evolution), Proc. Natl. Acad. Sci. USA 91, 10747–10751. 60 Stemmer, W.P.C. 1994, (Rapid Evolution of a Protein In Vitro by DNA Shuffling), Nature 370, 389–391. 61 Farinas, E.T., Bulter, T., Arnold, F.H. 2001, (Directed Enzyme Evolution), Curr. Opin. Biotechnol. 12, 545–551. 62 Minshull, J., Stemmer, W.P.C. 1999, (Protein Evolution by Molecular Breeding) Curr. Opin. Chem. Biol. 3, 284–290. 63 Crameri, A., Dawes, G., Rodriguez, E., Silver, S., Stemmer, W.P.C. 1997, (Molecular Evolution of an Arsenate Detoxification Pathway DNA Shuffling. Nat. Biotechnol. 15, 436–438. 64 Stemmer, W.P.C., Soong, N.W. 1999, (Molecular Breeding of Viruses for Targeting and Other Clinical Properties), Tumor Target 4, 59–62. 65 Powell, S.K., Kaloss, M.A., Pinkstaff, A., McKee, R., Burimski, I., Pensiero, M., Otto, E., Stemmer, W.P.C., Soong, N.W. 2000, (Breeding of Retroviruses by DNA Shuffling for Improved Stability and Processing Yields), Nat. Biotechnol. 18, 1279–1282. 66 Soong, N.W., Nomura, L., Pekrun, K., Reed, M., Sheppard, L., Dawes, G., Stemmer, W.P.C. 2000, (Molecular Breeding of Viruses), Nat. Genet. 25, 436–439. 67 Zhao, H., Giver, L., Shao, Z., Affholter, J.A., Arnold, F.H. 1998, (Molecular Evolution by Staggered Extension Process (StEP) In Vitro Recombination), Nat. Biotechnol. 16, 258–261. 68 Zha, D.X., Eipper, A., Reetz, M.T. 2003, (Assembly of Designed Oligonucleotides as an Efficient Method for Gene Recombination: A New Tool in Directed Evolution), Chembiochem. 4, 34–39. 69 Lutz, S., Patrick, W.M. 2004, (Novel Methods for Directed Evolution of Enzymes: Quality, not Quantity), Curr. Opin. Biotechnol. 15, 291–297. 70 Neylon, C. 2004, (Chemical and Biochemical Strategies for the Randomization of Protein Encoding DNA Sequences: Library Construction Methods for Directed Evolution), Nucleic Acids Res. 32, 1448–1459. 71 Ostermeier, M., Nixon, A.E., Shim, J.H., Benkovic, S.J. 1999, (Combinatorial Protein Engineering by Incremental Truncation), Proc. Natl. Acad. Sci. USA 96, 3562–3567. 72 Lutz, S., Benkovic, S.J. 2000, (Homologyindependent Protein Engineering), Curr. Opin. Biotechnol. 11, 319–324. 73 Lutz, S., Ostermeier, M., Moore, G.L., Maranas, C.D., Benkovic, S.J. 2001, (Creating Multiple-crossover DNA Libraries Independent of Sequence Identity), Proc. Natl. Acad. Sci. USA 98, 11248–11253. 74 Smith, G.P. 1985, (Filamentous Fusion Phage – Novel Expression Vectors that Display Cloned Antigens on the Virion Surface), Science 228, 1315–1317. 75 Fernandez-Gacio, A., Uguen, M., Fastrez, J. 2003, (Phage Display as a Tool for the Directed Evolution of Enzymes), Trends Biotechnol. 21, 408–414. 76 Lin, H.N., Cornish, V.W. 2002, (Screening and Selection Methods for Large-scale Analysis of Protein Function), Angew. Chem., Int. Ed. Engl. 41, 4403–4425. 77 Sieber, V., Plückthun, A., Schmid, F.X. 1998, (Selecting Proteins with Improved Stability by a Phage-based Method), Nat. Biotechnol. 16, 955–960. 78 Verhaert, R.M.D., Beekwilder, J., Olsthoorn, R., van Duin, J., Quax, W.J. 2002, (Phage Display Selects for Amylases with Improved Low pH Starch-binding), J Biotechnol. 96, 103–118. 79 Dröge, M.J., Rüggeberg, C.J., van der Sloot, A.M., Schimmel, J., Dijkstra, D.S., Verhaert, R.M.D., Reetz, M.T., Quax, W.J. 2003, (Binding of Phage Displayed Bacillus subtilis Lipase A to a Phosphonate Suicide Inhibitor), J. Biotechnol. 101, 19–28. 80 Reetz, M.T., Rüggeberg, C.J., Dröge, M.J., Quax, W.J. 2002, (Immobilization of Chiral Enzyme Inhibitors on Solid Supports by Amide-forming Coupling and Olefin Metathesis), Tetrahedron 58, 8465–8473.
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Industrial Biotransformations Edite
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Industrial Biotransformations Secon
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Contents Preface to the first editi
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5 Basics of Bioreaction Engineering
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X Preface to the first edition many
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XII Preface to the second edition E
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XIV List of Contributors Prof. Dr.
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2 1 History of Industrial Biotransf
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4 1 History of Industrial Biotransf
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6 1 History of Industrial Biotransf
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8 1 History of Industrial Biotransf
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10 1 History of Industrial Biotrans
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12 1 History of Industrial Biotrans
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14 1 History of Industrial Biotrans
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R' 16 O H N 1 History of Industrial
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18 1 History of Industrial Biotrans
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22 1 History of Industrial Biotrans
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24 1 History of Industrial Biotrans
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26 1 History of Industrial Biotrans
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28 1 History of Industrial Biotrans
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30 1 History of Industrial Biotrans
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32 1 History of Industrial Biotrans
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34 1 History of Industrial Biotrans
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36 1 History of Industrial Biotrans
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38 2 The Enzyme Classification Tab.
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40 2 The Enzyme Classification trib
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42 2 The Enzyme Classification EC 1
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44 2 The Enzyme Classification EC 1
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46 2 The Enzyme Classification EC 1
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48 2 The Enzyme Classification EC 2
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50 2 The Enzyme Classification EC 3
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52 2 The Enzyme Classification EC 3
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54 2 The Enzyme Classification 2.2.
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56 2 The Enzyme Classification The
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58 2 The Enzyme Classification EC 5
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- Page 160 and 161: Common name of enzyme Name of strai
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Alcohol dehydrogenase Acinetobacter
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Dehydrogenase Zygosaccharomyces rou
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Alcohol dehydrogenase Lactobacillus
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Alcohol dehydrogenase Lactobacillus
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Alcohol dehydrogenase Lactobacillus
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Carbonyl reductase Escherichia coli
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Aldehyde reductase Escherichia coli
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Lactate dehydrogenase Staphylococcu
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d-Lactate dehydrogenase Leuconostoc
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d-Lactate dehydrogenase Leuconostoc
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d-Sorbitol dehydrogenase Gluconobac
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d-Sorbitol dehydrogenase Gluconobac
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Dehydrogenase Geotrichum candidum 1
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Ketoreductase 1 = ethyl-4-chloro-3-
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Dehydrogenase Candida sorbophila N
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Dehydrogenase Candida sorbophila N
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Reductase Pichia methanolica 1 = Et
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Reductase Aureobasidium pullulans S
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Reductase Nocardia salmonicolor SC
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Glutamate dehydrogenase / Glucose 1
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Leucine dehydrogenase Bacillus spha
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Leucine dehydrogenase Bacillus spha
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Phenylalanine dehydrogenase / Forma
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d-Aminoacid oxidase Trijonopsis var
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d-Amino acid oxidase Trigonopsis va
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Nicotinic acid hydroxylase Achromob
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Nicotinic acid hydroxylase Achromob
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Catalase Microbial source 1) Reacti
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Oxygenase Arthrobacter sp. 1) React
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Naphthalene dioxygenase Pseudomonas
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Naphthalene dioxygenase Pseudomonas
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Benzoate dioxygenase Pseudomonas pu
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Cyclohexanone monooxygenase Acineto
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Cyclohexanone monooxygenase Acineto
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Oxygenase Escherichia coli OH OH 1
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Monooxygenases / Aryl alcohol dehyd
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Styrene monooxygenase Escherichia c
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Styrene monooxygenase Escherichia c
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Monooxygenase Pseudomonas putida H
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Monooxygenase Streptomyces sp. SC 1
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Oxygenase Nocardia autotropica 1) R
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Monooxygenase Nocardia corallina 1
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Monooxygenase Nocardia corallina
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Monooxygenase Nocardia corallina O
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Oxidase Pseudomonas oleovorans 1) R
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Reductase Baker’s yeast 1 = oxois
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Oxidase Rhodococcus erythropolis 2
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Desaturase Rhodococcus sp. 1) React
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Desaturase Rhodococcus sp. 3) Flow
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Oxidase Beauveria bassiana 1) React
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Oxidase Beauveria bassiana ● The
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Cyclodextrin glycosyltransferase Ba
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d-Amino acid transaminase Bacillus
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d-Amino acid transaminase Bacillus
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Transaminase Bacillus megaterium 1)
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Lipase Burkholderia plantarii 2 (R,
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Lipase Burkholderia plantarii 3) Fl
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Lipase Pseudomonas cepacia 1 = cis-
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Lipase Pseudomonas cepacia 5) Produ
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Lipase Pseudomonas cepacia 2 F 1 =
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Lipase Pseudomonas cepacia 6) Liter
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Lipase Mucor miehei Fig. 3.1.1.3 -
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Lipase Mucor miehei 6) Literature E
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Lipase Porcine pancreas 5) Product
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Lipase Pseudomonas fluorescens Fig.
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Lipase Pseudomonas fluorescens O O
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Lipase Candida cylindracea ● In c
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Lipase Candida antarctica 2 F 1) Re
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Lipase Candida antarctica ● It sh
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Lipase Candida antarctica ● The p
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Lipase Candida antarctica 3) Flow s
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Lipase Arthrobacter sp. ● For thi
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Lipase Serratia marescens MeO R MeO
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Lipase Serratia marescens Fig. 3.1.
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Lipase Pseudomonas cepacia 1) React
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Lipase Candida antarctica 1) Reacti
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Lipase Candida antarctica 4) Proces
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-Galactosidase Saccharomyces lactis
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Lipase Pseudomonas cepacia ● The
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Lactonase Fusarium oxysporum 1 = pa
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Lactonase Fusarium oxysporum Fig. 3
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Lactonase Fusarium oxysporum 5) Pro
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Glutaryl amidase Escherichia coli F
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Glutaryl amidase Escherichia coli 6
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Glutaryl amidase Pseudomonas sp. 3)
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a-Amylase / Amyloglucosidase Bacill
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Nucleosidase / Phosphorylase Erwini
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Aminopeptidase Pseudomonas putida 1
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Aminopeptidase Pseudomonas putida
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Aminopeptidase Pseudomonas putida 3
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Aminopeptidase Pseudomonas putida
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Carboxypeptidase B Pig Pancreas 3)
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Carboxypeptidase B Pig Pancreas 2)
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Carboxypeptidase B Pig Pancreas 3)
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Trypsin Pig Pancreas 2) Remarks ●
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Trypsin Pig Pancreas 2) Remarks ●
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Trypsin Pig Pancreas 2) Remarks ●
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Subtilisin Bacillus licheniformis 1
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Subtilisin Bacillus licheniformis 4
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Subtilisin Bacillus licheniformis
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Subtilisin Bacillus licheniformis 6
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Subtilisin Bacillus licheniformis
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Subtilisin Bacillus sp. EtOOC (R/S)
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Subtilisin Bacillus sp. drug discov
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Subtilisin Bacillus lentus 1 = (R,S
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Thermolysin Bacillus thermoproteoly
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Thermolysin Bacillus thermoproteoly
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Amidase Comamonas acidovorans 1) Re
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Amidase Klebsiella terrigena 2 H N
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Amidase Klebsiella terrigena 6) Lit
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Amidase Klebsiella oxytoca company:
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Urease Lactobacillus fermentum ●
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Penicillin amidase Escherichia coli
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Penicillin amidase Escherichia coli
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Penicillin amidase Bacillus megater
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Penicillin amidase Escherichia coli
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Penicillin amidase Escherichia coli
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Penicillin acylase Escherichia coli
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Penicillin acylase Escherichia coli
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Penicillin acylase Escherichia coli
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Aminoacylase Aspergillus niger 2 N
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Aminoacylase Aspergillus niger 3) F
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Aminoacylase Aspergillus oryzae S C
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Aminoacylase Aspergillus oryzae 3)
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d-Hydantoinase Bacillus brevis Fig.
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d-Hydantoinase Bacillus brevis 3) F
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Hydantoinase / Carbamoylase Pseudom
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l-Hydantoinase Arthrobacter sp. DSM
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l-Hydantoinase Arthrobacter sp. DSM
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-Lactamase Aureobacterium sp. 3) Fl
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-Lactamase Pseudomonas solanacearum
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Lactamase / Racemase Cryptococcus l
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Nitrilase Acidovorax facilis 1 = 2-
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Nitrilase Escherichia coli 1) React
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Nitrilase / Hydroxylase Agrobacteri
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Nitrilase / Hydroxylase Alcaligenes
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Dehalogenase Pseudomonas putida 1)
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Dehalogenase Pseudomonas putida 5)
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Haloalkane dehalogenase Alcaligenes
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Haloalkane dehalogenase Alcaligenes
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Haloalkane dehalogenase Enterobacte
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Halohydrin dehalogenase 1 = ethyl-(
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Pyruvate decarboxylase Saccharomyce
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Acetolactate decarboxylase Bacillus
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Aspartate b-decarboxylase Pseudomon
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Aspartate b-decarboxylase Pseudomon
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Oxynitrilase Hevea brasiliensis 1 =
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N-Acetyl-d-neuraminic acid aldolase
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N-Acetyl-d-neuraminic acid aldolase
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Tyrosine phenol lyase Erwinia herbi
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Fumarase Corynebacterium glutamicum
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Fumarase Corynebacterium glutamicum
- Page 478 and 479:
Fumarase Brevibacterium flavum 4) P
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Enoyl-CoA hydratase Candida rugosa
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Enoyl-CoA hydratase Candida rugosa
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Tryptophan synthase Escherichia col
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Malease Pseudomonas pseudoalcaligen
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Malease Pseudomonas pseudoalcaligen
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Nitrile hydratase Pseudomonas chlor
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Nitrile hydratase Rhodococcus rhodo
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Nitrile hydratase Rhodococcus rhodo
- Page 496 and 497:
Nitrile hydratase Rhodococcus rhodo
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Nitrile hydratase Rhodococcus rhodo
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Carnitine dehydratase Escherichia c
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Carnitine dehydratase Escherichia c
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Carnitine dehydratase Escherichia c
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Aspartase Escherichia coli 3) Flow
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Aspartase Escherichia coli 5) Produ
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Aspartase Brevibacterium flavum 3)
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l-Aspartase Escherichia coli 3) Flo
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l-Phenylalanine ammonia-lyase Rhodo
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Amino acid racemase Amycolatopsis o
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GlcNAc 2-epimerase Escherichia coli
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Xylose isomerase Bacillus coagulans
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Xylose isomerase Bacillus coagulans
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a-Glucosyl transferase Protaminobac
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516 7 Quantitative Analysis of Indu
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518 7 Quantitative Analysis of Indu
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520 7 Quantitative Analysis of Indu
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522 Index of enzyme name enzyme nam
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524 Index of enzyme name enzyme nam
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526 Index of strain strain enzyme n
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528 Index of strain strain enzyme n
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530 Index of strain strain enzyme n
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532 Index of company company strain
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534 Index of company company strain
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536 Index of starting material star
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538 Index of starting material star
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540 Index of starting material star
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542 Index of starting material star
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544 Index of starting material star
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546 Index of product product enzyme
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548 Index of product product enzyme
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550 Index of product product enzyme
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552 Index of product product enzyme
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554 Index of product product enzyme
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556 Index of product product enzyme