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(12) United States Patent (10) Patent No.: US 9,695.451 B2 Chen Et Al

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(12) United States Patent (10) Patent No.: US 9,695.451 B2 Chen Et Al US0096.95451B2 (12) United States Patent (10) Patent No.: US 9,695.451 B2 Chen et al. (45) Date of Patent: *Jul. 4, 2017 (54) POLYNUCLEOTIDES ENCODING (52) U.S. Cl. ENGINEERED IMINE REDUCTASES CPC ............ CI2P 13/02 (2013.01); C12N 9/0028 (2013.01); CI2P 13/001 (2013.01): CI2P (71) Applicant: CODEXIS, INC., Redwood City, CA 13/04 (2013.01); C12P 13/06 (2013.01); CI2P (US) 17/10 (2013.01); C12P 17/12 (2013.01); CI2P (72) Inventors: 'E'O O he, By- - - SN R J. 17/165CI2P (2013.01); 17/188 (2013.01);CI2P 17/185 C12Y (2013.01); 105/01 NESCO.ARS y (2013.01); C12Y 105/01023 (2013.01); C12Y Sukumaran, Singapore (SG), Derek 105/01024 (2013.01); C12Y 105/01028 Smith, Singapore (SG); Jeffrey C. (2013.01); Y02P 20/52 (2015.11) Moore, Westfield, NJ (US); Gregory (58) Field of Classification Search Hughes, Scotch Plains, NJ (US); Jacob CPC ..... Y02P 20/52; C12N 9/0028; C12N 9/0016: Janey, New York, NY (US); Gjalt W. C12P 13/001; C12P 17/10; C12P 13/02: Huisman, Redwood City, CA (US); C12P 13/04; C12P 13/06; C12P 17/12: Scott J. Novick, Palo Alto, CA (US); C12P 17/165; C12P 17/185; C12P Nicholas J. Agard, San Francisco, CA 17/188; C12P 21/02: C12Y 105/01028; (US); Oscar Alvizo, Fremont, CA (US); C12Y 105/01, C12Y 105/01023; C12Y it's AS Ms. Park, Sé 105/01024; C07K 14/61 Stefanie; Wan Ng Lin Minor, Yeo, RedwoodS1ngapore City, CA See application file for complete search history. (US) (56) References Cited (73) Assignee: Codexis, Inc., Redwood City, CA (US) U.S. PATENT DOCUMENTS (*) Notice: Subject to any disclaimer, the term of this patent is extended or adjusted under 35 7,202,070 B2 4/2007 Rozzell, Jr. U.S.C. 154(b) by 0 days. 7,423, 195 B2 9, 2008 Sticklen et al. 7,452,704 B2 11/2008 Esaki et al. This patent is Subject to a terminal dis- 2005, 0124040 A1 6/2005 Esaki et al. claimer. 2006/0205045 A1 9, 2006 Esaki et al. 2007/OOO9995 A1 1/2007 Bogosian et al. (21) Appl. No.: 15/286,900 OTHER PUBLICATIONS (22) Filed: Oct. 6, 2016 Abrahamson, M.J., et al., “Development of an Amine (65) Prior Publication Data Dehydrogenase for Synthesis of Chiral Amines.” Angew. Chem. Intl. Ed., 51:3969-3972 2012. US 2017/0022527 A1 Jan. 26, 2017 Asano, Y, et al., “A New NAD+-Dependent Opine Dehydrogenase from Arthrobacter sp. Strain IC.” J. Bacterol. 171 (8):4466-4471 Related U.S. ApplicationO O Data Baker,1989. P.J., et al., “A role for quaternary structure in the substrate (60) Continuation of application No. 15/048.887, filed on specificity of leucine dehydrogenase.” Structure, 3(7):693-705 Feb. 19, 2016, now Pat. No. 9,487,760, which is a 1995. continuation of application No. 14/887,943, filed on Bevan, M. et al., "Structure and transcription of the nopaline Oct. 20, 2015, now Pat. No. 9,296,993, which is a synthase gene region of T-DNA.” Nucleic Acids Research, division of application No. 13/890,944, filed on May 11(2):369-385 (1983. 9, 2013, now Pat. No. 9,193,957. (Continued) (60) Provisional application No. 61/646,100, filed on May Primary Examiner — Delia Ramirez 11, 2012. (74) Attorney, Agent, or Firm — Codexis, Inc. (51) Int. Cl. C7H 2L/00 (2006.01) (57) ABSTRACT CI2N 15/53 (2006.01) CI2N 15/63 (2006.01) The present disclosure provides engineered polypeptides CI2P 13/02 (2006.01) having imine reductase activity, polynucleotides encoding CI2N 9/06 (2006.01) the engineered imine reductases, host cells capable of CI2P I3/00 (2006.01) expressing the engineered imine reductases, and methods of CI2P 17/18 (2006.01) using these engineered polypeptides with a range of ketone CI2P I 7/10 (2006.01) and amine Substrate compounds to prepare secondary and CI2P I 7/12 (2006.01) tertiary amine product compounds. CI2P I 7/16 (2006.01) CI2P I3/06 (2006.01) CI2P I3/04 (2006.01) 7 Claims, No Drawings US 9,695.451 B2 Page 2 (56) References Cited Mihara, H., et al., "N-Methyl-L-amino acid dehydrogenase from Pseudomonas putida: A novel member of an unusual NAD(P)- dependent oxidoreductase Superfamily.” FEBS Journal, 272:1117 OTHER PUBLICATIONS 1123 2005. Britton, K.L., et al., “Crystallization of Arthrobacter sp. strain 1C Muller, A., et al., “Putative reaction mechanism of heterologously N-(1-D-carboxyethyl)-L-norvaline dehydrogenase and its complex expressed octopine dehydrogenase from the great scallop, Pecten with NAD+-.” Acta Cryst., D54:124-126 1998). maximus (L).” FEBS Journal, 274:6329-6339 (2007). Britton, K.L., et al., “Crystal structure and active site location of Peterson, P.E., et al., “The structure of bovine glutamate N-(1-D-carboxylethyl)-L-norvaline dehydrogenase,” Nature Struc dehydrogenase provides insights into the mechanism of allostery.” ture Biology, 5(7):593-601 1998. Structure, 7:769-782 1999. Brunhuber, N.M.W., et al., “Rhodococcus L-Phenylalanine Plese, B., et al., "Cloning and expression of a tauropine Dehydrogenase: Kinetics, Mechanism, and Structural Basis for dehydrogenase from the marine sponge Suberites domuncula, Mar Catalytic Specifity,” Biochemistry, 39.9174-9187 (2000. Biol, 153:1219-1232 2008. Dairi, T., et al., “Cloning, Nucleotide Sequencing, and Expression Plese, B., et al., “Strombine dehydrogenase in the demosponge of an Opine Dehydrogenase Gene from Arthrobacter sp. Strain 1C..” Suberites domuncula: Characterization and kinetic properties of the Applied and Environmental Microbiology, 61 (8):3169-3171 (1995). enzyme crucial for anaerobic metabolism,” Comparative Biochem Donkersloot, J.A., et al., “Cloning. Expression, Sequence Analysis, istry and Physiology, Part B, 154: 102-107 2009. and Site-directed Mutagenesis of the Tn5306-encoded Smits, S.H.J., et al., “A Structural Basis for Substrate Selectivity and N-(Carboxyethyl)ornithine Synthase from Lactococcus lactis K1.” Stereoselectivity in Octopine Dehydrogenase from Pecten maxi Bio. Chem., 270(20): 12226-12234 (1995). mus,” J. Mol. Biol. 381:200-211 2008. Endo, N. et al., “Purification, characterization, and cDNA cloning of Smits, S.H.J., et al., “Insights into the Mechanism of Ligand opine dehydrogenases from the polychaete rockworm Marphysa Binding to Octopine Dehydrogenase from Pecten maximus by Sanguinea, Comparative Biochemistry and Physiology, Part B. NMR and Crystallography.” PLoS One, 5(8): 1-10 |2010. 147:293-307 2007. UniProt F4A2G3 dated Jun. 28, 2011. Endo, N. et al., “cDNA cloning and primary structure comparison UniProt Q44297 dated Nov. 1, 1996. of tauropine dehydrogenase and beta-alanopine dehydrogenase Xuan, J.-W., et al., “Overlapping Reading Frames at the LYS5 from the limpet Cellana grata.” Fish Sci., 75: 1471-1479 2009. Locus in the Yeast Yarrowia lipolytica.” Molecular and Cellular Goto, M., et al., “Crystal Structures of Delta1-Piperideine-2- Biology, 10(9):4795-4806 1990. carboxylate/Delta1-Pyrroline-2-carboxylate Reductase Belonging Yip, K.S.P. et al., “The structure of Pyrococcus furiosus glutamate to a New Family of NAD(P)H-dependent Oxidoreductases,” J. Biol. dehydrogenase reveals a key role for ion-pair networks in main Chem., 280(49):40875-4.0884 2005. taining enzyme stability at extreme temperatures.” Structure, Kan-No, N., et al., “The amino acid sequence of tauropine 3(11): 1147-1158 (1995). dehydrogenase from the polychaete Arabella iricolor.’ Comparative International Search Report for International Application No. PCT/ Biochemistry and Physiology, Part B, 140:475-485 (2005). US2013/040377 dated Jul 18, 2013. Kan-No, N., et al., “Tauropine dehydrogenase from the marine Branden, C., et al., “Introduction to Protein Structure'. Published by Sponge Halichondria japonica is a homolog of omithine Garland Publishing, Inc., New York, New York, p. 247 (1991). cyclodeaminase/mu-crystallin.” Comparative Biochemistry and Seffernick, J.L., et al., “Melamine Deaminase and Atrazine Physiology, Part B, 141:331-339 (2005). Chlorohydrolase: 98 Percent Identical but Functionally Different.” Kato, Y., et al., “Stereoselective synthesis of opine-type secondary J. Bacteriol., 183:2405-2410 2001. amine carboxylic acids by a new enzyme opine dehydrogenase Use Witkowski, A., et al., “Conversion of a beta-ketoacyl synthase to a of recombinant enzymes,” J. Mol. Catalysis B: Enzymatic, 1:151 malonyl decarboxylase by replacement of the active-site cysteine 160 1996. with glutamine,” Biochemistry, 38(36): 11643-50 1999). Kimura, T., et al., “Complementary DNA Cloning and Molecular Sadowski, M.I., et al., “The sequence-structure relationship and Evolution of Opine Dehydrogenases in Some Marine Inverte protein function prediction.” Current Opinion in Structural Biology, brates.” Mar. Biotechnol. 6:493-502 (2005. 19:357-362 2009. US 9,695,451 B2 1. 2 POLYNUCLEOTDES ENCODING mus (great Scallop) (OpDH); ornithine synthase from Lac ENGINEERED IMINE REDUCTASES tococcus lactis K1 (CEOS); B-alanine opine dehydrogenase from Cellana grata (BADH); and tauropine dehydrogenase 1. CROSS REFERENCE TO RELATED from Suberites domuncula (Taul DH). The crystal structure of APPLICATIONS the opine dehydrogenase CENDH has been determined (see Britton et al., “Crystal structure and active site location of The present application is a Continuation of U.S. patent N-(1-D-carboxyethyl)-L-norvaline dehydrogenase.” Nat. application Ser. No. 15/048.887, filed Feb. 19, 2016, now Struct. Biol. 5(7): 593-601 (1998)). Another enzyme, U.S. Pat. No. 9,487,760, which is a Continuation of U.S. N-methyl L-amino acid dehydrogenase from Pseudomonas patent application Ser. No. 14/887,943, filed Oct. 20, 2015, 10 putida (NMDH) is known to have activity similar to opine now U.S. Pat. No. 9,296,993, which is a Divisional of U.S. dehydrogenases, reacting with O-keto acids and alkyl patent application Ser. No. 13/890,944, filed May 9, 2013, amines, but appears to have little or no sequence homology now U.S.
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