A β-alanine catabolism pathway containing a highly promiscuous ω-transaminase in the 12-aminododecanate-degrading Pseudomonas sp. strain AAC

Applied and Environmental Microbiology

Volumn 82, Issue 13, 2016, Pages 3846-3856

  Wilding, Matthew ^a   Peat, Thomas S ^a   Newman, Janet ^a   Scott, Colin ^a  

^a CSIRO   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIA; BIOCHEMISTRY; CRYSTAL STRUCTURE; DIMERS;

ACTIVE SITE POCKET; BUILDING BLOCKES; HISTIDINE RESIDUES; MULTIPLE FUNCTION; OMEGA-TRANSAMINASES; PHYSIOLOGICAL ROLES; POLYAMIDE MONOMERS; SUBSTRATE RANGE;

AMINO ACIDS;

AMINO ACID; BACTERIUM; CATABOLISM; CATALYSIS; CRYSTAL STRUCTURE; ENZYME; OXIDATION; PROTEIN; SUBSTRATE;

PSEUDOMONAS SP.;

ACETIC ACID DERIVATIVE; ACETYL COENZYME A; AMINOTRANSFERASE; BETA ALANINE;

CHEMISTRY; ENZYME ACTIVE SITE; ENZYME SPECIFICITY; ENZYMOLOGY; GENETICS; METABOLISM; MOLECULAR MODEL; PROTEIN CONFORMATION; PROTEIN MULTIMERIZATION; PSEUDOMONAS; X RAY CRYSTALLOGRAPHY;

ACETATES; ACETYL COENZYME A; BETA-ALANINE; CATALYTIC DOMAIN; CRYSTALLOGRAPHY, X-RAY; METABOLIC NETWORKS AND PATHWAYS; METABOLISM; MODELS, MOLECULAR; PROTEIN CONFORMATION; PROTEIN MULTIMERIZATION; PSEUDOMONAS; SUBSTRATE SPECIFICITY; TRANSAMINASES;

EID: 84976402643     PISSN: 00992240     EISSN: 10985336     Source Type: Journal    
DOI: 10.1128/AEM.00665-16     Document Type: Article

References (46)

1. Khersonsky O, Tawfik DS. 2010. Enzyme promiscuity: a mechanistic and evolutionary perspective. Annu Rev Biochem 79:471-505. http://dx.doi.org/10.1146/annurev-biochem-030409-143718.
2. Jensen RA. 1976. Enzyme recruitment in evolution of new function. Annu Rev Microbiol 30:409-425. http://dx.doi.org/10.1146/annurev.mi.30.100176.002205.
3. Hult K, Berglund P. 2007. Enzyme promiscuity: mechanism and applications. Trends Biotechnol 25:231-238. http://dx.doi.org/10.1016/j.tibtech.2007.03.002.
4. Lawrence PW. 2004. Evolution of enzymes for the metabolism of new chemical inputs into the environment. J Biol Chem 279:41259-41262. http://dx.doi.org/10.1074/jbc. R400014200.
5. Janssen DB, Dinkla IJT, Poelarends GJ, Terpstra P. 2005. Bacterial degradation of xenobiotic compounds: evolution and distribution of novel enzyme activities. Environ Microbiol 7:1868-1882. http://dx.doi.org/10.1111/j.1462-2920.2005.00966.x.
6. Bornscheuer UT, Kazlauskas RJ. 2004. Catalytic promiscuity in biocatalysis: using old enzymes to form new bonds and follow new pathways. Angew Chem Int Ed 43:6032-6040. http://dx.doi.org/10.1002/anie.200460416.
7. Malik MS, Park E-S, Shin J-S. 2012. Features and technical applications of ω-transaminases. Appl Microbiol Biotechnol 94:1163-1171. http://dx.doi.org/10.1007/s00253-012-4103-3.
8. Savile CK, Janey JM, MundorffEC, Moore JC, Tam S, Jarvis WR, Colbeck JC, Krebber A, Fleitz FJ, Brands J, Devine PN, Huisman GW, Hughes GJ. 2010. Biocatalytic asymmetric synthesis of chiral amines from ketones applied to sitagliptin manufacture. Science 329:305-309. http://dx.doi.org/10.1126/science.1188934.
9. Hirotsu K, Goto M, Okamoto A, Miyahara I. 2005. Dual substrate recognition of aminotransferases. Chem Rec 5:160-172. http://dx.doi.org/10.1002/tcr.20042.
10. Höhne M, Bornscheuer UT. 2012. Application of transaminases, p 779-820. In Drauz K, Groger H, May O (ed), Enzyme catalysis in organic synthesis, 3rd ed. Wiley-VCH Verlag GmbH, Weinheim, Germany.
11. Shin JS, Kim BG. 1999. Asymmetric synthesis of chiral amines with ω-transaminase. Biotechnol Bioeng 65:206-211. http://dx.doi.org/10.1002/(SICI)1097-0290(19991020)65:2<206::AID-BIT11>3.0.CO;2-9.
12. Matthias H, Uwe TB. 2009. Biocatalytic routes to optically active amines. ChemCatChem 1:42-51. http://dx.doi.org/10.1002/cctc.200900110.
13. Sayer C, Isupov MN, Westlake A, Littlechild JA. 2013. Structural studies of Pseudomonas and Chromobacterium ω-aminotransferases provide insights into their differing substrate specificity. Acta Crystallogr D Biol Crystallogr 69:564-576. http://dx.doi.org/10.1107/S0907444912051670.
14. Humble MS, Cassimjee KE, Håkansson M. 2012. Crystal structures of the Chromobacterium violaceum ω-transaminase reveal major structural rearrangements upon binding of coenzyme PLP. FEBS J 279:779-792. http://dx.doi.org/10.1111/j.1742-4658.2012.08468.x.
15. Mehta PK, Hale TI. 1993. Aminotransferases: demonstration of homology and division into evolutionary subgroups. Eur J Biochem 214:549-561. http://dx.doi.org/10.1111/j.1432-1033.1993.tb17953.x.
16. Cho BK, Park HY, Seo JH, Kim J, Kang TJ, Lee BS, Kim BG. 2008. Redesigning the substrate specificity of ω-aminotransferase for the kinetic resolution of aliphatic chiral amines. Biotechnol Bioeng 99:275-284. http://dx.doi.org/10.1002/bit.21591.
17. Wilding M, Walsh EFA, Dorrian SJ, Scott C. 2015. Identification of novel transaminases from a 12-aminododecanoic acid-metabolizing Pseudomonas strain. Microb Biotechnol 8:665-672. http://dx.doi.org/10.1111/1751-7915.12278.
18. Thiemens MH, Trogler WC. 1991. Nylon production: an unknown source of atmospheric nitrous oxide. Science 251:932-934. http://dx.doi.org/10.1126/science.251.4996.932.
19. Advisen, Ltd. 2013. Chemical companies: minimizing the risks of supply chain disruptions. Advisen, Ltd., New York, NY.
20. Lithner D, Larsson Å, Dave G. 2011. Environmental and health hazard ranking and assessment of plastic polymers based on chemical composition. Sci Total Environ 409:3309-3324. http://dx.doi.org/10.1016/j.scitotenv.2011.04.038.
21. Schrewe M, Ladkau N, Bühler B, Schmid A. 2013. Direct terminal alkylamino-functionalization via multistep biocatalysis in one recombinant whole-cell catalyst. Adv Synth Catal 355:1693-1697. http://dx.doi.org/10.1002/adsc.201200958.
22. Song J-W, Lee J-H, Bornscheuer UT, Park J-B. 2014. Microbial synthesis of medium-chain α, ω-dicarboxylic acids and ω-aminocarboxylic acids from renewable long-chain fatty acids. Adv Synth Catal 356:1782-1788. http://dx.doi.org/10.1002/adsc.201300784.
23. Bär HP, Drummond GI. 1966. On the mechanism of adenosine deaminase action. Biochem Biophys Res Commun 24:584-587. http://dx.doi.org/10.1016/0006-291X(66)90361-5.
24. Bergthorsson U, Andersson DI, Roth JR. 2007. Ohno's dilemma: evolution of new genes under continuous selection. Proc Natl Acad Sci U S A 104:17004-17009. http://dx.doi.org/10.1073/pnas.0707158104.
25. Kabsch W. 2010. XDS. Acta Crystallogr D 66:125-132. http://dx.doi.org/10.1107/S0907444909047337.
26. Evans P. 2006. Scaling and assessment of data quality. Acta Crystallogr D 62:72-82. http://dx.doi.org/10.1107/S0907444905036693.
27. McCoy AJ, Grosse-Kunstleve RW, Adams PD, Winn MD, Storoni LC, Read RJ. 2007. Phaser crystallographic software. J Appl Crystallogr 40: 658-674. http://dx.doi.org/10.1107/S0021889807021206.
28. Watanabe N, Sakabe K, Sakabe N, Higashi T, Sasaki K, Aibara S, Morita Y, Yonaha K, Toyama S, Fukutani H. 1989. Crystal structure analysis of omega-amino acid:pyruvate aminotransferase with a newly developed Weissenberg camera and an imaging plate using synchrotron radiation. J Biochem 105:1-3.
29. Emsley P, Lohkamp B, Scott WG, Cowtan K. 2010. Features and development of Coot. Acta Crystallogr D 66:486-501. http://dx.doi.org/10.1107/S0907444910007493.
30. Murshudov GN, Vagin AA, Dodson EJ. 1997. Refinement of macromolecular structures by the maximum-likelihood method. Acta CrystallogrD 53:240-255. http://dx.doi.org/10.1107/S0907444996012255.
31. Dundas J, Ouyang Z, Tseng J, Binkowski A, Turpaz Y, Liang J. 2006. CASTp: computed atlas of surface topography of proteins with structural and topographical mapping of functionally annotated residues. Nucleic Acids Res 34:W116-W118. http://dx.doi.org/10.1093/nar/gkl282.
32. Reetz MT, Kahakeaw D, Lohmer R. 2008. Addressing the numbers problem in directed evolution. ChemBioChem 9:1797-1804. http://dx.doi.org/10.1002/cbic.200800298.
33. Newman J, Seabrook S, Surjadi R, Williams C, Lucent D, Wilding M, Scott C, Peat T. 2013. Determination of the structure of the catabolic N-succinylornithine transaminase (AstC) from Escherichia coli. PLoS One 8:e58298. http://dx.doi.org/10.1371/journal.pone.0058298.
34. Bozell JJ, Petersen GR. 2010. Technology development for the production of biobased products from biorefinery carbohydrates: the US Department of Energy's "Top 10" revisited. Green Chem 12:539-554. http://dx.doi.org/10.1039/b922014c.
35. Krissinel E, Henrick K. 2007. Inference of macromolecular assemblies from crystalline state. J Mol Biol 372:774-797. http://dx.doi.org/10.1016/j.jmb.2007.05.022.
36. Oliveira EF, Cerqueira NMFSA, Fernandes PA, Ramos MJ. 2011. Mechanism of formation of the internal aldimine in pyridoxal 5'-phosphatedependent enzymes. J Am Chem Soc 133:15496-15505. http://dx.doi.org/10.1021/ja204229m.
37. Zu XL, Besant PG, Imhof A, Attwood PV. 2007. Mass spectrometric analysis of protein histidine phosphorylation. Amino Acids 32:347-357. http://dx.doi.org/10.1007/s00726-007-0493-4.
38. Stock AM, Robinson VL, Goudreau PN. 2000. Two-component signal transduction. Annu Rev Biochem 69:183-215. http://dx.doi.org/10.1146/annurev.biochem.69.1.183.
39. Besant PG, Attwood PV. 2005. Mammalian histidine kinases. Biochim Biophys Acta 1754:281-290. http://dx.doi.org/10.1016/j.bbapap.2005.07.026.
40. Besant PG, Tan E, Attwood PV. 2003. Mammalian protein histidine kinases. Int J Biochem Cell Biol 35:297-309. http://dx.doi.org/10.1016/S1357-2725(02)00257-1.
41. Goodwin GW, RougraffPM, Davis EJ, Harris RA. 1989. Purification and characterization of methylmalonate-semialdehyde dehydrogenase from rat liver. Identity to malonate-semialdehyde dehydrogenase. J Biol Chem 264:14965-14971.
42. Nakamura K, Bernheim F. 1961. Studies of malonic semialdehyde dehydrogenase from Pseudomonas aeruginosa. Biochim Biophys Acta 50:147-152. http://dx.doi.org/10.1016/0006-3002(61)91071-X.
43. Sokatch JR, Sanders LE, Marshall VP. 1968. Oxidation of methylmalonate semialdehyde to propionyl coenzyme A in Pseudomonas aeruginosa grown on valine. J Biol Chem 243:2500-2506.
44. Stines-Chaumeil C, Talfournier F, Branlant G. 2006. Mechanistic characterization of the MSDH (methylmalonate semialdehyde dehydrogenase) from Bacillus subtilis. Biochem J 395:107-115. http://dx.doi.org/10.1042/BJ20051525.
45. Steffen-Munsberg F, Vickers C, Thontowi A, Schätzle S, Tumlirsch T, Svedendahl Humble M, Land H, Berglund P, Bornscheuer UT, Höhne M. 2013. Connecting unexplored protein crystal structures to enzymatic function. ChemCatChem 5:150-153. http://dx.doi.org/10.1002/cctc.201200544.
46. Berglund P, Humble MS, Branneby C. 2012. C-X bond formation: transaminases as chiral catalysts: mechanism, engineering, and applications, p 390-401. In Carreira EM, Yamamoto H (ed), Comprehensive chirality. Elsevier, Amsterdam, Netherlands.