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Sándor E, Csuka P, Poppe L, Nagy J. Enantiocomplementary Bioreduction of 1-(Arylsulfanyl)propan-2-ones. Molecules 2024; 29:3858. [PMID: 39202937 PMCID: PMC11357645 DOI: 10.3390/molecules29163858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2024] [Revised: 08/05/2024] [Accepted: 08/13/2024] [Indexed: 09/03/2024] Open
Abstract
This study explored the enantiocomplementary bioreduction of substituted 1-(arylsulfanyl)propan-2-ones in batch mode using four wild-type yeast strains and two different recombinant alcohol dehydrogenases from Lactobacillus kefir and Rhodococcus aetherivorans. The selected yeast strains and recombinant alcohol dehydrogenases as whole-cell biocatalysts resulted in the corresponding 1-(arylsulfanyl)propan-2-ols with moderate to excellent conversions (60-99%) and high selectivities (ee > 95%). The best bioreductions-in terms of conversion (>90%) and enantiomeric excess (>99% ee)-at preparative scale resulted in the expected chiral alcohols with similar conversion and selectivity to the screening reactions.
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Affiliation(s)
| | | | - László Poppe
- Department of Organic Chemistry and Technology, Faculty of Chemical Technology and Biotechnology, Budapest University of Technology and Economics, Műegyetem rkp. 3, H-1111 Budapest, Hungary; (E.S.); (P.C.)
| | - József Nagy
- Department of Organic Chemistry and Technology, Faculty of Chemical Technology and Biotechnology, Budapest University of Technology and Economics, Műegyetem rkp. 3, H-1111 Budapest, Hungary; (E.S.); (P.C.)
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Zhang XJ, Yang F, Chen KL, Fang WM, Liu ZQ, Zheng YG. Efficient biosynthesis of Vibegron intermediate using a novel carbonyl reductase based on molecular modification of hydrogen bonding network regulation. Bioorg Chem 2023; 140:106788. [PMID: 37598433 DOI: 10.1016/j.bioorg.2023.106788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 07/26/2023] [Accepted: 08/13/2023] [Indexed: 08/22/2023]
Abstract
Vibegron is a novel, potent, highly selective β3-adrenergic receptor agonist for the treatment of overactive bladder with higher therapeutic capacity and lower side effects. Methyl(2S,3R)-2-((tert-butoxycarbonyl)amino)-3-hydroxy-3-phenylpropanoate ((2S,3R)-aminohydroxy ester) is a key chiral intermediate for the synthesis of Vibegron. A novel carbonyl reductase from Exiguobacterium sp. s126 (EaSDR6) was isolated using data mining technology from GenBank database with preferable catalytic activity. Hydrogen bond network regulation was performed using site-directed saturation mutagenesis and combination mutagenesis. The mutant EaSDR6A138L/S193A was obtained with the activity improvement by 4.58 folds compared with the wild type EaSDR6. The Km of EaSDR6A138L/S193A was decreased from 1.57 mM to 0.67 mM, kcat was increased by 2.17 folds, and the overall catalytic efficiency kcat/Km was increased by 5.07 folds. The organic-aqueous biphasic bioreaction system for the asymmetric synthesis of (2S,3R)-aminohydroxy ester was constructed for the first time. Under the substrate concentration of 150 g/L, the yield of (2S,3R)-aminohydroxy ester was > 99.99%, the e.e. was > 99.99%, and the spatiotemporal yield was 1.55 g/(L·h·g DCW) after 12 h reaction. While the substrate concentration was increased to 200 g/L and the reaction lasted for 36 h, the yield of (2S,3R)-aminohydroxy ester was > 99.99%, the e.e. was > 99.99% and the spatiotemporal yield was 1.05 g/(L·h·g DCW). The substrate concentration and spatiotemporal yield were higher than ever reported.
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Affiliation(s)
- Xiao-Jian Zhang
- National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China; Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China
| | - Fei Yang
- National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China; Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China
| | - Kai-Li Chen
- National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China; Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China
| | - Wei-Mei Fang
- National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China; Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China
| | - Zhi-Qiang Liu
- National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China; Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China.
| | - Yu-Guo Zheng
- National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China; Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China
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Stark F, Hoffmann A, Ihle N, Loderer C, Ansorge-Schumacher MB. Extended Scope and Understanding of Zinc-Dependent Alcohol Dehydrogenases for Reduction of Cyclic α-Diketones. Chembiochem 2023; 24:e202300290. [PMID: 37167138 DOI: 10.1002/cbic.202300290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 05/05/2023] [Accepted: 05/09/2023] [Indexed: 05/13/2023]
Abstract
Alcohol dehydrogenases (ADH) are important tools for generating chiral α-hydroxyketones. Previously, only the ADH of Thauera aromatica was known to convert cyclic α-diketones with appropriate preference. Here, we extend the spectrum of suitable enzymes by three alcohol dehydrogenases from Citrifermentans bemidjiense (CibADH), Deferrisoma camini (DecADH), and Thauera phenylacetica (ThpADH). Of these, DecADH is characterized by very high thermostability; CibADH and ThpADH convert α-halogenated cyclohexanones with increased activity. Otherwise, however, the substrate spectrum of all four ADHs is highly conserved. Structural considerations led to the conclusion that conversion of diketones requires not only the expansion of the active site into a large binding pocket, but also the circumferential modification of almost all amino acid residues that form the first shell of the binding pocket. The constellation appears to be overall highly specific for the relative positioning of the carbonyl functions and the size of the C-ring.
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Affiliation(s)
- Frances Stark
- Professur für Molekulare Biotechnologie, Technische Universität Dresden, 01062, Dresden, Germany
| | - Aaron Hoffmann
- Professur für Molekulare Biotechnologie, Technische Universität Dresden, 01062, Dresden, Germany
| | - Nadine Ihle
- Professur für Molekulare Biotechnologie, Technische Universität Dresden, 01062, Dresden, Germany
| | - Christoph Loderer
- Professur für Molekulare Biotechnologie, Technische Universität Dresden, 01062, Dresden, Germany
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5
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Shen W, Chen Y, Qiu S, Wang DN, Wang YJ, Zheng YG. Semi-rational engineering of a Kluyveromyces lactis aldo-keto reductase KlAKR for improved catalytic efficiency towards t-butyl 6-cyano-(3R, 5R)-dihydroxyhexanoate. Enzyme Microb Technol 2020; 132:109413. [DOI: 10.1016/j.enzmictec.2019.109413] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 08/13/2019] [Accepted: 08/19/2019] [Indexed: 12/24/2022]
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Wang DC, Li H, Xia SN, Xue YP, Zheng YG. Engineering of a keto acid reductase through reconstructing the substrate binding pocket to improve its activity. Catal Sci Technol 2019. [DOI: 10.1039/c8cy02586j] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Enzyme–substrate docking-guided point mutation of the substrate-binding pocket to generate mutant L244G/A250G/L245R with superior activity in the synthesis of (R)-2-hydroxy-4-phenylbutyric acid.
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Affiliation(s)
- Di-Chen Wang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province
- College of Biotechnology and Bioengineering
- Zhejiang University of Technology
- Hangzhou 310014
- China
| | - Heng Li
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province
- College of Biotechnology and Bioengineering
- Zhejiang University of Technology
- Hangzhou 310014
- China
| | - Shu-Ning Xia
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province
- College of Biotechnology and Bioengineering
- Zhejiang University of Technology
- Hangzhou 310014
- China
| | - Ya-Ping Xue
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province
- College of Biotechnology and Bioengineering
- Zhejiang University of Technology
- Hangzhou 310014
- China
| | - Yu-Guo Zheng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province
- College of Biotechnology and Bioengineering
- Zhejiang University of Technology
- Hangzhou 310014
- China
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Loderer C, Wagner D, Morgenstern F, Spieß A, Ansorge-Schumacher MB. Discovery of a novel thermostable Zn 2+ -dependent alcohol dehydrogenase from Chloroflexus aurantiacus through conserved domains mining. J Appl Microbiol 2018; 124:480-490. [PMID: 29224243 DOI: 10.1111/jam.13664] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Revised: 11/29/2017] [Accepted: 12/05/2017] [Indexed: 12/30/2022]
Abstract
AIMS The purpose of the study was to demonstrate feasibility of the Conserved Domains Database (CDD) for identification of novel biocatalysts with desirable properties from a class of well-characterized biocatalysts. METHODS AND RESULTS The thermostable ADH from Sulfolobus solfataricus with a broad substrate range was applied as a template for the search for novel thermostable ADHs via CDD. From the resulting hits, a putative ADH gene from the thermophilic organism Chloroflexus aurantiacus was cloned and expressed in Escherichia coli. The resulting enzyme was purified and characterized. With a temperature activity optimum of 70°C and a broad substrate spectrum especially for diketones, a versatile new biocatalyst was obtained. CONCLUSIONS Database-based mining in CDD is a suitable approach to obtain novel biocatalysts with desirable properties. Thereby, the available diversity of similar but not equal enzymes within this class can be increased. SIGNIFICANCE AND IMPACT OF THE STUDY For industrial applications, there is a demand for larger diversity of similar well-characterized enzymes in order to test them for a given process (biodiversity screening). For fundamental science, the comparison of enzymes with similar function but different sequence can provide insight into structure function relationships or the evolution of enzymes. This study gives a good example on how this demand can be efficiently met.
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Affiliation(s)
- C Loderer
- Institute for Microbiology, Technische Universität Dresden, Dresden, Germany
| | - D Wagner
- Enzyme Process Technology, RWTH Aachen University, Aachener Verfahrenstechnik, Aachen, Germany
| | - F Morgenstern
- Institute for Microbiology, Technische Universität Dresden, Dresden, Germany
| | - A Spieß
- Enzyme Process Technology, RWTH Aachen University, Aachener Verfahrenstechnik, Aachen, Germany.,Institute of Biochemical Engineering, TU Braunschweig, Braunschweig, Germany
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Fan LQ, Li MW, Qiu YJ, Chen QM, Jiang SJ, Shang YJ, Zhao LM. Increasing thermal stability of glutamate decarboxylase from Escherichia. coli by site-directed saturation mutagenesis and its application in GABA production. J Biotechnol 2018; 278:1-9. [PMID: 29660473 DOI: 10.1016/j.jbiotec.2018.04.009] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Revised: 11/03/2017] [Accepted: 04/12/2018] [Indexed: 01/05/2023]
Abstract
Gamma-amino butyric acid (GABA) is an important bio-product used in pharmaceuticals, functional foods, and a precursor of the biodegradable plastic polyamide 4 (Nylon 4). Glutamate decarboxylase B (GadB) from Escherichia. coli is a highly active biocatalyst that can convert l-glutamate to GABA. However, its practical application is limited by the poor thermostability and only active under acidic conditions of GadB. In this study, we performed site-directed saturation mutagenesis of the N-terminal residues of GadB from Escherichia coli to improve its thermostability. A triple mutant (M6, Gln5Ile/Val6Asp/Thr7Gln) showed higher thermostability, with a 5.6 times (560%) increase in half-life value at 45 °C, 8.7 °C rise in melting temperature (Tm) and a 14.3 °C rise in the temperature at which 50% of the initial activity remained after 15 min incubation (T1550), compared to wild-type enzyme. Protein 3D structure analysis showed that the induced new hydrogen bonds in the same polypeptide chain or between polypeptide chains in E. coli GadB homo-hexamer may be responsible for the improved thermostability. Increased thermostability contributed to increased GABA conversion ability. After 12 h conversion of 3 mol/L l-glutamate, GABA produced and mole conversion rate catalyzed by M6 whole cells was 297 g/L and 95%, respectively, while those by wild-type GAD was 273.5 g/L and 86.2%, respectively.
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Affiliation(s)
- Li-Qiang Fan
- State Key Laboratory of Bioreactor Engineering, R&D Center of Separation and Extraction Technology in Fermentation Industry, School of Biotechnology of East China University of Science and Technology, Shanghai, 200237, China.
| | - Ming-Wei Li
- State Key Laboratory of Bioreactor Engineering, R&D Center of Separation and Extraction Technology in Fermentation Industry, School of Biotechnology of East China University of Science and Technology, Shanghai, 200237, China
| | - Yong-Jun Qiu
- State Key Laboratory of Bioreactor Engineering, R&D Center of Separation and Extraction Technology in Fermentation Industry, School of Biotechnology of East China University of Science and Technology, Shanghai, 200237, China; Shanghai Collaborative Innovation Center for Biomanufacturing Technology(SCICBT), Shanghai, 200237, China
| | - Qi-Ming Chen
- State Key Laboratory of Bioreactor Engineering, R&D Center of Separation and Extraction Technology in Fermentation Industry, School of Biotechnology of East China University of Science and Technology, Shanghai, 200237, China; Shanghai Collaborative Innovation Center for Biomanufacturing Technology(SCICBT), Shanghai, 200237, China
| | - Si-Jing Jiang
- State Key Laboratory of Bioreactor Engineering, R&D Center of Separation and Extraction Technology in Fermentation Industry, School of Biotechnology of East China University of Science and Technology, Shanghai, 200237, China
| | - Yu-Jie Shang
- State Key Laboratory of Bioreactor Engineering, R&D Center of Separation and Extraction Technology in Fermentation Industry, School of Biotechnology of East China University of Science and Technology, Shanghai, 200237, China
| | - Li-Ming Zhao
- State Key Laboratory of Bioreactor Engineering, R&D Center of Separation and Extraction Technology in Fermentation Industry, School of Biotechnology of East China University of Science and Technology, Shanghai, 200237, China; Shanghai Collaborative Innovation Center for Biomanufacturing Technology(SCICBT), Shanghai, 200237, China.
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Engineering Streptomyces coelicolor Carbonyl Reductase for Efficient Atorvastatin Precursor Synthesis. Appl Environ Microbiol 2017; 83:AEM.00603-17. [PMID: 28389544 DOI: 10.1128/aem.00603-17] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Accepted: 04/04/2017] [Indexed: 11/20/2022] Open
Abstract
Streptomyces coelicolor CR1 (ScCR1) has been shown to be a promising biocatalyst for the synthesis of an atorvastatin precursor, ethyl-(S)-4-chloro-3-hydroxybutyrate [(S)-CHBE]. However, limitations of ScCR1 observed for practical application include low activity and poor stability. In this work, protein engineering was employed to improve the catalytic efficiency and stability of ScCR1. First, the crystal structure of ScCR1 complexed with NADH and cosubstrate 2-propanol was solved, and the specific activity of ScCR1 was increased from 38.8 U/mg to 168 U/mg (ScCR1I158V/P168S) by structure-guided engineering. Second, directed evolution was performed to improve the stability using ScCR1I158V/P168S as a template, affording a triple mutant, ScCR1A60T/I158V/P168S, whose thermostability (T5015, defined as the temperature at which 50% of initial enzyme activity is lost following a heat treatment for 15 min) and substrate tolerance (C5015, defined as the concentration at which 50% of initial enzyme activity is lost following incubation for 15 min) were 6.2°C and 4.7-fold higher than those of the wild-type enzyme. Interestingly, the specific activity of the triple mutant was further increased to 260 U/mg. Protein modeling and docking analysis shed light on the origin of the improved activity and stability. In the asymmetric reduction of ethyl-4-chloro-3-oxobutyrate (COBE) on a 300-ml scale, 100 g/liter COBE could be completely converted by only 2 g/liter of lyophilized ScCR1A60T/I158V/P168S within 9 h, affording an excellent enantiomeric excess (ee) of >99% and a space-time yield of 255 g liter-1 day-1 These results suggest high efficiency of the protein engineering strategy and good potential of the resulting variant for efficient synthesis of the atorvastatin precursor.IMPORTANCE Application of the carbonyl reductase ScCR1 in asymmetrically synthesizing (S)-CHBE, a key precursor for the blockbuster drug Lipitor, from COBE has been hindered by its low catalytic activity and poor thermostability and substrate tolerance. In this work, protein engineering was employed to improve the catalytic efficiency and stability of ScCR1. The catalytic efficiency, thermostability, and substrate tolerance of ScCR1 were significantly improved by structure-guided engineering and directed evolution. The engineered ScCR1 may serve as a promising biocatalyst for the biosynthesis of (S)-CHBE, and the protein engineering strategy adopted in this work would serve as a useful approach for future engineering of other reductases toward potential application in organic synthesis.
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Candida parapsilosis: A versatile biocatalyst for organic oxidation-reduction reactions. Bioorg Chem 2016; 68:187-213. [DOI: 10.1016/j.bioorg.2016.08.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Revised: 08/08/2016] [Accepted: 08/10/2016] [Indexed: 11/22/2022]
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Li A, Ye L, Yang X, Wang B, Yang C, Gu J, Yu H. Reconstruction of the Catalytic Pocket and Enzyme-Substrate Interactions To Enhance the Catalytic Efficiency of a Short-Chain Dehydrogenase/Reductase. ChemCatChem 2016. [DOI: 10.1002/cctc.201600921] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Aipeng Li
- Institute of Bioengineering, College of Chemical and Biological Engineering; Zhejiang University; 310027 Hangzhou P.R. China
| | - Lidan Ye
- Institute of Bioengineering, College of Chemical and Biological Engineering; Zhejiang University; 310027 Hangzhou P.R. China
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education; Zhejiang University; 310027 Hangzhou P.R. China
| | - Xiaohong Yang
- Institute of Bioengineering, College of Chemical and Biological Engineering; Zhejiang University; 310027 Hangzhou P.R. China
| | - Bei Wang
- College of Pharmaceutical Science; Zhejiang University of Technology; 310014 Hangzhou P.R. China
| | - Chengcheng Yang
- Institute of Bioengineering, College of Chemical and Biological Engineering; Zhejiang University; 310027 Hangzhou P.R. China
| | - Jiali Gu
- College of Life Science, Department of Materials Chemistry; Huzhou University; 313000 Huzhou P.R. China
| | - Hongwei Yu
- Institute of Bioengineering, College of Chemical and Biological Engineering; Zhejiang University; 310027 Hangzhou P.R. China
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Dhoke GV, Ensari Y, Davari MD, Ruff AJ, Schwaneberg U, Bocola M. What's My Substrate? Computational Function Assignment of Candida parapsilosis ADH5 by Genome Database Search, Virtual Screening, and QM/MM Calculations. J Chem Inf Model 2016; 56:1313-23. [PMID: 27387009 DOI: 10.1021/acs.jcim.6b00076] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Zinc-dependent medium chain reductase from Candida parapsilosis can be used in the reduction of carbonyl compounds to pharmacologically important chiral secondary alcohols. To date, the nomenclature of cpADH5 is differing (CPCR2/RCR/SADH) in the literature, and its natural substrate is not known. In this study, we utilized a substrate docking based virtual screening method combined with KEGG, MetaCyc pathway, and Candida genome databases search for the discovery of natural substrates of cpADH5. The virtual screening of 7834 carbonyl compounds from the ZINC database provided 94 aldehydes or methyl/ethyl ketones as putative carbonyl substrates. Out of which, 52 carbonyl substrates of cpADH5 with catalytically active docking pose were identified by employing mechanism based substrate docking protocol. Comparison of the virtual screening results with KEGG, MetaCyc database search, and Candida genome pathway analysis suggest that cpADH5 might be involved in the Ehrlich pathway (reduction of fusel aldehydes in leucine, isoleucine, and valine degradation). Our QM/MM calculations and experimental activity measurements affirmed that butyraldehyde substrates are the potential natural substrates of cpADH5, suggesting a carbonyl reductase role for this enzyme in butyraldehyde reduction in aliphatic amino acid degradation pathways. Phylogenetic tree analysis of known ADHs from Candida albicans shows that cpADH5 is close to caADH5. We therefore propose, according to the experimental substrate identification and sequence similarity, the common name butyraldehyde dehydrogenase cpADH5 for Candida parapsilosis CPCR2/RCR/SADH.
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Affiliation(s)
- Gaurao V Dhoke
- Lehrstuhl für Biotechnologie, RWTH Aachen University , Worringerweg 3, 52074 Aachen, Germany
| | - Yunus Ensari
- Lehrstuhl für Biotechnologie, RWTH Aachen University , Worringerweg 3, 52074 Aachen, Germany
| | - Mehdi D Davari
- Lehrstuhl für Biotechnologie, RWTH Aachen University , Worringerweg 3, 52074 Aachen, Germany
| | - Anna Joëlle Ruff
- Lehrstuhl für Biotechnologie, RWTH Aachen University , Worringerweg 3, 52074 Aachen, Germany
| | - Ulrich Schwaneberg
- Lehrstuhl für Biotechnologie, RWTH Aachen University , Worringerweg 3, 52074 Aachen, Germany.,DWI-Leibniz Institut für Interaktive Materialien , Forckenbeckstraße 50, 52056 Aachen, Germany
| | - Marco Bocola
- Lehrstuhl für Biotechnologie, RWTH Aachen University , Worringerweg 3, 52074 Aachen, Germany
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Activity improvement of a Kluyveromyces lactis aldo-keto reductase KlAKR via rational design. J Biotechnol 2016; 224:20-6. [DOI: 10.1016/j.jbiotec.2016.03.008] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2016] [Revised: 02/28/2016] [Accepted: 03/03/2016] [Indexed: 01/02/2023]
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Xu Q, Tao WY, Huang H, Li S. Highly efficient synthesis of ethyl (S)-4-chloro-3-hydroxybutanoate by a novel carbonyl reductase from Yarrowia lipolytica and using mannitol or sorbitol as cosubstrate. Biochem Eng J 2016. [DOI: 10.1016/j.bej.2015.11.010] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Redesigning alcohol dehydrogenases/reductases for more efficient biosynthesis of enantiopure isomers. Biotechnol Adv 2015; 33:1671-84. [DOI: 10.1016/j.biotechadv.2015.08.002] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Revised: 08/11/2015] [Accepted: 08/12/2015] [Indexed: 11/20/2022]
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16
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Wang X, Han S, Yang Z, Tang L. Improvement of the thermostability and activity of halohydrin dehalogenase from Agrobacterium radiobacter AD1 by engineering C-terminal amino acids. J Biotechnol 2015; 212:92-8. [DOI: 10.1016/j.jbiotec.2015.08.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Revised: 08/14/2015] [Accepted: 08/18/2015] [Indexed: 10/23/2022]
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17
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Loderer C, Dhoke GV, Davari MD, Kroutil W, Schwaneberg U, Bocola M, Ansorge-Schumacher MB. Investigation of Structural Determinants for the Substrate Specificity in the Zinc-Dependent Alcohol Dehydrogenase CPCR2 fromCandida parapsilosis. Chembiochem 2015; 16:1512-9. [DOI: 10.1002/cbic.201500100] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Indexed: 11/06/2022]
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Significantly improved thermostability of a reductase CgKR1 from Candida glabrata with a key mutation at Asp 138 for enhancing bioreduction of aromatic α-keto esters. J Biotechnol 2015; 203:54-61. [DOI: 10.1016/j.jbiotec.2015.02.035] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Revised: 02/14/2015] [Accepted: 02/28/2015] [Indexed: 01/03/2023]
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Hoebenreich S, Zilly FE, Acevedo-Rocha CG, Zilly M, Reetz MT. Speeding up directed evolution: Combining the advantages of solid-phase combinatorial gene synthesis with statistically guided reduction of screening effort. ACS Synth Biol 2015; 4:317-31. [PMID: 24921161 DOI: 10.1021/sb5002399] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Efficient and economic methods in directed evolution at the protein, metabolic, and genome level are needed for biocatalyst development and the success of synthetic biology. In contrast to random strategies, semirational approaches such as saturation mutagenesis explore the sequence space in a focused manner. Although several combinatorial libraries based on saturation mutagenesis have been reported using solid-phase gene synthesis, direct comparison with traditional PCR-based methods is currently lacking. In this work, we compare combinatorial protein libraries created in-house via PCR versus those generated by commercial solid-phase gene synthesis. Using descriptive statistics and probabilistic distributions on amino acid occurrence frequencies, the quality of the libraries was assessed and compared, revealing that the outsourced libraries are characterized by less bias and outliers than the PCR-based ones. Afterward, we screened all libraries following a traditional algorithm for almost complete library coverage and compared this approach with an emergent statistical concept suggesting screening a lower portion of the protein sequence space. Upon analyzing the biocatalytic landscapes and best hits of all combinatorial libraries, we show that the screening effort could have been reduced in all cases by more than 50%, while still finding at least one of the best mutants.
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Affiliation(s)
- Sabrina Hoebenreich
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
- Fachbereich
Chemie, Philipps-Universität Marburg, Hans-Meerwein-Straße, 35032 Marburg, Germany
| | - Felipe E. Zilly
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Carlos G. Acevedo-Rocha
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
- Fachbereich
Chemie, Philipps-Universität Marburg, Hans-Meerwein-Straße, 35032 Marburg, Germany
| | - Matías Zilly
- Fakultät
für Physik, Universität Duisburg-Essen, Lotharstraße 1, 47048 Duisburg, Germany
| | - Manfred T. Reetz
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
- Fachbereich
Chemie, Philipps-Universität Marburg, Hans-Meerwein-Straße, 35032 Marburg, Germany
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Grosch JH, Loderer C, Jestel T, Ansorge-Schumacher M, Spieß AC. Carbonyl reductase of Candida parapsilosis – Stability analysis and stabilization strategy. ACTA ACUST UNITED AC 2015. [DOI: 10.1016/j.molcatb.2014.12.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Zhao J, Kardashliev T, Joëlle Ruff A, Bocola M, Schwaneberg U. Lessons from diversity of directed evolution experiments by an analysis of 3,000 mutations. Biotechnol Bioeng 2014; 111:2380-9. [DOI: 10.1002/bit.25302] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Revised: 05/14/2014] [Accepted: 05/27/2014] [Indexed: 12/20/2022]
Affiliation(s)
- Jing Zhao
- Lehrstuhl für Biotechnologie; RWTH Aachen University; Worringerweg 3 52074 Aachen Germany
| | - Tsvetan Kardashliev
- Lehrstuhl für Biotechnologie; RWTH Aachen University; Worringerweg 3 52074 Aachen Germany
| | - Anna Joëlle Ruff
- Lehrstuhl für Biotechnologie; RWTH Aachen University; Worringerweg 3 52074 Aachen Germany
| | - Marco Bocola
- Lehrstuhl für Biotechnologie; RWTH Aachen University; Worringerweg 3 52074 Aachen Germany
| | - Ulrich Schwaneberg
- Lehrstuhl für Biotechnologie; RWTH Aachen University; Worringerweg 3 52074 Aachen Germany
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Man H, Gargiulo S, Frank A, Hollmann F, Grogan G. Structure of the NADH-dependent thermostable alcohol dehydrogenase TADH from Thermus sp. ATN1 provides a platform for engineering specificity and improved compatibility with inorganic cofactor-regeneration catalysts. ACTA ACUST UNITED AC 2014. [DOI: 10.1016/j.molcatb.2014.03.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Huang L, Ma HM, Yu HL, Xu JH. Altering the Substrate Specificity of ReductaseCgKR1 fromCandida glabrataby Protein Engineering for Bioreduction of Aromatic α-Keto Esters. Adv Synth Catal 2014. [DOI: 10.1002/adsc.201300775] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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Cloning, expression, and directed evolution of carbonyl reductase from Leifsonia xyli HS0904 with enhanced catalytic efficiency. Appl Microbiol Biotechnol 2014; 98:8591-601. [DOI: 10.1007/s00253-014-5770-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2014] [Revised: 04/09/2014] [Accepted: 04/10/2014] [Indexed: 01/03/2023]
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Chen XH, Wei P, Wang XT, Zong MH, Lou WY. A novel carbonyl reductase with anti-Prelog stereospecificity from Acetobacter sp. CCTCC M209061: purification and characterization. PLoS One 2014; 9:e94543. [PMID: 24740089 PMCID: PMC3989197 DOI: 10.1371/journal.pone.0094543] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2013] [Accepted: 03/18/2014] [Indexed: 11/20/2022] Open
Abstract
A novel carbonyl reductase (AcCR) catalyzing the asymmetric reduction of ketones to enantiopure alcohols with anti-Prelog stereoselectivity was found in Acetobacter sp. CCTCC M209061 and enriched 27.5-fold with an overall yield of 0.4% by purification. The enzyme showed a homotetrameric structure with an apparent molecular mass of 104 kDa and each subunit of 27 kDa. The gene sequence of AcCR was cloned and sequenced, and a 762 bp gene fragment was obtained. Either NAD(H) or NADP(H) can be used as coenzyme. For the reduction of 4'-chloroacetophenone, the Km value for NADH was around 25-fold greater than that for NADPH (0.66 mM vs 0.026 mM), showing that AcCR preferred NADPH over NADH. However, when NADH was used as cofactor, the response of AcCR activity to increasing concentration of 4'-chloroacetophenone was clearly sigmoidal with a Hill coefficient of 3.1, suggesting that the enzyme might possess four substrate-binding sites cooperating with each other The Vmax value for NADH-linked reduction was higher than that for NADPH-linked reduction (0.21 mM/min vs 0.17 mM/min). For the oxidation of isopropanol, the similar enzymological properties of AcCR were found using NAD+ or NADP+ as cofactor. Furthermore, a broad range of ketones such as aryl ketones, α-ketoesters and aliphatic ketones could be enantioselectively reduced into the corresponding chiral alcohols by this enzyme with high activity.
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Affiliation(s)
- Xiao-Hong Chen
- Lab of Applied Biocatalysis, College of Light Industry and Food Sciences, South China University of Technology, Guangzhou, Guangdong, China
| | - Ping Wei
- Lab of Applied Biocatalysis, College of Light Industry and Food Sciences, South China University of Technology, Guangzhou, Guangdong, China
| | - Xiao-Ting Wang
- State Key Laboratory of Pulp and Paper Engineering, South China University of Technology, Guangzhou, Guangdong, China
| | - Min-Hua Zong
- State Key Laboratory of Pulp and Paper Engineering, South China University of Technology, Guangzhou, Guangdong, China
| | - Wen-Yong Lou
- Lab of Applied Biocatalysis, College of Light Industry and Food Sciences, South China University of Technology, Guangzhou, Guangdong, China
- State Key Laboratory of Pulp and Paper Engineering, South China University of Technology, Guangzhou, Guangdong, China
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Clay D, Winkler CK, Tasnádi G, Faber K. Bioreduction and disproportionation of cyclohex-2-enone catalyzed by ene-reductase OYE-1 in 'micro-aqueous' organic solvents. Biotechnol Lett 2014; 36:1329-33. [PMID: 24563324 DOI: 10.1007/s10529-014-1494-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Accepted: 02/04/2014] [Indexed: 10/25/2022]
Abstract
The bioreduction and disproportionation of cyclohex-2-enone catalyzed by Old Yellow Enzyme 1 was investigated in presence of organic (co)solvents. Whereas the NADH-dependent bioreduction activity strongly decreased at elevated co-solvent concentrations due to the insolubility of the nicotinamide-cofactor, the NADH-free disproportionation was significantly improved in water-immiscible organic co-solvents at 90 % (v/v) with near-quantitative conversion. This positive effect was attributed to removal of the inhibiting co-product, phenol, from the enzyme's active site. The best co-solvents show high lipophilicity (logP) and a high potential to solubilize phenol (Kphenol). As a predictive parameter, the ratio of logP/Kphenol should be preferably ≥100.
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Affiliation(s)
- Dorina Clay
- Department of Chemistry, Organic & Bioorganic Chemistry, University of Graz, Heinrichstraße 28, 8010, Graz, Austria
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Man H, Loderer C, Ansorge-Schumacher MB, Grogan G. Structure of NADH-Dependent Carbonyl Reductase (CPCR2) from Candida parapsilosis
Provides Insight into Mutations that Improve Catalytic Properties. ChemCatChem 2014. [DOI: 10.1002/cctc.201300788] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Ni Y, Su Y, Li H, Zhou J, Sun Z. Scalable biocatalytic synthesis of optically pure ethyl (R)-2-hydroxy-4-phenylbutyrate using a recombinant E. coli with high catalyst yield. J Biotechnol 2013; 168:493-8. [DOI: 10.1016/j.jbiotec.2013.09.021] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2013] [Revised: 09/26/2013] [Accepted: 09/30/2013] [Indexed: 11/30/2022]
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Improvement of biocatalysts for industrial and environmental purposes by saturation mutagenesis. Biomolecules 2013; 3:778-811. [PMID: 24970191 PMCID: PMC4030971 DOI: 10.3390/biom3040778] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2013] [Revised: 09/22/2013] [Accepted: 09/23/2013] [Indexed: 11/16/2022] Open
Abstract
Laboratory evolution techniques are becoming increasingly widespread among protein engineers for the development of novel and designed biocatalysts. The palette of different approaches ranges from complete randomized strategies to rational and structure-guided mutagenesis, with a wide variety of costs, impacts, drawbacks and relevance to biotechnology. A technique that convincingly compromises the extremes of fully randomized vs. rational mutagenesis, with a high benefit/cost ratio, is saturation mutagenesis. Here we will present and discuss this approach in its many facets, also tackling the issue of randomization, statistical evaluation of library completeness and throughput efficiency of screening methods. Successful recent applications covering different classes of enzymes will be presented referring to the literature and to research lines pursued in our group. The focus is put on saturation mutagenesis as a tool for designing novel biocatalysts specifically relevant to production of fine chemicals for improving bulk enzymes for industry and engineering technical enzymes involved in treatment of waste, detoxification and production of clean energy from renewable sources.
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