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Li X, Jiang J, Li X, Liu D, Han M, Li W, Zhang H. Characterization and Application of a Novel Glucose Dehydrogenase with Excellent Organic Solvent Tolerance for Cofactor Regeneration in Carbonyl Reduction. Appl Biochem Biotechnol 2023; 195:7553-7567. [PMID: 37014512 DOI: 10.1007/s12010-023-04432-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/15/2023] [Indexed: 04/05/2023]
Abstract
An efficient cofactor regeneration system has been developed to provide a hydride source for the preparation of optically pure alcohols by carbonyl reductase-catalyzed asymmetric reduction. This system employed a novel glucose dehydrogenase (BcGDH90) from Bacillus cereus HBL-AI. The gene encoding BcGDH90 was found through the genome-wide functional annotation. Homology-built model study revealed that BcGDH90 was a homo-tetramer, and each subunit was composed of βD-αE-αF-αG-βG motif, which was responsible for substrate binding and tetramer formation. The gene of BcGDH90 was cloned and expressed in Escherichia coli. The recombinant BcGDH90 exhibited maximum activity of 45.3 U/mg at pH 9.0 and 40 °C. BcGDH90 showed high stability in a wide pH range of 4.0-10.0 and was stable after the incubation at 55 °C for 5 h. BcGDH90 was not a metal ion-dependent enzyme, but Zn2+ could seriously inhibit its activity. BcGDH90 displayed excellent tolerance to 90% of acetone, methanol, ethanol, n-propanol, and isopropanol. Furthermore, BcGDH90 was applied to regenerate NADPH for the asymmetric biosynthesis of (S)-(+)-1-phenyl-1,2-ethanediol ((S)-PED) from hydroxyacetophenone (2-HAP) with high concentration, which increased the final efficiency by 59.4%. These results suggest that BcGDH90 is potentially useful for coenzyme regeneration in the biological reduction.
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Affiliation(s)
- Xiaozheng Li
- College of Chemistry and Materials Science, Key Laboratory of Chemical Biology of Hebei Province, Laboratory of Medicinal Chemistry and Molecular Diagnosis of the Ministry of Education, Institute of Life Science and Green Development, Hebei University, Baoding, 071002, China
| | - Junpo Jiang
- College of Life Science, Microbial Technology Innovation Center for Feed of Hebei Province, Hebei Agricultural University, Baoding, 071001, China
| | - Xinyue Li
- College of Chemistry and Materials Science, Key Laboratory of Chemical Biology of Hebei Province, Laboratory of Medicinal Chemistry and Molecular Diagnosis of the Ministry of Education, Institute of Life Science and Green Development, Hebei University, Baoding, 071002, China
| | - Dexu Liu
- College of Chemistry and Materials Science, Key Laboratory of Chemical Biology of Hebei Province, Laboratory of Medicinal Chemistry and Molecular Diagnosis of the Ministry of Education, Institute of Life Science and Green Development, Hebei University, Baoding, 071002, China
| | - Mengnan Han
- College of Chemistry and Materials Science, Key Laboratory of Chemical Biology of Hebei Province, Laboratory of Medicinal Chemistry and Molecular Diagnosis of the Ministry of Education, Institute of Life Science and Green Development, Hebei University, Baoding, 071002, China
| | - Wei Li
- College of Chemistry and Materials Science, Key Laboratory of Chemical Biology of Hebei Province, Laboratory of Medicinal Chemistry and Molecular Diagnosis of the Ministry of Education, Institute of Life Science and Green Development, Hebei University, Baoding, 071002, China.
| | - Honglei Zhang
- College of Chemistry and Materials Science, Key Laboratory of Chemical Biology of Hebei Province, Laboratory of Medicinal Chemistry and Molecular Diagnosis of the Ministry of Education, Institute of Life Science and Green Development, Hebei University, Baoding, 071002, China.
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2
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Feng T, Liu J, Zhang X, Fan D, Bai Y. Protein engineering of multi-enzyme virus-like particle nanoreactors for enhanced chiral alcohol synthesis. NANOSCALE ADVANCES 2023; 5:6606-6616. [PMID: 38024302 PMCID: PMC10662152 DOI: 10.1039/d3na00515a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 10/17/2023] [Indexed: 12/01/2023]
Abstract
In the past decade, virus-like particles (VLPs) that can encapsulate single or multiple enzymes have been studied extensively as typical nanoreactors for biocatalysis in vitro, yet their catalytic efficiencies are usually inadequate for real applications. These biocatalytic nanoreactors should be engineered like their free-enzyme counterparts to improve their catalytic performance for potential applications. Herein we engineer biocatalytic VLPs for the enhanced synthesis of chiral alcohols. Different methods including directed evolution were applied to the entire bacteriophage P22 VLPs (except the coat protein), which encapsulated a carbonyl reductase from Scheffersomyces stipitis (SsCR) and a glucose dehydrogenase from Bacillus megaterium (BmGDH) in their capsids. The best variant, namely M5, showed an enhanced turnover frequency (TOF, min-1) up to 15-fold toward the majority of tested aromatic prochiral ketones, and gave up to 99% enantiomeric excess in the synthesis of chiral alcohol pharmaceutical intermediates. A comparison with the mutations of the free-enzyme counterparts showed that the same amino acid mutations led to different changes in the catalytic efficiencies of free and confined enzymes. Finally, the engineered M5 nanoreactor showed improved efficiency in the scale-up synthesis of chiral alcohols. The conversions of three substrates catalyzed by M5 were all higher than those catalyzed by the wild-type nanoreactor, demonstrating that enzyme-encapsulating VLPs can evolve to enhance their catalytic performance for potential applications.
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Affiliation(s)
- Taotao Feng
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing, East China University of Science and Technology Shanghai 200237 China
| | - Jiaxu Liu
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing, East China University of Science and Technology Shanghai 200237 China
| | - Xiaoyan Zhang
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing, East China University of Science and Technology Shanghai 200237 China
| | - Daidi Fan
- Shaanxi R&D Centre of Biomaterials and Fermentation Engineering, School of Chemical Engineering, Northwest University Xi'an Shaanxi 710069 China
| | - Yunpeng Bai
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing, East China University of Science and Technology Shanghai 200237 China
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3
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Sun Y, Xue W, Zhao J, Bao Q, Zhang K, Liu Y, Li H. Direct Electrochemistry of Glucose Dehydrogenase-Functionalized Polymers on a Modified Glassy Carbon Electrode and Its Molecular Recognition of Glucose. Int J Mol Sci 2023; 24:ijms24076152. [PMID: 37047124 PMCID: PMC10093998 DOI: 10.3390/ijms24076152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 03/21/2023] [Accepted: 03/23/2023] [Indexed: 04/14/2023] Open
Abstract
A glucose biosensor was layer-by-layer assembled on a modified glassy carbon electrode (GCE) from a nanocomposite of NAD(P)+-dependent glucose dehydrogenase, aminated polyethylene glycol (mPEG), carboxylic acid-functionalized multi-wall carbon nanotubes (fMWCNTs), and ionic liquid (IL) composite functional polymers. The electrochemical electrode was denoted as NF/IL/GDH/mPEG-fMWCNTs/GCE. The composite polymer membranes were characterized by cyclic voltammetry, ultraviolet-visible spectrophotometry, electrochemical impedance spectroscopy, scanning electron microscopy, and transmission electron microscopy. The cyclic voltammogram of the modified electrode had a pair of well-defined quasi-reversible redox peaks with a formal potential of -61 mV (vs. Ag/AgCl) at a scan rate of 0.05 V s-1. The heterogeneous electron transfer constant (ks) of GDH on the composite functional polymer-modified GCE was 6.5 s-1. The biosensor could sensitively recognize and detect glucose linearly from 0.8 to 100 µM with a detection limit down to 0.46 μM (S/N = 3) and a sensitivity of 29.1 nA μM-1. The apparent Michaelis-Menten constant (Kmapp) of the modified electrode was 0.21 mM. The constructed electrochemical sensor was compared with the high-performance liquid chromatography method for the determination of glucose in commercially available glucose injections. The results demonstrated that the sensor was highly accurate and could be used for the rapid and quantitative determination of glucose concentration.
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Affiliation(s)
- Yang Sun
- School of Life Sciences, Henan University, Kaifeng 475004, China
- Engineering Research Center for Applied Microbiology of Henan Province, Kaifeng 475004, China
| | - Weishi Xue
- School of Life Sciences, Henan University, Kaifeng 475004, China
- Engineering Research Center for Applied Microbiology of Henan Province, Kaifeng 475004, China
| | - Jianfeng Zhao
- School of Life Sciences, Henan University, Kaifeng 475004, China
- Engineering Research Center for Applied Microbiology of Henan Province, Kaifeng 475004, China
| | - Qianqian Bao
- School of Life Sciences, Henan University, Kaifeng 475004, China
- Engineering Research Center for Applied Microbiology of Henan Province, Kaifeng 475004, China
| | - Kailiang Zhang
- School of Life Sciences, Henan University, Kaifeng 475004, China
- Engineering Research Center for Applied Microbiology of Henan Province, Kaifeng 475004, China
| | - Yupeng Liu
- School of Life Sciences, Henan University, Kaifeng 475004, China
- Engineering Research Center for Applied Microbiology of Henan Province, Kaifeng 475004, China
| | - Hua Li
- School of Life Sciences, Henan University, Kaifeng 475004, China
- Engineering Research Center for Applied Microbiology of Henan Province, Kaifeng 475004, China
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4
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Fabrication of Fe3O4@SiO2@PDA-Ni2+ nanoparticles for one-step affinity immobilization and purification of His-tagged glucose dehydrogenase. Process Biochem 2023. [DOI: 10.1016/j.procbio.2023.02.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/27/2023]
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5
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Okuda-Shimazaki J, Yoshida H, Lee I, Kojima K, Suzuki N, Tsugawa W, Yamada M, Inaka K, Tanaka H, Sode K. Microgravity environment grown crystal structure information based engineering of direct electron transfer type glucose dehydrogenase. Commun Biol 2022; 5:1334. [PMID: 36473944 PMCID: PMC9727119 DOI: 10.1038/s42003-022-04286-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 11/21/2022] [Indexed: 12/12/2022] Open
Abstract
The heterotrimeric flavin adenine dinucleotide dependent glucose dehydrogenase is a promising enzyme for direct electron transfer (DET) principle-based glucose sensors within continuous glucose monitoring systems. We elucidate the structure of the subunit interface of this enzyme by preparing heterotrimer complex protein crystals grown under a space microgravity environment. Based on the proposed structure, we introduce inter-subunit disulfide bonds between the small and electron transfer subunits (5 pairs), as well as the catalytic and the electron transfer subunits (9 pairs). Without compromising the enzyme's catalytic efficiency, a mutant enzyme harboring Pro205Cys in the catalytic subunit, Asp383Cys and Tyr349Cys in the electron transfer subunit, and Lys155Cys in the small subunit, is determined to be the most stable of the variants. The developed engineered enzyme demonstrate a higher catalytic activity and DET ability than the wild type. This mutant retains its full activity below 70 °C as well as after incubation at 75 °C for 15 min - much higher temperatures than the current gold standard enzyme, glucose oxidase, is capable of withstanding.
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Affiliation(s)
- Junko Okuda-Shimazaki
- grid.10698.360000000122483208Joint Department of Biomedical Engineering, The University of North Carolina at Chapel Hill and North Carolina State University, Chapel Hill, NC27599 USA
| | - Hiromi Yoshida
- grid.258331.e0000 0000 8662 309XDepartment of Basic Life Science, Faculty of Medicine, Kagawa University, 1750-1 Ikenobe, Miki-cho, Kita-gun, Kagawa 761-0793 Japan
| | - Inyoung Lee
- grid.10698.360000000122483208Joint Department of Biomedical Engineering, The University of North Carolina at Chapel Hill and North Carolina State University, Chapel Hill, NC27599 USA
| | - Katsuhiro Kojima
- grid.136594.c0000 0001 0689 5974Graduate School of Engineering, Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588 Japan
| | - Nanoha Suzuki
- grid.136594.c0000 0001 0689 5974Graduate School of Engineering, Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588 Japan
| | - Wakako Tsugawa
- grid.136594.c0000 0001 0689 5974Graduate School of Engineering, Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588 Japan
| | - Mitsugu Yamada
- grid.62167.340000 0001 2220 7916JEM Utilization Center Human Spaceflight Technology Directorate, Japan Aerospace Exploration Agency (JAXA), 2-1-1 Sengen, Tsukuba-shi, Ibaraki 305-8505 Japan
| | - Koji Inaka
- grid.459744.fMaruwa Foods and Biosciences, 170-1 Tsutsui-cho, Yamato Koriyama-shi, Nara 639-1123 Japan
| | - Hiroaki Tanaka
- grid.459486.2Confocal Science Inc., Musashino Bldg, 5-14-15 Fukasawa, Setagaya-ku, Tokyo 158-0081 Japan
| | - Koji Sode
- grid.10698.360000000122483208Joint Department of Biomedical Engineering, The University of North Carolina at Chapel Hill and North Carolina State University, Chapel Hill, NC27599 USA
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Assessment of the Effects of Triticonazole on Soil and Human Health. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27196554. [PMID: 36235091 PMCID: PMC9572687 DOI: 10.3390/molecules27196554] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 09/19/2022] [Accepted: 09/26/2022] [Indexed: 11/28/2022]
Abstract
Triticonazole is a fungicide used to control diseases in numerous plants. The commercial product is a racemate containing (R)- and (S)-triticonazole and its residues have been found in vegetables, fruits, and drinking water. This study considered the effects of triticonazole on soil microorganisms and enzymes and human health by taking into account the enantiomeric structure when applicable. An experimental method was applied for assessing the effects of triticonazole on soil microorganisms and enzymes, and the effects of the stereoisomers on soil enzymes and human health were assessed using a computational approach. There were decreases in dehydrogenase and phosphatase activities and an increase in urease activity when barley and wheat seeds treated with various doses of triticonazole were sown in chernozem soil. At least 21 days were necessary for the enzymes to recover the activities. This was consistent with the diminution of the total number of soil microorganisms in the 14 days after sowing. Both stereoisomers were able to bind to human plasma proteins and were potentially inhibitors of human cytochromes, revealing cardiotoxicity and low endocrine disruption potential. As distinct effects, (R)-TTZ caused skin sensitization, carcinogenicity, and respiratory toxicity. There were no significant differences in the interaction energies of the stereoisomers and soil enzymes, but (S)-TTZ exposed higher interaction energies with plasma proteins and human cytochromes.
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Li Y, Luan P, Dong L, Liu J, Jiang L, Bai J, Liu F, Jiang Y. Asymmetric reduction of conjugated C C bonds by immobilized fusion of old yellow enzyme and glucose dehydrogenase. GREEN SYNTHESIS AND CATALYSIS 2022. [DOI: 10.1016/j.gresc.2022.10.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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8
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Li Y, Zhang R, Wang C, Forouhar F, Clarke OB, Vorobiev S, Singh S, Montelione GT, Szyperski T, Xu Y, Hunt JF. Oligomeric interactions maintain active-site structure in a noncooperative enzyme family. EMBO J 2022; 41:e108368. [PMID: 35801308 DOI: 10.15252/embj.2021108368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Revised: 04/07/2022] [Accepted: 04/16/2022] [Indexed: 11/09/2022] Open
Abstract
The evolutionary benefit accounting for widespread conservation of oligomeric structures in proteins lacking evidence of intersubunit cooperativity remains unclear. Here, crystal and cryo-EM structures, and enzymological data, demonstrate that a conserved tetramer interface maintains the active-site structure in one such class of proteins, the short-chain dehydrogenase/reductase (SDR) superfamily. Phylogenetic comparisons support a significantly longer polypeptide being required to maintain an equivalent active-site structure in the context of a single subunit. Oligomerization therefore enhances evolutionary fitness by reducing the metabolic cost of enzyme biosynthesis. The large surface area of the structure-stabilizing oligomeric interface yields a synergistic gain in fitness by increasing tolerance to activity-enhancing yet destabilizing mutations. We demonstrate that two paralogous SDR superfamily enzymes with different specificities can form mixed heterotetramers that combine their individual enzymological properties. This suggests that oligomerization can also diversify the functions generated by a given metabolic investment, enhancing the fitness advantage provided by this architectural strategy.
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Affiliation(s)
- Yaohui Li
- Key Laboratory of Industrial Biotechnology of Ministry of Education and School of Biotechnology, Jiangnan University, Wuxi, China.,Department of Biological Sciences, 702 Sherman Fairchild Center, MC2434, Columbia University, New York, NY, USA
| | - Rongzhen Zhang
- Key Laboratory of Industrial Biotechnology of Ministry of Education and School of Biotechnology, Jiangnan University, Wuxi, China
| | - Chi Wang
- Department of Biological Sciences, 702 Sherman Fairchild Center, MC2434, Columbia University, New York, NY, USA.,Cryo-Electron Microscopy Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Farhad Forouhar
- Department of Biological Sciences, 702 Sherman Fairchild Center, MC2434, Columbia University, New York, NY, USA.,Macromolecular Crystallography Shared Resource, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Oliver B Clarke
- Department of Physiology and Cellular Biophysics and Department of Anesthesiology, Columbia University Irving Medical Center, New York, NY, USA
| | - Sergey Vorobiev
- Department of Biological Sciences, 702 Sherman Fairchild Center, MC2434, Columbia University, New York, NY, USA
| | - Shikha Singh
- Department of Biological Sciences, 702 Sherman Fairchild Center, MC2434, Columbia University, New York, NY, USA
| | - Gaetano T Montelione
- Department of Chemistry & Chemical Biology and Center for Biotechnology & Interdisciplinary Sciences, Rensselaer Polytechnic Institute, Troy, NY, USA
| | - Thomas Szyperski
- Department of Chemistry, State University of New York at Buffalo, Buffalo, NY, USA
| | - Yan Xu
- Key Laboratory of Industrial Biotechnology of Ministry of Education and School of Biotechnology, Jiangnan University, Wuxi, China
| | - John F Hunt
- Department of Biological Sciences, 702 Sherman Fairchild Center, MC2434, Columbia University, New York, NY, USA
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9
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Yan Q, Zhang X, Chen Y, Guo B, Zhou P, Chen B, Huang Q, Wang JB. From Semirational to Rational Design: Developing a Substrate-Coupled System of Glucose Dehydrogenase for Asymmetric Synthesis. ACS Catal 2022. [DOI: 10.1021/acscatal.2c00705] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Qipeng Yan
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education) and Key Laboratory of Phytochemistry R&D of Hunan Province, College of Chemistry and Chemical Engineering, Hunan Normal University, 410081 Changsha, P. R. China
| | - Xinhua Zhang
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education) and Key Laboratory of Phytochemistry R&D of Hunan Province, College of Chemistry and Chemical Engineering, Hunan Normal University, 410081 Changsha, P. R. China
| | - Yingzhuang Chen
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education) and Key Laboratory of Phytochemistry R&D of Hunan Province, College of Chemistry and Chemical Engineering, Hunan Normal University, 410081 Changsha, P. R. China
| | - Bin Guo
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education) and Key Laboratory of Phytochemistry R&D of Hunan Province, College of Chemistry and Chemical Engineering, Hunan Normal University, 410081 Changsha, P. R. China
| | - Pei Zhou
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education) and Key Laboratory of Phytochemistry R&D of Hunan Province, College of Chemistry and Chemical Engineering, Hunan Normal University, 410081 Changsha, P. R. China
| | - Bo Chen
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education) and Key Laboratory of Phytochemistry R&D of Hunan Province, College of Chemistry and Chemical Engineering, Hunan Normal University, 410081 Changsha, P. R. China
| | - Qun Huang
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education) and Key Laboratory of Phytochemistry R&D of Hunan Province, College of Chemistry and Chemical Engineering, Hunan Normal University, 410081 Changsha, P. R. China
| | - Jian-bo Wang
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education) and Key Laboratory of Phytochemistry R&D of Hunan Province, College of Chemistry and Chemical Engineering, Hunan Normal University, 410081 Changsha, P. R. China
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10
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Crystal structure of L-arabinose 1-dehydrogenase as a short-chain reductase/dehydrogenase protein. Biochem Biophys Res Commun 2022; 604:14-21. [DOI: 10.1016/j.bbrc.2022.03.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 03/05/2022] [Indexed: 11/23/2022]
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11
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Tailoring an aldo-keto reductase KmAKR for robust thermostability and catalytic efficiency by stepwise evolution and structure-guided consensus engineering. Bioorg Chem 2021; 109:104712. [PMID: 33735657 DOI: 10.1016/j.bioorg.2021.104712] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Accepted: 01/28/2021] [Indexed: 01/13/2023]
Abstract
t-Butyl 6-cyano-(3R,5R)-dihydroxyhexanoate ((3R,5R)-2) is an advanced chiral diol intermediate of the cholesterol-lowering drug atorvastatin. KmAKRM5 (W297H/Y296W/K29H/Y28A/T63M) constructed in our previous work, displayed good biocatalytic performance on (3R,5R)-2. In the present work, stepwise evolution was applied to further enhance the thermostability and activity of KmAKRM5. For thermostability enhancement, N109 and S196 located far from the active site were picked out by structure-guided consensus engineering, and mutated by site-directed mutagenesis (SDM). For catalytic efficiency improvement, the residues A30 and T302 adjacent to the substrate-binding pocket were subjected to site-saturation mutagenesis (SSM). As a result, the "best" mutant KmAKRM9 (W297H/Y296W/K29H/Y28A/T63M/A30P/T302S/N109K/S196C) was developed, of which T5015 and Tm were 5.0 °C and 8.2 °C higher than those of KmAKRM5. Moreover, compared to KmAKRM5, KmAKRM9 displayed a 1.9-fold (846 vs 2436 min) and 6.7-fold (126 vs 972 min) longer half-lives at 40 and 50 °C, respectively. Structural analysis suggested that beneficial mutations introduced additional hydrophobic interactions and hydrogen bonds, contributing rigidification of the flexible loops and the increase of internal forces, hence increasing the thermostability and activity. 5 g DCW (dry cell weight) L-1KmAKRM9 completely reduced 350 g L-1t-butyl 6-cyano-(5R)-hydroxy-3-oxo-hexanoate ((5R)-1), within 3.7 h at 40 °C, yielding optically pure (3R,5R)-2 (d.e.p > 99.5%) with a space-time yield (STY) of 1.82 kg L-1 d-1. Hence, KmAKRM9 is a robust biocatalyst for the synthesis of (3R,5R)-2.
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12
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Yoshiwara K, Watanabe S, Watanabe Y. Crystal structure of l-rhamnose 1-dehydrogenase involved in the nonphosphorylative pathway of l-rhamnose metabolism in bacteria. FEBS Lett 2021; 595:637-646. [PMID: 33482017 DOI: 10.1002/1873-3468.14046] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Revised: 01/18/2021] [Accepted: 01/19/2021] [Indexed: 11/05/2022]
Abstract
Several microorganisms can utilize l-rhamnose as a carbon and energy source through the nonphosphorylative metabolic pathway, in which l-rhamnose 1-dehydrogenase (RhaDH) catalyzes the NAD(P)+ -dependent oxidization of l-rhamnose to l-rhamnono-1,4-lactone. We herein investigated the crystal structures of RhaDH from Azotobacter vinelandii in ligand-free, NAD+ -bound, NADP+ -bound, and l-rhamnose- and NAD+ -bound forms at 1.9, 2.1, 2.4, and 1.6 Å resolution, respectively. The significant interactions with the 2'-phosphate group of NADP+ , but not the 2'-hydroxyl group of NAD+ , were consistent with a preference for NADP+ over NAD+ . The C5-OH and C6-methyl groups of l-rhamnose were recognized by specific residues of RhaDH through hydrogen bonds and hydrophobic contact, respectively, which contribute to the different substrate specificities from other aldose 1-dehydrogenases in the short-chain dehydrogenase/reductase superfamily.
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Affiliation(s)
| | - Seiya Watanabe
- Faculty of Agriculture, Ehime University, Matsuyama, Japan.,Department of Bioscience, Graduate School of Agriculture, Ehime University, Matsuyama, Japan.,Center for Marine Environmental Studies (CMES), Ehime University, Matsuyama, Japan
| | - Yasunori Watanabe
- Faculty of Agriculture, Ehime University, Matsuyama, Japan.,Department of Bioscience, Graduate School of Agriculture, Ehime University, Matsuyama, Japan.,Faculty of Science, Yamagata University, Japan
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13
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Subramanian V, Lunin VV, Farmer SJ, Alahuhta M, Moore KT, Ho A, Chaudhari YB, Zhang M, Himmel ME, Decker SR. Phylogenetics-based identification and characterization of a superior 2,3-butanediol dehydrogenase for Zymomonas mobilis expression. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:186. [PMID: 33292448 PMCID: PMC7656694 DOI: 10.1186/s13068-020-01820-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 10/21/2020] [Indexed: 05/16/2023]
Abstract
BACKGROUND Zymomonas mobilis has recently been shown to be capable of producing the valuable platform biochemical, 2,3-butanediol (2,3-BDO). Despite this capability, the production of high titers of 2,3-BDO is restricted by several physiological parameters. One such bottleneck involves the conversion of acetoin to 2,3-BDO, a step catalyzed by 2,3-butanediol dehydrogenase (Bdh). Several Bdh enzymes have been successfully expressed in Z. mobilis, although a highly active enzyme is yet to be identified for expression in this host. Here, we report the application of a phylogenetic approach to identify and characterize a superior Bdh, followed by validation of its structural attributes using a mutagenesis approach. RESULTS Of the 11 distinct bdh genes that were expressed in Z. mobilis, crude extracts expressing Serratia marcescens Bdh (SmBdh) were found to have the highest activity (8.89 µmol/min/mg), when compared to other Bdh enzymes (0.34-2.87 µmol/min/mg). The SmBdh crystal structure was determined through crystallization with cofactor (NAD+) and substrate (acetoin) molecules bound in the active site. Active SmBdh was shown to be a tetramer with the active site populated by a Gln247 residue contributed by the diagonally opposite subunit. SmBdh showed a more extensive supporting hydrogen-bond network in comparison to the other well-studied Bdh enzymes, which enables improved substrate positioning and substrate specificity. This protein also contains a short α6 helix, which provides more efficient entry and exit of molecules from the active site, thereby contributing to enhanced substrate turnover. Extending the α6 helix to mimic the lower activity Enterobacter cloacae (EcBdh) enzyme resulted in reduction of SmBdh function to nearly 3% of the total activity. In great contrast, reduction of the corresponding α6 helix of the EcBdh to mimic the SmBdh structure resulted in ~ 70% increase in its activity. CONCLUSIONS This study has demonstrated that SmBdh is superior to other Bdhs for expression in Z. mobilis for 2,3-BDO production. SmBdh possesses unique structural features that confer biochemical advantage to this protein. While coordinated active site formation is a unique structural characteristic of this tetrameric complex, the smaller α6 helix and extended hydrogen network contribute towards improved activity and substrate promiscuity of the enzyme.
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Affiliation(s)
- Venkataramanan Subramanian
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO, 80401, USA.
| | - Vladimir V Lunin
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO, 80401, USA.
| | - Samuel J Farmer
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO, 80401, USA
| | - Markus Alahuhta
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO, 80401, USA
| | - Kyle T Moore
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO, 80401, USA
| | - Angela Ho
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO, 80401, USA
| | - Yogesh B Chaudhari
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO, 80401, USA
- Biodiversity and Ecosystem Research, Institute of Advanced Study in Science and Technology (IASST), Guwahati, Assam, India
| | - Min Zhang
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO, 80401, USA
| | - Michael E Himmel
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO, 80401, USA
| | - Stephen R Decker
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO, 80401, USA
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14
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Spano MB, Tran BH, Majumdar S, Weiss GA. 3D-Printed Labware for High-Throughput Immobilization of Enzymes. J Org Chem 2020; 85:8480-8488. [PMID: 32502347 PMCID: PMC9096805 DOI: 10.1021/acs.joc.0c00789] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
In continuous flow biocatalysis, chemical transformations can occur under milder, greener, more scalable, and safer conditions than conventional organic synthesis. However, the method typically involves extensive screening to optimize each enzyme's immobilization on its solid support material. The task of weighing solids for large numbers of experiments poses a bottleneck for screening enzyme immobilization conditions. For example, screening conditions often require multiple replicates exploring different support chemistries, buffer compositions, and temperatures. Thus, we report 3D-printed labware designed to measure and handle solids in multichannel format and expedite screening of enzyme immobilization conditions. To demonstrate the generality of these advances, alkaline phosphatase, glucose dehydrogenase, and laccase were screened for immobilization efficiency on seven resins. The results illustrate the requirements for optimization of each enzyme's loading and resin choice for optimal catalytic performance. Here, 3D-printed labware can decrease the requirements for an experimentalist's time by >95%. The approach to rapid optimization of enzyme immobilization is applicable to any enzyme and many solid support resins. Furthermore, the reported devices deliver precise and accurate aliquots of essentially any granular solid material.
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Affiliation(s)
- Michael B. Spano
- Department of Chemistry, University of California, Irvine, California, 92697-2025, United States of America
| | - Brandan H. Tran
- Department of Chemistry, University of California, Irvine, California, 92697-2025, United States of America
| | - Sudipta Majumdar
- Department of Chemistry, University of California, Irvine, California, 92697-2025, United States of America
| | - Gregory A. Weiss
- Department of Chemistry, University of California, Irvine, California, 92697-2025, United States of America
- Department of Molecular Biology and Biochemistry, University of California, Irvine, California, 92697-3900, United States of America
- Department of Pharmaceutical Sciences, University of California, Irvine, California, 92697-3958, United States of America
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15
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Stolarczyk K, Rogalski J, Bilewicz R. NAD(P)-dependent glucose dehydrogenase: Applications for biosensors, bioelectrodes, and biofuel cells. Bioelectrochemistry 2020; 135:107574. [PMID: 32498025 DOI: 10.1016/j.bioelechem.2020.107574] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Revised: 05/21/2020] [Accepted: 05/21/2020] [Indexed: 12/13/2022]
Abstract
This review discusses the physical and chemical properties of nicotinamide redox cofactor dependent glucose dehydrogenase (NAD(P) dependent GDH) and its extensive application in biosensors and bio-fuel cells. GDHs from different organisms show diverse biochemical properties (e.g., activity and stability) and preferences towards cofactors, such as nicotinamide adenine dinucleotide (NAD+) and nicotinamide adenine dinucleotide phosphate (NADP+). The (NAD(P)+) play important roles in biological electron transfer, however, there are some difficulties related to their application in devices that originate from their chemical properties and labile binding to the GDH enzyme. This review discusses the electrode modifications aimed at immobilising NAD+ or NADP+ cofactors and GDH at electrodes. Binding of the enzyme was achieved by appropriate protein engineering techniques, including polymerisation, hydrophobisation or hydrophilisation processes. Various enzyme-modified electrodes applied in biosensors, enzymatic fuel cells, and biobatteries are compared. Importantly, GDH can operate alone or as part of an enzymatic cascade, which often improves the functional parameters of the biofuel cell or simply allows use of cheaper fuels. Overall, this review explores how NAD(P)-dependent GDH has recently demonstrated high potential for use in various systems to generate electricity from biological sources for applications in implantable biomedical devices, wireless sensors, and portable electronic devices.
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Affiliation(s)
- Krzysztof Stolarczyk
- Faculty of Chemistry, University of Warsaw, Pasteura St. 1, 02-093 Warsaw, Poland
| | - Jerzy Rogalski
- Department of Biochemistry and Biotechnology, Maria Curie-Sklodowska University, Akademicka Str. 19, 20-031 Lublin, Poland
| | - Renata Bilewicz
- Faculty of Chemistry, University of Warsaw, Pasteura St. 1, 02-093 Warsaw, Poland.
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16
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Shah S, Sunder AV, Singh P, Wangikar PP. Characterization and Application of a Robust Glucose Dehydrogenase from Paenibacillus pini for Cofactor Regeneration in Biocatalysis. Indian J Microbiol 2020; 60:87-95. [PMID: 32089578 DOI: 10.1007/s12088-019-00834-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Accepted: 10/23/2019] [Indexed: 02/06/2023] Open
Abstract
Glucose dehydrogenases are important auxiliary enzymes in biocatalysis, employed in the regeneration of reduced nicotinamide cofactors for oxidoreductase catalysed reactions. Here we report the identification and characterization of a novel glucose-1-dehydrogenase (GDH) from Paenibacillus pini that prefers NAD+ as cofactor over NADP+. The purified recombinant P. pini GDH displayed a specific activity of 247.5 U/mg. The enzyme was stable in the pH range 4-8.5 and exhibited excellent thermostability till 50 °C for 24 h, even in the absence of NaCl or glycerol. Paenibacillus pini GDH was also tolerant to organic solvents, demonstrating its potential for recycling cofactors for biotransformation. The potential application of the enzyme was evaluated by coupling with a NAD+-dependent alcohol dehydrogenase for the reduction of acetophenone and ethyl-4-chloro-3-oxo-butanoate. Conversions higher than 95% were achieved within 2 h with low enzyme loading using lyophilized cell lysate, suggesting that P. pini GDH could be highly effective for recycling NADH in redox biocatalysis.
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Affiliation(s)
- Shikha Shah
- 1Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076 India
| | - Avinash Vellore Sunder
- 1Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076 India
| | - Pooja Singh
- 1Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076 India.,2Department of Biochemistry, Savitribai Phule Pune University, Pune, 411007 India
| | - Pramod P Wangikar
- 1Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076 India
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17
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Li T, Li R, Zhu T, Cui X, Li C, Cui Y, Wu B. Improving the System Performance of the Asymmetric Biosynthesis of d-Pantoic Acid by Using Artificially Self-Assembled Enzymes in Escherichia coli. ACS Biomater Sci Eng 2019; 6:219-224. [DOI: 10.1021/acsbiomaterials.9b01754] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Tao Li
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
- University of Chinese Academy of Sciences, Beijing 100101, PR China
| | - Ruifeng Li
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
- University of Chinese Academy of Sciences, Beijing 100101, PR China
| | - Tong Zhu
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
- University of Chinese Academy of Sciences, Beijing 100101, PR China
| | - Xuexian Cui
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
- University of Chinese Academy of Sciences, Beijing 100101, PR China
| | - Chuijian Li
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Yinglu Cui
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Bian Wu
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
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18
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Biochemical and structural investigation of sulfoacetaldehyde reductase from Klebsiella oxytoca. Biochem J 2019; 476:733-746. [PMID: 30718306 DOI: 10.1042/bcj20190005] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Revised: 01/25/2019] [Accepted: 02/01/2019] [Indexed: 11/17/2022]
Abstract
Sulfoacetaldehyde reductase (IsfD) is a member of the short-chain dehydrogenase/reductase (SDR) family, involved in nitrogen assimilation from aminoethylsulfonate (taurine) in certain environmental and human commensal bacteria. IsfD catalyzes the reversible NADPH-dependent reduction of sulfoacetaldehyde, which is generated by transamination of taurine, forming hydroxyethylsulfonate (isethionate) as a waste product. In the present study, the crystal structure of Klebsiella oxytoca IsfD in a ternary complex with NADPH and isethionate was solved at 2.8 Å, revealing residues important for substrate binding. IsfD forms a homotetramer in both crystal and solution states, with the C-terminal tail of each subunit interacting with the C-terminal tail of the diagonally opposite subunit, forming an antiparallel β sheet that constitutes part of the substrate-binding site. The sulfonate group of isethionate is stabilized by a hydrogen bond network formed by the residues Y148, R195, Q244 and a water molecule. In addition, F249 from the diagonal subunit restrains the conformation of Y148 to further stabilize the orientation of the sulfonate group. Mutation of any of these four residues into alanine resulted in a complete loss of catalytic activity for isethionate oxidation. Biochemical investigations of the substrate scope of IsfD, and bioinformatics analysis of IsfD homologs, suggest that IsfD is related to the promiscuous 3-hydroxyacid dehydrogenases with diverse metabolic functions.
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19
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Semi-rational engineering of carbonyl reductase YueD for efficient biosynthesis of halogenated alcohols with in situ cofactor regeneration. Biochem Eng J 2018. [DOI: 10.1016/j.bej.2018.05.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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20
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Nowak C, Pick A, Lommes P, Sieber V. Enzymatic Reduction of Nicotinamide Biomimetic Cofactors Using an Engineered Glucose Dehydrogenase: Providing a Regeneration System for Artificial Cofactors. ACS Catal 2017. [DOI: 10.1021/acscatal.7b00721] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Claudia Nowak
- Department
of Life Science Engineering, Straubing Center of Science, Technical University of Munich, Schulgasse 16, 94315 Straubing, Germany
| | - André Pick
- Department
of Life Science Engineering, Straubing Center of Science, Technical University of Munich, Schulgasse 16, 94315 Straubing, Germany
| | - Petra Lommes
- Department
of Life Science Engineering, Straubing Center of Science, Technical University of Munich, Schulgasse 16, 94315 Straubing, Germany
| | - Volker Sieber
- Department
of Life Science Engineering, Straubing Center of Science, Technical University of Munich, Schulgasse 16, 94315 Straubing, Germany
- TUM Catalysis Research Center, Ernst-Otto-Fischer-Straße 1, 85748 Garching, Germany
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21
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Ding H, Gao F, Yu Y, Chen B. Biochemical and Computational Insights on a Novel Acid-Resistant and Thermal-Stable Glucose 1-Dehydrogenase. Int J Mol Sci 2017; 18:ijms18061198. [PMID: 28587256 PMCID: PMC5486021 DOI: 10.3390/ijms18061198] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Revised: 05/30/2017] [Accepted: 05/30/2017] [Indexed: 11/29/2022] Open
Abstract
Due to the dual cofactor specificity, glucose 1-dehydrogenase (GDH) has been considered as a promising alternative for coenzyme regeneration in biocatalysis. To mine for potential GDHs for practical applications, several genes encoding for GDH had been heterogeneously expressed in Escherichia coli BL21 (DE3) for primary screening. Of all the candidates, GDH from Bacillus sp. ZJ (BzGDH) was one of the most robust enzymes. BzGDH was then purified to homogeneity by immobilized metal affinity chromatography and characterized biochemically. It displayed maximum activity at 45 °C and pH 9.0, and was stable at temperatures below 50 °C. BzGDH also exhibited a broad pH stability, especially in the acidic region, which could maintain around 80% of its initial activity at the pH range of 4.0–8.5 after incubating for 1 hour. Molecular dynamics simulation was conducted for better understanding the stability feature of BzGDH against the structural context. The in-silico simulation shows that BzGDH is stable and can maintain its overall structure against heat during the simulation at 323 K, which is consistent with the biochemical studies. In brief, the robust stability of BzGDH made it an attractive participant for cofactor regeneration on practical applications, especially for the catalysis implemented in acidic pH and high temperature.
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Affiliation(s)
- Haitao Ding
- Key Laboratory for Polar Science of State Oceanic Administration, Polar Research Institute of China, Shanghai 200136, China.
| | - Fen Gao
- East China Sea Fisheries Research Institute, Shanghai 200090, China.
| | - Yong Yu
- Key Laboratory for Polar Science of State Oceanic Administration, Polar Research Institute of China, Shanghai 200136, China.
| | - Bo Chen
- Key Laboratory for Polar Science of State Oceanic Administration, Polar Research Institute of China, Shanghai 200136, China.
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22
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Li J, Zhang R, Xu Y, Xiao R, Li K, Liu H, Jiang J, Zhou X, Li L, Zhou L, Gu Y. Ala258Phe substitution in Bacillus sp. YX-1 glucose dehydrogenase improves its substrate preference for xylose. Process Biochem 2017. [DOI: 10.1016/j.procbio.2017.03.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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23
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Haas J, Häckh M, Justus V, Müller M, Lüdeke S. Addition of a polyhistidine tag alters the regioselectivity of carbonyl reductase S1 from Candida magnoliae. Org Biomol Chem 2017; 15:10256-10264. [DOI: 10.1039/c7ob02666h] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A recombinant carbonyl reductase shows different regioselectivity with a C-terminal His-tag compared to the N-tagged enzyme toward the same triketide substrate. Highly selective synthesis of reference triketides allowed solving this conundrum.
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Affiliation(s)
- Julian Haas
- Institute of Pharmaceutical Sciences
- University of Freiburg
- 79104 Freiburg
- Germany
| | - Matthias Häckh
- Institute of Pharmaceutical Sciences
- University of Freiburg
- 79104 Freiburg
- Germany
| | - Viktor Justus
- Institute of Pharmaceutical Sciences
- University of Freiburg
- 79104 Freiburg
- Germany
| | - Michael Müller
- Institute of Pharmaceutical Sciences
- University of Freiburg
- 79104 Freiburg
- Germany
| | - Steffen Lüdeke
- Institute of Pharmaceutical Sciences
- University of Freiburg
- 79104 Freiburg
- Germany
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24
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Nitrated carbon nanoblisters for high-performance glucose dehydrogenase bioanodes. Biosens Bioelectron 2016; 77:860-5. [DOI: 10.1016/j.bios.2015.08.069] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Revised: 08/27/2015] [Accepted: 08/30/2015] [Indexed: 11/19/2022]
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25
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Pongtharangkul T, Chuekitkumchorn P, Suwanampa N, Payongsri P, Honda K, Panbangred W. Kinetic properties and stability of glucose dehydrogenase from Bacillus amyloliquefaciens SB5 and its potential for cofactor regeneration. AMB Express 2015; 5:68. [PMID: 26538191 PMCID: PMC4633474 DOI: 10.1186/s13568-015-0157-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2015] [Accepted: 10/27/2015] [Indexed: 11/10/2022] Open
Abstract
Glucose dehydrogenases (GluDH) from Bacillus species offer several advantages over other NAD(P)H regeneration systems including high stability, inexpensive substrate, thermodynamically favorable reaction and flexibility to regenerate both NADH and NADPH. In this research, characteristics of GluDH from Bacillus amyloliquefaciens SB5 (GluDH-BA) was reported for the first time. Despite a highly similar amino acid sequence when comparing with GluDH from Bacillus subtilis (GluDH-BS), GluDH-BA exhibited significantly higher specific activity (4.7-fold) and stability when pH was higher than 6. While an optimum activity of GluDH-BA was observed at a temperature of 50 °C, the enzyme was stable only up to 42 °C. GluDH-BA exhibited an extreme tolerance towards n-hexane and its respective alcohols. The productivity of GluDH obtained in this study (8.42 mg-GluDH/g-wet cells; 1035 U/g-wet cells) was among the highest productivity reported for recombinant E. coli. With its low KM-value towards glucose (5.5 mM) and NADP+ (0.05 mM), GluDH-BA was highly suitable for in vivo applications. In this work, a recombinant solvent-tolerant B. subtilis BA overexpressing GluDH-BA was developed and evaluated by coupling with B. subtilis overexpressing an enzyme P450 BM3 F87V for a whole-cell hydroxylation of n-hexane. Significantly higher products obtained clearly proved that B. subtilis BA was an effective cofactor regenerator, a valuable asset for bioproduction of value-added chemicals.
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Balabanova L, Golotin V, Podvolotskaya A, Rasskazov V. Genetically modified proteins: functional improvement and chimeragenesis. Bioengineered 2015. [PMID: 26211369 DOI: 10.1080/21655979.2015.1075674] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Abstract
This review focuses on the emerging role of site-specific mutagenesis and chimeragenesis for the functional improvement of proteins in areas where traditional protein engineering methods have been extensively used and practically exhausted. The novel path for the creation of the novel proteins has been created on the farther development of the new structure and sequence optimization algorithms for generating and designing the accurate structure models in result of x-ray crystallography studies of a lot of proteins and their mutant forms. Artificial genetic modifications aim to expand nature's repertoire of biomolecules. One of the most exciting potential results of mutagenesis or chimeragenesis finding could be design of effective diagnostics, bio-therapeutics and biocatalysts. A sampling of recent examples is listed below for the in vivo and in vitro genetically improvement of various binding protein and enzyme functions, with references for more in-depth study provided for the reader's benefit.
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Affiliation(s)
- Larissa Balabanova
- a G.B. Elyakov Pacific Institute of Bioorganic Chemistry; Far Eastern Branch; Russian Academy of Science ; Vladivostok , Russia.,b Far Eastern Federal University ; Vladivostok , Russia
| | - Vasily Golotin
- a G.B. Elyakov Pacific Institute of Bioorganic Chemistry; Far Eastern Branch; Russian Academy of Science ; Vladivostok , Russia.,b Far Eastern Federal University ; Vladivostok , Russia
| | | | - Valery Rasskazov
- a G.B. Elyakov Pacific Institute of Bioorganic Chemistry; Far Eastern Branch; Russian Academy of Science ; Vladivostok , Russia
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An S188V mutation alters substrate specificity of non-stereospecific α-haloalkanoic acid dehalogenase E (DehE). PLoS One 2015; 10:e0121687. [PMID: 25816329 PMCID: PMC4376737 DOI: 10.1371/journal.pone.0121687] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2014] [Accepted: 02/03/2015] [Indexed: 11/19/2022] Open
Abstract
The non-stereospecific α-haloalkanoic acid dehalogenase E (DehE) degrades many halogenated compounds but is ineffective against β-halogenated compounds such as 3-chloropropionic acid (3CP). Using molecular dynamics (MD) simulations and site-directed mutagenesis we show here that introducing the mutation S188V into DehE improves substrate specificity towards 3CP. MD simulations showed that residues W34, F37, and S188 of DehE were crucial for substrate binding. DehE showed strong binding ability for D-2-chloropropionic acid (D-2CP) and L-2-chloropropionic acid (L-2CP) but less affinity for 3CP. This reduced affinity was attributed to weak hydrogen bonding between 3CP and residue S188, as the carboxylate of 3CP forms rapidly interconverting hydrogen bonds with the backbone amide and side chain hydroxyl group of S188. By replacing S188 with a valine residue, we reduced the inter-molecular distance and stabilised bonding of the carboxylate of 3CP to hydrogens of the substrate-binding residues. Therefore, the S188V can act on 3CP, although its affinity is less strong than for D-2CP and L-2CP as assessed by Km. This successful alteration of DehE substrate specificity may promote the application of protein engineering strategies to other dehalogenases, thereby generating valuable tools for future bioremediation technologies.
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BdcA, a protein important for Escherichia coli biofilm dispersal, is a short-chain dehydrogenase/reductase that binds specifically to NADPH. PLoS One 2014; 9:e105751. [PMID: 25244619 PMCID: PMC4171110 DOI: 10.1371/journal.pone.0105751] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2014] [Accepted: 07/25/2014] [Indexed: 02/07/2023] Open
Abstract
The Escherichia coli protein BdcA (previously referred to as YjgI) plays a key role in the dispersal of cells from bacterial biofilms, and its constitutive activation provides an attractive therapeutic target for dismantling these communities. In order to investigate the function of BdcA at a molecular level, we integrated structural and functional studies. Our 2.05 Å structure of BdcA shows that it is a member of the NAD(P)(H)-dependent short-chain dehydrogenase/reductase (SDR) superfamily. Structural comparisons with other members of the SDR family suggested that BdcA binds NADP(H). This was demonstrated experimentally using thermal denaturation studies, which showed that BcdA binds specifically to NADPH. Subsequent ITC experiments further confirmed this result and reported a Kd of 25.9 µM. Thus, BdcA represents the newest member of the limited number of oxidoreductases shown to be involved in quorum sensing and biofilm dispersal.
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Ding H, Gao F, Liu D, Li Z, Xu X, Wu M, Zhao Y. Significant improvement of thermal stability of glucose 1-dehydrogenase by introducing disulfide bonds at the tetramer interface. Enzyme Microb Technol 2013; 53:365-72. [DOI: 10.1016/j.enzmictec.2013.08.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2013] [Revised: 07/30/2013] [Accepted: 08/06/2013] [Indexed: 10/26/2022]
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30
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Liang B, Lang Q, Tang X, Liu A. Simultaneously improving stability and specificity of cell surface displayed glucose dehydrogenase mutants to construct whole-cell biocatalyst for glucose biosensor application. BIORESOURCE TECHNOLOGY 2013; 147:492-498. [PMID: 24012845 DOI: 10.1016/j.biortech.2013.08.088] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2013] [Revised: 08/13/2013] [Accepted: 08/14/2013] [Indexed: 06/02/2023]
Abstract
The improved stability and substrate specificity of cell surface displayed glucose dehydrogenase (GDH) mutants by replacing four amino acids from Bacillus subtilis by using site-directed mutagenesis was systematically investigated. A series of mutated GDHs including E170R/Q252L, V149K/E170R/Q252L, E170R/Q252L/G259A and V149K/E170R/Q252L/G259A, were fused to the ice nucleation protein for displaying on cell surface of Eschericia coli. Q252L/E170R/V149K, Q252L/E170R/G259A and Q252L/E170R/V149K/G259A variants were found stable at a wide pH range and shown excellent thermostability. Especially, the Q252L/E170R/V149K/G259A mutant showed half-life of ~3.8days at 70 °C. Q252L/E170R/V149K/G259A variant exhibited the narrowest substrate specificity for d-glucose. The whole cell displayed GDH mutant could be cultured in a large scale with excellent enzyme activity and productivity. In addition, a sensitive and stable electrochemical glucose biosensor can be prepared using the GDH-mutant bacteria modified electrode. Thus, the whole cell biocatalysts are promising candidates for exploitation in a wide range of industrial applications.
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Affiliation(s)
- Bo Liang
- Laboratory for Biosensing, Qingdao Institute of Bioenergy & Bioprocess Technology, and Key Laboratory of Bioenergy, Chinese Academy of Sciences, 189 Songling Road, Qingdao 266101, China
| | - Qiaolin Lang
- Laboratory for Biosensing, Qingdao Institute of Bioenergy & Bioprocess Technology, and Key Laboratory of Bioenergy, Chinese Academy of Sciences, 189 Songling Road, Qingdao 266101, China
| | - Xiangjiang Tang
- Laboratory for Biosensing, Qingdao Institute of Bioenergy & Bioprocess Technology, and Key Laboratory of Bioenergy, Chinese Academy of Sciences, 189 Songling Road, Qingdao 266101, China
| | - Aihua Liu
- Laboratory for Biosensing, Qingdao Institute of Bioenergy & Bioprocess Technology, and Key Laboratory of Bioenergy, Chinese Academy of Sciences, 189 Songling Road, Qingdao 266101, China.
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31
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Yasutake Y, Nishioka T, Imoto N, Tamura T. A Single Mutation at the Ferredoxin Binding Site of P450 Vdh Enables Efficient Biocatalytic Production of 25-Hydroxyvitamin D3. Chembiochem 2013; 14:2284-91. [DOI: 10.1002/cbic.201300386] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2013] [Indexed: 01/08/2023]
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Singh RK, Tiwari MK, Singh R, Lee JK. From protein engineering to immobilization: promising strategies for the upgrade of industrial enzymes. Int J Mol Sci 2013; 14:1232-77. [PMID: 23306150 PMCID: PMC3565319 DOI: 10.3390/ijms14011232] [Citation(s) in RCA: 268] [Impact Index Per Article: 24.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2012] [Revised: 11/14/2012] [Accepted: 12/24/2012] [Indexed: 11/16/2022] Open
Abstract
Enzymes found in nature have been exploited in industry due to their inherent catalytic properties in complex chemical processes under mild experimental and environmental conditions. The desired industrial goal is often difficult to achieve using the native form of the enzyme. Recent developments in protein engineering have revolutionized the development of commercially available enzymes into better industrial catalysts. Protein engineering aims at modifying the sequence of a protein, and hence its structure, to create enzymes with improved functional properties such as stability, specific activity, inhibition by reaction products, and selectivity towards non-natural substrates. Soluble enzymes are often immobilized onto solid insoluble supports to be reused in continuous processes and to facilitate the economical recovery of the enzyme after the reaction without any significant loss to its biochemical properties. Immobilization confers considerable stability towards temperature variations and organic solvents. Multipoint and multisubunit covalent attachments of enzymes on appropriately functionalized supports via linkers provide rigidity to the immobilized enzyme structure, ultimately resulting in improved enzyme stability. Protein engineering and immobilization techniques are sequential and compatible approaches for the improvement of enzyme properties. The present review highlights and summarizes various studies that have aimed to improve the biochemical properties of industrially significant enzymes.
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Affiliation(s)
- Raushan Kumar Singh
- Department of Chemical Engineering, Konkuk University, 1 Hwayang-Dong, Gwangjin-Gu, Seoul 143-701, Korea.
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