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Ma W, Geng Q, Chen C, Zheng YC, Yu HL, Xu JH. Engineering a Formate Dehydrogenase for NADPH Regeneration. Chembiochem 2023; 24:e202300390. [PMID: 37455264 DOI: 10.1002/cbic.202300390] [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: 05/24/2023] [Revised: 07/09/2023] [Accepted: 07/11/2023] [Indexed: 07/18/2023]
Abstract
Nicotinamide adenine dinucleotide (NADH) and nicotinamide adenine dinucleotide phosphate (NADPH) constitute major hydrogen donors for oxidative/reductive bio-transformations. NAD(P)H regeneration systems coupled with formate dehydrogenases (FDHs) represent a dreamful method. However, most of the native FDHs are NAD+ -dependent and suffer from insufficient reactivity compared to other enzymatic tools, such as glucose dehydrogenase. An efficient and competitive NADP+ -utilizing FDH necessitates the availability and robustness of NADPH regeneration systems. Herein, we report the engineering of a new FDH from Candida dubliniensis (CdFDH), which showed no strict NAD+ preference by a structure-guided rational/semi-rational design. A combinatorial mutant CdFDH-M4 (D197Q/Y198R/Q199N/A372S/K371T/▵Q375/K167R/H16L/K159R) exhibited 75-fold intensification of catalytic efficiency (kcat /Km ). Moreover, CdFDH-M4 has been successfully employed in diverse asymmetric oxidative/reductive processes with cofactor total turnover numbers (TTNs) ranging from 135 to 986, making it potentially useful for NADPH-required biocatalytic transformations.
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Affiliation(s)
- Wei Ma
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Centre for Biomanufacturing, East China University of Science and Technology, Meilong Road 130, Shanghai, 200237, China
| | - Qiang Geng
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Centre for Biomanufacturing, East China University of Science and Technology, Meilong Road 130, Shanghai, 200237, China
| | - Cheng Chen
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Centre for Biomanufacturing, East China University of Science and Technology, Meilong Road 130, Shanghai, 200237, China
| | - Yu-Cong Zheng
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Centre for Biomanufacturing, East China University of Science and Technology, Meilong Road 130, Shanghai, 200237, China
| | - Hui-Lei Yu
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Centre for Biomanufacturing, East China University of Science and Technology, Meilong Road 130, Shanghai, 200237, China
| | - Jian-He Xu
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Centre for Biomanufacturing, East China University of Science and Technology, Meilong Road 130, Shanghai, 200237, China
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Acevedo‐Rocha CG, Sun Z, Reetz MT. Clarifying the Difference between Iterative Saturation Mutagenesis as a Rational Guide in Directed Evolution and OmniChange as a Gene Mutagenesis Technique. Chembiochem 2018; 19:2542-2544. [PMID: 30408315 DOI: 10.1002/cbic.201800372] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Indexed: 11/10/2022]
Affiliation(s)
| | - Zhoutong Sun
- Tianjin Institute of Industrial BiotechnologyChinese Academy of Sciences 32 West 7th Avenue, Tianjin Airport Economic Area Tianjin 300308 China
| | - Manfred T. Reetz
- Department of ChemistryPhilipps University 35032 Marburg Germany
- Max-Planck-Institut für Kohlenforschung Kaiser-Wilhelm-Platz 1 45470 Mülheim Germany
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Sutiono S, Carsten J, Sieber V. Structure-Guided Engineering of α-Keto Acid Decarboxylase for the Production of Higher Alcohols at Elevated Temperature. CHEMSUSCHEM 2018; 11:3335-3344. [PMID: 29953730 DOI: 10.1002/cssc.201800944] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 06/15/2018] [Indexed: 06/08/2023]
Abstract
Branched-chain keto acid decarboxylases (KDCs) are a class of enzymes that catalyze the decarboxylation of α-keto acids. They are key enzymes for production of higher alcohols in vivo and in vitro. However, the two most active KDCs (KivD and KdcA) have only moderate thermostability (<55 °C), which hinders the production of alcohols at high temperatures. Herein, structure-guided engineering toward improved thermostability of KdcA is outlined. Strategies such as stabilization of the catalytic center, surface engineering, and optimization of dimer interactions were applied. With seven amino acid substitutions, variant 7M.D showed an increase of the temperature at which 50 % of activity remains after one-hour incubation T1h50 by 14.8 °C without compromising its substrate specificity. 7M.D exhibited greater than 400-fold improvement of half-life at 70 °C and greater than 600-fold increase in process stability in the presence of 4 % isobutanol at 50 °C. 7M.D is more promising for the production of higher alcohols in thermophiles (>65 °C) and in cell-free applications.
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Affiliation(s)
- Samuel Sutiono
- Chair of Chemistry of Biogenic Resources, TUM Campus Straubing for Biotechnology and Sustainability, Technical University of Munich, Schulgasse 16, 94315, Straubing, Germany
| | - Jörg Carsten
- Catalytic Research Center, Technical University of Munich, Ernst-Otto-Fischer-Straße 1, 85748, Garching, Germany
| | - Volker Sieber
- Chair of Chemistry of Biogenic Resources, TUM Campus Straubing for Biotechnology and Sustainability, Technical University of Munich, Schulgasse 16, 94315, Straubing, Germany
- Catalytic Research Center, Technical University of Munich, Ernst-Otto-Fischer-Straße 1, 85748, Garching, Germany
- Straubing Branch BioCat, Fraunhofer IGB, Schulgasse 11a, 94315, Straubing, Germany
- School of Chemistry and Molecular Biosciences, The University of Queensland, 68 Copper Road, St., Lucia, 4072, Australia
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d-lyxose isomerase and its application for functional sugar production. Appl Microbiol Biotechnol 2018; 102:2051-2062. [DOI: 10.1007/s00253-018-8746-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Revised: 12/26/2017] [Accepted: 12/27/2017] [Indexed: 12/31/2022]
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Sun Z, Lonsdale R, Kong XD, Xu JH, Zhou J, Reetz MT. Reshaping an Enzyme Binding Pocket for Enhanced and Inverted Stereoselectivity: Use of Smallest Amino Acid Alphabets in Directed Evolution. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201501809] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Sun Z, Lonsdale R, Kong XD, Xu JH, Zhou J, Reetz MT. Reshaping an Enzyme Binding Pocket for Enhanced and Inverted Stereoselectivity: Use of Smallest Amino Acid Alphabets in Directed Evolution. Angew Chem Int Ed Engl 2015; 54:12410-5. [DOI: 10.1002/anie.201501809] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Indexed: 01/06/2023]
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Wagner N, Bosshart A, Failmezger J, Bechtold M, Panke S. A Separation-Integrated Cascade Reaction to Overcome Thermodynamic Limitations in Rare-Sugar Synthesis. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201411279] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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Wagner N, Bosshart A, Failmezger J, Bechtold M, Panke S. A Separation-Integrated Cascade Reaction to Overcome Thermodynamic Limitations in Rare-Sugar Synthesis. Angew Chem Int Ed Engl 2015; 54:4182-6. [DOI: 10.1002/anie.201411279] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Indexed: 12/31/2022]
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Bosshart A, Hee CS, Bechtold M, Schirmer T, Panke S. Directed Divergent Evolution of a ThermostableD-Tagatose Epimerase towards Improved Activity for Two Hexose Substrates. Chembiochem 2015; 16:592-601. [DOI: 10.1002/cbic.201402620] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2014] [Indexed: 12/31/2022]
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