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Watanabe S, Ito M, Kigawa T. DiRect: Site-directed mutagenesis method for protein engineering by rational design. Biochem Biophys Res Commun 2021; 551:107-113. [PMID: 33725571 DOI: 10.1016/j.bbrc.2021.03.021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 03/04/2021] [Indexed: 12/13/2022]
Abstract
Site-directed mutagenesis (SDM), an indispensable method in molecular biology and protein engineering, is rather time-consuming and laborious. Protein engineering, especially that of enzymes, nowadays increasingly relies on rational design approaches in which both SDM and protein expression are the bottlenecks because they are generally based on the recombinant DNA technology. Here, we developed a new PCR-based mutagenesis method, DiRect, that achieves high performance in product quality (≥99% substitution) without recombinant DNA technology. We applied DiRect in combination with a cell-free protein expression system to an industrially relevant enzyme, nicotinamide adenine dinucleotide phosphate-dependent 3-quinuclidinone reductase from Rhodotorula rubra. In a single round of screening, 90 newly designed mutant proteins were produced within two days, and an unreported mutant (Q135I) exhibiting much higher thermostability than the wild-type enzyme was successfully identified within one extra day. Thus, DiRect is a simple, efficient, and potentially scalable SDM method.
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Affiliation(s)
- Satoru Watanabe
- Laboratory for Cellular Structural Biology, RIKEN Center for Biosystems Dynamics Research (BDR), 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan; Laboratory for Biomolecular Structure and Dynamics, RIKEN Quantitative Biology Center (QBiC), 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan
| | - Masahiro Ito
- Laboratory for Cellular Structural Biology, RIKEN Center for Biosystems Dynamics Research (BDR), 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan; Laboratory for Biomolecular Structure and Dynamics, RIKEN Quantitative Biology Center (QBiC), 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan
| | - Takanori Kigawa
- Laboratory for Cellular Structural Biology, RIKEN Center for Biosystems Dynamics Research (BDR), 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan; Laboratory for Biomolecular Structure and Dynamics, RIKEN Quantitative Biology Center (QBiC), 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan.
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Doden HL, Pollet RM, Mythen SM, Wawrzak Z, Devendran S, Cann I, Koropatkin NM, Ridlon JM. Structural and biochemical characterization of 20β-hydroxysteroid dehydrogenase from Bifidobacterium adolescentis strain L2-32. J Biol Chem 2019; 294:12040-12053. [PMID: 31209107 DOI: 10.1074/jbc.ra119.009390] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 06/11/2019] [Indexed: 01/20/2023] Open
Abstract
Anaerobic bacteria inhabiting the human gastrointestinal tract have evolved various enzymes that modify host-derived steroids. The bacterial steroid-17,20-desmolase pathway cleaves the cortisol side chain, forming pro-androgens predicted to impact host physiology. Bacterial 20β-hydroxysteroid dehydrogenase (20β-HSDH) regulates cortisol side-chain cleavage by reducing the C-20 carboxyl group on cortisol, yielding 20β-dihydrocortisol. Recently, the gene encoding 20β-HSDH in Butyricicoccus desmolans ATCC 43058 was reported, and a nonredundant protein search yielded a candidate 20β-HSDH gene in Bifidobacterium adolescentis strain L2-32. B. adolescentis 20β-HSDH could regulate cortisol side-chain cleavage by limiting pro-androgen formation in bacteria such as Clostridium scindens and 21-dehydroxylation by Eggerthella lenta Here, the putative B. adolescentis 20β-HSDH was cloned, overexpressed, and purified. 20β-HSDH activity was confirmed through whole-cell and pure enzymatic assays, and it is specific for cortisol. Next, we solved the structures of recombinant 20β-HSDH in both the apo- and holo-forms at 2.0-2.2 Å resolutions, revealing close overlap except for rearrangements near the active site. Interestingly, the structures contain a large, flexible N-terminal region that was investigated by gel-filtration chromatography and CD spectroscopy. This extended N terminus is important for protein stability because deletions of varying lengths caused structural changes and reduced enzymatic activity. A nonconserved extended N terminus was also observed in several short-chain dehydrogenase/reductase family members. B. adolescentis strains capable of 20β-HSDH activity could alter glucocorticoid metabolism in the gut and thereby serve as potential probiotics for the management of androgen-dependent diseases.
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Affiliation(s)
- Heidi L Doden
- Microbiome Metabolic Engineering Theme, Carl R. Woese Institute for Genomic Biology, Urbana, Illinois 61801; Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
| | - Rebecca M Pollet
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan 48109
| | - Sean M Mythen
- Microbiome Metabolic Engineering Theme, Carl R. Woese Institute for Genomic Biology, Urbana, Illinois 61801; Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
| | - Zdzislaw Wawrzak
- Northwestern Synchrotron Research Center-LS-CAT, Northwestern University, Argonne, Illinois 60439
| | - Saravanan Devendran
- Microbiome Metabolic Engineering Theme, Carl R. Woese Institute for Genomic Biology, Urbana, Illinois 61801; Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
| | - Isaac Cann
- Microbiome Metabolic Engineering Theme, Carl R. Woese Institute for Genomic Biology, Urbana, Illinois 61801; Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801; Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
| | - Nicole M Koropatkin
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan 48109
| | - Jason M Ridlon
- Microbiome Metabolic Engineering Theme, Carl R. Woese Institute for Genomic Biology, Urbana, Illinois 61801; Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801; Cancer Center of Illinois, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801; Division of Nutritional Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801.
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Jia Z, Ma H, Huang Y, Huang Y, Ren P, Song S, Hu M, Tao Y. Production of (R)-3-quinuclidinol by a whole-cell biocatalyst with high efficiency. BIOCATAL BIOTRANSFOR 2017. [DOI: 10.1080/10242422.2017.1400019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Zhenhua Jia
- Biology Institute, Hebei Academy of sciences, Shijiazhuang, P. R. China
| | - Hong Ma
- Biology Institute, Hebei Academy of sciences, Shijiazhuang, P. R. China
| | - Yali Huang
- Biology Institute, Hebei Academy of sciences, Shijiazhuang, P. R. China
| | - Yuanyuan Huang
- Biology Institute, Hebei Academy of sciences, Shijiazhuang, P. R. China
| | - Pengju Ren
- Biology Institute, Hebei Academy of sciences, Shijiazhuang, P. R. China
| | - Shuishan Song
- Biology Institute, Hebei Academy of sciences, Shijiazhuang, P. R. China
| | - Meirong Hu
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing, P.R. China
| | - Yong Tao
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing, P.R. China
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Liu ZQ, Wu L, Zhang XJ, Xue YP, Zheng YG. Directed Evolution of Carbonyl Reductase from Rhodosporidium toruloides and Its Application in Stereoselective Synthesis of tert-Butyl (3R,5S)-6-Chloro-3,5-dihydroxyhexanoate. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2017; 65:3721-3729. [PMID: 28425285 DOI: 10.1021/acs.jafc.7b00866] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
tert-Butyl (3R,5S)-6-chloro-3,5-dihydroxyhexanoate ((3R,5S)-CDHH) is a key intermediate of atorvastatin and rosuvastatin synthesis. Carbonyl reductase RtSCR9 from Rhodosporidium toruloides exhibited excellent activity toward tert-butyl (S)-6-chloro-5-hydroxy-3-oxohexanoate ((S)-CHOH). For the activity of RtSCR9 to be improved, random mutagenesis and site-saturation mutagenesis were performed. Three positive mutants were obtained (mut-Gln95Asp, mut-Ile144Lys, and mut-Phe156Gln). These mutants exhibited 1.94-, 3.03-, and 1.61-fold and 1.93-, 3.15-, and 1.97-fold improvement in the specific activity and kcat/Km, respectively. Asymmetric reduction of (S)-CHOH by mut-Ile144Lys coupled with glucose dehydrogenase was conducted. The yield and enantiomeric excess of (3R,5S)-CDHH reached 98 and 99%, respectively, after 8 h bioconversion in a single batch reaction with 1 M (S)-CHOH, and the space-time yield reached 542.83 mmol L-1 h-1 g-1 wet cell weight. This study presents a new carbonyl reductase for efficient synthesis of (3R,5S)-CDHH.
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Affiliation(s)
- Zhi-Qiang Liu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering and ‡Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology , Hangzhou 310014, China
| | - Lin Wu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering and ‡Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology , Hangzhou 310014, China
| | - Xiao-Jian Zhang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering and ‡Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology , Hangzhou 310014, China
| | - Ya-Ping Xue
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering and ‡Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology , Hangzhou 310014, China
| | - Yu-Guo Zheng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering and ‡Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology , Hangzhou 310014, China
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Kataoka M, Miyakawa T, Shimizu S, Tanokura M. Enzymes useful for chiral compound synthesis: structural biology, directed evolution, and protein engineering for industrial use. Appl Microbiol Biotechnol 2016; 100:5747-57. [DOI: 10.1007/s00253-016-7603-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Revised: 04/30/2016] [Accepted: 05/02/2016] [Indexed: 10/21/2022]
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Tanokura M, Miyakawa T, Guan L, Hou F. Structural analysis of enzymes used for bioindustry and bioremediation. Biosci Biotechnol Biochem 2015; 79:1391-401. [DOI: 10.1080/09168451.2015.1052770] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Abstract
Microbial enzymes have been widely applied in the large-scale, bioindustrial manufacture of food products and pharmaceuticals due to their high substrate specificity and stereoselectivity, and their effectiveness under mild conditions with low environmental burden. At the same time, bioremedial techniques using microbial enzymes have been developed to solve the problem of industrial waste, particularly with respect to persistent chemicals and toxic substances. And finally, structural studies of these enzymes have revealed the mechanistic basis of enzymatic reactions, including the stereoselectivity and binding specificity of substrates and cofactors. The obtained structural insights are useful not only to deepen our understanding of enzymes with potential bioindustrial and/or bioremedial application, but also for the functional improvement of enzymes through rational protein engineering. This review shows the structural bases for various types of enzymatic reactions, including the substrate specificity accompanying cofactor-controlled and kinetic mechanisms.
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Affiliation(s)
- Masaru Tanokura
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Takuya Miyakawa
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Lijun Guan
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Feng Hou
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
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Hou F, Miyakawa T, Kataoka M, Takeshita D, Kumashiro S, Uzura A, Urano N, Nagata K, Shimizu S, Tanokura M. Structural basis for high substrate-binding affinity and enantioselectivity of 3-quinuclidinone reductase AtQR. Biochem Biophys Res Commun 2014; 446:911-5. [PMID: 24642255 DOI: 10.1016/j.bbrc.2014.03.030] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2014] [Accepted: 03/09/2014] [Indexed: 11/28/2022]
Abstract
(R)-3-Quinuclidinol, a useful compound for the synthesis of various pharmaceuticals, can be enantioselectively produced from 3-quinuclidinone by 3-quinuclidinone reductase. Recently, a novel NADH-dependent 3-quinuclidionone reductase (AtQR) was isolated from Agrobacterium tumefaciens, and showed much higher substrate-binding affinity (>100 fold) than the reported 3-quinuclidionone reductase (RrQR) from Rhodotorula rubra. Here, we report the crystal structure of AtQR at 1.72 Å. Three NADH-bound protomers and one NADH-free protomer form a tetrameric structure in an asymmetric unit of crystals. NADH not only acts as a proton donor, but also contributes to the stability of the α7 helix. This helix is a unique and functionally significant part of AtQR and is related to form a deep catalytic cavity. AtQR has all three catalytic residues of the short-chain dehydrogenases/reductases family and the hydrophobic wall for the enantioselective reduction of 3-quinuclidinone as well as RrQR. An additional residue on the α7 helix, Glu197, exists near the active site of AtQR. This acidic residue is considered to form a direct interaction with the amine part of 3-quinuclidinone, which contributes to substrate orientation and enhancement of substrate-binding affinity. Mutational analyses also support that Glu197 is an indispensable residue for the activity.
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Affiliation(s)
- Feng Hou
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Takuya Miyakawa
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Michihiko Kataoka
- Division of Applied Life Sciences, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai 559-8531, Japan; Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Daijiro Takeshita
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Shoko Kumashiro
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Atsuko Uzura
- Research & Development Center, Nagase & Co., Ltd., 2-2-3 Muratani, Nishi-ku, Kobe 651-2241, Japan
| | - Nobuyuki Urano
- Division of Applied Life Sciences, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai 559-8531, Japan; Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Koji Nagata
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Sakayu Shimizu
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan; Faculty of Bioenvironmental Science, Kyoto Gakuen University, Sogabe-cho, Kameoka 621-8555, Japan
| | - Masaru Tanokura
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan.
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