1
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Zhang L, Sun Z, Xu G, Ni Y. Classification and functional origins of stereocomplementary alcohol dehydrogenases for asymmetric synthesis of chiral secondary alcohols: A review. Int J Biol Macromol 2024; 270:132238. [PMID: 38729463 DOI: 10.1016/j.ijbiomac.2024.132238] [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: 01/28/2024] [Revised: 04/17/2024] [Accepted: 05/07/2024] [Indexed: 05/12/2024]
Abstract
Alcohol dehydrogenases (ADHs) mediated biocatalytic asymmetric reduction of ketones have been widely applied in the synthesis of optically active secondary alcohols with highly reactive hydroxyl groups ligated to the stereogenic carbon and divided into (R)- and (S)-configurations. Stereocomplementary ADHs could be applied in the synthesis of both enantiomers and are increasingly accepted as the "first of choice" in green chemistry due to the high atomic economy, low environmental factor, 100 % theoretical yield, and high environmentally friendliness. Due to the equal importance of complementary alcohols, development of stereocomplementary ADHs draws increasing attention. This review is committed to summarize recent advance in discovery of naturally evolved and tailor-made stereocomplementary ADHs, unveil the molecular mechanism of stereoselective catalysis in views of classification and functional basis, and provide guidance for further engineering the stereoselectivity of ADHs for the industrial biosynthesis of chiral secondary alcohol of industrial relevance.
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Affiliation(s)
- Lu Zhang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, China
| | - Zewen Sun
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, China
| | - Guochao Xu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, China.
| | - Ye Ni
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, China.
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2
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Honda Malca S, Duss N, Meierhofer J, Patsch D, Niklaus M, Reiter S, Hanlon SP, Wetzl D, Kuhn B, Iding H, Buller R. Effective engineering of a ketoreductase for the biocatalytic synthesis of an ipatasertib precursor. Commun Chem 2024; 7:46. [PMID: 38418529 PMCID: PMC10902378 DOI: 10.1038/s42004-024-01130-5] [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: 08/25/2023] [Accepted: 02/15/2024] [Indexed: 03/01/2024] Open
Abstract
Semi-rational enzyme engineering is a powerful method to develop industrial biocatalysts. Profiting from advances in molecular biology and bioinformatics, semi-rational approaches can effectively accelerate enzyme engineering campaigns. Here, we present the optimization of a ketoreductase from Sporidiobolus salmonicolor for the chemo-enzymatic synthesis of ipatasertib, a potent protein kinase B inhibitor. Harnessing the power of mutational scanning and structure-guided rational design, we created a 10-amino acid substituted variant exhibiting a 64-fold higher apparent kcat and improved robustness under process conditions compared to the wild-type enzyme. In addition, the benefit of algorithm-aided enzyme engineering was studied to derive correlations in protein sequence-function data, and it was found that the applied Gaussian processes allowed us to reduce enzyme library size. The final scalable and high performing biocatalytic process yielded the alcohol intermediate with ≥ 98% conversion and a diastereomeric excess of 99.7% (R,R-trans) from 100 g L-1 ketone after 30 h. Modelling and kinetic studies shed light on the mechanistic factors governing the improved reaction outcome, with mutations T134V, A238K, M242W and Q245S exerting the most beneficial effect on reduction activity towards the target ketone.
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Affiliation(s)
- Sumire Honda Malca
- Institute of Chemistry and Biotechnology, Zurich University of Applied Sciences, Einsiedlerstrasse 31, 8820 Wädenswil, Switzerland
| | - Nadine Duss
- Institute of Chemistry and Biotechnology, Zurich University of Applied Sciences, Einsiedlerstrasse 31, 8820 Wädenswil, Switzerland
| | - Jasmin Meierhofer
- Institute of Chemistry and Biotechnology, Zurich University of Applied Sciences, Einsiedlerstrasse 31, 8820 Wädenswil, Switzerland
- Analytical Research and Development, MSD Werthenstein BioPharma GmbH, Industrie Nord 1, 6105 Schachen, Switzerland
| | - David Patsch
- Institute of Chemistry and Biotechnology, Zurich University of Applied Sciences, Einsiedlerstrasse 31, 8820 Wädenswil, Switzerland
| | - Michael Niklaus
- Institute of Chemistry and Biotechnology, Zurich University of Applied Sciences, Einsiedlerstrasse 31, 8820 Wädenswil, Switzerland
| | - Stefanie Reiter
- Institute of Chemistry and Biotechnology, Zurich University of Applied Sciences, Einsiedlerstrasse 31, 8820 Wädenswil, Switzerland
- Manufacturing Science and Technology, Fisher Clinical Services GmbH, Biotech Innovation Park, 2543 Lengnau, Switzerland
| | - Steven Paul Hanlon
- Process Chemistry and Catalysis, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Dennis Wetzl
- Process Chemistry and Catalysis, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, 4070 Basel, Switzerland
- Nonclinical Drug Development, Boehringer Ingelheim International GmbH, Birkendorfer Strasse 65, 88397 Biberach an der Riss, Germany
| | - Bernd Kuhn
- Pharmaceutical Research and Early Development, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Hans Iding
- Process Chemistry and Catalysis, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Rebecca Buller
- Institute of Chemistry and Biotechnology, Zurich University of Applied Sciences, Einsiedlerstrasse 31, 8820 Wädenswil, Switzerland.
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3
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Yue X, Li Y, Yang L, Sang D, Huang Z, Chen F. Sustainable asymmetric synthesis of diltiazem precursor enabled by recombinant Escherichia coli whole cells co-expressing an engineered ketoreductase and glucose dehydrogenase. Biotechnol J 2024; 19:e2300250. [PMID: 38048389 DOI: 10.1002/biot.202300250] [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] [Received: 05/29/2023] [Revised: 11/20/2023] [Accepted: 11/29/2023] [Indexed: 12/06/2023]
Abstract
As a key synthetic intermediate of the cardiovascular drug diltiazem, methyl (2R,3S)-3-(4-methoxyphenyl) glycidate ((2R,3S)-MPGM) (1) is accessible via the ring closure of chlorohydrin (3S)-methyl 2-chloro-3-hydroxy-3-(4-methoxyphenyl)propanoate ((3S)-2). We report the efficient reduction of methyl 2-chloro-3-(4-methoxyphenyl)-3-oxo-propanoate (3) to (3S)-2 using an engineered enzyme SSCRM2 possessing 4.5-fold improved specific activity, which was obtained through the structure-guided site-saturation mutagenesis of the ketoreductase SSCR by reliving steric hindrance and undesired interactions. With the combined use of the co-expression fine-tuning strategy, a recombinant E. coli (pET28a-RBS-SSCRM2 /pACYCDuet-GDH), co-expressing SSCRM2 and glucose dehydrogenase, was constructed and optimized for protein expression. After optimizing the reaction conditions, whole-cell-catalyzed complete reduction of industrially relevant 300 g L-1 of 3 was realized, affording (3S)-2 with 99% ee and a space-time yield of 519.1 g∙L-1 ∙d-1 , representing the highest record for the biocatalytic synthesis of (3S)-2 reported to date. The E-factor of this biocatalytic synthesis was 24.5 (including water). Chiral alcohol (3S)-2 generated in this atom-economic synthesis was transformed to (2R,3S)-MPGM in 95% yield with 99% ee.
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Affiliation(s)
- Xiaoping Yue
- Engineering Center of Catalysis and Synthesis for Chiral Molecules, Department of Chemistry, Fudan University, Shanghai, P. R. China
- Shanghai Engineering Research Center of Industrial Asymmetric Catalysis of Chiral Drugs, Shanghai, P. R. China
- Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu, P. R. China
| | - Yitong Li
- Engineering Center of Catalysis and Synthesis for Chiral Molecules, Department of Chemistry, Fudan University, Shanghai, P. R. China
- Shanghai Engineering Research Center of Industrial Asymmetric Catalysis of Chiral Drugs, Shanghai, P. R. China
- Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu, P. R. China
| | - Lin Yang
- School of Health, Jiangxi Normal University, Nanchang, P. R. China
| | - Di Sang
- Engineering Center of Catalysis and Synthesis for Chiral Molecules, Department of Chemistry, Fudan University, Shanghai, P. R. China
- Shanghai Engineering Research Center of Industrial Asymmetric Catalysis of Chiral Drugs, Shanghai, P. R. China
| | - Zedu Huang
- Engineering Center of Catalysis and Synthesis for Chiral Molecules, Department of Chemistry, Fudan University, Shanghai, P. R. China
- Shanghai Engineering Research Center of Industrial Asymmetric Catalysis of Chiral Drugs, Shanghai, P. R. China
| | - Fener Chen
- Engineering Center of Catalysis and Synthesis for Chiral Molecules, Department of Chemistry, Fudan University, Shanghai, P. R. China
- Shanghai Engineering Research Center of Industrial Asymmetric Catalysis of Chiral Drugs, Shanghai, P. R. China
- Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu, P. R. China
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4
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Hu X, Liu W, Yan Y, Deng H, Cai Y. Tropinone reductase: A comprehensive review on its role as the key enzyme in tropane alkaloids biosynthesis. Int J Biol Macromol 2023; 253:127377. [PMID: 37839598 DOI: 10.1016/j.ijbiomac.2023.127377] [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: 07/09/2023] [Revised: 09/28/2023] [Accepted: 10/09/2023] [Indexed: 10/17/2023]
Abstract
TAs, including hyoscyamine and scopolamine, were used to treat neuromuscular disorders ranging from nerve agent poisoning to Parkinson's disease. Tropinone reductase I (TR-I; EC 1.1.1.206) catalyzed the conversion of tropinone into tropine in the biosynthesis of TAs, directing the metabolic flow towards hyoscyamine and scopolamine. Tropinone reductase II (TR-II; EC 1.1.1.236) was responsible for the conversion of tropinone into pseudotropine, diverting the metabolic flux towards calystegine A3. The regulation of metabolite flow through both branches of the TAs pathway seemed to be influenced by the enzymatic activity of both enzymes and their accessibility to the precursor tropinone. The significant interest in the utilization of metabolic engineering for the efficient production of TAs has highlighted the importance of TRs as crucial enzymes that govern both the direction of metabolic flow and the yield of products. This review discussed recent advances for the TRs sources, properties, protein structure and biocatalytic mechanisms, and a detailed overview of its crucial role in the metabolism and synthesis of TAs was summarized. Furthermore, we conducted a detailed investigation into the evolutionary origins of these two TRs. A prospective analysis of potential challenges and applications of TRs was presented.
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Affiliation(s)
- Xiaoxiang Hu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Wenjing Liu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Yi Yan
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Huaxiang Deng
- Center for Synthetic Biochemistry, Institute of Synthetic Biology, Institutes of Advanced Technologies, Shenzhen, China
| | - Yujie Cai
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China.
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5
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Zhu L, Cui Y, Chen X, Zhang H, Feng J, Wu Q, Zhu D. Synthesis of single stereoisomers of 2,2-disubstituted 3-hydroxycyclohexane-1-ones via enzymatic desymmetric reduction of the 1,3-cyclohexanediones. GREEN SYNTHESIS AND CATALYSIS 2021. [DOI: 10.1016/j.gresc.2021.04.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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6
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Liu ZL. Reasons for 2-furaldehyde and 5-hydroxymethyl-2-furaldehyde resistance in Saccharomyces cerevisiae: current state of knowledge and perspectives for further improvements. Appl Microbiol Biotechnol 2021; 105:2991-3007. [PMID: 33830300 DOI: 10.1007/s00253-021-11256-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 03/16/2021] [Accepted: 03/23/2021] [Indexed: 11/25/2022]
Abstract
Common toxic compounds 2-furaldehyde (furfural) and 5-hydroxymethyl-2-furaldehyde (HMF) are formed from dehydration of pentose and hexose, respectively, during decomposition of lignocellulosic biomass polymers. Furfural and HMF represent a major class of aldehyde toxic chemicals that inhibit microbial growth and interfere with subsequent fermentation for production of renewable fuels and chemicals. Understanding mechanisms of yeast tolerance aids development of tolerant strains as the most economic means to overcome the toxicity. This review updates current knowledge on yeast resistance to these toxic chemicals obtained from rapid advances in the past few years. Findings are largely exemplified by an adapted strain NRRL Y-50049 compared with its progenitor, the industrial yeast Saccharomyces cerevisiae type strain NRRL Y-12632. Newly characterized molecular phenotypes distinguished acquired resistant components of Y-50049 from innate stress response of its progenitor Y-12632. These findings also raised important questions on how to address more deeply ingrained changes in addition to local renovations for yeast adaptation. An early review on understandings of yeast tolerance to these inhibitory compounds is available and its contents omitted here to avoid redundancy. Controversial and confusing issues on identification of yeast resistance to furfural and HMF are further clarified aiming improved future research. Propositions and perspectives on research understanding molecular mechanisms of yeast resistance and future improvements are also presented. KEY POINTS: • Distinguished adapted resistance from innate stress response in yeast. • Defined pathway-based molecular phenotypes of yeast resistance. • Proposed genomic insight and perspectives on yeast resistance and adaptation.
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Affiliation(s)
- Z Lewis Liu
- National Center for Agricultural Utilization Research, Bioenergy Research Unit, USDA Agricultural Research Service, 1815 N. University Street, Peoria, IL, 61604, USA.
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7
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Zhou J, Xu G, Ni Y. Stereochemistry in Asymmetric Reduction of Bulky–Bulky Ketones by Alcohol Dehydrogenases. ACS Catal 2020. [DOI: 10.1021/acscatal.0c02646] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Jieyu Zhou
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122 Jiangsu, China
| | - Guochao Xu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122 Jiangsu, China
| | - Ye Ni
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122 Jiangsu, China
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8
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Li J, Feng J, Chen X, Gong J, Cui Y, Zhang H, Bu D, Wu Q, Zhu D. Structure-Guided Directed Evolution of a Carbonyl Reductase Enables the Stereoselective Synthesis of (2S,3S)-2,2-Disubstituted-3-hydroxycyclopentanones via Desymmetric Reduction. Org Lett 2020; 22:3444-3448. [PMID: 32319785 DOI: 10.1021/acs.orglett.0c00892] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Juan Li
- National Engineering Laboratory for Industrial Enzymes and Tianjin Engineering Research Center of Biocatalytic Technology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West Seventh Avenue, Tianjin Airport Economic
Area, Tianjin 300308, China
- University of Chinese Academy of Sciences, No.19(A) Yuquan Road, Shijingshan District, Beijing 100049, China
| | - Jinhui Feng
- National Engineering Laboratory for Industrial Enzymes and Tianjin Engineering Research Center of Biocatalytic Technology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West Seventh Avenue, Tianjin Airport Economic
Area, Tianjin 300308, China
| | - Xi Chen
- National Engineering Laboratory for Industrial Enzymes and Tianjin Engineering Research Center of Biocatalytic Technology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West Seventh Avenue, Tianjin Airport Economic
Area, Tianjin 300308, China
| | - Jingyao Gong
- National Engineering Laboratory for Industrial Enzymes and Tianjin Engineering Research Center of Biocatalytic Technology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West Seventh Avenue, Tianjin Airport Economic
Area, Tianjin 300308, China
- Department of Medicinal Chemistry, School of Pharmacy Southwest Medical University, Luzhou, Sichuan 646000, China
| | - Yunfeng Cui
- National Engineering Laboratory for Industrial Enzymes and Tianjin Engineering Research Center of Biocatalytic Technology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West Seventh Avenue, Tianjin Airport Economic
Area, Tianjin 300308, China
| | - Hongliu Zhang
- National Engineering Laboratory for Industrial Enzymes and Tianjin Engineering Research Center of Biocatalytic Technology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West Seventh Avenue, Tianjin Airport Economic
Area, Tianjin 300308, China
| | - Dandan Bu
- National Engineering Laboratory for Industrial Enzymes and Tianjin Engineering Research Center of Biocatalytic Technology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West Seventh Avenue, Tianjin Airport Economic
Area, Tianjin 300308, China
| | - Qiaqing Wu
- National Engineering Laboratory for Industrial Enzymes and Tianjin Engineering Research Center of Biocatalytic Technology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West Seventh Avenue, Tianjin Airport Economic
Area, Tianjin 300308, China
| | - Dunming Zhu
- National Engineering Laboratory for Industrial Enzymes and Tianjin Engineering Research Center of Biocatalytic Technology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West Seventh Avenue, Tianjin Airport Economic
Area, Tianjin 300308, China
- University of Chinese Academy of Sciences, No.19(A) Yuquan Road, Shijingshan District, Beijing 100049, China
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9
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Sudhakara S, Ramakrishnan C, Gromiha MM, Chadha A. New insights into the stereospecific reduction by an (S) specific carbonyl reductase from Candida parapsilosis ATCC 7330: experimental and QM/MM studies. Catal Sci Technol 2020. [DOI: 10.1039/d0cy01170c] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The quantum mechanics/molecular mechanics study of an (S) specific carbonyl reductase from C. parapsilosis ATCC 7330 showing a dual kinetic response for the reduction of ketones and α-ketoesters suggests different reaction mechanisms for the same.
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Affiliation(s)
- Sneha Sudhakara
- Laboratory of Bioorganic Chemistry
- Department of Biotechnology
- Bhupat and Jyoti Mehta School of Biosciences
- Indian Institute of Technology Madras
- Chennai 600036
| | - Chandrasekaran Ramakrishnan
- Protein Bioinformatics lab
- Department of Biotechnology
- Bhupat and Jyoti Mehta School of Biosciences
- Indian Institute of Technology Madras
- Chennai 600036
| | - M. Michael Gromiha
- Protein Bioinformatics lab
- Department of Biotechnology
- Bhupat and Jyoti Mehta School of Biosciences
- Indian Institute of Technology Madras
- Chennai 600036
| | - Anju Chadha
- Laboratory of Bioorganic Chemistry
- Department of Biotechnology
- Bhupat and Jyoti Mehta School of Biosciences
- Indian Institute of Technology Madras
- Chennai 600036
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10
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Significantly enhancing the biocatalytic synthesis of chiral alcohols by semi-rationally engineering an anti-Prelog carbonyl reductase from Acetobacter sp. CCTCC M209061. MOLECULAR CATALYSIS 2019. [DOI: 10.1016/j.mcat.2019.110613] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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11
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Mittmann E, Hu Y, Peschke T, Rabe KS, Niemeyer CM, Bräse S. Chemoenzymatic Synthesis ofO‐Containing Heterocycles fromα‐Diazo Esters. ChemCatChem 2019. [DOI: 10.1002/cctc.201901602] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Esther Mittmann
- Karlsruhe Institute of Technology (KIT)Institute for Biological Interfaces (IBG 1) Hermann-von-Helmholtz-Platz 76344 Eggenstein-Leopoldschafen Germany
| | - Yuling Hu
- Karlsruhe Institute of Technology (KIT)Institute of Organic Chemistry (IOC) Fritz-Haber-Weg 6 76131 Karlsruhe Germany
| | - Theo Peschke
- Karlsruhe Institute of Technology (KIT)Institute for Biological Interfaces (IBG 1) Hermann-von-Helmholtz-Platz 76344 Eggenstein-Leopoldschafen Germany
- Novartis Pharma AGChemical and Analytical Development (CHAD) 4056 Basel Switzerland
| | - Kersten S. Rabe
- Karlsruhe Institute of Technology (KIT)Institute for Biological Interfaces (IBG 1) Hermann-von-Helmholtz-Platz 76344 Eggenstein-Leopoldschafen Germany
| | - Christof M. Niemeyer
- Karlsruhe Institute of Technology (KIT)Institute for Biological Interfaces (IBG 1) Hermann-von-Helmholtz-Platz 76344 Eggenstein-Leopoldschafen Germany
- Karlsruhe Institute of Technology (KIT)Institute of Organic Chemistry (IOC) Fritz-Haber-Weg 6 76131 Karlsruhe Germany
| | - Stefan Bräse
- Karlsruhe Institute of Technology (KIT)Institute of Organic Chemistry (IOC) Fritz-Haber-Weg 6 76131 Karlsruhe Germany
- Karlsruhe Institute of Technology (KIT)Institute of Toxicology and Genetics (IOC) Hermann-von-Helmholtz-Platz 76344 Eggenstein-Leopoldschafen Germany
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12
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Li A, Yuchi Q, Li X, Pang W, Li B, Xue F, Zhang L. Discovery of a novel ortho-haloacetophenones-specific carbonyl reductase from Bacillus aryabhattai and insight into the molecular basis for its catalytic performance. Int J Biol Macromol 2019; 138:781-790. [PMID: 31351953 DOI: 10.1016/j.ijbiomac.2019.07.153] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 07/23/2019] [Accepted: 07/24/2019] [Indexed: 12/25/2022]
Abstract
To exploit robust biocatalysts for chiral 1-(2-halophenyl)ethanols synthesis, an ortho-haloacetophenones-specific carbonyl reductase (BaSDR1) gene from Bacillus aryabhattai was cloned and expressed in Escherichia coli. The impressive properties regarding BaSDR1 application include preference for NADH as coenzyme, noticeable tolerance against high cosubstrate concentration, and remarkable catalytic performance over a broad pH range from 5.0 to 10.0. The optimal temperature was 35 °C, with a half-life of 3.1 h at 35 °C and 0.75 h at 45 °C, respectively. Notably, BaSDR1 displayed excellent catalytic performance toward various ortho-haloacetophenones, providing chiral 1-(2-halophenyl)ethanols with 99% ee for all the substrates tested. Most importantly, the docking results indicated that the enzyme-substrate interactions and the steric hindrance of halogen atoms act in a push-pull manner in regulating enzyme catalytic ability. These results provide valuable clues for the structure-function relationships of BaSDR1 and the role of halogen groups in catalytic performance, and offer important reference for protein engineering and mining of functional compounds.
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Affiliation(s)
- Aipeng Li
- School of Life Sciences, Northwestern Polytechnical University, 710072 Xi'an, China; Research & Development Institute of Northwestern Polytechnical University in Shenzhen, 518057 Shenzhen, China
| | - Qingxiao Yuchi
- School of Life Sciences, Northwestern Polytechnical University, 710072 Xi'an, China
| | - Xue Li
- School of Life Sciences, Northwestern Polytechnical University, 710072 Xi'an, China
| | - Wei Pang
- School of Life Sciences, Northwestern Polytechnical University, 710072 Xi'an, China
| | - Bin Li
- School of Life Sciences, Northwestern Polytechnical University, 710072 Xi'an, China
| | - Feng Xue
- School of Marine and Bioengineering, Yancheng Institute of Technology, 224051 Yancheng, China.
| | - Lianbing Zhang
- School of Life Sciences, Northwestern Polytechnical University, 710072 Xi'an, China.
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13
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An J, Nie Y, Xu Y. Structural insights into alcohol dehydrogenases catalyzing asymmetric reductions. Crit Rev Biotechnol 2019; 39:366-379. [DOI: 10.1080/07388551.2019.1566205] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Jianhong An
- School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China
- School of Ophthalmology and Optometry, and Eye Hospital, Wenzhou Medical University, Wenzhou, China
- State Key Laboratory of Optometry, Ophthalmology and Vision Science, Wenzhou, China
| | - Yao Nie
- School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China
- International Joint Research Laboratory for Brewing Microbiology, Applied Enzymology at Jiangnan University, Wuxi, China
| | - Yan Xu
- School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China
- International Joint Research Laboratory for Brewing Microbiology, Applied Enzymology at Jiangnan University, Wuxi, China
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
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14
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Zhou J, Wang Y, Xu G, Wu L, Han R, Schwaneberg U, Rao Y, Zhao YL, Zhou J, Ni Y. Structural Insight into Enantioselective Inversion of an Alcohol Dehydrogenase Reveals a "Polar Gate" in Stereorecognition of Diaryl Ketones. J Am Chem Soc 2018; 140:12645-12654. [PMID: 30247889 DOI: 10.1021/jacs.8b08640] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Diaryl ketones are important building blocks for synthesizing pharmaceuticals and are generally regarded as "difficult-to-reduce" ketones due to the large steric hindrance of their two bulky aromatic side chains. Alcohol dehydrogenase from Kluyveromyces polyspora ( KpADH) has been identified as a robust biocatalyst due to its high conversion of diaryl ketone substrate (4-chlorophenyl)(pyridine-2-yl)ketone (CPMK) with a moderate R-selectivity of 82% ee. To modulate the stereoselectivity of KpADH, a "polarity scanning" strategy was proposed, in which six key residues inside and at the entrance of the substrate binding pocket were identified. After iterative combinatorial mutagenesis, variants Mu-R2 and Mu-S5 with enhanced (99.2% ee, R) and inverted (97.8% ee, S) stereoselectivity were obtained. The crystal structures of KpADH and two mutants in complex with NADPH were resolved to elucidate the evolution of enantioselective inversion. Based on MD simulation, Mu-R2-CPMKProR and Mu-S5-CPMKProS were more favorable in the formation of prereaction states. Interestingly, a quadrilateral plane formed by α-carbons of four residues (N136, V161, C237, and G214) was identified at the entrance of the substrate binding pocket of Mu-S5; this plane acts as a "polar gate" for substrates. Due to the discrepancy in charge characteristics between chlorophenyl and pyridine substituents, the pro- S orientation of CPMK is defined when it passes through the "polar gate" in Mu-S5, whereas the similar plane in wild-type is blocked by several aromatic residues. Our result paves the way for engineering stereocomplementary ADH toward bulky diaryl ketones and provides structural insight into the mechanism of stereoselective inversion.
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Affiliation(s)
- Jieyu Zhou
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology , Jiangnan University , Wuxi , 214122 Jiangsu , China
| | - Yue Wang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology , Jiangnan University , Wuxi , 214122 Jiangsu , China
| | - Guochao Xu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology , Jiangnan University , Wuxi , 214122 Jiangsu , China
| | - Lian Wu
- State Key Laboratory of Bio-organic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis , Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences , Shanghai 200032 , China
| | - Ruizhi Han
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology , Jiangnan University , Wuxi , 214122 Jiangsu , China
| | - Ulrich Schwaneberg
- Institute of Biotechnology , RWTH Aachen University , Worringerweg 3 , 52074 Aachen , Germany
| | - Yijian Rao
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology , Jiangnan University , Wuxi , 214122 Jiangsu , China
| | - Yi-Lei Zhao
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology , Shanghai Jiao Tong University , Shanghai 200240 , China
| | - Jiahai Zhou
- State Key Laboratory of Bio-organic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis , Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences , Shanghai 200032 , China
| | - Ye Ni
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology , Jiangnan University , Wuxi , 214122 Jiangsu , China
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15
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Rönnander J, Ljunggren J, Hedenström E, Wright SAI. Biotransformation of vanillin into vanillyl alcohol by a novel strain of Cystobasidium laryngis isolated from decaying wood. AMB Express 2018; 8:137. [PMID: 30143905 PMCID: PMC6109037 DOI: 10.1186/s13568-018-0666-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 08/17/2018] [Indexed: 11/19/2022] Open
Abstract
Vanillin is an aromatic aldehyde found as a component of lignocellulosic material, and in the cured pods of orchidaceae plants. Like other phenolic substances, vanillin has antimicrobial activity and can be extracted from lignin either by a thermo-chemical process or through microbial degradation. Vanillin, can serve as a model monomer in biodegradation studies of lignin. In the present study, a yeast isolated from decaying wood on the Faroe Islands, was identified as Cystobasidium laryngis strain FMYD002, based on internal transcribed spacer sequence analysis. It demonstrated the ability to convert vanillin to vanillyl alcohol, as detected by ultra-high performance liquid chromatography-quadrupole-time-of-flight. Structural analysis of vanillyl alcohol was carried out by using gas chromatography-mass spectrometry and 1H NMR spectroscopy, and further verified by synthesis. The reduction of vanillin to vanillyl alcohol has been documented for only a few species of fungi. However, to our knowledge, this biotransformation has not yet been reported for basidiomycetous yeast species, nor for any representative of the subphylum Pucciniomycotina. The biotransformation capability of the present strain might prove useful in the industrial utilisation of lignocellulosic residues.
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Affiliation(s)
- Jonas Rönnander
- Faculty of Engineering and Sustainable Development, University of Gävle, 80176, Gävle, Sweden.
| | - Joel Ljunggren
- Department of Chemical Engineering, Mid Sweden University, 85170, Sundsvall, Sweden
| | - Erik Hedenström
- Department of Chemical Engineering, Mid Sweden University, 85170, Sundsvall, Sweden
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16
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Liu ZL. Understanding the tolerance of the industrial yeast Saccharomyces cerevisiae against a major class of toxic aldehyde compounds. Appl Microbiol Biotechnol 2018; 102:5369-5390. [PMID: 29725719 DOI: 10.1007/s00253-018-8993-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Revised: 04/03/2018] [Accepted: 04/05/2018] [Indexed: 12/27/2022]
Abstract
Development of the next-generation biocatalyst is vital for fermentation-based industrial applications and a sustainable bio-based economy. Overcoming the major class of toxic compounds associated with lignocellulose-to-biofuels conversion is one of the significant challenges for new strain development. A significant number of investigations have been made to understand mechanisms of the tolerance for industrial yeast. It is humbling to learn how complicated the cell's response to the toxic chemicals is and how little we have known about yeast tolerance in the universe of the living cell. This study updates our current knowledge on the tolerance of industrial yeast against aldehyde inhibitory compounds at cellular, molecular and the genomic levels. It is comprehensive yet specific based on reproducible evidence and cross confirmed findings from different investigations using varied experimental approaches. This research approaches a rational foundation toward a more comprehensive understanding on the yeast tolerance. Discussions and perspectives are also proposed for continued exploring the puzzle of the yeast tolerance to aid the next-generation biocatalyst development.
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Affiliation(s)
- ZongLin Lewis Liu
- The US Department of Agriculture, Agricultural Research Service, National Center for Agricultural Utilization Research, Bioenergy Research Unit, 1815 N University Street, Peoria, IL, 61604, USA.
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17
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Chen X, Zhang H, Feng J, Wu Q, Zhu D. Molecular Basis for the High Activity and Enantioselectivity of the Carbonyl Reductase from Sporobolomyces salmonicolor toward α-Haloacetophenones. ACS Catal 2018. [DOI: 10.1021/acscatal.8b00591] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Xi Chen
- National Engineering Laboratory for Industrial Enzymes and Tianjin Engineering Research Center of Biocatalytic Technology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Hongliu Zhang
- National Engineering Laboratory for Industrial Enzymes and Tianjin Engineering Research Center of Biocatalytic Technology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Jinhui Feng
- National Engineering Laboratory for Industrial Enzymes and Tianjin Engineering Research Center of Biocatalytic Technology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Qiaqing Wu
- National Engineering Laboratory for Industrial Enzymes and Tianjin Engineering Research Center of Biocatalytic Technology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Dunming Zhu
- National Engineering Laboratory for Industrial Enzymes and Tianjin Engineering Research Center of Biocatalytic Technology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
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18
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Zheng GW, Liu YY, Chen Q, Huang L, Yu HL, Lou WY, Li CX, Bai YP, Li AT, Xu JH. Preparation of Structurally Diverse Chiral Alcohols by Engineering Ketoreductase CgKR1. ACS Catal 2017. [DOI: 10.1021/acscatal.7b01933] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Gao-Wei Zheng
- State
Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation
Center for Biomanufacturing, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Yuan-Yang Liu
- State
Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation
Center for Biomanufacturing, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Qi Chen
- State
Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation
Center for Biomanufacturing, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Lei Huang
- State
Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation
Center for Biomanufacturing, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Hui-Lei Yu
- State
Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation
Center for Biomanufacturing, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Wen-Yong Lou
- Lab
of Applied Biocatalysis, School of Food Science and Engineering, South China University of Technology, Guangzhou 510640, Guangdong, China
| | - Chun-Xiu Li
- State
Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation
Center for Biomanufacturing, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Yun-Peng Bai
- State
Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation
Center for Biomanufacturing, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Ai-Tao Li
- Department
of Biocatalysis, Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz
1, Mülheim an der Ruhr 45470, Germany
| | - Jian-He Xu
- State
Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation
Center for Biomanufacturing, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
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19
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Tavanti M, Parmeggiani F, Castellanos JRG, Mattevi A, Turner NJ. One-Pot Biocatalytic Double Oxidation of α-Isophorone for the Synthesis of Ketoisophorone. ChemCatChem 2017. [DOI: 10.1002/cctc.201700620] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Michele Tavanti
- Manchester Institute of Biotechnology (MIB); School of Chemistry; The University of Manchester; 131 Princess Street M1 7DN Manchester United Kingdom
| | - Fabio Parmeggiani
- Manchester Institute of Biotechnology (MIB); School of Chemistry; The University of Manchester; 131 Princess Street M1 7DN Manchester United Kingdom
| | - J. Rubén Gómez Castellanos
- Department of Biology and Biotechnology “Lazzaro Spallanzani”; University of Pavia; Via Ferrata 9 27100 Pavia Italy
| | - Andrea Mattevi
- Department of Biology and Biotechnology “Lazzaro Spallanzani”; University of Pavia; Via Ferrata 9 27100 Pavia Italy
| | - Nicholas J. Turner
- Manchester Institute of Biotechnology (MIB); School of Chemistry; The University of Manchester; 131 Princess Street M1 7DN Manchester United Kingdom
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20
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Li A, Ye L, Yang X, Yang C, Gu J, Yu H. Structure-guided stereoselectivity inversion of a short-chain dehydrogenase/reductase towards halogenated acetophenones. Chem Commun (Camb) 2016; 52:6284-7. [DOI: 10.1039/c6cc00051g] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The structure-guided rational design of an NADH-dependent short-chain dehydrogenase/reductase (SDR) reversed the stereoselectivity towards halogenated acetophenones from Prelog to anti-Prelog.
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Affiliation(s)
- Aipeng Li
- Institute of Bioengineering
- College of Chemical and Biological Engineering
- Zhejiang University
- Hangzhou 310027
- P. R. China
| | - Lidan Ye
- Institute of Bioengineering
- College of Chemical and Biological Engineering
- Zhejiang University
- Hangzhou 310027
- P. R. China
| | - Xiaohong Yang
- Institute of Bioengineering
- College of Chemical and Biological Engineering
- Zhejiang University
- Hangzhou 310027
- P. R. China
| | - Chengcheng Yang
- Institute of Bioengineering
- College of Chemical and Biological Engineering
- Zhejiang University
- Hangzhou 310027
- P. R. China
| | - Jiali Gu
- College of Life Science
- Department of Materials Chemistry
- Huzhou University
- Huzhou 313000
- P. R. China
| | - Hongwei Yu
- Institute of Bioengineering
- College of Chemical and Biological Engineering
- Zhejiang University
- Hangzhou 310027
- P. R. China
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21
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Zhang D, Chen X, Chi J, Feng J, Wu Q, Zhu D. Semi–Rational Engineering a Carbonyl Reductase for the Enantioselective Reduction of β-Amino Ketones. ACS Catal 2015. [DOI: 10.1021/acscatal.5b00226] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Dalong Zhang
- National
Engineering Laboratory for Industrial Enzymes and Tianjin Engineering
Center for Biocatalytic Technology, Tianjin Institute of Industrial
Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Xi Chen
- National
Engineering Laboratory for Industrial Enzymes and Tianjin Engineering
Center for Biocatalytic Technology, Tianjin Institute of Industrial
Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Jing Chi
- National
Engineering Laboratory for Industrial Enzymes and Tianjin Engineering
Center for Biocatalytic Technology, Tianjin Institute of Industrial
Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jinhui Feng
- National
Engineering Laboratory for Industrial Enzymes and Tianjin Engineering
Center for Biocatalytic Technology, Tianjin Institute of Industrial
Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Qiaqing Wu
- National
Engineering Laboratory for Industrial Enzymes and Tianjin Engineering
Center for Biocatalytic Technology, Tianjin Institute of Industrial
Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Dunming Zhu
- National
Engineering Laboratory for Industrial Enzymes and Tianjin Engineering
Center for Biocatalytic Technology, Tianjin Institute of Industrial
Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
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22
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Chen R, Liu X, Wang J, Lin J, Wei D. Cloning, expression, and characterization of an anti-Prelog stereospecific carbonyl reductase from Gluconobacter oxydans DSM2343. Enzyme Microb Technol 2014; 70:18-27. [PMID: 25659628 DOI: 10.1016/j.enzmictec.2014.12.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Revised: 12/09/2014] [Accepted: 12/11/2014] [Indexed: 10/24/2022]
Abstract
A new anti-Prelog stereospecific carbonyl reductase (GoKR) from Gluconobacter oxydans DSM2343 was cloned and identified in Escherichia coli. This GoKR formed a homo-tetramer with a subunit size of approximately 27.0kDa. GoKR exhibited full activity with NADPH but not with NADH as a cofactor. The optimal pH and temperature were 9.0 and 30°C, respectively. GoKR reduced various ketones, including aliphatic and aromatic ketones, α- and β-keto esters. Aromatic ketones were reduced to (R)-enantiomers, whereas keto esters were reduced to (S)-hydroxy esters with different enantioselectivities. The data indicate that GoKR does not obey Prelog's rule and exhibits anti-Prelog enantiopreference. Enzyme-substrate-cofactor docking analysis showed that hydride transfer occurred at the si faces of carbonyl group for ethyl 4-chloro-3-oxobutanoate (COBE), which was then selectively reduced to the chiral (S)-alcohol. Excellent enantioselectivities were obtained for reducing COBE and ethyl 2-oxo-4-phenylbutyrate into the corresponding (S)-type products. These products are important for synthesizing HMG-CoA reductase (statins) and angiotensin-converting enzyme inhibitors, respectively.
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Affiliation(s)
- Rong Chen
- State Key Laboratory of Bioreactor Engineering, New World Institute of Biotechnology, East China University of Science and Technology, Shanghai 200237, China; Center for Biomedicine and Health, Division of Basical Medicine, Hangzhou Normal University, Hangzhou 310012, China
| | - Xu Liu
- State Key Laboratory of Bioreactor Engineering, New World Institute of Biotechnology, East China University of Science and Technology, Shanghai 200237, China
| | - Jiale Wang
- State Key Laboratory of Bioreactor Engineering, New World Institute of Biotechnology, East China University of Science and Technology, Shanghai 200237, China
| | - Jinping Lin
- State Key Laboratory of Bioreactor Engineering, New World Institute of Biotechnology, East China University of Science and Technology, Shanghai 200237, China.
| | - Dongzhi Wei
- State Key Laboratory of Bioreactor Engineering, New World Institute of Biotechnology, East China University of Science and Technology, Shanghai 200237, China.
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23
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Pan H, Zhou R, Louie GV, Mühlemann JK, Bomati EK, Bowman ME, Dudareva N, Dixon RA, Noel JP, Wang X. Structural studies of cinnamoyl-CoA reductase and cinnamyl-alcohol dehydrogenase, key enzymes of monolignol biosynthesis. THE PLANT CELL 2014; 26:3709-27. [PMID: 25217505 PMCID: PMC4213152 DOI: 10.1105/tpc.114.127399] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2014] [Revised: 07/27/2014] [Accepted: 08/08/2014] [Indexed: 05/18/2023]
Abstract
The enzymes cinnamoyl-CoA reductase (CCR) and cinnamyl alcohol dehydrogenase (CAD) catalyze the two key reduction reactions in the conversion of cinnamic acid derivatives into monolignol building blocks for lignin polymers in plant cell walls. Here, we describe detailed functional and structural analyses of CCRs from Medicago truncatula and Petunia hybrida and of an atypical CAD (CAD2) from M. truncatula. These enzymes are closely related members of the short-chain dehydrogenase/reductase (SDR) superfamily. Our structural studies support a reaction mechanism involving a canonical SDR catalytic triad in both CCR and CAD2 and an important role for an auxiliary cysteine unique to CCR. Site-directed mutants of CAD2 (Phe226Ala and Tyr136Phe) that enlarge the phenolic binding site result in a 4- to 10-fold increase in activity with sinapaldehyde, which in comparison to the smaller coumaraldehyde and coniferaldehyde substrates is disfavored by wild-type CAD2. This finding demonstrates the potential exploitation of rationally engineered forms of CCR and CAD2 for the targeted modification of monolignol composition in transgenic plants. Thermal denaturation measurements and structural comparisons of various liganded and unliganded forms of CCR and CAD2 highlight substantial conformational flexibility of these SDR enzymes, which plays an important role in the establishment of catalytically productive complexes of the enzymes with their NADPH and phenolic substrates.
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Affiliation(s)
- Haiyun Pan
- Plant Biology Division, Samuel Roberts Noble Foundation, Ardmore, Oklahoma 73401
| | - Rui Zhou
- Plant Biology Division, Samuel Roberts Noble Foundation, Ardmore, Oklahoma 73401
| | - Gordon V Louie
- Howard Hughes Medical Institute, Jack H. Skirball Center for Chemical Biology and Proteomics, The Salk Institute for Biological Studies, La Jolla, California 92037
| | - Joëlle K Mühlemann
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907
| | - Erin K Bomati
- Howard Hughes Medical Institute, Jack H. Skirball Center for Chemical Biology and Proteomics, The Salk Institute for Biological Studies, La Jolla, California 92037 Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92037
| | - Marianne E Bowman
- Howard Hughes Medical Institute, Jack H. Skirball Center for Chemical Biology and Proteomics, The Salk Institute for Biological Studies, La Jolla, California 92037
| | - Natalia Dudareva
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907
| | - Richard A Dixon
- Department of Biological Sciences, University of North Texas, Denton, Texas 76203-5017
| | - Joseph P Noel
- Howard Hughes Medical Institute, Jack H. Skirball Center for Chemical Biology and Proteomics, The Salk Institute for Biological Studies, La Jolla, California 92037 Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92037
| | - Xiaoqiang Wang
- Plant Biology Division, Samuel Roberts Noble Foundation, Ardmore, Oklahoma 73401
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24
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Guo PC, Bao ZZ, Ma XX, Xia Q, Li WF. Structural insights into the cofactor-assisted substrate recognition of yeast methylglyoxal/isovaleraldehyde reductase Gre2. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1844:1486-92. [PMID: 24879127 DOI: 10.1016/j.bbapap.2014.05.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Revised: 05/06/2014] [Accepted: 05/19/2014] [Indexed: 02/06/2023]
Abstract
Saccharomyces cerevisiae Gre2 (EC1.1.1.283) serves as a versatile enzyme that catalyzes the stereoselective reduction of a broad range of substrates including aliphatic and aromatic ketones, diketones, as well as aldehydes, using NADPH as the cofactor. Here we present the crystal structures of Gre2 from S. cerevisiae in an apo-form at 2.00Å and NADPH-complexed form at 2.40Å resolution. Gre2 forms a homodimer, each subunit of which contains an N-terminal Rossmann-fold domain and a variable C-terminal domain, which participates in substrate recognition. The induced fit upon binding to the cofactor NADPH makes the two domains shift toward each other, producing an interdomain cleft that better fits the substrate. Computational simulation combined with site-directed mutagenesis and enzymatic activity analysis enabled us to define a potential substrate-binding pocket that determines the stringent substrate stereoselectivity for catalysis.
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Affiliation(s)
- Peng-Chao Guo
- State Key Laboratory of Silkworm Genome Biology, Southwest University, 216, Tiansheng Road, Beibei, Chongqing 400716, People's Republic of China; Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, People's Republic of China
| | - Zhang-Zhi Bao
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, People's Republic of China
| | - Xiao-Xiao Ma
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, People's Republic of China
| | - Qingyou Xia
- State Key Laboratory of Silkworm Genome Biology, Southwest University, 216, Tiansheng Road, Beibei, Chongqing 400716, People's Republic of China
| | - Wei-Fang Li
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, People's Republic of China.
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25
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Huang L, Ma HM, Yu HL, Xu JH. Altering the Substrate Specificity of ReductaseCgKR1 fromCandida glabrataby Protein Engineering for Bioreduction of Aromatic α-Keto Esters. Adv Synth Catal 2014. [DOI: 10.1002/adsc.201300775] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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26
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Enantioselectivity and Enzyme-Substrate Docking Studies of a Ketoreductase from Sporobolomyces salmonicolor (SSCR) and Saccharomyces cerevisiae (YOL151w). INTERNATIONAL SCHOLARLY RESEARCH NOTICES 2014; 2014:124289. [PMID: 27350963 PMCID: PMC4897451 DOI: 10.1155/2014/124289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Revised: 05/26/2014] [Accepted: 06/04/2014] [Indexed: 11/18/2022]
Abstract
Models for two ketoreductases were created and used to predict the stereoselectivity of the enzymes. One was based on the crystal structure of Sporobolomyces salmonicolor. This model was used to predict the stereoselectivity for 46 ketone reductions using this enzyme; only 6 were incorrectly predicted. The stereochemistries of the products were compared to the experimental values found in the literature. The Prelog rules were also used to predict the stereoselectivity for this enzyme; however the Prelog rules seem to be highly substrate dependent. As a result, predicting stereoselectivity of KREDs is more complicated than is allowed for with just substrate size and geometry. This enzyme showed Prelog docking geometry for 13 substrates if the enzyme is assumed to prefer an anti-Prelog docking geometry. For SSCR the molecular modeling proved to be a better method for predicting stereoselectivity of the enzymes. The second model was a homology model for YOL151w based on the enzyme crystal structure of Sporobolomyces salmonicolor carbonyl reductase, SSCR. In this homology model, 14 compounds were docked and the predicted stereochemistry was compared to the literature values. Of these, 5 were incorrectly predicted.
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27
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Prelog and anti-Prelog stereoselectivity of two ketoreductases from Candida glabrata. Biotechnol Lett 2013; 35:1469-73. [PMID: 23690040 DOI: 10.1007/s10529-013-1228-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2013] [Accepted: 05/01/2013] [Indexed: 10/26/2022]
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28
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Ma H, Yang L, Ni Y, Zhang J, Li CX, Zheng GW, Yang H, Xu JH. Stereospecific Reduction of Methyl o-Chlorobenzoylformate at 300 g⋅L−1 without Additional Cofactor using a Carbonyl Reductase Mined from Candida glabrata. Adv Synth Catal 2012. [DOI: 10.1002/adsc.201100366] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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29
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Zheng C, Choquer M, Zhang B, Ge H, Hu S, Ma H, Chen S. LongSAGE gene-expression profiling of Botrytis cinerea germination suppressed by resveratrol, the major grapevine phytoalexin. Fungal Biol 2011; 115:815-32. [PMID: 21872179 DOI: 10.1016/j.funbio.2011.06.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2010] [Revised: 06/13/2011] [Accepted: 06/15/2011] [Indexed: 12/11/2022]
Abstract
The ascomycetes Botrytis cinerea is one of the most studied necrotrophic phytopathogens and one of the main fungal parasites of grapevine. As a defense mechanism, grapevine produces a phytoalexin compound, resveratrol, which inhibits germination of the fungal conidium before it can penetrate the plant barriers and lead to host cell necrotrophy. To elucidate the effect of resveratrol on transcriptional regulation in B. cinerea germlings, two LongSAGE (long serial analysis of gene expression) libraries were generated in vitro for gene-expression profiling: 41 428 tags and among them, 15 665 unitags were obtained from resveratrol-treated B. cinerea germlings and 41 358 tags, among them, 16 362 unitags were obtained from non-treated B. cinerea germlings. In-silico analysis showed that about half of these unitags match known genes in the complete B. cinerea genome sequence. Comparison of unitag frequencies between libraries highlighted 110 genes that were transcriptionally regulated in the presence of resveratrol: 53 and 57 genes were significantly down- and upregulated, respectively. Manual curation of their putative functional categories showed that primary metabolism of germinating conidia appears to be markedly affected under resveratrol treatment, along with changes in other putative metabolic pathways, such as resveratrol detoxification and virulence-effector secretion, in B. cinerea germlings. We propose a hypothetical model of cross talk between B. cinerea germinating conidia and resveratrol-producing grapevine at the very early steps of infection.
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Affiliation(s)
- Chuanlin Zheng
- College of Agriculture and Biotechnology, China Agricultural University, Beijing
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30
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Nie Y, Xiao R, Xu Y, Montelione GT. Novel anti-Prelog stereospecific carbonyl reductases from Candida parapsilosis for asymmetric reduction of prochiral ketones. Org Biomol Chem 2011; 9:4070-8. [PMID: 21505708 DOI: 10.1039/c0ob00938e] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The application of biocatalysis to the synthesis of chiral molecules is one of the greenest technologies for the replacement of chemical routes due to its environmentally benign reaction conditions and unparalleled chemo-, regio- and stereoselectivities. We have been interested in searching for carbonyl reductase enzymes and assessing their substrate specificity and stereoselectivity. We now report a gene cluster identified in Candida parapsilosis that consists of four open reading frames including three putative stereospecific carbonyl reductases (scr1, scr2, and scr3) and an alcohol dehydrogenase (cpadh). These newly identified three stereospecific carbonyl reductases (SCRs) showed high catalytic activities for producing (S)-1-phenyl-1,2-ethanediol from 2-hydroxyacetophenone with NADPH as the coenzyme. Together with CPADH, all four enzymes from this cluster are carbonyl reductases with novel anti-Prelog stereoselectivity. SCR1 and SCR3 exhibited distinct specificities to acetophenone derivatives and chloro-substituted 2-hydroxyacetophenones, and especially very high activities towards ethyl 4-chloro-3-oxobutyrate, a β-ketoester with important pharmaceutical potential. Our study also showed that genomic mining is a powerful tool for the discovery of new enzymes.
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Affiliation(s)
- Yao Nie
- Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, New Jersey 08854, USA
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Richter N, Hummel W. Biochemical characterisation of a NADPH-dependent carbonyl reductase from Neurospora crassa reducing α- and β-keto esters. Enzyme Microb Technol 2011; 48:472-9. [PMID: 22113019 DOI: 10.1016/j.enzmictec.2011.02.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2010] [Revised: 02/06/2011] [Accepted: 02/07/2011] [Indexed: 10/18/2022]
Abstract
A gene encoding an NADPH-dependent carbonyl reductase from Neurospora crassa (nccr) was cloned and heterologously expressed in Escherichia coli. The enzyme (NcCR) was purified and biochemically characterised. NcCR exhibited a restricted substrate spectrum towards various ketones, and the highest activity (468U/mg) was observed with dihydroxyacetone. However, NcCR proved to be very selective in the reduction of different α- and β-keto esters. Several compounds were converted to the corresponding hydroxy ester in high enantiomeric excess (ee) at high conversion rates. The enantioselectivity of NcCR for the reduction of ethyl 4-chloro-3-oxobutanoate showed a strong dependence on temperature. This effect was studied in detail, revealing that the ee could be substantially increased by decreasing the temperature from 40 °C (78.8%) to -3 °C (98.0%). When the experimental conditions were optimised to improve the optical purity of the product, (S)-4-chloro-3-hydroxybutanoate (ee 98.0%) was successfully produced on a 300 mg (1.8 mmol) scale using NcCR at -3 °C.
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Affiliation(s)
- Nina Richter
- evocatal GmbH, Merowingerplatz 1a, 40225 Düsseldorf, Germany
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Li H, Yang Y, Zhu D, Hua L, Kantardjieff K. Highly Enantioselective Mutant Carbonyl Reductases Created via Structure-Based Site-Saturation Mutagenesis. J Org Chem 2010; 75:7559-64. [DOI: 10.1021/jo101541n] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Hongmei Li
- Department of Chemistry, Southern Methodist University, Dallas, Texas 75275, United States
| | - Yan Yang
- Department of Chemistry, Southern Methodist University, Dallas, Texas 75275, United States
| | - Dunming Zhu
- State Engineering Laboratory for Industrial Enzymes, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- Department of Chemistry, Southern Methodist University, Dallas, Texas 75275, United States
| | - Ling Hua
- Department of Chemistry, Southern Methodist University, Dallas, Texas 75275, United States
- China Research Center, Genencor, A Danisco Division, Shanghai 200335, China
| | - Katherine Kantardjieff
- Department of Chemistry, California State Polytechnic University, Pomona, California 91768, United States
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Breicha K, Müller M, Hummel W, Niefind K. Crystallization and preliminary crystallographic analysis of Gre2p, an NADP(+)-dependent alcohol dehydrogenase from Saccharomyces cerevisiae. Acta Crystallogr Sect F Struct Biol Cryst Commun 2010; 66:838-41. [PMID: 20606287 PMCID: PMC2898475 DOI: 10.1107/s1744309110018889] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2010] [Accepted: 05/20/2010] [Indexed: 11/10/2022]
Abstract
Gre2p [Genes de respuesta a estres (stress-response gene)] from Saccharomyces cerevisiae is a monomeric enzyme of 342 amino acids with a molecular weight of 38.1 kDa. The enzyme catalyses both the stereospecific reduction of keto compounds and the oxidation of various hydroxy compounds and alcohols by the simultaneous consumption of the cofactor NADPH and formation of NADP(+). Crystals of a Gre2p complex with NADP(+) were grown using PEG 8000 as a precipitant. They belong to the monoclinic space group P2(1). The current diffraction resolution is 3.2 A. In spite of the monomeric nature of Gre2p in solution, packing and self-rotation calculations revealed the existence of two Gre2p protomers per asymmetric unit related by a twofold noncrystallographic axis.
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Affiliation(s)
- Klaus Breicha
- Institut für Biochemie, Department für Chemie, Universität zu Köln, Zülpicher Strasse 47, D-50674 Köln, Germany
| | - Marion Müller
- Institut für Molekulare Enzymtechnologie, Heinrich-Heine Universität Düsseldorf im Forschungszentrum Jülich, D-52426 Jülich, Germany
| | - Werner Hummel
- Institut für Molekulare Enzymtechnologie, Heinrich-Heine Universität Düsseldorf im Forschungszentrum Jülich, D-52426 Jülich, Germany
| | - Karsten Niefind
- Institut für Biochemie, Department für Chemie, Universität zu Köln, Zülpicher Strasse 47, D-50674 Köln, Germany
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Jung J, Park HJ, Uhm KN, Kim D, Kim HK. Asymmetric synthesis of (S)-ethyl-4-chloro-3-hydroxy butanoate using a Saccharomyces cerevisiae reductase: enantioselectivity and enzyme-substrate docking studies. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2010; 1804:1841-9. [PMID: 20601218 DOI: 10.1016/j.bbapap.2010.06.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2010] [Revised: 06/05/2010] [Accepted: 06/14/2010] [Indexed: 11/25/2022]
Abstract
Ethyl (S)-4-chloro-3-hydroxy butanoate (ECHB) is a building block for the synthesis of hypercholesterolemia drugs. In this study, various microbial reductases have been cloned and expressed in Escherichia coli. Their reductase activities toward ethyl-4-chloro oxobutanoate (ECOB) have been assayed. Amidst them, Baker's yeast YDL124W, YOR120W, and YOL151W reductases showed high activities. YDL124W produced (S)-ECHB exclusively, whereas YOR120W and YOL151W made (R)-form alcohol. The homology models and docking models with ECOB and NADPH elucidated their substrate specificities and enantioselectivities. A glucose dehydrogenase-coupling reaction was used as NADPH recycling system to perform continuously the reduction reaction. Recombinant E. coli cell co-expressing YDL124W and Bacillus subtilis glucose dehydrogenase produced (S)-ECHB exclusively.
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Affiliation(s)
- Jihye Jung
- Division of Biotechnology, The Catholic University of Korea, Bucheon 420-743, Republic of Korea
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Stereochemistry of furfural reduction by a Saccharomyces cerevisiae aldehyde reductase that contributes to in situ furfural detoxification. Appl Environ Microbiol 2010; 76:4926-32. [PMID: 20525870 DOI: 10.1128/aem.00542-10] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Ari1p from Saccharomyces cerevisiae, recently identified as an intermediate-subclass short-chain dehydrogenase/reductase, contributes in situ to the detoxification of furfural. Furfural inhibits efficient ethanol production by yeast, particularly when the carbon source is acid-treated lignocellulose, which contains furfural at a relatively high concentration. NADPH is Ari1p's best known hydride donor. Here we report the stereochemistry of the hydride transfer step, determined by using (4R)-[4-(2)H]NADPD and (4S)-[4-(2)H]NADPD and unlabeled furfural in Ari1p-catalyzed reactions and following the deuterium atom into products 2-furanmethanol or NADP(+). Analysis of the products demonstrates unambiguously that Ari1p directs hydride transfer from the si face of NADPH to the re face of furfural. The singular orientation of substrates enables construction of a model of the Michaelis complex in the Ari1p active site. The model reveals hydrophobic residues near the furfural binding site that, upon mutation, may increase specificity for furfural and enhance enzyme performance. Using (4S)-[4-(2)H]NADPD and NADPH as substrates, primary deuterium kinetic isotope effects of 2.2 and 2.5 were determined for the steady-state parameters k(cat)(NADPH) and k(cat)/K(m)(NADPH), respectively, indicating that hydride transfer is partially rate limiting to catalysis.
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Engineering cofactor preference of ketone reducing biocatalysts: A mutagenesis study on a γ-diketone reductase from the yeast Saccharomyces cerevisiae serving as an example. Int J Mol Sci 2010; 11:1735-58. [PMID: 20480039 PMCID: PMC2871135 DOI: 10.3390/ijms11041735] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2010] [Revised: 03/24/2010] [Accepted: 04/06/2010] [Indexed: 11/18/2022] Open
Abstract
The synthesis of pharmaceuticals and catalysts more and more relies on enantiopure chiral building blocks. These can be produced in an environmentally benign and efficient way via bioreduction of prochiral ketones catalyzed by dehydrogenases. A productive source of these biocatalysts is the yeast Saccharomyces cerevisiae, whose genome also encodes a reductase catalyzing the sequential reduction of the γ-diketone 2,5-hexanedione furnishing the diol (2S,5S)-hexanediol and the γ-hydroxyketone (5S)-hydroxy-2-hexanone in high enantio- as well as diastereoselectivity (ee and de >99.5%). This enzyme prefers NADPH as the hydrogen donating cofactor. As NADH is more stable and cheaper than NADPH it would be more effective if NADH could be used in cell-free bioreduction systems. To achieve this, the cofactor binding site of the dehydrogenase was altered by site-directed mutagenesis. The results show that the rational approach based on a homology model of the enzyme allowed us to generate a mutant enzyme having a relaxed cofactor preference and thus is able to use both NADPH and NADH. Results obtained from other mutants are discussed and point towards the limits of rationally designed mutants.
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Asymmetric synthesis of (S)-3-chloro-1-phenyl-1-propanol using Saccharomyces cerevisiae reductase with high enantioselectivity. Appl Microbiol Biotechnol 2010; 87:185-93. [PMID: 20111861 DOI: 10.1007/s00253-010-2442-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2009] [Revised: 01/06/2010] [Accepted: 01/06/2010] [Indexed: 10/19/2022]
Abstract
3-Chloro-1-phenyl-1-propanol is used as a chiral intermediate in the synthesis of antidepressant drugs. Various microbial reductases were expressed in Escherichia coli, and their activities toward 3-chloro-1-phenyl-1-propanone were evaluated. The yeast reductase YOL151W (GenBank locus tag) exhibited the highest level of activity and exclusively generated the (S)-alcohol. Recombinant YOL151W was purified by Ni-nitrilotriacetic acid (Ni-NTA) and desalting column chromatography. It displayed an optimal temperature and pH of 40 degrees C and 7.5-8.0, respectively. The glucose dehydrogenase coupling reaction was introduced as an NADPH regeneration system. NaOH solution was occasionally added to maintain the reaction solution pH within the range of 7.0-7.5. By using this reaction system, the substrate (30 mM) could be completely converted to the (S)-alcohol product with an enantiomeric excess value of 100%. A homology model of YOL151W was constructed based on the structure of Sporobolomyces salmonicolor carbonyl reductase (Protein Data Bank ID: 1Y1P). A docking model of YOL151W with NADPH and 3-chloro-1-phenyl-1-propanone was then constructed, which showed that the cofactor and substrate bound tightly to the active site of the enzyme in the lowest free energy state and explained how the (S)-alcohol was produced exclusively in the reduction process.
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Müller M, Katzberg M, Bertau M, Hummel W. Highly efficient and stereoselective biosynthesis of (2S,5S)-hexanediol with a dehydrogenase from Saccharomyces cerevisiae. Org Biomol Chem 2010; 8:1540-50. [DOI: 10.1039/b920869k] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Liu X, Walsh CT. Cyclopiazonic acid biosynthesis in Aspergillus sp.: characterization of a reductase-like R* domain in cyclopiazonate synthetase that forms and releases cyclo-acetoacetyl-L-tryptophan. Biochemistry 2009; 48:8746-57. [PMID: 19663400 DOI: 10.1021/bi901123r] [Citation(s) in RCA: 119] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The fungal neurotoxin alpha-cyclopiazonic acid (CPA), a nanomolar inhibitor of Ca2+-ATPase, has a pentacyclic indole tetramic acid scaffold that arises from one molecule of tryptophan, acetyl-CoA, malonyl-CoA, and dimethylallyl pyrophosphate by consecutive action of three enzymes, CpaS, CpaD, and CpaO. CpaS is a hybrid, two module polyketide synthase-nonribosomal peptide synthetase (PKS-NRPS) that makes and releases cyclo-acetoacetyl-L-tryptophan (cAATrp), the tetramic acid that serves as substrate for subsequent prenylation and oxidative cyclization to the five ring CPA scaffold. The NRPS module in CpaS has a predicted four-domain organization of condensation, adenylation, thiolation, and reductase* (C-A-T-R*), where R* lacks the critical Ser-Tyr-Lys catalytic triad of the short chain dehydrogenase/reductase (SDR) superfamily. By heterologous overproduction in Escherichia coli of the 56 kDa Aspergillus flavus CpaS TR* didomain and the single T and R* domains, we demonstrate that CpaS catalyzes a Dieckmann-type cyclization on the N-acetoacetyl-Trp intermediate bound in thioester linkage to the phosphopantetheinyl arm of the T domain to form and release cAATrp. This occurs without any participation of NAD(P)H, so R* does not function as a canonical SDR family member. Use of the T and R* domains in in trans assays enabled multiple turnovers and evaluation of specific mutants. Mutation of the D3803 residue in the R* domain, conserved in other fungal tetramate synthetases, abolished activity both in in trans and in cis (TR*) activity assays. It is likely that cyclization of beta-ketoacylaminoacyl-S-pantetheinyl intermediates to released tetramates represents a default cyclization/release route for redox-incompetent R* domains embedded in NRPS assembly lines.
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Affiliation(s)
- Xinyu Liu
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, Massachusetts 02115, USA
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Liu ZL, Moon J. A novel NADPH-dependent aldehyde reductase gene from Saccharomyces cerevisiae NRRL Y-12632 involved in the detoxification of aldehyde inhibitors derived from lignocellulosic biomass conversion. Gene 2009; 446:1-10. [PMID: 19577617 DOI: 10.1016/j.gene.2009.06.018] [Citation(s) in RCA: 98] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2009] [Revised: 06/16/2009] [Accepted: 06/19/2009] [Indexed: 10/20/2022]
Abstract
Aldehyde inhibitors such as furfural, 5-hydroxymethylfurfural, anisaldehyde, benzaldehyde, cinnamaldehyde, and phenylaldehyde are commonly generated during lignocellulosic biomass conversion process for low-cost cellulosic ethanol production that interferes with subsequent microbial growth and fermentation. In situ detoxification of the aldehyde inhibitors is possible by the tolerant ethanologenic yeast that involves multiple genes including numerous functional reductases. In this study, we report a novel aldehyde reductase gene clone Y63 from ethanologenic yeast Saccharomyces cerevisiae NRRL Y12632, representing the uncharacterized ORF YGL157W, which demonstrated NADPH-dependent reduction activities toward at least 14 aldehyde substrates. The identity of gene clone Y63 is the same with YGL157W of SGD since a variation of only 35 nucleotides in genomic sequence and three amino acid residues were observed between the two that share the same length of 347 residues in size. As one among the highly induced genes, YGL157W of Y-12632 showed significantly high levels of transcript abundance in response to furfural and HMF challenges. Based on the deduced amino acid sequence and the most conserved functional motif analyses including closely related reductases from five other yeast species to this date, YGL157W was identified as a member of the subclass 'intermediate' of the SDR (short-chain dehydrogenase/reductase) superfamily with the following typical characteristics: the most conserved catalytic site to lie at Tyr(169)-X-X-X-Lys(173); an indispensable reduction catalytic triad at Ser(131), Tyr(169), and Lys(173), and an approved cofactor-binding motif at Gly(11)-X-X-Gly(14)-X-X-Ala(17) near the N-terminus. YGL039W, YDR541C, and YOL151W (GRE2) appeared to be the similar type of enzymes falling into the same category of the intermediate subfamily.
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Affiliation(s)
- Z Lewis Liu
- U.S. Department of Agriculture, Agricultural Research Service, National Center for Agricultural Utilization Research, 1815 N University St., Peoria, IL 61604, USA.
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41
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Ser67Asp and His68Asp substitutions in candida parapsilosis carbonyl reductase alter the coenzyme specificity and enantioselectivity of ketone reduction. Appl Environ Microbiol 2009; 75:2176-83. [PMID: 19201968 DOI: 10.1128/aem.02519-08] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A short-chain carbonyl reductase (SCR) from Candida parapsilosis catalyzes an anti-Prelog reduction of 2-hydroxyacetophenone to (S)-1-phenyl-1,2-ethanediol (PED) and exhibits coenzyme specificity for NADPH over NADH. By using site-directed mutagenesis, the mutants were designed with different combinations of Ser67Asp, His68Asp, and Pro69Asp substitutions inside or adjacent to the coenzyme binding pocket. All mutations caused a significant shift of enantioselectivity toward the (R)-configuration during 2-hydroxyacetophenone reduction. The S67D/H68D mutant produced (R)-PED with high optical purity and yield in the NADH-linked reaction. By kinetic analysis, the S67D/H68D mutant resulted in a nearly 10-fold increase and a 20-fold decrease in the k(cat)/K(m) value when NADH and NADPH were used as the cofactors, respectively, but maintaining a k(cat) value essentially the same with respect to wild-type SCR. The ratio of K(d) (dissociation constant) values between NADH and NADPH for the S67D/H68D mutant and SCR were 0.28 and 1.9 respectively, which indicates that the S67D/H68D mutant has a stronger preference for NADH and weaker binding for NADPH. Moreover, the S67D/H68D enzyme exhibited a secondary structure and melting temperature similar to the wild-type form. It was also found that NADH provided maximal protection against thermal and urea denaturation for S67D/H68D, in contrast to the effective protection by NADP(H) for the wild-type enzyme. Thus, the double point mutation S67D/H68D successfully converted the coenzyme specificity of SCR from NADP(H) to NAD(H) as well as the product enantioselectivity without disturbing enzyme stability. This work provides a protein engineering approach to modify the coenzyme specificity and enantioselectivity of ketone reduction for short-chain reductases.
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Halo LM, Marshall JW, Yakasai AA, Song Z, Butts CP, Crump MP, Heneghan M, Bailey AM, Simpson TJ, Lazarus CM, Cox RJ. Authentic Heterologous Expression of the Tenellin Iterative Polyketide Synthase Nonribosomal Peptide Synthetase Requires Coexpression with an Enoyl Reductase. Chembiochem 2008; 9:585-94. [PMID: 18266306 DOI: 10.1002/cbic.200700390] [Citation(s) in RCA: 111] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Laura M Halo
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK
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43
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Zhu D, Yang Y, Majkowicz S, Pan THY, Kantardjieff K, Hua L. Inverting the Enantioselectivity of a Carbonyl Reductase via Substrate−Enzyme Docking-Guided Point Mutation. Org Lett 2008; 10:525-8. [DOI: 10.1021/ol702638j] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Dunming Zhu
- Department of Chemistry, Southern Methodist University, Dallas, Texas 75275, and W. M. Keck Foundation Center for Molecular Structure and Department of Chemistry and Biochemistry, California State UniversityFullerton, Fullerton, California 92834
| | - Yan Yang
- Department of Chemistry, Southern Methodist University, Dallas, Texas 75275, and W. M. Keck Foundation Center for Molecular Structure and Department of Chemistry and Biochemistry, California State UniversityFullerton, Fullerton, California 92834
| | - Stephanie Majkowicz
- Department of Chemistry, Southern Methodist University, Dallas, Texas 75275, and W. M. Keck Foundation Center for Molecular Structure and Department of Chemistry and Biochemistry, California State UniversityFullerton, Fullerton, California 92834
| | - Thoris Hsin-Yuan Pan
- Department of Chemistry, Southern Methodist University, Dallas, Texas 75275, and W. M. Keck Foundation Center for Molecular Structure and Department of Chemistry and Biochemistry, California State UniversityFullerton, Fullerton, California 92834
| | - Katherine Kantardjieff
- Department of Chemistry, Southern Methodist University, Dallas, Texas 75275, and W. M. Keck Foundation Center for Molecular Structure and Department of Chemistry and Biochemistry, California State UniversityFullerton, Fullerton, California 92834
| | - Ling Hua
- Department of Chemistry, Southern Methodist University, Dallas, Texas 75275, and W. M. Keck Foundation Center for Molecular Structure and Department of Chemistry and Biochemistry, California State UniversityFullerton, Fullerton, California 92834
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Gherardini PF, Wass MN, Helmer-Citterich M, Sternberg MJE. Convergent Evolution of Enzyme Active Sites Is not a Rare Phenomenon. J Mol Biol 2007; 372:817-45. [PMID: 17681532 DOI: 10.1016/j.jmb.2007.06.017] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2006] [Revised: 05/14/2007] [Accepted: 06/08/2007] [Indexed: 02/03/2023]
Abstract
Since convergent evolution of enzyme active sites was first identified in serine proteases, other individual instances of this phenomenon have been documented. However, a systematic analysis assessing the frequency of this phenomenon across enzyme space is still lacking. This work uses the Query3d structural comparison algorithm to integrate for the first time detailed knowledge about catalytic residues, available through the Catalytic Site Atlas (CSA), with the evolutionary information provided by the Structural Classification of Proteins (SCOP) database. This study considers two modes of convergent evolution: (i) mechanistic analogues which are enzymes that use the same mechanism to perform related, but possibly different, reactions (considered here as sharing the first three digits of the EC number); and (ii) transformational analogues which catalyse exactly the same reaction (identical EC numbers), but may use different mechanisms. Mechanistic analogues were identified in 15% (26 out of 169) of the three-digit EC groups considered, showing that this phenomenon is not rare. Furthermore 11 of these groups also contain transformational analogues. The catalytic triad is the most widespread active site; the results of the structural comparison show that this mechanism, or variations thereof, is present in 23 superfamilies. Transformational analogues were identified for 45 of the 951 four-digit EC numbers present within the CSA and about half of these were also mechanistic analogues exhibiting convergence of their active sites. This analysis has also been extended to the whole Protein Data Bank to provide a complete and manually curated list of the all the transformational analogues whose structure is classified in SCOP. The results of this work show that the phenomenon of convergent evolution is not rare, especially when considering large enzymatic families.
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Affiliation(s)
- Pier Federico Gherardini
- Biochemistry Building, Division of Molecular Biosciences, Imperial College London, London SW7 2AZ, UK
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45
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Nie Y, Xu Y, Mu XQ, Wang HY, Yang M, Xiao R. Purification, characterization, gene cloning, and expression of a novel alcohol dehydrogenase with anti-prelog stereospecificity from Candida parapsilosis. Appl Environ Microbiol 2007; 73:3759-64. [PMID: 17435004 PMCID: PMC1932682 DOI: 10.1128/aem.02185-06] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2006] [Accepted: 03/31/2007] [Indexed: 11/20/2022] Open
Abstract
An alcohol dehydrogenase from Candida parapsilosis CCTCC M203011 was characterized along with its biochemical activity and structural gene. The amino acid sequence shows similarity to those of the short-chain dehydrogenase/reductases but no overall identity to known proteins. This enzyme with unusual stereospecificity catalyzes an anti-Prelog reduction of 2-hydroxyacetophenone to (S)-1-phenyl-1,2-ethanediol.
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Affiliation(s)
- Yao Nie
- Key Laboratory of Industrial Biotechnology of Ministry of Education, School of Biotechnology, Southern Yangtze University, Wuxi 214122, People's Republic of China
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Petit P, Granier T, d'Estaintot BL, Manigand C, Bathany K, Schmitter JM, Lauvergeat V, Hamdi S, Gallois B. Crystal structure of grape dihydroflavonol 4-reductase, a key enzyme in flavonoid biosynthesis. J Mol Biol 2007; 368:1345-57. [PMID: 17395203 DOI: 10.1016/j.jmb.2007.02.088] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2007] [Revised: 02/21/2007] [Accepted: 02/23/2007] [Indexed: 10/23/2022]
Abstract
The nicotinamide adenine dinucleotide phosphate (NADPH)-dependent enzyme dihydroflavonol 4-reductase (DFR) catalyzes a late step in the biosynthesis of anthocyanins and condensed tannins, two flavonoid classes of importance to plant survival and human nutrition. This enzyme has been widely investigated in many plant species, but little is known about its structural and biochemical properties. To provide a basis for detailed structure-function studies, the crystal structure of Vitis vinifera DFR, heterologously expressed in Escherichia coli, has been determined at 1.8 A resolution. The 3D structure of the ternary complex obtained with the oxidized form of nicotinamide adenine dinucleotide phosphate and dihydroquercetin, one of the DFR substrates, presents common features with the short-chain dehydrogenase/reductase family, i.e., an N-terminal domain adopting a Rossmann fold and a variable C-terminal domain, which participates in substrate binding. The structure confirms the importance of the 131-156 region, which lines the substrate binding site and enlightens the role of a specific residue at position 133 (Asn or Asp), assumed to control substrate recognition. The activity of the wild-type enzyme and its variant N133D has been quantified in vitro, using dihydroquercetin or dihydrokaempferol. Our results demonstrate that position 133 cannot be solely responsible for the recognition of the B-ring hydroxylation pattern of dihydroflavonols.
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Affiliation(s)
- Pierre Petit
- Chimie et Biologie des Membranes et des Nanoobjets, UMR CNRS 5248, Bâtiment B8, Avenue des Facultés, Université Bordeaux 1, 33405 Talence Cedex, France
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Cundari TR, Dinescu A, Zhu D, Hua L. A molecular modeling study on the enantioselectivity of aryl alkyl ketone reductions by a NADPH-dependent carbonyl reductase. J Mol Model 2007; 13:685-90. [PMID: 17279371 DOI: 10.1007/s00894-007-0168-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2006] [Accepted: 12/08/2006] [Indexed: 11/25/2022]
Abstract
Automated structural analysis of Sporobolomyces salmonicolor carbonyl reductase (SSCR) indicates that the two largest potential receptor sites are in the vicinity of the nicotinamide reductant. The largest receptor site is a scalene triangle with sides of approximately 8 A by 9 A by 13 A, which is narrow in width; one corner is surrounded by hydrophilic residues that can favorably bond with the ketone oxygen. Docking aryl alkyl ketones shows a distinct preference for binding to the largest receptor site, and for conformations that place the carbonyl oxygen of the substrate in the hydrophilic corner of the largest receptor site. Favorable docking conformations for aryl alkyl ketones fall into two low-energy ensembles. These conformational ensembles are distinguished by the positions of the substituents, presenting either the Si- or Re-face of the ketone to the nicotinamide reductant. For the ketones investigated here, there is a correspondence between the major enantiomer of the alcohol obtained from the reduction of the ketone and the conformer found to have the most stable interaction energy with the receptor site in all cases. The receptor site modeling, docking simulations, molecular dynamics, and enzyme-substrate geometry optimizations lead to a model for understanding the enantioselectivity of this NADPH-dependent carbonyl reductase.
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Affiliation(s)
- Thomas R Cundari
- Department of Chemistry, Center for Advanced Scientific Computing and Modeling, University of North Texas, Box 305070, Denton, TX 76203-5070, USA
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Zhu D, Hua L. Enantioselective Enzymatic Reductions of Sterically Bulky Aryl Alkyl Ketones Catalyzed by a NADPH-Dependent Carbonyl Reductase. J Org Chem 2006; 71:9484-6. [PMID: 17137377 DOI: 10.1021/jo061571y] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The enantioselective reductions of aryl alkyl ketones, ArC(O)R, with a diverse number of alkyl groups have been achieved with an isolated carbonyl reductase from Sporobolomyces salmonicolor. Of special interest is the observation that ketones with sterically bulky alkyl groups could be reduced to the corresponding alcohols in excellent optical purity. An unusual alkyl chain-induced enantiopreference reversal was observed but was shown to be consistent with the enzyme-substrate docking calculations.
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Affiliation(s)
- Dunming Zhu
- Department of Chemistry, Southern Methodist University, Dallas, Texas 75275, USA
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Zhu D, Yang Y, Buynak JD, Hua L. Stereoselective ketone reduction by a carbonyl reductase from Sporobolomyces salmonicolor. Substrate specificity, enantioselectivity and enzyme-substrate docking studies. Org Biomol Chem 2006; 4:2690-5. [PMID: 16826293 DOI: 10.1039/b606001c] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In our effort to search for effective carbonyl reductases, the activity and enantioselectivity of a carbonyl reductase from Sporobolomyces salmonicolor have been evaluated toward the reduction of a variety of ketones. This carbonyl reductase (SSCR) reduces a broad spectrum of ketones including aliphatic and aromatic ketones, as well as alpha- and beta-ketoesters. Among these substrates, SSCR shows highest activity for the reduction of alpha-ketoesters. Aromatic alpha-ketoesters are reduced to (S)-alpha-hydroxy esters, while (R)-enantiomers are obtained from the reduction of aliphatic counterparts. This interesting observation is consistent with enzyme-substrate docking studies, which show that hydride transfer occurs at the different faces of carbonyl group for aromatic and aliphatic alpha-ketoesters. It is worthy to note that sterically bulky ketone substrates, such as 2'-methoxyacetophenone, 1-adamantyl methyl ketone, ethyl 4,4-dimethyl-3-oxopentanoate and ethyl 3,3-dimethyl-2-oxobutanoate, are reduced to the corresponding alcohols with excellent optical purity. Thus, SSCR possesses an unusually broad substrate specificity and is especially useful for the reduction of ketones with sterically bulky substituents.
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Affiliation(s)
- Dunming Zhu
- Department of Chemistry, Southern Methodist University, Dallas, Texas 75275-0314, USA
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