151
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Zachos I, Nowak C, Sieber V. Biomimetic cofactors and methods for their recycling. Curr Opin Chem Biol 2018; 49:59-66. [PMID: 30336443 DOI: 10.1016/j.cbpa.2018.10.003] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 09/30/2018] [Accepted: 10/02/2018] [Indexed: 12/19/2022]
Abstract
Nicotinamide cofactor biomimetics (NCBs) belong to a class of compounds that, as the name suggests, mimic the structures and functions of natural nicotinamide cofactors, namely nicotinamide adenine dinucleotide and nicotinamide adenine dinucleotide phosphate and their corresponding reduced forms. The first set of NCBs was discovered in the 1930s; these were initially used to study the chemical properties of this class of cofactors as well as understand nicotinamide binding of oxidoreductases. Since then, various NCBs, enzymes, and recycling systems have evolved and lately, new NCBs have been developed and used to run biocatalytic reactions.
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Affiliation(s)
- Ioannis Zachos
- Chair of Chemistry of Biogenic Resources, Technical University of Munich, Campus Straubing for Biotechnology and Sustainability, Schulgasse 16, 94315 Straubing, Germany
| | - Claudia Nowak
- Chair of Chemistry of Biogenic Resources, Technical University of Munich, Campus Straubing for Biotechnology and Sustainability, Schulgasse 16, 94315 Straubing, Germany; Current address: Dr. Ebeling & Assoc. GmbH, Hamburg, Germany
| | - Volker Sieber
- Chair of Chemistry of Biogenic Resources, Technical University of Munich, Campus Straubing for Biotechnology and Sustainability, Schulgasse 16, 94315 Straubing, Germany; Catalysis Research Center, Technical University of Munich, Garching, Germany; Fraunhofer Institute of InterfacialBiotechnology (IGB), Bio-, Electro- and Chemo Catalysis (BioCat) Branch, Straubing, Germany; School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Qld, Australia.
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152
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Dalal KS, Padvi SA, Wagh YB, Dalal DS, Chaudhari BL. Lipase from Porcine Pancreas: An Efficient Biocatalyst for the Synthesis of ortho
-Aminocarbonitriles. ChemistrySelect 2018. [DOI: 10.1002/slct.201802352] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Kiran S. Dalal
- School of Life Sciences; Kavayitri Bahinabai Chaudhari North Maharashtra University; Jalgaon 425 001 (MS) India
| | - Swapnil A. Padvi
- School of Chemical Sciences; Kavayitri Bahinabai Chaudhari North Maharashtra University; Jalgaon 425 001 (MS) India
| | - Yogesh B. Wagh
- School of Chemical Sciences; Kavayitri Bahinabai Chaudhari North Maharashtra University; Jalgaon 425 001 (MS) India
| | - Dipak S. Dalal
- School of Chemical Sciences; Kavayitri Bahinabai Chaudhari North Maharashtra University; Jalgaon 425 001 (MS) India
| | - Bhushan L. Chaudhari
- School of Life Sciences; Kavayitri Bahinabai Chaudhari North Maharashtra University; Jalgaon 425 001 (MS) India
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153
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A reusable magnetic nickel nanoparticle based catalyst for the aqueous synthesis of diverse heterocycles and their evaluation as potential anti-bacterial agent. Bioorg Med Chem 2018; 26:5018-5028. [DOI: 10.1016/j.bmc.2018.08.033] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2018] [Revised: 08/15/2018] [Accepted: 08/26/2018] [Indexed: 11/22/2022]
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154
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Abstract
In the period 1985 to 1995 applications of biocatalysis, driven by the need for more sustainable manufacture of chemicals and catalytic, (enantio)selective methods for the synthesis of pharmaceutical intermediates, largely involved the available hydrolases. This was followed, in the next two decades, by revolutionary developments in protein engineering and directed evolution for the optimisation of enzyme function and performance that totally changed the biocatalysis landscape. In the same period, metabolic engineering and synthetic biology revolutionised the use of whole cell biocatalysis in the synthesis of commodity chemicals by fermentation. In particular, developments in the enzymatic enantioselective synthesis of chiral alcohols and amines are highlighted. Progress in enzyme immobilisation facilitated applications under harsh industrial conditions, such as in organic solvents. The emergence of biocatalytic or chemoenzymatic cascade processes, often with co-immobilised enzymes, has enabled telescoping of multi-step processes. Discovering and inventing new biocatalytic processes, based on (meta)genomic sequencing, evolving enzyme promiscuity, chemomimetic biocatalysis, artificial metalloenzymes, and the introduction of non-canonical amino acids into proteins, are pushing back the limits of biocatalysis function. Finally, the integral role of biocatalysis in developing a biobased carbon-neutral economy is discussed.
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Affiliation(s)
- Roger A Sheldon
- Molecular Sciences Institute, School of Chemistry, University of the Witwatersrand, Johannesburg, South Africa.
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155
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Diaminopelargonic acid transaminase from Psychrobacter cryohalolentis is active towards (S)-(-)-1-phenylethylamine, aldehydes and α-diketones. Appl Microbiol Biotechnol 2018; 102:9621-9633. [DOI: 10.1007/s00253-018-9310-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 07/09/2018] [Accepted: 08/07/2018] [Indexed: 11/25/2022]
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156
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Cui J, Ren S, Sun B, Jia S. Optimization protocols and improved strategies for metal-organic frameworks for immobilizing enzymes: Current development and future challenges. Coord Chem Rev 2018. [DOI: 10.1016/j.ccr.2018.05.004] [Citation(s) in RCA: 89] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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157
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Evolutionary repurposing of a sulfatase: A new Michaelis complex leads to efficient transition state charge offset. Proc Natl Acad Sci U S A 2018; 115:E7293-E7302. [PMID: 30012610 DOI: 10.1073/pnas.1607817115] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The recruitment and evolutionary optimization of promiscuous enzymes is key to the rapid adaptation of organisms to changing environments. Our understanding of the precise mechanisms underlying enzyme repurposing is, however, limited: What are the active-site features that enable the molecular recognition of multiple substrates with contrasting catalytic requirements? To gain insights into the molecular determinants of adaptation in promiscuous enzymes, we performed the laboratory evolution of an arylsulfatase to improve its initially weak phenylphosphonate hydrolase activity. The evolutionary trajectory led to a 100,000-fold enhancement of phenylphosphonate hydrolysis, while the native sulfate and promiscuous phosphate mono- and diester hydrolyses were only marginally affected (≤50-fold). Structural, kinetic, and in silico characterizations of the evolutionary intermediates revealed that two key mutations, T50A and M72V, locally reshaped the active site, improving access to the catalytic machinery for the phosphonate. Measured transition state (TS) charge changes along the trajectory suggest the creation of a new Michaelis complex (E•S, enzyme-substrate), with enhanced leaving group stabilization in the TS for the promiscuous phosphonate (βleavinggroup from -1.08 to -0.42). Rather than altering the catalytic machinery, evolutionary repurposing was achieved by fine-tuning the molecular recognition of the phosphonate in the Michaelis complex, and by extension, also in the TS. This molecular scenario constitutes a mechanistic alternative to adaptation solely based on enzyme flexibility and conformational selection. Instead, rapid functional transitions between distinct chemical reactions rely on the high reactivity of permissive active-site architectures that allow multiple substrate binding modes.
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158
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Engleder M, Pichler H. On the current role of hydratases in biocatalysis. Appl Microbiol Biotechnol 2018; 102:5841-5858. [PMID: 29785499 PMCID: PMC6013536 DOI: 10.1007/s00253-018-9065-7] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Revised: 04/27/2018] [Accepted: 04/27/2018] [Indexed: 11/06/2022]
Abstract
Water addition to carbon-carbon double bonds provides access to value-added products from inexpensive organic feedstock. This interesting but relatively little-studied reaction is catalysed by hydratases in a highly regio- and enantiospecific fashion with excellent atom economy. Considering that asymmetric hydration of (non-activated) carbon-carbon double bonds is virtually impossible with current organic chemistry, enzymatic hydration reactions are highly attractive for industrial applications. Hydratases have been known for several decades but their biocatalytic potential has only been explored over the past 15 years. As a result, a considerable amount of information on this enzyme group has become available, enabling their development for practical applications. This review focuses on hydratases catalysing water addition to non-activated carbon-carbon double bonds, and examines hydratases from a biochemical, structural and mechanistic angle. Current challenges and opportunities in hydration biocatalysis are discussed, and, ultimately, their potential for organic synthesis is highlighted.
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Affiliation(s)
- Matthias Engleder
- Austrian Centre of Industrial Biotechnology (acib), Petersgasse 14, 8010, Graz, Austria
- Institute of Molecular Biotechnology, Graz University of Technology, NAWI Graz, BioTechMed Graz, Petersgasse 8010, Graz, Austria
| | - Harald Pichler
- Austrian Centre of Industrial Biotechnology (acib), Petersgasse 14, 8010, Graz, Austria.
- Institute of Molecular Biotechnology, Graz University of Technology, NAWI Graz, BioTechMed Graz, Petersgasse 8010, Graz, Austria.
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159
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Frese A, Barrass SV, Sutton PW, Adams JP, Grogan G. An Aminocaprolactam Racemase from Ochrobactrum anthropi with Promiscuous Amino Acid Ester Racemase Activity. Chembiochem 2018; 19:1711-1715. [PMID: 29897155 DOI: 10.1002/cbic.201800265] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Indexed: 01/01/2023]
Abstract
The kinetic resolution of amino acid esters (AAEs) is a useful synthetic strategy for the preparation of single-enantiomer amino acids. The development of an enzymatic dynamic kinetic resolution (DKR) process for AAEs, which would give a theoretical yield of 100 % of the enantiopure product, would require an amino acid ester racemase (AAER); however, no such enzyme has been described. We have identified low AAER activity of 15 U mg-1 in a homologue of a PLP-dependent α-amino ϵ-caprolactam racemase (ACLR) from Ochrobactrum anthropi. We have determined the structure of this enzyme, OaACLR, to a resolution of 1.87 Å and, by using structure-guided saturation mutagenesis, in combination with a colorimetric screen for AAER activity, we have identified a mutant, L293C, in which the promiscuous AAER activity of this enzyme towards l-phenylalanine methyl ester is improved 3.7-fold.
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Affiliation(s)
- Amina Frese
- York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York, YO10 5DD, UK
| | - Sarah V Barrass
- York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York, YO10 5DD, UK
| | - Peter W Sutton
- GSK Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, UK
- Present address: Department of Chemical, Biological and Environmental Engineering, Bioprocess Engineering and Applied Biocatalysis Group, Engineering School, Campus de la UAB, 08193, Bellaterra (Cerdanyola del Vallés), Barcelona, Spain
| | - Joe P Adams
- GSK Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, UK
| | - Gideon Grogan
- York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York, YO10 5DD, UK
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160
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Wang Y, Zhang C, An S, Fang X, Yu D. Engineering substrate promiscuity in 2,4-dichlorophenol hydroxylase by in silico design. RSC Adv 2018; 8:21184-21190. [PMID: 35539933 PMCID: PMC9080915 DOI: 10.1039/c8ra03229g] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2018] [Accepted: 06/04/2018] [Indexed: 11/21/2022] Open
Abstract
2,4-Dichlorophenol hydroxylase (2,4-DCP hydroxylase) is a key enzyme in the degradation of 2,4-dichlorophenoxyacetic acid in the hydroxylation step in many bacteria. Our previous study demonstrated that a 2,4-DCP hydroxylase (TfdB-JLU) exhibits broad substrate specificity for chlorophenols (CPs) and their homologues. In this study, TfdB-JLU has been engineered by rational design to further broaden its substrate scope towards CPs. We dissect the architectures of enzymes from oxidoreductase families to discover their underlying structural sources of substrate promiscuity. A homology model of TfdB-JLU has been built and docking experiments of this homology model with its natural substrate 2,4-DCP reveal that the phenyl rings of 2,4-DCP form strong interactions with residues His47, Ile48, Trp222, Pro316, and Phe424. These residues are found to be important for substrate binding in the active site. Then, the site-directed mutagenesis strategy has been applied for redesigning substrate promiscuity in TfdB-JLU. The TfdB-JLU-P316Q variant obtained shows a significant enhancement of activity (up to 3.4-fold) toward 10 CP congeners compared to wild-type TfdB-JLU. Interestingly, the active improvements of TfdB-JLU-P316Q toward CP congeners show significant difference, especially for active improvements of positional congeners such as 3-CP (1.1-fold) compared to 4-CP (3.0-fold), as well as 2,3-DCP (1.2-fold) compared to 2,5-DCP (3.4-fold). Structural analysis results indicate that the improvement in substrate promiscuity of the variant enzyme compared to the wild-type enzyme is possibly due to the increase of non-bonding interaction. The results suggest that exploiting enzyme-substrate promiscuity is promising, which would provide a starting point for designing and engineering novel biological catalysts for pollution removal.
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Affiliation(s)
- Ye Wang
- College of Life Science, Jilin University 2699 Qianjin Street Changchun 130012 P. R. China
| | - Chengkai Zhang
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, College of Life Science, Jilin University 2699 Qianjin Street Changchun 130012 P. R. China +86-431-85155240 +86-431-85155249
| | - Song An
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, College of Life Science, Jilin University 2699 Qianjin Street Changchun 130012 P. R. China +86-431-85155240 +86-431-85155249
| | - Xuexun Fang
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, College of Life Science, Jilin University 2699 Qianjin Street Changchun 130012 P. R. China +86-431-85155240 +86-431-85155249
| | - Dahai Yu
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, College of Life Science, Jilin University 2699 Qianjin Street Changchun 130012 P. R. China +86-431-85155240 +86-431-85155249
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161
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Hernández K, Szekrenyi A, Clapés P. Nucleophile Promiscuity of Natural and Engineered Aldolases. Chembiochem 2018; 19:1353-1358. [DOI: 10.1002/cbic.201800135] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Indexed: 01/01/2023]
Affiliation(s)
- Karel Hernández
- Department of Chemical Biology and Molecular Modelling; Catalonia Institute for Advanced Chemistry IQAC-CSIC; Jordi Girona 18-26 08034 Barcelona Spain
| | - Anna Szekrenyi
- Institut für Organische Chemie und Biochemie; Technische Universität Darmstadt; Alarich-Weiss-Strasse 4 64287 Darmstadt Germany
| | - Pere Clapés
- Department of Chemical Biology and Molecular Modelling; Catalonia Institute for Advanced Chemistry IQAC-CSIC; Jordi Girona 18-26 08034 Barcelona Spain
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162
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Dobrzanski T, Gravina F, Steckling B, Olchanheski LR, Sprenger RF, Espírito Santo BC, Galvão CW, Reche PM, Prestes RA, Pileggi SAV, Campos FR, Azevedo RA, Sadowsky MJ, Beltrame FL, Pileggi M. Bacillus megaterium strains derived from water and soil exhibit differential responses to the herbicide mesotrione. PLoS One 2018; 13:e0196166. [PMID: 29694403 PMCID: PMC5918998 DOI: 10.1371/journal.pone.0196166] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Accepted: 04/06/2018] [Indexed: 02/07/2023] Open
Abstract
The intense use of herbicides for weed control in agriculture causes selection pressure on soil microbiota and water ecosystems, possibly resulting in changes to microbial processes, such as biogeochemical cycles. These xenobiotics may increase the production of reactive oxygen species and consequently affect the survival of microorganisms, which need to develop strategies to adapt to these conditions and maintain their ecological functionality. This study analyzed the adaptive responses of bacterial isolates belonging to the same species, originating from two different environments (water and soil), and subjected to selection pressure by herbicides. The effects of herbicide Callisto and its active ingredient, mesotrione, induced different adaptation strategies on the cellular, enzymatic, and structural systems of two Bacillus megaterium isolates obtained from these environments. The lipid saturation patterns observed may have affected membrane permeability in response to this herbicide. Moreover, this may have led to different levels of responses involving superoxide dismutase and catalase activities, and enzyme polymorphisms. Due to these response systems, the strain isolated from water exhibited higher growth rates than did the soil strain, in evaluations made in oligotrophic culture media, which would be more like that found in semi-pristine aquatic environments. The influence of the intracellular oxidizing environments, which changed the mode of degradation of mesotrione in our experimental model and produced different metabolites, can also be observed in soil and water at sites related to agriculture. Since the different metabolites may present different levels of toxicity, we suggest that this fact should be considered in studies on the fate of agrochemicals in different environments.
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Affiliation(s)
- Tatiane Dobrzanski
- Laboratório de Microbiologia Ambiental, Setor de Ciências Biológicas e da Saúde, Departamento de Biologia Estrutural, Molecular e Genética, Universidade Estadual de Ponta Grossa, Ponta Grossa, Paraná, Brazil
| | - Fernanda Gravina
- Laboratório de Microbiologia Ambiental, Setor de Ciências Biológicas e da Saúde, Departamento de Biologia Estrutural, Molecular e Genética, Universidade Estadual de Ponta Grossa, Ponta Grossa, Paraná, Brazil
| | - Bruna Steckling
- Laboratório de Microbiologia Ambiental, Setor de Ciências Biológicas e da Saúde, Departamento de Biologia Estrutural, Molecular e Genética, Universidade Estadual de Ponta Grossa, Ponta Grossa, Paraná, Brazil
| | - Luiz R. Olchanheski
- Laboratório de Biologia Molecular e Ecologia Microbiana, Instituto de Ciências Biomédicas, Departamento de Microbiologia, Universidade de São Paulo, São Paulo, São Paulo, Brazil
| | - Ricardo F. Sprenger
- Separare - Núcleo de Cromatografia, Departamento de Química, Universidade Federal de São Carlos, São Carlos, São Paulo, Brazil
| | - Bruno C. Espírito Santo
- Laboratório de Biotecnologia Microbiana, Departamento de Biotecnologia, Genética e Biologia Celular, Universidade Estadual de Maringá, Maringá, Paraná, Brazil
| | - Carolina W. Galvão
- Laboratório de Biologia Molecular Microbiana, Setor de Ciências Biológicas e da Saúde, Departamento de Biologia Estrutural, Molecular e Genética, Universidade Estadual de Ponta Grossa, Ponta Grossa, Paraná, Brazil
| | - Péricles M. Reche
- Laboratório de Pesquisa em Recursos Hídricos, Setor de Ciências Biológicas e da Saúde, Departamento de Enfermagem e Saúde Pública, Universidade Estadual de Ponta Grossa, Ponta Grossa, Paraná, Brazil
| | - Rosilene A. Prestes
- Departamento Acadêmico, Campus Ponta Grossa, Universidade Tecnológica Federal do Paraná, UTFPR, Campus Ponta Grossa, Ponta Grossa, Paraná, Brazil
| | - Sônia A. V. Pileggi
- Laboratório de Microbiologia Ambiental, Setor de Ciências Biológicas e da Saúde, Departamento de Biologia Estrutural, Molecular e Genética, Universidade Estadual de Ponta Grossa, Ponta Grossa, Paraná, Brazil
| | - Francinete R. Campos
- Laboratório de Biociências e Espectrometria de Massas, Departamento de Farmácia, Universidade Federal do Paraná, Curitiba, Paraná, Brazil
| | - Ricardo A. Azevedo
- Departamento de Genética, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Piracicaba, São Paulo, Brazil
| | - Michael J. Sadowsky
- Department of Soil, Water, and Climate, and The Biotechnology Institute, University of Minnesota, Saint Paul, Minnesota, United States of America
| | - Flávio L. Beltrame
- Laboratório de Fitoterapia, Tecnologia e Química de Produtos Naturais, Departamento de Ciências Farmacêuticas, Setor de Ciências Biológicas e da Saúde, Universidade Estadual de Ponta Grossa, Ponta Grossa, Paraná, Brazil
| | - Marcos Pileggi
- Laboratório de Microbiologia Ambiental, Setor de Ciências Biológicas e da Saúde, Departamento de Biologia Estrutural, Molecular e Genética, Universidade Estadual de Ponta Grossa, Ponta Grossa, Paraná, Brazil
- * E-mail:
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163
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Żądło-Dobrowolska A, Schmidt NG, Kroutil W. Promiscuous activity of C-acyltransferase from Pseudomonas protegens: synthesis of acetanilides in aqueous buffer. Chem Commun (Camb) 2018; 54:3387-3390. [PMID: 29553154 PMCID: PMC5885802 DOI: 10.1039/c8cc00290h] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A C-acyltransferase was found to show promiscuous activity catalyzing C–N bond formation in aqueous buffer instead of C–C bond formation.
Amide bond formation has considerable significance in synthetic chemistry. Although the C-acyltransferase from Pseudomonas protegens has been found to catalyze C–C bond formation in nature as well as in in vitro experiments with non-natural substrates, it is now shown that the enzyme is also able to catalyze amide formation using aniline derivatives as substrates with promiscuous activity. Importantly, the amide formation was enabled in aqueous buffer. Identifying phenyl acetate as the most suitable acetyl donor, the products were obtained with up to >99% conversion and up to 99% isolated yield.
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Affiliation(s)
- Anna Żądło-Dobrowolska
- Institute of Chemistry, University of Graz, NAWI Graz, BioTechMed Graz, Harrachgasse 21/3, Graz, Austria.
| | - Nina G Schmidt
- Institute of Chemistry, University of Graz, NAWI Graz, BioTechMed Graz, Harrachgasse 21/3, Graz, Austria. and Austrian Centre of Industrial Biotechnology, acib GmbH, Graz, Austria
| | - Wolfgang Kroutil
- Institute of Chemistry, University of Graz, NAWI Graz, BioTechMed Graz, Harrachgasse 21/3, Graz, Austria. and Austrian Centre of Industrial Biotechnology, acib GmbH, Graz, Austria
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164
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Bathellier C, Tcherkez G, Lorimer GH, Farquhar GD. Rubisco is not really so bad. PLANT, CELL & ENVIRONMENT 2018; 41:705-716. [PMID: 29359811 DOI: 10.1111/pce.13149] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Revised: 01/09/2018] [Accepted: 01/09/2018] [Indexed: 05/19/2023]
Abstract
Ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) is the most widespread carboxylating enzyme in autotrophic organisms. Its kinetic and structural properties have been intensively studied for more than half a century. Yet important aspects of the catalytic mechanism remain poorly understood, especially the oxygenase reaction. Because of its relatively modest turnover rate (a few catalytic events per second) and the competitive inhibition by oxygen, Rubisco is often viewed as an inefficient catalyst for CO2 fixation. Considerable efforts have been devoted to improving its catalytic efficiency, so far without success. In this review, we re-examine Rubisco's catalytic performance by comparison with other chemically related enzymes. We find that Rubisco is not especially slow. Furthermore, considering both the nature and the complexity of the chemical reaction, its kinetic properties are unremarkable. Although not unique to Rubisco, oxygenation is not systematically observed in enolate and enamine forming enzymes and cannot be considered as an inevitable consequence of the mechanism. It is more likely the result of a compromise between chemical and metabolic imperatives. We argue that a better description of Rubisco mechanism is still required to better understand the link between CO2 and O2 reactivity and the rationale of Rubisco diversification and evolution.
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Affiliation(s)
- Camille Bathellier
- Research School of Biology, College of Science, Australian National University, Canberra, 2601, ACT, Australia
| | - Guillaume Tcherkez
- Research School of Biology, College of Science, Australian National University, Canberra, 2601, ACT, Australia
| | - George H Lorimer
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD, 27042, USA
| | - Graham D Farquhar
- Research School of Biology, College of Science, Australian National University, Canberra, 2601, ACT, Australia
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165
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Payer SE, Pollak H, Glueck SM, Faber K. A Rational Active-Site Redesign Converts a Decarboxylase into a C=C Hydratase: "Tethered Acetate" Supports Enantioselective Hydration of 4-Hydroxystyrenes. ACS Catal 2018. [PMID: 29527405 PMCID: PMC5838639 DOI: 10.1021/acscatal.7b04293] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The promiscuous regio- and stereoselective hydration of 4-hydroxystyrenes catalyzed by ferulic acid decarboxylase from Enterobacter sp. (FDC_Es) depends on bicarbonate bound in the active site, which serves as a proton relay activating a water molecule for nucleophilic attack on a quinone methide electrophile. This "cofactor" is crucial for achieving improved conversions and high stereoselectivities for (S)-configured benzylic alcohol products. Similar effects were observed with simple aliphatic carboxylic acids as additives. A rational redesign of the active site by replacing the bicarbonate or acetate "cofactor" with a newly introduced side-chain carboxylate from an adjacent amino acid yielded mutants that efficiently acted as C=C hydratases. A single-point mutation of valine 46 to glutamate or aspartate improved the hydration activity by 40% and boosted the stereoselectivity 39-fold in the absence of bicarbonate or acetate.
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Affiliation(s)
- Stefan E. Payer
- Austrian Centre of
Industrial Biotechnology and ‡Department of Chemistry, University of Graz, Heinrichstrasse 28/2, 8010 Graz, Austria
| | - Hannah Pollak
- Austrian Centre of
Industrial Biotechnology and ‡Department of Chemistry, University of Graz, Heinrichstrasse 28/2, 8010 Graz, Austria
| | - Silvia M. Glueck
- Austrian Centre of
Industrial Biotechnology and ‡Department of Chemistry, University of Graz, Heinrichstrasse 28/2, 8010 Graz, Austria
| | - Kurt Faber
- Austrian Centre of
Industrial Biotechnology and ‡Department of Chemistry, University of Graz, Heinrichstrasse 28/2, 8010 Graz, Austria
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166
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Dwivedee BP, Soni S, Sharma M, Bhaumik J, Laha JK, Banerjee UC. Promiscuity of Lipase-Catalyzed Reactions for Organic Synthesis: A Recent Update. ChemistrySelect 2018. [DOI: 10.1002/slct.201702954] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Bharat P. Dwivedee
- Department of Pharmaceutical Technology (Biotechnology); National Institute of Pharmaceutical Education and Research; S.A.S. Nagar 160062 Punjab India
| | - Surbhi Soni
- Department of Biotechnology; National Institute of Pharmaceutical Education and Research, S.A.S. Nagar; 160062 Punjab India
| | - Misha Sharma
- Department of Pharmaceutical Technology (Process Chemistry); National Institute of Pharmaceutical Education and Research; S.A.S. Nagar 160062 Punjab India
| | - Jayeeta Bhaumik
- Department of Pharmaceutical Technology (Biotechnology); National Institute of Pharmaceutical Education and Research; S.A.S. Nagar 160062 Punjab India
| | - Joydev K. Laha
- Department of Pharmaceutical Technology (Process Chemistry); National Institute of Pharmaceutical Education and Research; S.A.S. Nagar 160062 Punjab India
| | - Uttam C. Banerjee
- Department of Pharmaceutical Technology (Biotechnology); National Institute of Pharmaceutical Education and Research; S.A.S. Nagar 160062 Punjab India
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167
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Ye D, Guan KL, Xiong Y. Metabolism, Activity, and Targeting of D- and L-2-Hydroxyglutarates. Trends Cancer 2018; 4:151-165. [PMID: 29458964 PMCID: PMC5884165 DOI: 10.1016/j.trecan.2017.12.005] [Citation(s) in RCA: 148] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2017] [Revised: 12/11/2017] [Accepted: 12/12/2017] [Indexed: 12/30/2022]
Abstract
Isocitrate dehydrogenases (IDH1/2) are frequently mutated in multiple types of human cancer, resulting in neomorphic enzymes that convert α-ketoglutarate (α-KG) to 2-hydroxyglutarate (2-HG). The current view on the mechanism of IDH mutation holds that 2-HG acts as an antagonist of α-KG to competitively inhibit the activity of α-KG-dependent dioxygenases, including those involved in histone and DNA demethylation. Recent studies have implicated 2-HG in activities beyond epigenetic modification. Multiple enzymes have been discovered that lack mutations but that can nevertheless produce 2-HG promiscuously under hypoxic or acidic conditions. Therapies are being developed to treat IDH-mutant cancers by targeting either the mutant IDH enzymes directly or the pathways sensitized by 2-HG.
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Affiliation(s)
- Dan Ye
- Molecular and Cell Biology Lab, Institute of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China; Department of General Surgery, Huashan Hospital, Fudan University, Shanghai 200040, China.
| | - Kun-Liang Guan
- Molecular and Cell Biology Lab, Institute of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China; Department of Pharmacology and Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093, USA
| | - Yue Xiong
- Molecular and Cell Biology Lab, Institute of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China; Department of Biochemistry and Biophysics, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
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168
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Martínez-Martínez M, Coscolín C, Santiago G, Chow J, Stogios PJ, Bargiela R, Gertler C, Navarro-Fernández J, Bollinger A, Thies S, Méndez-García C, Popovic A, Brown G, Chernikova TN, García-Moyano A, Bjerga GEK, Pérez-García P, Hai T, Del Pozo MV, Stokke R, Steen IH, Cui H, Xu X, Nocek BP, Alcaide M, Distaso M, Mesa V, Peláez AI, Sánchez J, Buchholz PCF, Pleiss J, Fernández-Guerra A, Glöckner FO, Golyshina OV, Yakimov MM, Savchenko A, Jaeger KE, Yakunin AF, Streit WR, Golyshin PN, Guallar V, Ferrer M, The INMARE Consortium. Determinants and Prediction of Esterase Substrate Promiscuity Patterns. ACS Chem Biol 2018; 13:225-234. [PMID: 29182315 DOI: 10.1021/acschembio.7b00996] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Esterases receive special attention because of their wide distribution in biological systems and environments and their importance for physiology and chemical synthesis. The prediction of esterases' substrate promiscuity level from sequence data and the molecular reasons why certain such enzymes are more promiscuous than others remain to be elucidated. This limits the surveillance of the sequence space for esterases potentially leading to new versatile biocatalysts and new insights into their role in cellular function. Here, we performed an extensive analysis of the substrate spectra of 145 phylogenetically and environmentally diverse microbial esterases, when tested with 96 diverse esters. We determined the primary factors shaping their substrate range by analyzing substrate range patterns in combination with structural analysis and protein-ligand simulations. We found a structural parameter that helps rank (classify) the promiscuity level of esterases from sequence data at 94% accuracy. This parameter, the active site effective volume, exemplifies the topology of the catalytic environment by measuring the active site cavity volume corrected by the relative solvent accessible surface area (SASA) of the catalytic triad. Sequences encoding esterases with active site effective volumes (cavity volume/SASA) above a threshold show greater substrate spectra, which can be further extended in combination with phylogenetic data. This measure provides also a valuable tool for interrogating substrates capable of being converted. This measure, found to be transferred to phosphatases of the haloalkanoic acid dehalogenase superfamily and possibly other enzymatic systems, represents a powerful tool for low-cost bioprospecting for esterases with broad substrate ranges, in large scale sequence data sets.
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Affiliation(s)
| | - Cristina Coscolín
- Institute of Catalysis, Consejo Superior de Investigaciones Científicas, 28049 Madrid, Spain
| | - Gerard Santiago
- Barcelona Supercomputing Center (BSC), 08034 Barcelona, Spain
| | - Jennifer Chow
- Biozentrum Klein Flottbek, Mikrobiologie & Biotechnologie, Universität Hamburg, 22609 Hamburg, Germany
| | - Peter J. Stogios
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, M5S 3E5 Toronto, Ontario, Canada
| | - Rafael Bargiela
- Institute of Catalysis, Consejo Superior de Investigaciones Científicas, 28049 Madrid, Spain
| | - Christoph Gertler
- School of Biological Sciences, Bangor University, LL57 2UW Bangor, United Kingdom
| | - José Navarro-Fernández
- Institute of Catalysis, Consejo Superior de Investigaciones Científicas, 28049 Madrid, Spain
| | - Alexander Bollinger
- Institut für Molekulare Enzymtechnologie, Heinrich-Heine-Universität Düsseldorf, 52425 Jülich, Germany
| | - Stephan Thies
- Institut für Molekulare Enzymtechnologie, Heinrich-Heine-Universität Düsseldorf, 52425 Jülich, Germany
| | - Celia Méndez-García
- Department of Functional Biology-IUBA, Universidad de Oviedo, 33006 Oviedo, Spain
| | - Ana Popovic
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, M5S 3E5 Toronto, Ontario, Canada
| | - Greg Brown
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, M5S 3E5 Toronto, Ontario, Canada
| | | | | | - Gro E. K. Bjerga
- Uni Research AS, Center for Applied Biotechnology, 5006 Bergen, Norway
| | - Pablo Pérez-García
- Biozentrum Klein Flottbek, Mikrobiologie & Biotechnologie, Universität Hamburg, 22609 Hamburg, Germany
| | - Tran Hai
- School of Biological Sciences, Bangor University, LL57 2UW Bangor, United Kingdom
| | - Mercedes V. Del Pozo
- Institute of Catalysis, Consejo Superior de Investigaciones Científicas, 28049 Madrid, Spain
| | - Runar Stokke
- Department of Biology and KG Jebsen Centre for Deep Sea Research, University of Bergen, 5020 Bergen, Norway
| | - Ida H. Steen
- Department of Biology and KG Jebsen Centre for Deep Sea Research, University of Bergen, 5020 Bergen, Norway
| | - Hong Cui
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, M5S 3E5 Toronto, Ontario, Canada
| | - Xiaohui Xu
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, M5S 3E5 Toronto, Ontario, Canada
| | - Boguslaw P. Nocek
- Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, 60439 Illinois, United States
| | - María Alcaide
- Institute of Catalysis, Consejo Superior de Investigaciones Científicas, 28049 Madrid, Spain
| | - Marco Distaso
- School of Biological Sciences, Bangor University, LL57 2UW Bangor, United Kingdom
| | - Victoria Mesa
- Department of Functional Biology-IUBA, Universidad de Oviedo, 33006 Oviedo, Spain
| | - Ana I. Peláez
- Department of Functional Biology-IUBA, Universidad de Oviedo, 33006 Oviedo, Spain
| | - Jesús Sánchez
- Department of Functional Biology-IUBA, Universidad de Oviedo, 33006 Oviedo, Spain
| | - Patrick C. F. Buchholz
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, 70569 Stuttgart, Germany
| | - Jürgen Pleiss
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, 70569 Stuttgart, Germany
| | - Antonio Fernández-Guerra
- Jacobs University Bremen gGmbH, Bremen, Germany
- Max Planck Institute for Marine Microbiology, 28359 Bremen, Germany
- University of Oxford, Oxford e-Research Centre, Oxford, United Kingdom
| | - Frank O. Glöckner
- Jacobs University Bremen gGmbH, Bremen, Germany
- Max Planck Institute for Marine Microbiology, 28359 Bremen, Germany
| | - Olga V. Golyshina
- School of Biological Sciences, Bangor University, LL57 2UW Bangor, United Kingdom
| | - Michail M. Yakimov
- Institute for Coastal Marine Environment, Consiglio Nazionale delle Ricerche, 98122 Messina, Italy
- Immanuel Kant Baltic Federal University, 236041 Kaliningrad, Russia
| | - Alexei Savchenko
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, M5S 3E5 Toronto, Ontario, Canada
| | - Karl-Erich Jaeger
- Institut für Molekulare Enzymtechnologie, Heinrich-Heine-Universität Düsseldorf, 52425 Jülich, Germany
- Institute for Bio- and Geosciences IBG-1: Biotechnology, Forschunsgzentrum Jülich GmbH, 52425 Jülich, Germany
| | - Alexander F. Yakunin
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, M5S 3E5 Toronto, Ontario, Canada
| | - Wolfgang R. Streit
- Biozentrum Klein Flottbek, Mikrobiologie & Biotechnologie, Universität Hamburg, 22609 Hamburg, Germany
| | - Peter N. Golyshin
- School of Biological Sciences, Bangor University, LL57 2UW Bangor, United Kingdom
| | - Víctor Guallar
- Barcelona Supercomputing Center (BSC), 08034 Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain
| | - Manuel Ferrer
- Institute of Catalysis, Consejo Superior de Investigaciones Científicas, 28049 Madrid, Spain
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169
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Yun EJ, Oh EJ, Liu JJ, Yu S, Kim DH, Kwak S, Kim KH, Jin YS. Promiscuous activities of heterologous enzymes lead to unintended metabolic rerouting in Saccharomyces cerevisiae engineered to assimilate various sugars from renewable biomass. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:140. [PMID: 29785207 PMCID: PMC5950193 DOI: 10.1186/s13068-018-1135-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2018] [Accepted: 04/28/2018] [Indexed: 05/08/2023]
Abstract
BACKGROUND Understanding the global metabolic network, significantly perturbed upon promiscuous activities of foreign enzymes and different carbon sources, is crucial for systematic optimization of metabolic engineering of yeast Saccharomyces cerevisiae. Here, we studied the effects of promiscuous activities of overexpressed enzymes encoded by foreign genes on rerouting of metabolic fluxes of an engineered yeast capable of assimilating sugars from renewable biomass by profiling intracellular and extracellular metabolites. RESULTS Unbiased metabolite profiling of the engineered S. cerevisiae strain EJ4 revealed promiscuous enzymatic activities of xylose reductase and xylitol dehydrogenase on galactose and galactitol, respectively, resulting in accumulation of galactitol and tagatose during galactose fermentation. Moreover, during glucose fermentation, a trisaccharide consisting of glucose accumulated outside of the cells probably owing to the promiscuous and transglycosylation activity of β-glucosidase expressed for hydrolyzing cellobiose. Meanwhile, higher accumulation of fatty acids and secondary metabolites was observed during xylose and cellobiose fermentations, respectively. CONCLUSIONS The heterologous enzymes functionally expressed in S. cerevisiae showed promiscuous activities that led to unintended metabolic rerouting in strain EJ4. Such metabolic rerouting could result in a low yield and productivity of a final product due to the formation of unexpected metabolites. Furthermore, the global metabolic network can be significantly regulated by carbon sources, thus yielding different patterns of metabolite production. This metabolomic study can provide useful information for yeast strain improvement and systematic optimization of yeast metabolism to manufacture bio-based products.
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Affiliation(s)
- Eun Ju Yun
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801 USA
- Department of Biotechnology, Graduate School, Korea University, Seoul, 02841 South Korea
| | - Eun Joong Oh
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801 USA
| | - Jing-Jing Liu
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801 USA
| | - Sora Yu
- Department of Biotechnology, Graduate School, Korea University, Seoul, 02841 South Korea
| | - Dong Hyun Kim
- Department of Biotechnology, Graduate School, Korea University, Seoul, 02841 South Korea
| | - Suryang Kwak
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801 USA
| | - Kyoung Heon Kim
- Department of Biotechnology, Graduate School, Korea University, Seoul, 02841 South Korea
| | - Yong-Su Jin
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801 USA
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170
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Zhang F, Wang YH, Tang X, Wu R. Catalytic promiscuity of the non-native FPP substrate in the TEAS enzyme: non-negligible flexibility of the carbocation intermediate. Phys Chem Chem Phys 2018; 20:15061-15073. [DOI: 10.1039/c8cp02262c] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
By QM(DFT)/MM MD simulations, it has been revealed that the non-native substrate catalytic promiscuity of TEAS (one of the sesquiterpene cyclases) is mostly attributable to its notable conformational flexibility of the branching intermediate bisabolyl cation.
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Affiliation(s)
- Fan Zhang
- School of Pharmaceutical Sciences
- Sun Yat-sen University
- Guangzhou 510006
- China
| | - Yong-Heng Wang
- School of Pharmaceutical Sciences
- Sun Yat-sen University
- Guangzhou 510006
- China
| | - Xiaowen Tang
- School of Pharmaceutical Sciences
- Sun Yat-sen University
- Guangzhou 510006
- China
| | - Ruibo Wu
- School of Pharmaceutical Sciences
- Sun Yat-sen University
- Guangzhou 510006
- China
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171
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Cassimjee KE, Hendil-Forssell P, Volkov A, Krog A, Malmo J, Aune TEV, Knecht W, Miskelly IR, Moody TS, Svedendahl Humble M. Streamlined Preparation of Immobilized Candida antarctica Lipase B. ACS OMEGA 2017; 2:8674-8677. [PMID: 30023589 PMCID: PMC6045393 DOI: 10.1021/acsomega.7b01510] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/08/2017] [Accepted: 11/22/2017] [Indexed: 06/08/2023]
Abstract
Candida antarctica lipase B (CalB) was efficiently expressed (6.2 g L-1) in Escherichia coli by utilizing an N-terminal tag cassette and the XylS/Pm expression system in a fed-batch bioreactor; subsequent direct binding to EziG from crude extracts resulted in an immobilized catalyst with superior activity to Novozym 435.
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Affiliation(s)
| | | | - Alexey Volkov
- EnginZyme
AB, Teknikringen 38A, SE-114 28 Stockholm, Sweden
| | - Anne Krog
- Vectron
Biosolutions AS, Abels
gt 5, 7030 Trondheim, Norway
| | - Jostein Malmo
- Vectron
Biosolutions AS, Abels
gt 5, 7030 Trondheim, Norway
| | | | - Wolfgang Knecht
- Lund
Protein Production Platform, Lund University, Sölvegatan 35, SE-223 62 Lund, Sweden
| | - Iain R. Miskelly
- Department
of Biocatalysis and Isotope Chemistry, Almac
Group Limited, 20 Seagoe
Industrial Estate, Craigavon BT63 5QD, U.K.
- Arran
Chemical Company Limited, Unit 1 Monksland Industrial Estate, Athlone, County Roscommon N37 DN24, Ireland
| | - Thomas S. Moody
- Department
of Biocatalysis and Isotope Chemistry, Almac
Group Limited, 20 Seagoe
Industrial Estate, Craigavon BT63 5QD, U.K.
- Arran
Chemical Company Limited, Unit 1 Monksland Industrial Estate, Athlone, County Roscommon N37 DN24, Ireland
| | - Maria Svedendahl Humble
- School of
Biotechnology, Division of Industrial Biotechnology, Albanova University
Centre, KTH Royal Institute of Technology, SE-106 91 Stockholm, Sweden
- Pharem
Biotech AB, Biovation
Park, Forskargatan 20 J, SE-151 36 Södertälje, Sweden
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172
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Kelly SA, Pohle S, Wharry S, Mix S, Allen CCR, Moody TS, Gilmore BF. Application of ω-Transaminases in the Pharmaceutical Industry. Chem Rev 2017; 118:349-367. [PMID: 29251912 DOI: 10.1021/acs.chemrev.7b00437] [Citation(s) in RCA: 202] [Impact Index Per Article: 28.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Chiral amines are valuable building blocks for the pharmaceutical industry. ω-TAms have emerged as an exciting option for their synthesis, offering a potential "green alternative" to overcome the drawbacks associated with conventional chemical methods. In this review, we explore the application of ω-TAms for pharmaceutical production. We discuss the diverse array of reactions available involving ω-TAms and process considerations of their use in both kinetic resolution and asymmetric synthesis. With the aid of specific drug intermediates and APIs, we chart the development of ω-TAms using protein engineering and their contribution to elegant one-pot cascades with other enzymes, including carbonyl reductases (CREDs), hydrolases and monoamine oxidases (MAOs), providing a comprehensive overview of their uses, beginning with initial applications through to the present day.
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Affiliation(s)
- Stephen A Kelly
- School of Pharmacy, Queen's University Belfast , Belfast BT9 7BL, N. Ireland, U.K
| | - Stefan Pohle
- Almac , Department of Biocatalysis & Isotope Chemistry, 20 Seagoe Industrial Estate, Craigavon BT63 5QD, N. Ireland, U.K
| | - Scott Wharry
- Almac , Department of Biocatalysis & Isotope Chemistry, 20 Seagoe Industrial Estate, Craigavon BT63 5QD, N. Ireland, U.K
| | - Stefan Mix
- Almac , Department of Biocatalysis & Isotope Chemistry, 20 Seagoe Industrial Estate, Craigavon BT63 5QD, N. Ireland, U.K
| | - Christopher C R Allen
- School of Biological Sciences, Queen's University Belfast , Belfast BT9 7BL, N. Ireland, U.K
| | - Thomas S Moody
- Almac , Department of Biocatalysis & Isotope Chemistry, 20 Seagoe Industrial Estate, Craigavon BT63 5QD, N. Ireland, U.K.,Arran Chemical Company Limited , Unit 1 Monksland Industrial Estate, Athlone, Co. Roscommon, Ireland
| | - Brendan F Gilmore
- School of Pharmacy, Queen's University Belfast , Belfast BT9 7BL, N. Ireland, U.K
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173
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Ding X, Zhang XD, Dong CL, Guan Z, He YH. Enzyme-Catalyzed Cascade Michael/Cyclization Reaction for the Synthesis of 3,4-Dihydropyran Derivatives by Using a Protease. Catal Letters 2017. [DOI: 10.1007/s10562-017-2275-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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174
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Evolution of a flipped pathway creates metabolic innovation in tomato trichomes through BAHD enzyme promiscuity. Nat Commun 2017; 8:2080. [PMID: 29234041 PMCID: PMC5727100 DOI: 10.1038/s41467-017-02045-7] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Accepted: 11/03/2017] [Indexed: 01/29/2023] Open
Abstract
Plants produce hundreds of thousands of structurally diverse specialized metabolites via multistep biosynthetic networks, including compounds of ecological and therapeutic importance. These pathways are restricted to specific plant groups, and are excellent systems for understanding metabolic evolution. Tomato and other plants in the nightshade family synthesize protective acylated sugars in the tip cells of glandular trichomes on stems and leaves. We describe a metabolic innovation in wild tomato species that contributes to acylsucrose structural diversity. A small number of amino acid changes in two acylsucrose acyltransferases alter their acyl acceptor preferences, resulting in reversal of their order of reaction and increased product diversity. This study demonstrates how small numbers of amino acid changes in multiple pathway enzymes can lead to diversification of specialized metabolites in plants. It also highlights the power of a combined genetic, genomic and in vitro biochemical approach to identify the evolutionary mechanisms leading to metabolic novelty. Plants produce large numbers of structurally diverse metabolites through multistep pathways that often use the same precursors. Here the authors utilize the pathway leading to the production of acylated sucroses in the tomato plant to illustrate how metabolite diversity can arise through biochemical pathway evolution.
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175
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Guezane-Lakoud S, Toffano M, Aribi-Zouioueche L. Promiscuous lipase catalyzed a new P-C bond formation: Green and efficient protocol for one-pot synthesis of α-aminophosphonates. HETEROATOM CHEMISTRY 2017. [DOI: 10.1002/hc.21408] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Samia Guezane-Lakoud
- Ecocompatible Asymmetric Catalysis Laboratory (LCAE); Badji Mokhtar Annaba-University; Annaba Algeria
| | - Martial Toffano
- Equipe de Catalyse Moléculaire-ICMMO- CNRS UMR8182 Bât 420; Université Paris-Sud; Orsay France
| | - Louisa Aribi-Zouioueche
- Ecocompatible Asymmetric Catalysis Laboratory (LCAE); Badji Mokhtar Annaba-University; Annaba Algeria
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176
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177
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178
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Dai L, Tao F, Tang H, Guo Y, Shen Y, Xu P. Directing enzyme devolution for biosynthesis of alkanols and 1,n-alkanediols from natural polyhydroxy compounds. Metab Eng 2017; 44:70-80. [DOI: 10.1016/j.ymben.2017.09.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2017] [Revised: 09/07/2017] [Accepted: 09/13/2017] [Indexed: 12/01/2022]
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179
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Jia HY, Zong MH, Yu HL, Li N. Dehydrogenase-Catalyzed Oxidation of Furanics: Exploitation of Hemoglobin Catalytic Promiscuity. CHEMSUSCHEM 2017; 10:3524-3528. [PMID: 28786206 DOI: 10.1002/cssc.201701288] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Revised: 08/06/2017] [Indexed: 06/07/2023]
Abstract
The catalytic promiscuity of hemoglobin (Hb) was explored for regenerating oxidized nicotinamide cofactors [NAD(P)+ ]. With H2 O2 as oxidant, Hb efficiently oxidized NAD(P)H into NAD(P)+ within 30 min. The new NAD(P)+ regeneration system was coupled with horse liver alcohol dehydrogenase (HLADH) for the oxidation of bio-based furanics such as furfural and 5-hydroxymethylfurfural (HMF). The target acids (e.g., 2,5-furandicarboxylic acid, FDCA) were prepared with moderate-to-good yields. The enzymatic regeneration method was applied in l-glutamic dehydrogenase (DH)-mediated oxidative deamination of lglutamate and for l-lactic-DH-mediated oxidation of l-lactate, which furnished α-ketoglutarate and pyruvate in yields of 97 % and 81 %, respectively. A total turnover number (TTON) of up to approximately 5000 for cofactor and an E factor of less than 110 were obtained in the bi-enzymatic cascade synthesis of α-ketoglutarate. Overall, a proof-of-concept based on catalytic promiscuity of Hb was provided for in situ regeneration of NAD(P)+ in DH-catalyzed oxidation reactions.
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Affiliation(s)
- Hao-Yu Jia
- State Key Laboratory of Pulp and Paper Engineering, School of Food Science and Engineering, South China University of Technology, 381 Wushan Road, Guangzhou, 510640, P.R. China
| | - Min-Hua Zong
- State Key Laboratory of Pulp and Paper Engineering, School of Food Science and Engineering, South China University of Technology, 381 Wushan Road, Guangzhou, 510640, P.R. 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, P.R. China
| | - Ning Li
- State Key Laboratory of Pulp and Paper Engineering, School of Food Science and Engineering, South China University of Technology, 381 Wushan Road, Guangzhou, 510640, P.R. China
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180
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Freund GS, O’Brien TE, Vinson L, Carlin DA, Yao A, Mak WS, Tagkopoulos I, Facciotti MT, Tantillo DJ, Siegel JB. Elucidating Substrate Promiscuity within the FabI Enzyme Family. ACS Chem Biol 2017; 12:2465-2473. [PMID: 28820936 DOI: 10.1021/acschembio.7b00400] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The rapidly growing appreciation of enzymes' catalytic and substrate promiscuity may lead to their expanded use in the fields of chemical synthesis and industrial biotechnology. Here, we explore the substrate promiscuity of enoyl-acyl carrier protein reductases (commonly known as FabI) and how that promiscuity is a function of inherent reactivity and the geometric demands of the enzyme's active site. We demonstrate that these enzymes catalyze the reduction of a wide range of substrates, particularly α,β-unsaturated aldehydes. In addition, we demonstrate that a combination of quantum mechanical hydride affinity calculations and molecular docking can be used to rapidly categorize compounds that FabI can use as substrates. The results here provide new insight into the determinants of catalysis for FabI and set the stage for the development of a new assay for drug discovery, organic synthesis, and novel biocatalysts.
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Affiliation(s)
- Gabriel S. Freund
- Genome
Center, University of California Davis, One Shields Avenue, Davis, California 95616, United States
- Department
of Mathematics, University of California Davis, Davis, California United States
| | - Terrence E. O’Brien
- Genome
Center, University of California Davis, One Shields Avenue, Davis, California 95616, United States
- Department
of Chemistry, University of California Davis, Davis, California United States
| | - Logan Vinson
- Genome
Center, University of California Davis, One Shields Avenue, Davis, California 95616, United States
| | - Dylan Alexander Carlin
- Genome
Center, University of California Davis, One Shields Avenue, Davis, California 95616, United States
- Biophysics
Graduate Group, University of California Davis, Davis, California United States
| | - Andrew Yao
- Genome
Center, University of California Davis, One Shields Avenue, Davis, California 95616, United States
| | - Wai Shun Mak
- Genome
Center, University of California Davis, One Shields Avenue, Davis, California 95616, United States
- Department
of Chemistry, University of California Davis, Davis, California United States
| | - Ilias Tagkopoulos
- Genome
Center, University of California Davis, One Shields Avenue, Davis, California 95616, United States
- Department
of Computer Science, University of California Davis, Davis, California United States
| | - Marc T. Facciotti
- Genome
Center, University of California Davis, One Shields Avenue, Davis, California 95616, United States
- Department
of Biomedical Engineering, University of California, Davis, California United States
| | - Dean J. Tantillo
- Department
of Chemistry, University of California Davis, Davis, California United States
| | - Justin B. Siegel
- Genome
Center, University of California Davis, One Shields Avenue, Davis, California 95616, United States
- Department
of Chemistry, University of California Davis, Davis, California United States
- Department of Biochemistry & Molecular Medicine, University of CaliforniaDavis, Davis, California United States
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181
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Sharma AK, Jaiswal SK, Chaudhary N, Sharma VK. A novel approach for the prediction of species-specific biotransformation of xenobiotic/drug molecules by the human gut microbiota. Sci Rep 2017; 7:9751. [PMID: 28852076 PMCID: PMC5575299 DOI: 10.1038/s41598-017-10203-6] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 08/07/2017] [Indexed: 11/09/2022] Open
Abstract
The human gut microbiota is constituted of a diverse group of microbial species harbouring an enormous metabolic potential, which can alter the metabolism of orally administered drugs leading to individual/population-specific differences in drug responses. Considering the large heterogeneous pool of human gut bacteria and their metabolic enzymes, investigation of species-specific contribution to xenobiotic/drug metabolism by experimental studies is a challenging task. Therefore, we have developed a novel computational approach to predict the metabolic enzymes and gut bacterial species, which can potentially carry out the biotransformation of a xenobiotic/drug molecule. A substrate database was constructed for metabolic enzymes from 491 available human gut bacteria. The structural properties (fingerprints) from these substrates were extracted and used for the development of random forest models, which displayed average accuracies of up to 98.61% and 93.25% on cross-validation and blind set, respectively. After the prediction of EC subclass, the specific metabolic enzyme (EC) is identified using a molecular similarity search. The performance was further evaluated on an independent set of FDA-approved drugs and other clinically important molecules. To our knowledge, this is the only available approach implemented as 'DrugBug' tool for the prediction of xenobiotic/drug metabolism by metabolic enzymes of human gut microbiota.
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Affiliation(s)
- Ashok K Sharma
- Metagenomics and Systems Biology Laboratory, Indian Institute of Science Education and Research, Bhopal, Madhya Pradesh, India
| | - Shubham K Jaiswal
- Metagenomics and Systems Biology Laboratory, Indian Institute of Science Education and Research, Bhopal, Madhya Pradesh, India
| | - Nikhil Chaudhary
- Metagenomics and Systems Biology Laboratory, Indian Institute of Science Education and Research, Bhopal, Madhya Pradesh, India
| | - Vineet K Sharma
- Metagenomics and Systems Biology Laboratory, Indian Institute of Science Education and Research, Bhopal, Madhya Pradesh, India.
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182
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Koszelewski D, Paprocki D, Madej A, Borys F, Brodzka A, Ostaszewski R. Enzymatic Tandem Approach to Knoevenagel Condensation of Acetaldehyde with Acidic Methylene Compounds in Organic Media. European J Org Chem 2017. [DOI: 10.1002/ejoc.201700936] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Dominik Koszelewski
- Institute of Organic Chemistry; Polish Academy of Sciences; Kasprzaka 44/52 01-224 Warsaw Poland
| | - Daniel Paprocki
- Institute of Organic Chemistry; Polish Academy of Sciences; Kasprzaka 44/52 01-224 Warsaw Poland
| | - Arleta Madej
- Institute of Organic Chemistry; Polish Academy of Sciences; Kasprzaka 44/52 01-224 Warsaw Poland
| | - Filip Borys
- Institute of Organic Chemistry; Polish Academy of Sciences; Kasprzaka 44/52 01-224 Warsaw Poland
| | - Anna Brodzka
- Institute of Organic Chemistry; Polish Academy of Sciences; Kasprzaka 44/52 01-224 Warsaw Poland
| | - Ryszard Ostaszewski
- Institute of Organic Chemistry; Polish Academy of Sciences; Kasprzaka 44/52 01-224 Warsaw Poland
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183
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Sandoval BA, Meichan AJ, Hyster TK. Enantioselective Hydrogen Atom Transfer: Discovery of Catalytic Promiscuity in Flavin-Dependent 'Ene'-Reductases. J Am Chem Soc 2017; 139:11313-11316. [PMID: 28780870 DOI: 10.1021/jacs.7b05468] [Citation(s) in RCA: 90] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Flavin has long been known to function as a single electron reductant in biological settings, but this reactivity has rarely been observed with flavoproteins used in organic synthesis. Here we describe the discovery of an enantioselective radical dehalogenation pathway for α-bromoesters using flavin-dependent 'ene'-reductases. Mechanistic experiments support the role of flavin hydroquinone as a single electron reductant, flavin semiquinone as the hydrogen atom source, and the enzyme as the source of chirality.
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Affiliation(s)
- Braddock A Sandoval
- Department of Chemistry, Princeton University , Princeton, New Jersey 08544, United States
| | - Andrew J Meichan
- Department of Chemistry, Princeton University , Princeton, New Jersey 08544, United States
| | - Todd K Hyster
- Department of Chemistry, Princeton University , Princeton, New Jersey 08544, United States
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184
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Affiliation(s)
- Toshiyuki Itoh
- Department
of Chemistry and Biotechnology, Graduate School of Engineering and ‡Center for Research
on Green Sustainable Chemistry, Tottori University, 4-101 Koyama-minami, Tottori 680-8552, Japan
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185
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Roth S, Präg A, Wechsler C, Marolt M, Ferlaino S, Lüdeke S, Sandon N, Wetzl D, Iding H, Wirz B, Müller M. Extended Catalytic Scope of a Well-Known Enzyme: Asymmetric Reduction of Iminium Substrates by Glucose Dehydrogenase. Chembiochem 2017; 18:1703-1706. [PMID: 28722796 DOI: 10.1002/cbic.201700261] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Indexed: 11/10/2022]
Abstract
NADP(H)-dependent imine reductases (IREDs) are of interest in biocatalytic research due to their ability to generate chiral amines from imine/iminium substrates. In reaction protocols involving IREDs, glucose dehydrogenase (GDH) is generally used to regenerate the expensive cofactor NADPH by oxidation of d-glucose to gluconolactone. We have characterized different IREDs with regard to reduction of a set of bicyclic iminium compounds and have utilized 1 H NMR and GC analyses to determine degree of substrate conversion and product enantiomeric excess (ee). All IREDs reduced the tested iminium compounds to the corresponding chiral amines. Blank experiments without IREDs also showed substrate conversion, however, thus suggesting an iminium reductase activity of GDH. This unexpected observation was confirmed by additional experiments with GDHs of different origin. The reduction of C=N bonds with good levels of conversion (>50 %) and excellent enantioselectivity (up to >99 % ee) by GDH represents a promiscuous catalytic activity of this enzyme.
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Affiliation(s)
- Sebastian Roth
- Institut für Pharmazeutische Wissenschaften, Albert-Ludwigs-Universität Freiburg, Albertstrasse 25, 79104, Freiburg, Germany
| | - Andreas Präg
- Institut für Pharmazeutische Wissenschaften, Albert-Ludwigs-Universität Freiburg, Albertstrasse 25, 79104, Freiburg, Germany
| | - Cindy Wechsler
- Institut für Pharmazeutische Wissenschaften, Albert-Ludwigs-Universität Freiburg, Albertstrasse 25, 79104, Freiburg, Germany
| | - Marija Marolt
- Institut für Pharmazeutische Wissenschaften, Albert-Ludwigs-Universität Freiburg, Albertstrasse 25, 79104, Freiburg, Germany
| | - Sascha Ferlaino
- Institut für Pharmazeutische Wissenschaften, Albert-Ludwigs-Universität Freiburg, Albertstrasse 25, 79104, Freiburg, Germany
| | - Steffen Lüdeke
- Institut für Pharmazeutische Wissenschaften, Albert-Ludwigs-Universität Freiburg, Albertstrasse 25, 79104, Freiburg, Germany
| | - Nicolas Sandon
- Process Chemistry and Catalysis, F. Hoffmann-La Roche, Ltd., 4070, Basel, Switzerland
| | - Dennis Wetzl
- Process Chemistry and Catalysis, F. Hoffmann-La Roche, Ltd., 4070, Basel, Switzerland
| | - Hans Iding
- Process Chemistry and Catalysis, F. Hoffmann-La Roche, Ltd., 4070, Basel, Switzerland
| | - Beat Wirz
- Process Chemistry and Catalysis, F. Hoffmann-La Roche, Ltd., 4070, Basel, Switzerland
| | - Michael Müller
- Institut für Pharmazeutische Wissenschaften, Albert-Ludwigs-Universität Freiburg, Albertstrasse 25, 79104, Freiburg, Germany
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186
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Martínez-Núñez MA, Rodríguez-Escamilla Z, Rodríguez-Vázquez K, Pérez-Rueda E. Tracing the Repertoire of Promiscuous Enzymes along the Metabolic Pathways in Archaeal Organisms. Life (Basel) 2017; 7:life7030030. [PMID: 28703743 PMCID: PMC5617955 DOI: 10.3390/life7030030] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Revised: 07/09/2017] [Accepted: 07/10/2017] [Indexed: 01/10/2023] Open
Abstract
The metabolic pathways that carry out the biochemical transformations sustaining life depend on the efficiency of their associated enzymes. In recent years, it has become clear that promiscuous enzymes have played an important role in the function and evolution of metabolism. In this work we analyze the repertoire of promiscuous enzymes in 89 non-redundant genomes of the Archaea cellular domain. Promiscuous enzymes are defined as those proteins with two or more different Enzyme Commission (E.C.) numbers, according the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. From this analysis, it was found that the fraction of promiscuous enzymes is lower in Archaea than in Bacteria. A greater diversity of superfamily domains is associated with promiscuous enzymes compared to specialized enzymes, both in Archaea and Bacteria, and there is an enrichment of substrate promiscuity rather than catalytic promiscuity in the archaeal enzymes. Finally, the presence of promiscuous enzymes in the metabolic pathways was found to be heterogeneously distributed at the domain level and in the phyla that make up the Archaea. These analyses increase our understanding of promiscuous enzymes and provide additional clues to the evolution of metabolism in Archaea.
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Affiliation(s)
- Mario Alberto Martínez-Núñez
- Laboratorio de Estudios Ecogenómicos, Facultad de Ciencias, Unidad Académica de Ciencias y Tecnología de la UNAM en Yucatán, Universidad Nacional Autónoma de México, Carretera Sierra Papacal-Chuburna Km. 5, C.P. 97302, Mérida, Yucatán, Mexico.
| | - Zuemy Rodríguez-Escamilla
- Departamento de Microbiología, Instituto de Biotecnología, Universidad Nacional, Autónoma de México, C.P. 62210, Cuernavaca, Morelos, Mexico.
| | - Katya Rodríguez-Vázquez
- Instituto de Investigaciones en Matemáticas Aplicadas y en Sistemas, Universidad Nacional Autónoma de México, Ciudad Universitaria, C.P. 04510, Ciudad de México, Mexico.
| | - Ernesto Pérez-Rueda
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, C.P. 62210, Cuernavaca, Morelos, Mexico.
- Instituto de Investigaciones en Matemáticas Aplicadas y en Sistemas, Universidad Nacional Autónoma de México, Unidad Académica Yucatán, Carretera Sierra Papacal-Chuburna Km. 5, C.P. 97302, Mérida, Yucatán, Mexico.
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187
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Sharma P, Guptasarma P. Endoglucanase activity at a second site in Pyrococcus furiosus triosephosphate isomerase-Promiscuity or compensation for a metabolic handicap? FEBS Open Bio 2017; 7:1126-1143. [PMID: 28781953 PMCID: PMC5537068 DOI: 10.1002/2211-5463.12249] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Revised: 03/05/2017] [Accepted: 05/23/2017] [Indexed: 01/16/2023] Open
Abstract
The eight‐stranded (β/α)8 barrel fold known as the Triosephosphate isomerase (TIM) barrel is the most commonly observed fold in enzymes, displaying an eightfold structural symmetry. The sequences and structures of different TIM barrel enzymes suggest that nature exploits the modularity inherent in the eightfold symmetry to generate enzymes with diverse enzymatic activities and, in certain cases, more than one catalytic activity per enzyme. Here, we report the discovery, verification, and characterization of such an additional activity, a novel endoglucanase/cellulase activity in what is otherwise a triosephosphate isomerase from the hyperthermophile archaeon Pyrococcus furiosus (PfuTIM). The activity is seen in two different ranges of temperatures, with one maximum at 40 °C and a second maximum close to 100 °C. The endoglucanase/cellulase activity is inhibited by norharman, a TIM inhibitor, which is suspected to bind at a site different to that of the regular substrate, glyceraldehyde‐3‐phosphate (G3P). However, endoglucanase/cellulose activity is not inhibited either by G3P analogs or by glycine‐scanning mutations involving residues in loops 1, 4, and 6 of PfuTIM, which are known to be important for TIM activity. It appears, therefore, that two different sites on PfuTIM are responsible for the observed TIM and endoglucanase activities. We discuss possible correlations between this discovery and certain unusual features of the glycolytic pathway in P. furiosus. Enzyme Pyrococcus furiosus Triosephosphate isomerase (EC:5.3.1.1)
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Affiliation(s)
- Prerna Sharma
- Department of Biological Sciences Centre for Protein Science Design and Engineering (CPSDE) Indian Institute of Science Education and Research (IISER) Mohali Punjab.,Division of Protein Science and Engineering CSIR- Institute of Microbial Technology Chandigarh India
| | - Purnananda Guptasarma
- Department of Biological Sciences Centre for Protein Science Design and Engineering (CPSDE) Indian Institute of Science Education and Research (IISER) Mohali Punjab.,Division of Protein Science and Engineering CSIR- Institute of Microbial Technology Chandigarh India
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188
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Piazzetta P, Marino T, Russo N. Mechanistic Explanation of the Weak Carbonic Anhydrase's Esterase Activity. Molecules 2017; 22:E1009. [PMID: 28629166 PMCID: PMC6152773 DOI: 10.3390/molecules22061009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Revised: 06/08/2017] [Accepted: 06/13/2017] [Indexed: 11/16/2022] Open
Abstract
In order to elucidate the elementary mechanism of the promiscuous esterase activity of human carbonic anhydrase (h-CA), we present an accurate theoretical investigation on the hydrolysis of fully-acetylated d-glucose functionalized as sulfamate. This h-CA's inhibitor is of potential relevance in cancer therapy. The study has been performed within the framework of three-layer ONIOM (QM-high:QM'-medium:MM-low) hybrid approach. The computations revealed that the hydrolysis process is not energetically favored, in agreement with the observed weak carbonic anhydrase's esterase activity.
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Affiliation(s)
- Paolo Piazzetta
- Dipartimento di Chimica e Tecnologie Chimiche (CTC), Università della Calabria, 87036 Arcavacata di Rende (CS), Italy.
| | - Tiziana Marino
- Dipartimento di Chimica e Tecnologie Chimiche (CTC), Università della Calabria, 87036 Arcavacata di Rende (CS), Italy.
| | - Nino Russo
- Dipartimento di Chimica e Tecnologie Chimiche (CTC), Università della Calabria, 87036 Arcavacata di Rende (CS), Italy.
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189
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Bayer CD, van Loo B, Hollfelder F. Specificity Effects of Amino Acid Substitutions in Promiscuous Hydrolases: Context-Dependence of Catalytic Residue Contributions to Local Fitness Landscapes in Nearby Sequence Space. Chembiochem 2017; 18:1001-1015. [PMID: 28464395 PMCID: PMC5488252 DOI: 10.1002/cbic.201600657] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Indexed: 12/18/2022]
Abstract
Catalytic promiscuity can facilitate evolution of enzyme functions-a multifunctional catalyst may act as a springboard for efficient functional adaptation. We test the effect of single mutations on multiple activities in two groups of promiscuous AP superfamily members to probe this hypothesis. We quantify the effect of site-saturating mutagenesis of an analogous, nucleophile-flanking residue in two superfamily members: an arylsulfatase (AS) and a phosphonate monoester hydrolase (PMH). Statistical analysis suggests that no one physicochemical characteristic alone explains the mutational effects. Instead, these effects appear to be dominated by their structural context. Likewise, the effect of changing the catalytic nucleophile itself is not reaction-type-specific. Mapping of "fitness landscapes" of four activities onto the possible variation of a chosen sequence position revealed tremendous potential for respecialization of AP superfamily members through single-point mutations, highlighting catalytic promiscuity as a powerful predictor of adaptive potential.
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Affiliation(s)
- Christopher D. Bayer
- Department of BiochemistryUniversity of Cambridge80 Tennis Court RoadCB2 1GACambridgeUK
- Present address: c-LEcta GmbHPerlickstrasse 504103LeipzigGermany
| | - Bert van Loo
- Department of BiochemistryUniversity of Cambridge80 Tennis Court RoadCB2 1GACambridgeUK
- Present address: Institute for Evolution and BiodiversityUniversity of MünsterHüfferstrasse 148149MünsterGermany
| | - Florian Hollfelder
- Department of BiochemistryUniversity of Cambridge80 Tennis Court RoadCB2 1GACambridgeUK
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190
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Payer SE, Sheng X, Pollak H, Wuensch C, Steinkellner G, Himo F, Glueck SM, Faber K. Exploring the Catalytic Promiscuity of Phenolic Acid Decarboxylases: Asymmetric, 1,6-Conjugate Addition of Nucleophiles Across 4-Hydroxystyrene. Adv Synth Catal 2017; 359:2066-2075. [PMID: 28713228 PMCID: PMC5488193 DOI: 10.1002/adsc.201700247] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Revised: 04/02/2017] [Indexed: 01/29/2023]
Abstract
The catalytic promiscuity of a ferulic acid decarboxylase from Enterobacter sp. (FDC_Es) and phenolic acid decarboxylases (PADs) for the asymmetric conjugate addition of water across the C=C bond of hydroxystyrenes was extended to the N‐, C‐ and S‐nucleophiles methoxyamine, cyanide and propanethiol to furnish the corresponding addition products in up to 91% ee. The products obtained from the biotransformation employing the most suitable enzyme/nucleophile pairs were isolated and characterized after optimizing the reaction conditions. Finally, a mechanistic rationale supported by quantum mechanical calculations for the highly (S)‐selective addition of cyanide is proposed. ![]()
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Affiliation(s)
- Stefan E Payer
- Department of Chemistry University of Graz Heinrichstrasse 28, A-8010 Graz Austria
| | - Xiang Sheng
- Arrhenius Laboratory Department of Organic Chemistry Stockholm University SE-106 91 Stockholm Sweden
| | - Hannah Pollak
- Department of Chemistry University of Graz Heinrichstrasse 28, A-8010 Graz Austria
| | - Christiane Wuensch
- Austrian Centre of Industrial Biotechnology (ACIB) c/o Department of Chemistry University of Graz Heinrichstrasse 28, A-8010 Graz Austria.,Department of Chemistry University of Graz Heinrichstrasse 28, A-8010 Graz Austria
| | - Georg Steinkellner
- Austrian Centre of Industrial Biotechnology (ACIB) c/o Department of Chemistry University of Graz Heinrichstrasse 28, A-8010 Graz Austria.,Center for Molecular Biosciences University of Graz Humboldtstrasse 508010 Graz Austria
| | - Fahmi Himo
- Arrhenius Laboratory Department of Organic Chemistry Stockholm University SE-106 91 Stockholm Sweden
| | - Silvia M Glueck
- Austrian Centre of Industrial Biotechnology (ACIB) c/o Department of Chemistry University of Graz Heinrichstrasse 28, A-8010 Graz Austria.,Department of Chemistry University of Graz Heinrichstrasse 28, A-8010 Graz Austria
| | - Kurt Faber
- Department of Chemistry University of Graz Heinrichstrasse 28, A-8010 Graz Austria
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191
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High-Resolution X-Ray Structures of Two Functionally Distinct Members of the Cyclic Amide Hydrolase Family of Toblerone Fold Enzymes. Appl Environ Microbiol 2017; 83:AEM.03365-16. [PMID: 28235873 DOI: 10.1128/aem.03365-16] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2016] [Accepted: 02/15/2017] [Indexed: 01/28/2023] Open
Abstract
The Toblerone fold was discovered recently when the first structure of the cyclic amide hydrolase, AtzD (a cyanuric acid hydrolase), was elucidated. We surveyed the cyclic amide hydrolase family, finding a strong correlation between phylogenetic distribution and specificity for either cyanuric acid or barbituric acid. One of six classes (IV) could not be tested due to a lack of expression of the proteins from it, and another class (V) had neither cyanuric acid nor barbituric acid hydrolase activity. High-resolution X-ray structures were obtained for a class VI barbituric acid hydrolase (1.7 Å) from a Rhodococcus species and a class V cyclic amide hydrolase (2.4 Å) from a Frankia species for which we were unable to identify a substrate. Both structures were homologous with the tetrameric Toblerone fold enzyme AtzD, demonstrating a high degree of structural conservation within the cyclic amide hydrolase family. The barbituric acid hydrolase structure did not contain zinc, in contrast with early reports of zinc-dependent activity for this enzyme. Instead, each barbituric acid hydrolase monomer contained either Na+ or Mg2+, analogous to the structural metal found in cyanuric acid hydrolase. The Frankia cyclic amide hydrolase contained no metal but instead formed unusual, reversible, intermolecular vicinal disulfide bonds that contributed to the thermal stability of the protein. The active sites were largely conserved between the three enzymes, differing at six positions, which likely determine substrate specificity.IMPORTANCE The Toblerone fold enzymes catalyze an unusual ring-opening hydrolysis with cyclic amide substrates. A survey of these enzymes shows that there is a good correlation between physiological function and phylogenetic distribution within this family of enzymes and provide insights into the evolutionary relationships between the cyanuric acid and barbituric acid hydrolases. This family of enzymes is structurally and mechanistically distinct from other enzyme families; however, to date the structure of just two, physiologically identical, enzymes from this family has been described. We present two new structures: a barbituric acid hydrolase and an enzyme of unknown function. These structures confirm that members of the CyAH family have the unusual Toblerone fold, albeit with some significant differences.
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192
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193
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Hinzpeter F, Gerland U, Tostevin F. Optimal Compartmentalization Strategies for Metabolic Microcompartments. Biophys J 2017; 112:767-779. [PMID: 28256236 PMCID: PMC5340097 DOI: 10.1016/j.bpj.2016.11.3194] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Revised: 11/18/2016] [Accepted: 11/28/2016] [Indexed: 11/16/2022] Open
Abstract
Intracellular compartmentalization of cooperating enzymes is a strategy that is frequently used by cells. Segregation of enzymes that catalyze sequential reactions can alleviate challenges such as toxic pathway intermediates, competing metabolic reactions, and slow reaction rates. Inspired by nature, synthetic biologists also seek to encapsulate engineered metabolic pathways within vesicles or proteinaceous shells to enhance the yield of industrially and pharmaceutically useful products. Although enzymatic compartments have been extensively studied experimentally, a quantitative understanding of the underlying design principles is still lacking. Here, we study theoretically how the size and enzymatic composition of compartments should be chosen so as to maximize the productivity of a model metabolic pathway. We find that maximizing productivity requires compartments larger than a certain critical size. The enzyme density within each compartment should be tuned according to a power-law scaling in the compartment size. We explain these observations using an analytically solvable, well-mixed approximation. We also investigate the qualitatively different compartmentalization strategies that emerge in parameter regimes where this approximation breaks down. Our results suggest that the different sizes and enzyme packings of α- and β-carboxysomes each constitute an optimal compartmentalization strategy given the properties of their respective protein shells.
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Affiliation(s)
- Florian Hinzpeter
- Department of Physics, Technische Universität München, Garching, Germany.
| | - Ulrich Gerland
- Department of Physics, Technische Universität München, Garching, Germany
| | - Filipe Tostevin
- Department of Physics, Technische Universität München, Garching, Germany
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194
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Metabolic anchor reactions for robust biorefining. Metab Eng 2017; 40:1-4. [PMID: 28232136 PMCID: PMC5368410 DOI: 10.1016/j.ymben.2017.02.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Revised: 02/03/2017] [Accepted: 02/19/2017] [Indexed: 11/20/2022]
Abstract
Microbial cell factories based on renewable carbon sources are fundamental to a sustainable bio-economy. The economic feasibility of producer cells requires robust performance balancing growth and production. However, the inherent competition between these two objectives often leads to instability and reduces productivity. While algorithms exist to design metabolic network reduction strategies for aligning these objectives, the biochemical basis of the growth-product coupling has remained unresolved. Here, we reveal key reactions in the cellular biochemical repertoire as universal anchor reactions for aligning cell growth and production. A necessary condition for a reaction to be an anchor is that it splits a substrate into two or more molecules. By searching the currently known biochemical reaction space, we identify 62 C-C cleaving anchor reactions, such as isocitrate lyase (EC 4.1.3.1) and L-tryptophan indole-lyase (EC 4.1.99.1), which are relevant for biorefining. The here identified anchor reactions mark network nodes for basing growth-coupled metabolic engineering and novel pathway designs.
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195
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Ferre FT, Resende JA, Schultz J, Mangrich AS, Faria RB, Rocha AB, Scarpellini M. Catalytic promiscuity of mononuclear copper(II) complexes in mild conditions: Catechol and cyclohexane oxidations. Polyhedron 2017. [DOI: 10.1016/j.poly.2016.11.045] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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196
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Enzyme-catalyzed direct three-component aza-Diels–Alder reaction using lipase from Candida sp. 99–125. CHINESE CHEM LETT 2017. [DOI: 10.1016/j.cclet.2016.10.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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197
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Gajęcka M, Zielonka Ł, Gajęcki M. Activity of Zearalenone in the Porcine Intestinal Tract. Molecules 2016; 22:E18. [PMID: 28029134 PMCID: PMC6155780 DOI: 10.3390/molecules22010018] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2016] [Revised: 12/21/2016] [Accepted: 12/21/2016] [Indexed: 12/16/2022] Open
Abstract
This study demonstrates that low doses (somewhat above the No Observed Adverse Effect Level, NOAEL) of the mycoestrogen zearalenone (ZEN) and its metabolites display multispecificity towards various biological targets in gilts. The observed responses in gilts were surprising. The presence of ZEN and zearalenols (ZELs) did not evoke a response in the porcine gastrointestinal tract, which was attributed to dietary tolerance. Lymphocyte proliferation was intensified in jejunal mesenteric lymph nodes, and lymphocyte counts increased in the jejunal epithelium with time of exposure. In the distal digestive tract, fecal bacterial counts decreased, the activity of fecal bacterial enzymes and lactic acid bacteria increased, and cecal water was characterized by higher genotoxicity. The accompanying hyperestrogenism led to changes in mRNA activity of selected enzymes (cytochrome P450, hydroxysteroid dehydrogenases, nitric oxide synthases) and receptors (estrogen and progesterone receptors), and it stimulated post-translational modifications which play an important role in non-genomic mechanisms of signal transmission. Hyperestrogenism influences the regulation of the host's steroid hormones (estron, estradiol and progesteron), it affects the virulence of bacterial genes encoding bacterial hydroxysteroid dehydrogenases (HSDs), and it participates in detoxification processes by slowing down intestinal activity, provoking energy deficits and promoting antiporter activity at the level of enterocytes. In most cases, hyperestrogenism fulfils all of the above roles. The results of this study indicate that low doses of ZEN alleviate inflammatory processes in the digestive system, in particular in the proximal and distal intestinal tract, and increase body weight gains in gilts.
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Affiliation(s)
- Magdalena Gajęcka
- Department of Veterinary Prevention and Feed Hygiene, Faculty of Veterinary Medicine, University of Warmia and Mazury in Olsztyn, Oczapowskiego 13/29, 10-718 Olsztyn, Poland.
- Department of Epizootiology, Faculty of Veterinary Medicine, University of Warmia and Mazury in Olsztyn, Oczapowskiego 13/01, 10-718 Olsztyn, Poland.
| | - Łukasz Zielonka
- Department of Veterinary Prevention and Feed Hygiene, Faculty of Veterinary Medicine, University of Warmia and Mazury in Olsztyn, Oczapowskiego 13/29, 10-718 Olsztyn, Poland.
| | - Maciej Gajęcki
- Department of Veterinary Prevention and Feed Hygiene, Faculty of Veterinary Medicine, University of Warmia and Mazury in Olsztyn, Oczapowskiego 13/29, 10-718 Olsztyn, Poland.
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198
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Baier F, Copp JN, Tokuriki N. Evolution of Enzyme Superfamilies: Comprehensive Exploration of Sequence–Function Relationships. Biochemistry 2016; 55:6375-6388. [DOI: 10.1021/acs.biochem.6b00723] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- F. Baier
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - J. N. Copp
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - N. Tokuriki
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
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199
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Graf MMH, Maurer M, Oostenbrink C. Free-energy calculations of residue mutations in a tripeptide using various methods to overcome inefficient sampling. J Comput Chem 2016; 37:2597-605. [PMID: 27634475 PMCID: PMC5082540 DOI: 10.1002/jcc.24488] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Revised: 08/22/2016] [Accepted: 08/24/2016] [Indexed: 01/19/2023]
Abstract
Previous free-energy calculations have shown that the seemingly simple transformation of the tripeptide KXK to KGK in water holds some unobvious challenges concerning the convergence of the forward and backward thermodynamic integration processes (i.e., hysteresis). In the current study, the central residue X was either alanine, serine, glutamic acid, lysine, phenylalanine, or tyrosine. Interestingly, the transformation from alanine to glycine yielded the highest hysteresis in relation to the extent of the chemical change of the side chain. The reason for that could be attributed to poor sampling of φ2 /ψ2 dihedral angles along the transformation. Altering the nature of alanine's Cβ atom drastically improved the sampling and at the same time led to the identification of high energy barriers as cause for it. Consequently, simple strategies to overcome these barriers are to increase simulation time (computationally expensive) or to use enhanced sampling techniques such as Hamiltonian replica exchange molecular dynamics and one-step perturbation. © 2016 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc.
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Affiliation(s)
- Michael M H Graf
- Institute of Molecular Modeling and Simulation, Department of Material Sciences and Process Engineering, BOKU, University of Natural Resources and Life Sciences, Muthgasse 18, AT-1190, Vienna, Austria
| | - Manuela Maurer
- Institute of Molecular Modeling and Simulation, Department of Material Sciences and Process Engineering, BOKU, University of Natural Resources and Life Sciences, Muthgasse 18, AT-1190, Vienna, Austria
| | - Chris Oostenbrink
- Institute of Molecular Modeling and Simulation, Department of Material Sciences and Process Engineering, BOKU, University of Natural Resources and Life Sciences, Muthgasse 18, AT-1190, Vienna, Austria.
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200
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Liang YR, Wu Q, Lin XF. Effect of Additives on the Selectivity and Reactivity of Enzymes. CHEM REC 2016; 17:90-121. [PMID: 27490244 DOI: 10.1002/tcr.201600016] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Indexed: 01/05/2023]
Abstract
Enzymes have been widely used as efficient, eco-friendly, and biodegradable catalysts in organic chemistry due to their mild reaction conditions and high selectivity and efficiency. In recent years, the catalytic promiscuity of many enzymes in unnatural reactions has been revealed and studied by chemists and biochemists, which has expanded the application potential of enzymes. To enhance the selectivity and activity of enzymes in their natural or promiscuous reactions, many methods have been recommended, such as protein engineering, process engineering, and media engineering. Among them, the additive approach is very attractive because of its simplicity to use and high efficiency. In this paper, we will review the recent developments about the applications of additives to improve the catalytic performances of enzymes in their natural and promiscuous reactions. These additives include water, organic bases, water mimics, cosolvents, crown ethers, salts, surfactants, and some particular molecular additives.
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Affiliation(s)
- Yi-Ru Liang
- Department of Chemistry, Zhejiang University, Hangzhou, 310027, P. R. China
| | - Qi Wu
- Department of Chemistry, Zhejiang University, Hangzhou, 310027, P. R. China
| | - Xian-Fu Lin
- Department of Chemistry, Zhejiang University, Hangzhou, 310027, P. R. China
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