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Li Y, Zhang P, Sun Z, Li H, Ge R, Sheng X, Zhang W. Peroxygenase-Catalyzed Selective Synthesis of Calcitriol Starting from Alfacalcidol. Antioxidants (Basel) 2022; 11:antiox11061044. [PMID: 35739941 PMCID: PMC9220053 DOI: 10.3390/antiox11061044] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Revised: 05/19/2022] [Accepted: 05/20/2022] [Indexed: 12/10/2022] Open
Abstract
Calcitriol is an active analog of vitamin D3 and has excellent physiological activities in regulating healthy immune function. To synthesize the calcitriol compound, the concept of total synthesis is often adopted, which typically involves multiple steps and results in an overall low yield. Herein, we envisioned an enzymatic approach for the synthesis of calcitriol. Peroxygenase from Agrocybe aegerita (AaeUPO) was used as a catalyst to hydroxylate the C-H bond at the C-25 position of alfacalcidol and yielded the calcitriol in a single step. The enzymatic reaction yielded 80.3% product formation in excellent selectivity, with a turnover number up to 4000. In a semi-preparative scale synthesis, 72% isolated yield was obtained. It was also found that AaeUPO is capable of hydroxylating the C-H bond at the C-1 position of vitamin D3, thereby enabling the calcitriol synthesis directly from vitamin D3.
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Affiliation(s)
- Yuanying Li
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; (Y.L.); (P.Z.); (Z.S.); (H.L.); (R.G.); (X.S.)
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China
| | - Pengpeng Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; (Y.L.); (P.Z.); (Z.S.); (H.L.); (R.G.); (X.S.)
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China
| | - Zhoutong Sun
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; (Y.L.); (P.Z.); (Z.S.); (H.L.); (R.G.); (X.S.)
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China
| | - Huanhuan Li
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; (Y.L.); (P.Z.); (Z.S.); (H.L.); (R.G.); (X.S.)
- School of Chemical Engineering and Technology, Xi’an Jiaotong University, Xi’an 710000, China
| | - Ran Ge
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; (Y.L.); (P.Z.); (Z.S.); (H.L.); (R.G.); (X.S.)
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China
| | - Xiang Sheng
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; (Y.L.); (P.Z.); (Z.S.); (H.L.); (R.G.); (X.S.)
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China
| | - Wuyuan Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; (Y.L.); (P.Z.); (Z.S.); (H.L.); (R.G.); (X.S.)
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China
- Correspondence: ; Tel.: +86-22-8486-6462
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2
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Structural Characterization of Two Short Unspecific Peroxygenases: Two Different Dimeric Arrangements. Antioxidants (Basel) 2022; 11:antiox11050891. [PMID: 35624755 PMCID: PMC9137552 DOI: 10.3390/antiox11050891] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 04/26/2022] [Accepted: 04/28/2022] [Indexed: 11/17/2022] Open
Abstract
Unspecific peroxygenases (UPOs) are extracellular fungal enzymes of biotechnological interest as self-sufficient (and more stable) counterparts of cytochrome P450 monooxygenases, the latter being present in most living cells. Expression hosts and structural information are crucial for exploiting UPO diversity (over eight thousand UPO-type genes were identified in sequenced genomes) in target reactions of industrial interest. However, while many thousands of entries in the Protein Data Bank include molecular coordinates of P450 enzymes, only 19 entries correspond to UPO enzymes, and UPO structures from only two species (Agrocybe aegerita and Hypoxylon sp.) have been published to date. In the present study, two UPOs from the basidiomycete Marasmius rotula (rMroUPO) and the ascomycete Collariella virescens (rCviUPO) were crystallized after sequence optimization and Escherichia coli expression as active soluble enzymes. Crystals of rMroUPO and rCviUPO were obtained at sufficiently high resolution (1.45 and 1.95 Å, respectively) and the corresponding structures were solved by molecular replacement. The crystal structures of the two enzymes (and two mutated variants) showed dimeric proteins. Complementary biophysical and molecular biology studies unveiled the diverse structural bases of the dimeric nature of the two enzymes. Intermolecular disulfide bridge and parallel association between two α-helices, among other interactions, were identified at the dimer interfaces. Interestingly, one of the rCviUPO variants incorporated the ability to produce fatty acid diepoxides—reactive compounds with valuable cross-linking capabilities—due to removal of the enzyme C-terminal tail located near the entrance of the heme access channel. In conclusion, different dimeric arrangements could be described in (short) UPO crystal structures.
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3
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Enzymatic Epoxidation of Long-Chain Terminal Alkenes by Fungal Peroxygenases. Antioxidants (Basel) 2022; 11:antiox11030522. [PMID: 35326172 PMCID: PMC8944640 DOI: 10.3390/antiox11030522] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 03/01/2022] [Accepted: 03/07/2022] [Indexed: 02/01/2023] Open
Abstract
Terminal alkenes are among the most attractive starting materials for the synthesis of epoxides, which are essential and versatile intermediate building blocks for the pharmaceutical, flavoring, and polymer industries. Previous research on alkene epoxidation has focused on the use of several oxidizing agents and/or different enzymes, including cytochrome P450 monooxygenases, as well as microbial whole-cell catalysts that have several drawbacks. Alternatively, we explored the ability of unspecific peroxygenases (UPOs) to selectively epoxidize terminal alkenes. UPOs are attractive biocatalysts because they are robust extracellular enzymes and only require H2O2 as cosubstrate. Here, we show how several UPOs, such as those from Cyclocybe (Agrocybe) aegerita (AaeUPO), Marasmius rotula (MroUPO), Coprinopsis cinerea (rCciUPO), Humicola insolens (rHinUPO), and Daldinia caldariorum (rDcaUPO), are able to catalyze the epoxidation of long-chain terminal alkenes (from C12:1 to C20:1) after an initial optimization of several reaction parameters (cosolvent, cosubstrate, and pH). In addition to terminal epoxides, alkenols and other hydroxylated derivatives of the alkenes were formed. Although all UPOs were able to convert and epoxidize the alkenes, notable differences were observed between them, with rCciUPO being responsible for the highest substrate turnover and MroUPO being the most selective with respect to terminal epoxidation. The potential of peroxygenases for epoxidizing long-chain terminal alkenes represents an interesting and green alternative to the existing synthesis technologies.
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Li K, Yang Q, Zhang P, Zhang W. Research Progress of Peroxygenase-Catalyzed Reactions Driven by in-situ Generation of H 2 O 2. CHINESE J ORG CHEM 2022. [DOI: 10.6023/cjoc202108052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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5
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Affiliation(s)
- Judith Münch
- Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120, Halle, Saale, Germany
| | - Pascal Püllmann
- Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120, Halle, Saale, Germany
| | - Wuyuan Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West seventh Avenue, Tianjin 300308, China
- National Technology Innovation Center of Synthetic Biology, 32 West seventh Avenue, Tianjin 300308, China
| | - Martin J. Weissenborn
- Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120, Halle, Saale, Germany
- Institute of Chemistry, MartinLuther-University Halle-Wittenberg, Kurt-Mothes-Strasse 2, 06120, Halle, Saale, Germany
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Knorrscheidt A, Soler J, Hünecke N, Püllmann P, Garcia-Borràs M, Weissenborn MJ. Accessing Chemo- and Regioselective Benzylic and Aromatic Oxidations by Protein Engineering of an Unspecific Peroxygenase. ACS Catal 2021; 11:7327-7338. [PMID: 34631225 PMCID: PMC8496131 DOI: 10.1021/acscatal.1c00847] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 05/21/2021] [Indexed: 01/12/2023]
Abstract
![]()
Unspecific
peroxygenases (UPOs) enable oxyfunctionalizations of
a broad substrate range with unparalleled activities. Tailoring these
enzymes for chemo- and regioselective transformations represents a
grand challenge due to the difficulties in their heterologous productions.
Herein, we performed protein engineering in Saccharomyces
cerevisiae using the MthUPO from Myceliophthora thermophila. More than 5300 transformants
were screened. This protein engineering led to a significant reshaping
of the active site as elucidated by computational modelling. The reshaping
was responsible for the increased oxyfunctionalization activity, with
improved kcat/Km values of up to 16.5-fold for the model substrate 5-nitro-1,3-benzodioxole.
Moreover, variants were identified with high chemo- and regioselectivities
in the oxyfunctionalization of aromatic and benzylic carbons, respectively.
The benzylic hydroxylation was demonstrated to perform with enantioselectivities
of up to 95% ee. The proposed evolutionary protocol
and rationalization of the enhanced activities and selectivities acquired
by MthUPO variants represent a step forward toward
the use and implementation of UPOs in biocatalytic synthetic pathways
of industrial interest.
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Affiliation(s)
- Anja Knorrscheidt
- Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120 Halle, Germany
| | - Jordi Soler
- Institut de Química Computacional i Catàlisi and Departament de Química, Universitat de Girona, Carrer Maria Aurèlia Capmany 69, 17003 Girona, Catalonia, Spain
| | - Nicole Hünecke
- Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120 Halle, Germany
| | - Pascal Püllmann
- Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120 Halle, Germany
| | - Marc Garcia-Borràs
- Institut de Química Computacional i Catàlisi and Departament de Química, Universitat de Girona, Carrer Maria Aurèlia Capmany 69, 17003 Girona, Catalonia, Spain
| | - Martin J. Weissenborn
- Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120 Halle, Germany
- Institute of Chemistry, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 2, 06120 Halle, Germany
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7
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Immobilization of the Peroxygenase from Agrocybe aegerita. The Effect of the Immobilization pH on the Features of an Ionically Exchanged Dimeric Peroxygenase. Catalysts 2021. [DOI: 10.3390/catal11050560] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
This paper outlines the immobilization of the recombinant dimeric unspecific peroxygenase from Agrocybe aegerita (rAaeUPO). The enzyme was quite stable (remaining unaltered its activity after 35 h at 47 °C and pH 7.0). Phosphate destabilized the enzyme, while glycerol stabilized it. The enzyme was not immobilized on glyoxyl-agarose supports, while it was immobilized albeit in inactive form on vinyl-sulfone-activated supports. rAaeUPO immobilization on glutaraldehyde pre-activated supports gave almost quantitative immobilization yield and retained some activity, but the biocatalyst was very unstable. Its immobilization via anion exchange on PEI supports also produced good immobilization yields, but the rAaeUPO stability dropped. However, using aminated agarose, the enzyme retained stability and activity. The stability of the immobilized enzyme strongly depended on the immobilization pH, being much less stable when rAaeUPO was adsorbed at pH 9.0 than when it was immobilized at pH 7.0 or pH 5.0 (residual activity was almost 0 for the former and 80% for the other preparations), presenting stability very similar to that of the free enzyme. This is a very clear example of how the immobilization pH greatly affects the final biocatalyst performance.
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8
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Advances in enzymatic oxyfunctionalization of aliphatic compounds. Biotechnol Adv 2021; 51:107703. [PMID: 33545329 DOI: 10.1016/j.biotechadv.2021.107703] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Revised: 01/17/2021] [Accepted: 01/25/2021] [Indexed: 12/27/2022]
Abstract
Selective oxyfunctionalizations of aliphatic compounds are difficult chemical reactions, where enzymes can play an important role due to their stereo- and regio-selectivity and operation under mild reaction conditions. P450 monooxygenases are well-known biocatalysts that mediate oxyfunctionalization reactions in different living organisms (from bacteria to humans). Unspecific peroxygenases (UPOs), discovered in fungi, have arisen as "dream biocatalysts" of great biotechnological interest because they catalyze the oxyfunctionalization of aliphatic and aromatic compounds, avoiding the necessity of expensive cofactors and regeneration systems, and only depending on H2O2 for their catalysis. Here, we summarize recent advances in aliphatic oxyfunctionalization reactions by UPOs, as well as the molecular determinants of the enzyme structures responsible for their activities, emphasizing the differences found between well-known P450s and the novel fungal peroxygenases.
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Municoy M, González-Benjumea A, Carro J, Aranda C, Linde D, Renau-Mínguez C, Ullrich R, Hofrichter M, Guallar V, Gutiérrez A, Martínez AT. Fatty-Acid Oxygenation by Fungal Peroxygenases: From Computational Simulations to Preparative Regio- and Stereoselective Epoxidation. ACS Catal 2020. [DOI: 10.1021/acscatal.0c03165] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Martí Municoy
- Barcelona Supercomputing Center, Jordi Girona 29, Barcelona E-08034, Spain
| | | | - Juan Carro
- Centro de Investigaciones Biológicas Margarita Salas, CSIC, Ramiro de Maeztu 9, Madrid E-28040, Spain
| | - Carmen Aranda
- Instituto de Recursos Naturales y Agrobiología de Sevilla, CSIC, Reina Mercedes 10, Seville E-41012, Spain
| | - Dolores Linde
- Centro de Investigaciones Biológicas Margarita Salas, CSIC, Ramiro de Maeztu 9, Madrid E-28040, Spain
| | - Chantal Renau-Mínguez
- Centro de Investigaciones Biológicas Margarita Salas, CSIC, Ramiro de Maeztu 9, Madrid E-28040, Spain
| | - René Ullrich
- Technische Universität Dresden, International Institute Zittau, Markt 23, Zittau D-02763, Germany
| | - Martin Hofrichter
- Technische Universität Dresden, International Institute Zittau, Markt 23, Zittau D-02763, Germany
| | - Victor Guallar
- Barcelona Supercomputing Center, Jordi Girona 29, Barcelona E-08034, Spain
- ICREA, Passeig Lluís Companys 23, Barcelona E-08010, Spain
| | - Ana Gutiérrez
- Instituto de Recursos Naturales y Agrobiología de Sevilla, CSIC, Reina Mercedes 10, Seville E-41012, Spain
| | - Angel T. Martínez
- Centro de Investigaciones Biológicas Margarita Salas, CSIC, Ramiro de Maeztu 9, Madrid E-28040, Spain
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10
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Wang Z, Jian Y, Han Y, Fu Z, Lu D, Wu J, Liu Z. Recent progress in enzymatic functionalization of carbon-hydrogen bonds for the green synthesis of chemicals. Chin J Chem Eng 2020. [DOI: 10.1016/j.cjche.2020.06.040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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11
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Roda S, Santiago G, Guallar V. Mapping enzyme-substrate interactions: its potential to study the mechanism of enzymes. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2020; 122:1-31. [PMID: 32951809 DOI: 10.1016/bs.apcsb.2020.06.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
With the increase of the need to use more sustainable processes for the industry in our society, the modeling of enzymes has become crucial to fully comprehend their mechanism of action and use this knowledge to enhance and design their properties. A lot of methods to study enzymes computationally exist and they have been classified on sequence-based, structure-based, and the more new artificial intelligence-based ones. Albeit the abundance of methods to help predict the function of an enzyme, molecular modeling is crucial when trying to understand the enzyme mechanism, as they aim to correlate atomistic information with experimental data. Among them, methods that simulate the system dynamics at a molecular mechanics level of theory (classical force fields) have shown to offer a comprehensive study. In this book chapter, we will analyze these techniques, emphasizing the importance of precise modeling of enzyme-substrate interactions. In the end, a brief explanation of the transference of the information from research studies to the industry is given accompanied with two examples of family enzymes where their modeling has helped their exploitation.
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Affiliation(s)
- Sergi Roda
- Barcelona Supercomputing Center (BSC), Barcelona, Spain
| | | | - Victor Guallar
- Barcelona Supercomputing Center (BSC), Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
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12
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Babot ED, Aranda C, Del Rı O JC, Ullrich R, Kiebist J, Scheibner K, Hofrichter M, Martı Nez AT, Gutiérrez A. Selective Oxygenation of Ionones and Damascones by Fungal Peroxygenases. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:5375-5383. [PMID: 32292026 DOI: 10.1021/acs.jafc.0c01019] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Apocarotenoids are among the most highly valued fragrance constituents, being also appreciated as synthetic building blocks. This work shows the ability of unspecific peroxygenases (UPOs, EC1.11.2.1) from several fungi, some of them being described recently, to catalyze the oxyfunctionalization of α- and β-ionones and α- and β-damascones. Enzymatic reactions yielded oxygenated products such as hydroxy, oxo, carboxy, and epoxy derivatives that are interesting compounds for the flavor and fragrance and pharmaceutical industries. Although variable regioselectivity was observed depending on the substrate and enzyme, oxygenation was preferentially produced at the allylic position in the ring, being especially evident in the reaction with α-ionone, forming 3-hydroxy-α-ionone and/or 3-oxo-α-ionone. Noteworthy were the reactions with damascones, in the course of which some UPOs oxygenated the terminal position of the side chain, forming oxygenated derivatives (i.e., the corresponding alcohol, aldehyde, and carboxylic acid) at C-10, which were predominant in the Agrocybe aegerita UPO reactions, and first reported here.
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Affiliation(s)
- Esteban D Babot
- Instituto de Recursos Naturales y Agrobiologı́a de Sevilla, CSIC, Av. Reina Mercedes 10, E-41012 Seville, Spain
| | - Carmen Aranda
- Instituto de Recursos Naturales y Agrobiologı́a de Sevilla, CSIC, Av. Reina Mercedes 10, E-41012 Seville, Spain
| | - José C Del Rı O
- Instituto de Recursos Naturales y Agrobiologı́a de Sevilla, CSIC, Av. Reina Mercedes 10, E-41012 Seville, Spain
| | - René Ullrich
- Department of Bio- and Environmental Sciences, TU Dresden, International Institute Zittau, Markt 23, 02763 Zittau, Germany
| | - Jan Kiebist
- JenaBios GmbH, Löbstedter Str. 80, 07749 Jena, Germany
| | | | - Martin Hofrichter
- Department of Bio- and Environmental Sciences, TU Dresden, International Institute Zittau, Markt 23, 02763 Zittau, Germany
| | - Angel T Martı Nez
- Centro de Investigaciones Biológicas Margarita Salas, CSIC, Ramiro de Maeztu 9, E-28040 Madrid, Spain
| | - Ana Gutiérrez
- Instituto de Recursos Naturales y Agrobiologı́a de Sevilla, CSIC, Av. Reina Mercedes 10, E-41012 Seville, Spain
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13
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Discovery of processive catalysis by an exo-hydrolase with a pocket-shaped active site. Nat Commun 2019; 10:2222. [PMID: 31110237 PMCID: PMC6527550 DOI: 10.1038/s41467-019-09691-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 03/22/2019] [Indexed: 11/08/2022] Open
Abstract
Substrates associate and products dissociate from enzyme catalytic sites rapidly, which hampers investigations of their trajectories. The high-resolution structure of the native Hordeum exo-hydrolase HvExoI isolated from seedlings reveals that non-covalently trapped glucose forms a stable enzyme-product complex. Here, we report that the alkyl β-d-glucoside and methyl 6-thio-β-gentiobioside substrate analogues perfused in crystalline HvExoI bind across the catalytic site after they displace glucose, while methyl 2-thio-β-sophoroside attaches nearby. Structural analyses and multi-scale molecular modelling of nanoscale reactant movements in HvExoI reveal that upon productive binding of incoming substrates, the glucose product modifies its binding patterns and evokes the formation of a transient lateral cavity, which serves as a conduit for glucose departure to allow for the next catalytic round. This path enables substrate-product assisted processive catalysis through multiple hydrolytic events without HvExoI losing contact with oligo- or polymeric substrates. We anticipate that such enzyme plasticity could be prevalent among exo-hydrolases. Enzyme substrates and products often diffuse too rapidly to assess the catalytic implications of these movements. Here, the authors characterise the structural basis of product and substrate diffusion for an exo-hydrolase and discover a substrate-product assisted processive catalytic mechanism.
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15
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Aranda C, Municoy M, Guallar V, Kiebist J, Scheibner K, Ullrich R, del Río JC, Hofrichter M, Martínez AT, Gutiérrez A. Selective synthesis of 4-hydroxyisophorone and 4-ketoisophorone by fungal peroxygenases. Catal Sci Technol 2019. [DOI: 10.1039/c8cy02114g] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Some fungal peroxygenases (UPOs) selectively oxidize α-isophorone to 4-hydroxyisophorone (4HIP) and 4-ketoisophorone (4KIP) while others are less selective or unable.
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Affiliation(s)
- Carmen Aranda
- Instituto de Recursos Naturales y Agrobiología de Sevilla
- CSIC
- E-41012 Seville
- Spain
| | | | - Víctor Guallar
- Barcelona Supercomputing Center
- Barcelona
- Spain
- ICREA Passeig Lluís Companys 23
- Barcelona
| | | | | | - René Ullrich
- TU Dresden
- Department of Bio- and Environmental Sciences
- 02763 Zittau
- Germany
| | - José C. del Río
- Instituto de Recursos Naturales y Agrobiología de Sevilla
- CSIC
- E-41012 Seville
- Spain
| | - Martin Hofrichter
- TU Dresden
- Department of Bio- and Environmental Sciences
- 02763 Zittau
- Germany
| | | | - Ana Gutiérrez
- Instituto de Recursos Naturales y Agrobiología de Sevilla
- CSIC
- E-41012 Seville
- Spain
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16
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Dong J, Fernández‐Fueyo E, Hollmann F, Paul CE, Pesic M, Schmidt S, Wang Y, Younes S, Zhang W. Biocatalytic Oxidation Reactions: A Chemist's Perspective. Angew Chem Int Ed Engl 2018; 57:9238-9261. [PMID: 29573076 PMCID: PMC6099261 DOI: 10.1002/anie.201800343] [Citation(s) in RCA: 271] [Impact Index Per Article: 45.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Indexed: 01/25/2023]
Abstract
Oxidation chemistry using enzymes is approaching maturity and practical applicability in organic synthesis. Oxidoreductases (enzymes catalysing redox reactions) enable chemists to perform highly selective and efficient transformations ranging from simple alcohol oxidations to stereoselective halogenations of non-activated C-H bonds. For many of these reactions, no "classical" chemical counterpart is known. Hence oxidoreductases open up shorter synthesis routes based on a more direct access to the target products. The generally very mild reaction conditions may also reduce the environmental impact of biocatalytic reactions compared to classical counterparts. In this Review, we critically summarise the most important recent developments in the field of biocatalytic oxidation chemistry and identify the most pressing bottlenecks as well as promising solutions.
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Affiliation(s)
- JiaJia Dong
- Department of BiotechnologyDelft University of Technologyvan der Maasweg 92629HZDelftThe Netherlands
| | - Elena Fernández‐Fueyo
- Department of BiotechnologyDelft University of Technologyvan der Maasweg 92629HZDelftThe Netherlands
| | - Frank Hollmann
- Department of BiotechnologyDelft University of Technologyvan der Maasweg 92629HZDelftThe Netherlands
| | - Caroline E. Paul
- Department of BiotechnologyDelft University of Technologyvan der Maasweg 92629HZDelftThe Netherlands
| | - Milja Pesic
- Department of BiotechnologyDelft University of Technologyvan der Maasweg 92629HZDelftThe Netherlands
| | - Sandy Schmidt
- Department of BiotechnologyDelft University of Technologyvan der Maasweg 92629HZDelftThe Netherlands
| | - Yonghua Wang
- School of Food Science and EngineeringSouth China University of TechnologyGuangzhou510640P. R. China
| | - Sabry Younes
- Department of BiotechnologyDelft University of Technologyvan der Maasweg 92629HZDelftThe Netherlands
| | - Wuyuan Zhang
- Department of BiotechnologyDelft University of Technologyvan der Maasweg 92629HZDelftThe Netherlands
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17
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Dong J, Fernández-Fueyo E, Hollmann F, Paul CE, Pesic M, Schmidt S, Wang Y, Younes S, Zhang W. Biokatalytische Oxidationsreaktionen - aus der Sicht eines Chemikers. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201800343] [Citation(s) in RCA: 84] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- JiaJia Dong
- Department of Biotechnology; Delft University of Technology; van der Maasweg 9 2629HZ Delft Niederlande
| | - Elena Fernández-Fueyo
- Department of Biotechnology; Delft University of Technology; van der Maasweg 9 2629HZ Delft Niederlande
| | - Frank Hollmann
- Department of Biotechnology; Delft University of Technology; van der Maasweg 9 2629HZ Delft Niederlande
| | - Caroline E. Paul
- Department of Biotechnology; Delft University of Technology; van der Maasweg 9 2629HZ Delft Niederlande
| | - Milja Pesic
- Department of Biotechnology; Delft University of Technology; van der Maasweg 9 2629HZ Delft Niederlande
| | - Sandy Schmidt
- Department of Biotechnology; Delft University of Technology; van der Maasweg 9 2629HZ Delft Niederlande
| | - Yonghua Wang
- School of Food Science and Engineering; South China University of Technology; Guangzhou 510640 P. R. China
| | - Sabry Younes
- Department of Biotechnology; Delft University of Technology; van der Maasweg 9 2629HZ Delft Niederlande
| | - Wuyuan Zhang
- Department of Biotechnology; Delft University of Technology; van der Maasweg 9 2629HZ Delft Niederlande
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18
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Aranda C, Ullrich R, Kiebist J, Scheibner K, del Río JC, Hofrichter M, Martínez AT, Gutiérrez A. Selective synthesis of the resveratrol analogue 4,4′-dihydroxy-trans-stilbene and stilbenoids modification by fungal peroxygenases. Catal Sci Technol 2018. [DOI: 10.1039/c8cy00272j] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Different unspecific peroxygenases (UPOs) catalyze the hydroxylation or epoxidation of trans-stilbene and other stilbenoids yielding resveratrol analogs and other compounds.
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Affiliation(s)
- Carmen Aranda
- Instituto de Recursos Naturales y Agrobiología de Sevilla
- CSIC
- E-41012 Seville
- Spain
| | - René Ullrich
- Department of Bio- and Environmental Sciences
- TU Dresden
- 02763 Zittau
- Germany
| | | | | | - José C. del Río
- Instituto de Recursos Naturales y Agrobiología de Sevilla
- CSIC
- E-41012 Seville
- Spain
| | - Martin Hofrichter
- Department of Bio- and Environmental Sciences
- TU Dresden
- 02763 Zittau
- Germany
| | | | - Ana Gutiérrez
- Instituto de Recursos Naturales y Agrobiología de Sevilla
- CSIC
- E-41012 Seville
- Spain
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19
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Olmedo A, del Río JC, Kiebist J, Ullrich R, Hofrichter M, Scheibner K, Martínez AT, Gutiérrez A. Fatty Acid Chain Shortening by a Fungal Peroxygenase. Chemistry 2017; 23:16985-16989. [PMID: 29083064 PMCID: PMC5725704 DOI: 10.1002/chem.201704773] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Indexed: 11/08/2022]
Abstract
A recently discovered peroxygenase from the fungus Marasmius rotula (MroUPO) is able to catalyze the progressive one-carbon shortening of medium and long-chain mono- and dicarboxylic acids by itself alone, in the presence of H2 O2 . The mechanism, analyzed using H218 O2 , starts with an α-oxidation catalyzed by MroUPO generating an α-hydroxy acid, which is further oxidized by the enzyme to a reactive α-keto intermediate whose decarboxylation yields the one-carbon shorter fatty acid. Compared with the previously characterized peroxygenase of Agrocybe aegerita, a wider heme access channel, enabling fatty acid positioning with the carboxylic end near the heme cofactor (as seen in one of the crystal structures available) could be at the origin of the unique ability of MroUPO shortening carboxylic acid chains.
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Affiliation(s)
- Andrés Olmedo
- Instituto de Recursos Naturales y Agrobiología de Sevilla, CSICReina Mercedes 1041012SevilleSpain
| | - José C. del Río
- Instituto de Recursos Naturales y Agrobiología de Sevilla, CSICReina Mercedes 1041012SevilleSpain
| | - Jan Kiebist
- JenaBios GmbHLöbstedter Str. 8007749JenaGermany
| | | | | | | | - Angel T. Martínez
- Centro de Investigaciones Biológicas, CSICRamiro de Maeztu 928040MadridSpain
| | - Ana Gutiérrez
- Instituto de Recursos Naturales y Agrobiología de Sevilla, CSICReina Mercedes 1041012SevilleSpain
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20
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Martínez AT, Ruiz-Dueñas FJ, Camarero S, Serrano A, Linde D, Lund H, Vind J, Tovborg M, Herold-Majumdar OM, Hofrichter M, Liers C, Ullrich R, Scheibner K, Sannia G, Piscitelli A, Pezzella C, Sener ME, Kılıç S, van Berkel WJ, Guallar V, Lucas MF, Zuhse R, Ludwig R, Hollmann F, Fernández-Fueyo E, Record E, Faulds CB, Tortajada M, Winckelmann I, Rasmussen JA, Gelo-Pujic M, Gutiérrez A, del Río JC, Rencoret J, Alcalde M. Oxidoreductases on their way to industrial biotransformations. Biotechnol Adv 2017. [DOI: 10.1016/j.biotechadv.2017.06.003] [Citation(s) in RCA: 130] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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21
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Gygli G, Lucas MF, Guallar V, van Berkel WJH. The ins and outs of vanillyl alcohol oxidase: Identification of ligand migration paths. PLoS Comput Biol 2017; 13:e1005787. [PMID: 28985219 PMCID: PMC5646868 DOI: 10.1371/journal.pcbi.1005787] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Revised: 10/18/2017] [Accepted: 09/21/2017] [Indexed: 01/03/2023] Open
Abstract
Vanillyl alcohol oxidase (VAO) is a homo-octameric flavoenzyme belonging to the VAO/PCMH family. Each VAO subunit consists of two domains, the FAD-binding and the cap domain. VAO catalyses, among other reactions, the two-step conversion of p-creosol (2-methoxy-4-methylphenol) to vanillin (4-hydroxy-3-methoxybenzaldehyde). To elucidate how different ligands enter and exit the secluded active site, Monte Carlo based simulations have been performed. One entry/exit path via the subunit interface and two additional exit paths have been identified for phenolic ligands, all leading to the si side of FAD. We argue that the entry/exit path is the most probable route for these ligands. A fourth path leading to the re side of FAD has been found for the co-ligands dioxygen and hydrogen peroxide. Based on binding energies and on the behaviour of ligands in these four paths, we propose a sequence of events for ligand and co-ligand migration during catalysis. We have also identified two residues, His466 and Tyr503, which could act as concierges of the active site for phenolic ligands, as well as two other residues, Tyr51 and Tyr408, which could act as a gateway to the re side of FAD for dioxygen. Most of the residues in the four paths are also present in VAO’s closest relatives, eugenol oxidase and p-cresol methylhydroxylase. Key path residues show movements in our simulations that correspond well to conformations observed in crystal structures of these enzymes. Preservation of other path residues can be linked to the electron acceptor specificity and oligomerisation state of the three enzymes. This study is the first comprehensive overview of ligand and co-ligand migration in a member of the VAO/PCMH family, and provides a proof of concept for the use of an unbiased method to sample this process. Enzymes are bionanomachines, which speed up chemical reactions in organisms. To understand how they achieve that, we need to study their mechanisms. Computational enzymology can show us what happens in the enzyme’s active site during a reaction. But molecules need first to reach the active site before a reaction can start. The process of substrate entry and product exit to the active site is often neglected when studying enzymes. However, these two events are of fundamental importance to the proper functioning of any enzyme. We are interested in these dynamic processes to complete our understanding of the mode of action of enzymes. In our work, we have studied substrate and product migration in vanillyl alcohol oxidase. This enzyme can produce the flavour vanillin and enantiopure alcohols, but also catalyses other reactions. The named products are of interest to the flavour- and fine-chemical industries.
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Affiliation(s)
- Gudrun Gygli
- Laboratory of Biochemistry, Wageningen University & Research, Stippeneng 4, WE Wageningen, The Netherlands
| | - Maria Fátima Lucas
- Joint BSC-IRB Research Program in Computational Biology, Barcelona Supercomputing Center, Jordi Girona 29, Barcelona, Spain
| | - Victor Guallar
- Joint BSC-IRB Research Program in Computational Biology, Barcelona Supercomputing Center, Jordi Girona 29, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluís Companys 23, Barcelona, Spain
| | - Willem J. H. van Berkel
- Laboratory of Biochemistry, Wageningen University & Research, Stippeneng 4, WE Wageningen, The Netherlands
- * E-mail:
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22
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Wang Y, Lan D, Durrani R, Hollmann F. Peroxygenases en route to becoming dream catalysts. What are the opportunities and challenges? Curr Opin Chem Biol 2017; 37:1-9. [DOI: 10.1016/j.cbpa.2016.10.007] [Citation(s) in RCA: 145] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Revised: 10/12/2016] [Accepted: 10/13/2016] [Indexed: 01/09/2023]
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23
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Lucas MF, Monza E, Jørgensen LJ, Ernst HA, Piontek K, Bjerrum MJ, Martinez ÁT, Camarero S, Guallar V. Simulating Substrate Recognition and Oxidation in Laccases: From Description to Design. J Chem Theory Comput 2017; 13:1462-1467. [PMID: 28187256 DOI: 10.1021/acs.jctc.6b01158] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
To meet the very specific requirements demanded by industry, proteins must be appropriately tailored. Engineering laccases, to improve the oxidation of small molecules, with applications in multiple fields, is, however, a difficult task. Most efforts have concentrated on increasing the redox potential of the enzyme, but in recent work, we have pursued an alternate strategy to engineering these biocatalysts. In particular, we have found that redesigning substrate binding at the T1 pocket, guided by in silico methodologies, to be a more consistent option. In this work, we evaluate the robustness of our computational approach to estimate activity, emphasizing the importance of the binding event in laccase reactivity. Strengths and weaknesses of the protocol are discussed along with its potential for scoring large numbers of protein sequences and thus its significance in protein engineering.
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Affiliation(s)
- Maria Fátima Lucas
- Joint BSC-CRG-IRB Research Program in Computational Biology, Barcelona Supercomputing Center , Jordi Girona 29, E-08034 Barcelona, Spain.,Anaxomics Biotech , Balmes 89, E-08008 Barcelona, Spain
| | - Emanuele Monza
- Joint BSC-CRG-IRB Research Program in Computational Biology, Barcelona Supercomputing Center , Jordi Girona 29, E-08034 Barcelona, Spain
| | - Lise J Jørgensen
- Department of Chemistry, University of Copenhagen , Universitetsparken 5, DK-2100 Copenhagen Ø, C., Denmark
| | - Heidi A Ernst
- Department of Chemistry, University of Copenhagen , Universitetsparken 5, DK-2100 Copenhagen Ø, C., Denmark
| | - Klaus Piontek
- University of Freiburg , Albertstraße 21, D-79104 Freiburg im Breisgau, Germany
| | - Morten J Bjerrum
- Department of Chemistry, University of Copenhagen , Universitetsparken 5, DK-2100 Copenhagen Ø, C., Denmark
| | - Ángel T Martinez
- Centro de Investigaciones Biológicas, CSIC , Ramiro de Maeztu 9, E-28040 Madrid, Spain
| | - Susana Camarero
- Centro de Investigaciones Biológicas, CSIC , Ramiro de Maeztu 9, E-28040 Madrid, Spain
| | - Víctor Guallar
- Joint BSC-CRG-IRB Research Program in Computational Biology, Barcelona Supercomputing Center , Jordi Girona 29, E-08034 Barcelona, Spain.,ICREA , Passeig Lluís Companys 23, E-08010 Barcelona, Spain
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24
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Olmedo A, Aranda C, del Río JC, Kiebist J, Scheibner K, Martínez AT, Gutiérrez A. From Alkanes to Carboxylic Acids: Terminal Oxygenation by a Fungal Peroxygenase. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201605430] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Andrés Olmedo
- Instituto de Recursos Naturales y Agrobiología de Sevilla; CSIC; Reina Mercedes 10 41012 Seville Spain
| | - Carmen Aranda
- Instituto de Recursos Naturales y Agrobiología de Sevilla; CSIC; Reina Mercedes 10 41012 Seville Spain
| | - José C. del Río
- Instituto de Recursos Naturales y Agrobiología de Sevilla; CSIC; Reina Mercedes 10 41012 Seville Spain
| | | | | | - Angel T. Martínez
- Centro de Investigaciones Biológicas; CSIC; Ramiro de Maeztu 9 28040 Madrid Spain
| | - Ana Gutiérrez
- Instituto de Recursos Naturales y Agrobiología de Sevilla; CSIC; Reina Mercedes 10 41012 Seville Spain
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25
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Olmedo A, Aranda C, del Río JC, Kiebist J, Scheibner K, Martínez AT, Gutiérrez A. From Alkanes to Carboxylic Acids: Terminal Oxygenation by a Fungal Peroxygenase. Angew Chem Int Ed Engl 2016; 55:12248-51. [DOI: 10.1002/anie.201605430] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Revised: 06/29/2016] [Indexed: 11/10/2022]
Affiliation(s)
- Andrés Olmedo
- Instituto de Recursos Naturales y Agrobiología de Sevilla; CSIC; Reina Mercedes 10 41012 Seville Spain
| | - Carmen Aranda
- Instituto de Recursos Naturales y Agrobiología de Sevilla; CSIC; Reina Mercedes 10 41012 Seville Spain
| | - José C. del Río
- Instituto de Recursos Naturales y Agrobiología de Sevilla; CSIC; Reina Mercedes 10 41012 Seville Spain
| | | | | | - Angel T. Martínez
- Centro de Investigaciones Biológicas; CSIC; Ramiro de Maeztu 9 28040 Madrid Spain
| | - Ana Gutiérrez
- Instituto de Recursos Naturales y Agrobiología de Sevilla; CSIC; Reina Mercedes 10 41012 Seville Spain
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