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Sheng X, Himo F. Mechanisms of metal-dependent non-redox decarboxylases from quantum chemical calculations. Comput Struct Biotechnol J 2021; 19:3176-3186. [PMID: 34141138 PMCID: PMC8187880 DOI: 10.1016/j.csbj.2021.05.044] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 05/24/2021] [Accepted: 05/24/2021] [Indexed: 11/18/2022] Open
Abstract
Quantum chemical calculations are today an extremely valuable tool for studying enzymatic reaction mechanisms. In this mini-review, we summarize our recent work on several metal-dependent decarboxylases, where we used the so-called cluster approach to decipher the details of the reaction mechanisms, including elucidation of the identity of the metal cofactors and the origins of substrate specificity. Decarboxylases are of growing potential for biocatalytic applications, as they can be used in the synthesis of novel compounds of, e.g., pharmaceutical interest. They can also be employed in the reverse direction, providing a strategy to synthesize value‐added chemicals by CO2 fixation. A number of non-redox metal-dependent decarboxylases from the amidohydrolase superfamily have been demonstrated to have promiscuous carboxylation activities and have attracted great attention in the recent years. The computational mechanistic studies provide insights that are important for the further modification and utilization of these enzymes in industrial processes. The discussed enzymes are: 5‐carboxyvanillate decarboxylase, γ‐resorcylate decarboxylase, 2,3‐dihydroxybenzoic acid decarboxylase, and iso-orotate decarboxylase.
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Key Words
- 2,3-DHBD, 2,3‐dihydroxybenzoic acid decarboxylase
- 2,6-DHBD, 2,6‐dihydroxybenzoic acid decarboxylase
- 2-NR, 2-nitroresorcinol
- 5-CV, 5-carboxyvanillate
- 5-NV, 5-nitrovanillate
- 5caU, 5-carboxyuracil
- AHS, amidohydrolase superfamily
- Biocatalysis
- Decarboxylase
- Density functional theory
- IDCase, iso-orotate decarboxylase
- LigW, 5‐carboxyvanillate decarboxylase
- MIMS, membrane inlet mass spectrometry
- QM/MM, quantum mechanics/molecular mechanics
- Reaction mechanism
- Transition state
- γ-RS, γ-resorcylate
- γ-RSD, γ‐resorcylate decarboxylase
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Affiliation(s)
- Xiang Sheng
- National Engineering Laboratory for Industrial Enzymes and Tianjin Engineering Research Center of Biocatalytic Technology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, and National Technology Innovation Center for Synthetic Biology, Tianjin 300308, PR China
| | - Fahmi Himo
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, SE-10691 Stockholm, Sweden
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2
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Hofer G, Sheng X, Braeuer S, Payer SE, Plasch K, Goessler W, Faber K, Keller W, Himo F, Glueck SM. Metal Ion Promiscuity and Structure of 2,3-Dihydroxybenzoic Acid Decarboxylase of Aspergillus oryzae. Chembiochem 2021; 22:652-656. [PMID: 33090643 PMCID: PMC7894528 DOI: 10.1002/cbic.202000600] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 10/06/2020] [Indexed: 12/19/2022]
Abstract
Broad substrate tolerance and excellent regioselectivity, as well as independence from sensitive cofactors have established benzoic acid decarboxylases from microbial sources as efficient biocatalysts. Robustness under process conditions makes them particularly attractive for preparative-scale applications. The divalent metal-dependent enzymes are capable of catalyzing the reversible non-oxidative (de)carboxylation of a variety of electron-rich (hetero)aromatic substrates analogously to the chemical Kolbe-Schmitt reaction. Elemental mass spectrometry supported by crystal structure elucidation and quantum chemical calculations verified the presence of a catalytically relevant Mg2+ complexed in the active site of 2,3-dihydroxybenoic acid decarboxylase from Aspergillus oryzae (2,3-DHBD_Ao). This unique example with respect to the nature of the metal is in contrast to mechanistically related decarboxylases, which generally have Zn2+ or Mn2+ as the catalytically active metal.
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Affiliation(s)
- Gerhard Hofer
- Institute of Molecular BiosciencesBioTechMed GrazUniversity of Graz8010GrazAustria
| | - Xiang Sheng
- Department of Organic ChemistryArrhenius LaboratoryStockholm University10691StockholmSweden
| | - Simone Braeuer
- Department of Chemistry, Analytical ChemistryUniversity of Graz8010GrazAustria
| | - Stefan E. Payer
- Department of Chemistry, Organic & Bioorganic ChemistryUniversity of Graz8010GrazAustria
| | - Katharina Plasch
- Department of Chemistry, Organic & Bioorganic ChemistryUniversity of Graz8010GrazAustria
| | - Walter Goessler
- Department of Chemistry, Analytical ChemistryUniversity of Graz8010GrazAustria
| | - Kurt Faber
- Department of Chemistry, Organic & Bioorganic ChemistryUniversity of Graz8010GrazAustria
| | - Walter Keller
- Institute of Molecular BiosciencesBioTechMed GrazUniversity of Graz8010GrazAustria
| | - Fahmi Himo
- Department of Organic ChemistryArrhenius LaboratoryStockholm University10691StockholmSweden
| | - Silvia M. Glueck
- Department of Chemistry, Organic & Bioorganic ChemistryUniversity of Graz8010GrazAustria
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3
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Payer SE, Faber K, Glueck SM. Non-Oxidative Enzymatic (De)Carboxylation of (Hetero)Aromatics and Acrylic Acid Derivatives. Adv Synth Catal 2019; 361:2402-2420. [PMID: 31379472 PMCID: PMC6644310 DOI: 10.1002/adsc.201900275] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 04/16/2019] [Indexed: 12/20/2022]
Abstract
The utilization of carbon dioxide as a C1-building block for the production of valuable chemicals has recently attracted much interest. Whereas chemical CO2 fixation is dominated by C-O and C-N bond forming reactions, the development of novel concepts for the carboxylation of C-nucleophiles, which leads to the formation of carboxylic acids, is highly desired. Beside transition metal catalysis, biocatalysis has emerged as an attractive method for the highly regioselective (de)carboxylation of electron-rich (hetero)aromatics, which has been recently further expanded to include conjugated α,β-unsaturated (acrylic) acid derivatives. Depending on the type of substrate, different classes of enzymes have been explored for (i) the ortho-carboxylation of phenols catalyzed by metal-dependent ortho-benzoic acid decarboxylases and (ii) the side-chain carboxylation of para-hydroxystyrenes mediated by metal-independent phenolic acid decarboxylases. Just recently, the portfolio of bio-carboxylation reactions was complemented by (iii) the para-carboxylation of phenols and the decarboxylation of electron-rich heterocyclic and acrylic acid derivatives mediated by prenylated FMN-dependent decarboxylases, which is the main focus of this review. Bio(de)carboxylation processes proceed under physiological reaction conditions employing bicarbonate or (pressurized) CO2 when running in the energetically uphill carboxylation direction. Aiming to facilitate the application of these enzymes in preparative-scale biotransformations, their catalytic mechanism and substrate scope are analyzed in this review.
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Affiliation(s)
- Stefan E. Payer
- Institute of ChemistryUniversity of GrazHeinrichstrasse 288010GrazAustria
| | - Kurt Faber
- Institute of ChemistryUniversity of GrazHeinrichstrasse 288010GrazAustria
| | - Silvia M. Glueck
- Institute of ChemistryUniversity of GrazHeinrichstrasse 288010GrazAustria
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4
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Kirimura K, Araki M, Ishihara M, Ishii Y. Expanding Substrate Specificity of Salicylate Decarboxylase by Site-directed Mutagenesis for Expansion of the Entrance Region Connecting to the Substrate Access Tunnel. CHEM LETT 2019. [DOI: 10.1246/cl.180755] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Kohtaro Kirimura
- Department of Applied Chemistry, Faculty of Science and Engineering, Waseda University, 3-4-1 Ohkubo, Shinjuku-ku, Tokyo 169-8555, Japan
| | - Masahiro Araki
- Department of Applied Chemistry, Faculty of Science and Engineering, Waseda University, 3-4-1 Ohkubo, Shinjuku-ku, Tokyo 169-8555, Japan
| | - Mana Ishihara
- Department of Applied Chemistry, Faculty of Science and Engineering, Waseda University, 3-4-1 Ohkubo, Shinjuku-ku, Tokyo 169-8555, Japan
| | - Yoshitaka Ishii
- Department of Applied Chemistry, Faculty of Science and Engineering, Waseda University, 3-4-1 Ohkubo, Shinjuku-ku, Tokyo 169-8555, Japan
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Sheng X, Plasch K, Payer SE, Ertl C, Hofer G, Keller W, Braeuer S, Goessler W, Glueck SM, Himo F, Faber K. Reaction Mechanism and Substrate Specificity of Iso-orotate Decarboxylase: A Combined Theoretical and Experimental Study. Front Chem 2018; 6:608. [PMID: 30619817 PMCID: PMC6305744 DOI: 10.3389/fchem.2018.00608] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Accepted: 11/27/2018] [Indexed: 01/04/2023] Open
Abstract
The C-C bond cleavage catalyzed by metal-dependent iso-orotate decarboxylase (IDCase) from the thymidine salvage pathway is of interest for the elucidation of a (hypothetical) DNA demethylation pathway. IDCase appears also as a promising candidate for the synthetic regioselective carboxylation of N-heteroaromatics. Herein, we report a joint experimental-theoretical study to gain insights into the metal identity, reaction mechanism, and substrate specificity of IDCase. In contrast to previous assumptions, the enzyme is demonstrated by ICPMS/MS measurements to contain a catalytically relevant Mn2+ rather than Zn2+. Quantum chemical calculations revealed that decarboxylation of the natural substrate (5-carboxyuracil) proceeds via a (reverse) electrophilic aromatic substitution with formation of CO2. The occurrence of previously proposed tetrahedral carboxylate intermediates with concomitant formation of HCO3- could be ruled out on the basis of prohibitively high energy barriers. In contrast to related o-benzoic acid decarboxylases, such as γ-resorcylate decarboxylase and 5-carboxyvanillate decarboxylase, which exhibit a relaxed substrate tolerance for phenolic acids, IDCase shows high substrate fidelity. Structural and energy comparisons suggest that this is caused by a unique hydrogen bonding of the heterocyclic natural substrate (5-carboxyuracil) to the surrounding residues. Analysis of calculated energies also shows that the reverse carboxylation of uracil is impeded by a strongly disfavored uphill reaction.
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Affiliation(s)
- Xiang Sheng
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, Stockholm, Sweden
| | - Katharina Plasch
- Institute of Chemistry, Organic & Bioorganic Chemistry, University of Graz, Graz, Austria
| | - Stefan E Payer
- Institute of Chemistry, Organic & Bioorganic Chemistry, University of Graz, Graz, Austria
| | - Claudia Ertl
- Institute of Chemistry, Organic & Bioorganic Chemistry, University of Graz, Graz, Austria
| | - Gerhard Hofer
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
| | - Walter Keller
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
| | - Simone Braeuer
- Institute of Chemistry, Analytical Chemistry, University of Graz, Graz, Austria
| | - Walter Goessler
- Institute of Chemistry, Analytical Chemistry, University of Graz, Graz, Austria
| | - Silvia M Glueck
- Institute of Chemistry, Organic & Bioorganic Chemistry, University of Graz, Graz, Austria.,Austrian Centre of Industrial Biotechnology (ACIB GmbH), Graz, Austria
| | - Fahmi Himo
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, Stockholm, Sweden
| | - Kurt Faber
- Institute of Chemistry, Organic & Bioorganic Chemistry, University of Graz, Graz, Austria
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6
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Sheng X, Patskovsky Y, Vladimirova A, Bonanno JB, Almo SC, Himo F, Raushel FM. Mechanism and Structure of γ-Resorcylate Decarboxylase. Biochemistry 2018; 57:3167-3175. [PMID: 29283551 DOI: 10.1021/acs.biochem.7b01213] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
γ-Resorcylate decarboxylase (γ-RSD) has evolved to catalyze the reversible decarboxylation of 2,6-dihydroxybenzoate to resorcinol in a nonoxidative fashion. This enzyme is of significant interest because of its potential for the production of γ-resorcylate and other benzoic acid derivatives under environmentally sustainable conditions. Kinetic constants for the decarboxylation of 2,6-dihydroxybenzoate catalyzed by γ-RSD from Polaromonas sp. JS666 are reported, and the enzyme is shown to be active with 2,3-dihydroxybenzoate, 2,4,6-trihydroxybenzoate, and 2,6-dihydroxy-4-methylbenzoate. The three-dimensional structure of γ-RSD with the inhibitor 2-nitroresorcinol (2-NR) bound in the active site is reported. 2-NR is directly ligated to a Mn2+ bound in the active site, and the nitro substituent of the inhibitor is tilted significantly from the plane of the phenyl ring. The inhibitor exhibits a binding mode different from that of the substrate bound in the previously determined structure of γ-RSD from Rhizobium sp. MTP-10005. On the basis of the crystal structure of the enzyme from Polaromonas sp. JS666, complementary density functional calculations were performed to investigate the reaction mechanism. In the proposed reaction mechanism, γ-RSD binds 2,6-dihydroxybenzoate by direct coordination of the active site manganese ion to the carboxylate anion of the substrate and one of the adjacent phenolic oxygens. The enzyme subsequently catalyzes the transfer of a proton to C1 of γ-resorcylate prior to the actual decarboxylation step. The reaction mechanism proposed previously, based on the structure of γ-RSD from Rhizobium sp. MTP-10005, is shown to be associated with high energies and thus less likely to be correct.
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Affiliation(s)
- Xiang Sheng
- Department of Organic Chemistry, Arrhenius Laboratory , Stockholm University , SE-106 91 Stockholm , Sweden
| | - Yury Patskovsky
- Albert Einstein College of Medicine , 1300 Morris Park Avenue , Bronx , New York 10461 , United States
| | - Anna Vladimirova
- Department of Chemistry , Texas A&M University , College Station , Texas 77842 , United States
| | - Jeffrey B Bonanno
- Albert Einstein College of Medicine , 1300 Morris Park Avenue , Bronx , New York 10461 , United States
| | - Steven C Almo
- Albert Einstein College of Medicine , 1300 Morris Park Avenue , Bronx , New York 10461 , United States
| | - Fahmi Himo
- Department of Organic Chemistry, Arrhenius Laboratory , Stockholm University , SE-106 91 Stockholm , Sweden
| | - Frank M Raushel
- Department of Chemistry , Texas A&M University , College Station , Texas 77842 , United States
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7
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Payer SE, Marshall SA, Bärland N, Sheng X, Reiter T, Dordic A, Steinkellner G, Wuensch C, Kaltwasser S, Fisher K, Rigby SEJ, Macheroux P, Vonck J, Gruber K, Faber K, Himo F, Leys D, Pavkov‐Keller T, Glueck SM. Regioselective para-Carboxylation of Catechols with a Prenylated Flavin Dependent Decarboxylase. Angew Chem Int Ed Engl 2017; 56:13893-13897. [PMID: 28857436 PMCID: PMC5656893 DOI: 10.1002/anie.201708091] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Indexed: 11/18/2022]
Abstract
The utilization of CO2 as a carbon source for organic synthesis meets the urgent demand for more sustainability in the production of chemicals. Herein, we report on the enzyme-catalyzed para-carboxylation of catechols, employing 3,4-dihydroxybenzoic acid decarboxylases (AroY) that belong to the UbiD enzyme family. Crystal structures and accompanying solution data confirmed that AroY utilizes the recently discovered prenylated FMN (prFMN) cofactor, and requires oxidative maturation to form the catalytically competent prFMNiminium species. This study reports on the in vitro reconstitution and activation of a prFMN-dependent enzyme that is capable of directly carboxylating aromatic catechol substrates under ambient conditions. A reaction mechanism for the reversible decarboxylation involving an intermediate with a single covalent bond between a quinoid adduct and cofactor is proposed, which is distinct from the mechanism of prFMN-associated 1,3-dipolar cycloadditions in related enzymes.
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Affiliation(s)
- Stefan E. Payer
- Department of Chemistry, Organic & Bioorganic ChemistryUniversity of Graz, NAWI Graz, BioTechMed GrazHeinrichstrasse 28/28010GrazAustria
| | - Stephen A. Marshall
- Manchester Institute of BiotechnologyUniversity of Manchester131 Princess StreetManchesterM1 7DNUK
| | - Natalie Bärland
- Max Planck Institute of BiophysicsMax-von-Laue Strasse 360438Frankfurt am MainGermany
| | - Xiang Sheng
- Department of Organic ChemistryArrhenius LaboratoryStockholm University10691StockholmSweden
| | - Tamara Reiter
- Austrian Centre of Industrial Biotechnology (ACIB)Austria
| | - Andela Dordic
- Institute of Molecular BiosciencesUniversity of Graz, NAWI Graz, BioTechMed GrazHumboldtstrasse 508010GrazAustria
- Austrian Centre of Industrial Biotechnology (ACIB)Austria
| | - Georg Steinkellner
- Institute of Molecular BiosciencesUniversity of Graz, NAWI Graz, BioTechMed GrazHumboldtstrasse 508010GrazAustria
- Austrian Centre of Industrial Biotechnology (ACIB)Austria
| | | | - Susann Kaltwasser
- Max Planck Institute of BiophysicsMax-von-Laue Strasse 360438Frankfurt am MainGermany
| | - Karl Fisher
- Manchester Institute of BiotechnologyUniversity of Manchester131 Princess StreetManchesterM1 7DNUK
| | - Stephen E. J. Rigby
- Manchester Institute of BiotechnologyUniversity of Manchester131 Princess StreetManchesterM1 7DNUK
| | - Peter Macheroux
- Institute of BiochemistryGraz University of TechnologyPetersgasse 128010GrazAustria
| | - Janet Vonck
- Max Planck Institute of BiophysicsMax-von-Laue Strasse 360438Frankfurt am MainGermany
| | - Karl Gruber
- Institute of Molecular BiosciencesUniversity of Graz, NAWI Graz, BioTechMed GrazHumboldtstrasse 508010GrazAustria
| | - Kurt Faber
- Department of Chemistry, Organic & Bioorganic ChemistryUniversity of Graz, NAWI Graz, BioTechMed GrazHeinrichstrasse 28/28010GrazAustria
| | - Fahmi Himo
- Department of Organic ChemistryArrhenius LaboratoryStockholm University10691StockholmSweden
| | - David Leys
- Manchester Institute of BiotechnologyUniversity of Manchester131 Princess StreetManchesterM1 7DNUK
| | - Tea Pavkov‐Keller
- Institute of Molecular BiosciencesUniversity of Graz, NAWI Graz, BioTechMed GrazHumboldtstrasse 508010GrazAustria
- Austrian Centre of Industrial Biotechnology (ACIB)Austria
| | - Silvia M. Glueck
- Department of Chemistry, Organic & Bioorganic ChemistryUniversity of Graz, NAWI Graz, BioTechMed GrazHeinrichstrasse 28/28010GrazAustria
- Austrian Centre of Industrial Biotechnology (ACIB)Austria
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8
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Payer SE, Marshall SA, Bärland N, Sheng X, Reiter T, Dordic A, Steinkellner G, Wuensch C, Kaltwasser S, Fisher K, Rigby SEJ, Macheroux P, Vonck J, Gruber K, Faber K, Himo F, Leys D, Pavkov-Keller T, Glueck SM. Regioselektivepara-Carboxylierung von Catecholen mit einer Prenylflavin-abhängigen Decarboxylase. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201708091] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Stefan E. Payer
- Institut für Chemie, Organische & Bioorganische Chemie; Universität Graz, NAWI Graz, BioTechMed Graz; Heinrichstraße 28/2 8010 Graz Österreich
| | - Stephen A. Marshall
- Manchester Institute of Biotechnology; University of Manchester; 131 Princess Street Manchester M1 7DN Großbritannien
| | - Natalie Bärland
- Max-Planck-Institut für Biophysik; Max-Von-Laue-Straße 3 60438 Frankfurt am Main Deutschland
| | - Xiang Sheng
- Department of Organic Chemistry; Arrhenius Laboratory; Stockholm University; 10691 Stockholm Schweden
| | - Tamara Reiter
- Austrian Centre of Industrial Biotechnology (ACIB); Österreich
| | - Andela Dordic
- Institut für Molekulare Biowissenschaften; Universität Graz, NAWI Graz, BioTechMed Graz; Humboldtstraße 50 8010 Graz Österreich
- Austrian Centre of Industrial Biotechnology (ACIB); Österreich
| | - Georg Steinkellner
- Institut für Molekulare Biowissenschaften; Universität Graz, NAWI Graz, BioTechMed Graz; Humboldtstraße 50 8010 Graz Österreich
- Austrian Centre of Industrial Biotechnology (ACIB); Österreich
| | | | - Susann Kaltwasser
- Max-Planck-Institut für Biophysik; Max-Von-Laue-Straße 3 60438 Frankfurt am Main Deutschland
| | - Karl Fisher
- Manchester Institute of Biotechnology; University of Manchester; 131 Princess Street Manchester M1 7DN Großbritannien
| | - Stephen E. J. Rigby
- Manchester Institute of Biotechnology; University of Manchester; 131 Princess Street Manchester M1 7DN Großbritannien
| | - Peter Macheroux
- Institut für Biochemie; Technische Universität Graz; Petersgasse 12 8010 Graz Österreich
| | - Janet Vonck
- Max-Planck-Institut für Biophysik; Max-Von-Laue-Straße 3 60438 Frankfurt am Main Deutschland
| | - Karl Gruber
- Institut für Molekulare Biowissenschaften; Universität Graz, NAWI Graz, BioTechMed Graz; Humboldtstraße 50 8010 Graz Österreich
| | - Kurt Faber
- Institut für Chemie, Organische & Bioorganische Chemie; Universität Graz, NAWI Graz, BioTechMed Graz; Heinrichstraße 28/2 8010 Graz Österreich
| | - Fahmi Himo
- Department of Organic Chemistry; Arrhenius Laboratory; Stockholm University; 10691 Stockholm Schweden
| | - David Leys
- Manchester Institute of Biotechnology; University of Manchester; 131 Princess Street Manchester M1 7DN Großbritannien
| | - Tea Pavkov-Keller
- Institut für Molekulare Biowissenschaften; Universität Graz, NAWI Graz, BioTechMed Graz; Humboldtstraße 50 8010 Graz Österreich
- Austrian Centre of Industrial Biotechnology (ACIB); Österreich
| | - Silvia M. Glueck
- Institut für Chemie, Organische & Bioorganische Chemie; Universität Graz, NAWI Graz, BioTechMed Graz; Heinrichstraße 28/2 8010 Graz Österreich
- Austrian Centre of Industrial Biotechnology (ACIB); Österreich
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Pesci L, Gurikov P, Liese A, Kara S. Amine-Mediated Enzymatic Carboxylation of Phenols Using CO 2 as Substrate Increases Equilibrium Conversions and Reaction Rates. Biotechnol J 2017; 12. [PMID: 28862371 DOI: 10.1002/biot.201700332] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Revised: 08/18/2017] [Indexed: 01/08/2023]
Abstract
A variety of strategies is applied to alleviate thermodynamic and kinetic limitations in biocatalytic carboxylation of metabolites in vivo. A key feature to consider in enzymatic carboxylations is the nature of the cosubstrate: CO2 or its hydrated form, bicarbonate. The substrate binding and activation mechanism determine what the actual carboxylation agent is. Dihydroxybenzoic acid (de)carboxylases catalyze the reversible regio-selective ortho-(de)carboxylation of phenolics. These enzymes have attracted considerable attention in the last 10 years due to their potential in substituting harsh conditions typical of chemical carboxylations (100-200 °C, 5-100 bar) with, ideally, greener ones (20-40 °C, 1 bar). They are reported to use bicarbonate as substrate, needed in large excess to overcome thermodynamic and kinetic limitations. Therefore, CO2 can be used as substrate by these enzymes only if it is converted into bicarbonate in situ. In this contribution, we report the simultaneous amine-mediated conversion of CO2 into bicarbonate and the ortho-carboxylation of different phenolic molecules catalyzed by 2,3-dihydroxybenzoic acid (de)carboxylase from Aspergillus oryzae. Our results show that under the newly developed conditions a significant thermodynamic (up to twofold increase in conversion) and kinetic improvement (up to approx. fivefold increase in rate) of the biocatalytic carboxylation of catechol is achieved.
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Affiliation(s)
- Lorenzo Pesci
- Institute of Technical Biocatalysis, Hamburg University of Technology, Denickestr. 15, Hamburg 21073, Germany
| | - Pavel Gurikov
- Institute of Thermal Separation Processes, Hamburg University of Technology, Hamburg, Germany
| | - Andreas Liese
- Institute of Technical Biocatalysis, Hamburg University of Technology, Denickestr. 15, Hamburg 21073, Germany
| | - Selin Kara
- Institute of Technical Biocatalysis, Hamburg University of Technology, Denickestr. 15, Hamburg 21073, Germany
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10
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Recent Progress and Novel Applications in Enzymatic Conversion of Carbon Dioxide. ENERGIES 2017. [DOI: 10.3390/en10040473] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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11
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Plasch K, Resch V, Hitce J, Popłoński J, Faber K, Glueck SM. Regioselective Enzymatic Carboxylation of Bioactive (Poly)phenols. Adv Synth Catal 2017; 359:959-965. [PMID: 28450825 PMCID: PMC5396361 DOI: 10.1002/adsc.201601046] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Revised: 11/21/2016] [Indexed: 11/07/2022]
Abstract
In order to extend the applicability of the regioselective enzymatic carboxylation of phenols, the substrate scope of o-benzoic acid (de)carboxylases has been investigated towards complex molecules with an emphasis on flavouring agents and polyphenols possessing antioxidant properties. o-Hydroxycarboxylic acid products were obtained with perfect regioselectivity, in moderate to excellent yields. The applicability of this method was proven by the regioselective bio-carboxylation of resveratrol on a preparative scale with 95% yield.
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Affiliation(s)
- Katharina Plasch
- Department of Chemistry, Organic & Bioorganic ChemistryUniversity of GrazHeinrichstrasse 28A-8010GrazAustria
| | - Verena Resch
- Department of Chemistry, Organic & Bioorganic ChemistryUniversity of GrazHeinrichstrasse 28A-8010GrazAustria
| | - Julien Hitce
- L'Oréal Research & Innovation30 bis rue Maurice Berteaux95500Le ThillayFrance
| | - Jarosław Popłoński
- Department of ChemistryWrocław University of Environmental and Life Sciencesul. C. K. Norwida 2550-375WrocławPoland
| | - Kurt Faber
- Department of Chemistry, Organic & Bioorganic ChemistryUniversity of GrazHeinrichstrasse 28A-8010GrazAustria
| | - Silvia M. Glueck
- Department of Chemistry, Organic & Bioorganic ChemistryUniversity of GrazHeinrichstrasse 28A-8010GrazAustria
- Austrian Centre of Industrial Biotechnology (ACIB)University of GrazHeinrichstrasse 28A-8010GrazAustria
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Wuensch C, Pavkov-Keller T, Steinkellner G, Gross J, Fuchs M, Hromic A, Lyskowski A, Fauland K, Gruber K, Glueck SM, Faber K. Regioselective Enzymatic β-Carboxylation of para-Hydroxy- styrene Derivatives Catalyzed by Phenolic Acid Decarboxylases. Adv Synth Catal 2015; 357:1909-1918. [PMID: 26190963 PMCID: PMC4498466 DOI: 10.1002/adsc.201401028] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Revised: 01/07/2015] [Indexed: 11/17/2022]
Abstract
We report on a 'green' method for the utilization of carbon dioxide as C1 unit for the regioselective synthesis of (E)-cinnamic acids via regioselective enzymatic carboxylation of para-hydroxystyrenes. Phenolic acid decarboxylases from bacterial sources catalyzed the β-carboxylation of para-hydroxystyrene derivatives with excellent regio- and (E/Z)-stereoselectivity by exclusively acting at the β-carbon atom of the C=C side chain to furnish the corresponding (E)-cinnamic acid derivatives in up to 40% conversion at the expense of bicarbonate as carbon dioxide source. Studies on the substrate scope of this strategy are presented and a catalytic mechanism is proposed based on molecular modelling studies supported by mutagenesis of amino acid residues in the active site.
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Affiliation(s)
- Christiane Wuensch
- Austrian Centre of Industrial Biotechnology, c/o Department of Chemistry, Organic & Bioorganic Chemistry, Heinrichstrasse 28, University of Graz 8010 Graz, Austria ; Department of Chemistry, Organic & Bioorganic Chemistry, Heinrichstrasse 28, University of Graz 8010 Graz, Austria, ; phone: (+43)-316-380-5332 ; e-mail: or
| | - Tea Pavkov-Keller
- Austrian Centre of Industrial Biotechnology, c/o Department of Chemistry, Organic & Bioorganic Chemistry, Heinrichstrasse 28, University of Graz 8010 Graz, Austria ; Institute of Molecular Biosciences, Humboldtstrasse 50, University of Graz 8010 Graz, Austria
| | - Georg Steinkellner
- Austrian Centre of Industrial Biotechnology, c/o Department of Chemistry, Organic & Bioorganic Chemistry, Heinrichstrasse 28, University of Graz 8010 Graz, Austria ; Institute of Molecular Biosciences, Humboldtstrasse 50, University of Graz 8010 Graz, Austria
| | - Johannes Gross
- Austrian Centre of Industrial Biotechnology, c/o Department of Chemistry, Organic & Bioorganic Chemistry, Heinrichstrasse 28, University of Graz 8010 Graz, Austria ; Department of Chemistry, Organic & Bioorganic Chemistry, Heinrichstrasse 28, University of Graz 8010 Graz, Austria, ; phone: (+43)-316-380-5332 ; e-mail: or
| | - Michael Fuchs
- Department of Chemistry, Organic & Bioorganic Chemistry, Heinrichstrasse 28, University of Graz 8010 Graz, Austria, ; phone: (+43)-316-380-5332 ; e-mail: or
| | - Altijana Hromic
- Austrian Centre of Industrial Biotechnology, c/o Department of Chemistry, Organic & Bioorganic Chemistry, Heinrichstrasse 28, University of Graz 8010 Graz, Austria ; Institute of Molecular Biosciences, Humboldtstrasse 50, University of Graz 8010 Graz, Austria
| | - Andrzej Lyskowski
- Austrian Centre of Industrial Biotechnology, c/o Department of Chemistry, Organic & Bioorganic Chemistry, Heinrichstrasse 28, University of Graz 8010 Graz, Austria ; Institute of Molecular Biosciences, Humboldtstrasse 50, University of Graz 8010 Graz, Austria
| | - Kerstin Fauland
- Austrian Centre of Industrial Biotechnology, c/o Department of Chemistry, Organic & Bioorganic Chemistry, Heinrichstrasse 28, University of Graz 8010 Graz, Austria ; Institute of Molecular Biosciences, Humboldtstrasse 50, University of Graz 8010 Graz, Austria
| | - Karl Gruber
- Institute of Molecular Biosciences, Humboldtstrasse 50, University of Graz 8010 Graz, Austria
| | - Silvia M Glueck
- Austrian Centre of Industrial Biotechnology, c/o Department of Chemistry, Organic & Bioorganic Chemistry, Heinrichstrasse 28, University of Graz 8010 Graz, Austria ; Department of Chemistry, Organic & Bioorganic Chemistry, Heinrichstrasse 28, University of Graz 8010 Graz, Austria, ; phone: (+43)-316-380-5332 ; e-mail: or
| | - Kurt Faber
- Department of Chemistry, Organic & Bioorganic Chemistry, Heinrichstrasse 28, University of Graz 8010 Graz, Austria, ; phone: (+43)-316-380-5332 ; e-mail: or
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Stoychev SD, Conifer CM, Uhe A, Hölscher M, Leitner W. A DFT study of ruthenium pincer carboxylate complexes as potential catalysts for the direct carboxylation of arenes with CO2- meridional versus facial coordination. Dalton Trans 2014; 43:11180-9. [PMID: 24723201 DOI: 10.1039/c4dt00294f] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A recent DFT study of the ruthenium pincer benzoate complex [Ru(PNP)(PhCOO)2] I (PNP = 2,6-bis(diphenylphosphanyl)lutidine) in its meridional form has revealed mer-I to be a promising catalyst lead structure for the direct insertion of CO2 into the C-H bonds of arenes, such as benzene. After the successful synthesis of I, its solid state structure interestingly and unexpectedly showed the pincer ligand to adopt the facial rather than the meridional coordination mode. Recalculation of the catalytic cycle with fac-I including all relevant local minima and transition states revealed (a) fac-I to be significantly more stable (6.1 kcal mol(-1)) than mer-I, (b) that the energetic span (ES; i.e. the effective activation barrier) for the cycle with fac-I amounts to 38.8 kcal mol(-1), while the cycle with mer-I has an ES of 25.5 kcal mol(-1) only. These results are a hint that fac-I is catalytically inactive. Experimental testing of fac-I showed indeed no product formation, which is in full accordance with the computations. To reduce the spatial flexibility of the pincer ligand, its CH2 groups were replaced by O atoms. The resulting complex [Ru(PONOP)(PhCOO)2] II (PONOP = 2,6-bis(diphenylphosphinito)pyridine) was used for the calculation of the catalytic cycle in benzene as the solvent. Gratifyingly, the starting complex mer-II is more stable than fac-II by 1.9 kcal mol(-1) in benzene as the solvent. Consequently, mer-II should be available experimentally. As with fac-I, also fac-II generates a catalytic cycle with a high ES (37.1 kcal mol(-1)), while mer-II generates a cycle with a significantly lower ES (27.2 kcal mol(-1)) indicating mer-II to be a potentially active catalyst. A possible explanation of the much lower ES in the case of the meridionally coordinated species is found in the stronger interaction of the substrate with the metal center in the arene-σ-bond complex. As a result the issue that is created by the mer/fac isomerism can be resolved by creating spatially less flexible structures.
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Affiliation(s)
- S D Stoychev
- Institut für Technische und Makromolekulare Chemie, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany.
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Wuensch C, Gross J, Steinkellner G, Lyskowski A, Gruber K, Glueck SM, Faber K. Regioselective ortho-carboxylation of phenols catalyzed by benzoic acid decarboxylases: a biocatalytic equivalent to the Kolbe–Schmitt reaction. RSC Adv 2014. [DOI: 10.1039/c3ra47719c] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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Pushing the equilibrium of regio-complementary carboxylation of phenols and hydroxystyrene derivatives. J Biotechnol 2013; 168:264-70. [PMID: 23880442 DOI: 10.1016/j.jbiotec.2013.07.017] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2013] [Revised: 06/18/2013] [Accepted: 07/12/2013] [Indexed: 11/22/2022]
Abstract
The enzymatic carboxylation of electron-rich aromatics, which represents a promising 'green' equivalent to the chemical Kolbe-Schmitt reaction, is thermodynamically disfavored and is therefore impeded by incomplete conversions. Optimization of the reaction conditions, such as pH, temperature, substrate concentration and the use of organic co-solvents and/or ionic liquids allowed to push the conversion in favor of carboxylation by a factor of up to 50%. Careful selection of the type of bicarbonate salt used as CO2 source was crucial to ensure optimal activities. Among two types of carboxylases tested with their natural substrates, benzoic acid decarboxylase from Rhizobium sp. proved to be significantly more stable than phenolic acid decarboxylase from Mycobacterium colombiense; it tolerated reaction temperatures of up to 50 °C and substrate concentrations of up to 100mM and allowed efficient biocatalyst recycling.
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Ienaga S, Kosaka S, Honda Y, Ishii Y, Kirimura K. p-Aminosalicylic Acid Production by Enzymatic Kolbe–Schmitt Reaction Using Salicylic Acid Decarboxylases Improved through Site-Directed Mutagenesis. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2013. [DOI: 10.1246/bcsj.20130006] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Saori Ienaga
- Department of Applied Chemistry, Faculty of Science and Engineering, Waseda University
| | - Sachiyo Kosaka
- Department of Applied Chemistry, Faculty of Science and Engineering, Waseda University
| | - Yuki Honda
- Department of Applied Chemistry, Faculty of Science and Engineering, Waseda University
| | - Yoshitaka Ishii
- Environmental Information and Science Course, School of Social Information Studies, Otsuma Women’s University
| | - Kohtaro Kirimura
- Department of Applied Chemistry, Faculty of Science and Engineering, Waseda University
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LC-QTOF/MS metabolomic profiles in human plasma after a 5-week high dietary fiber intake. Anal Bioanal Chem 2013; 405:4799-809. [PMID: 23535740 DOI: 10.1007/s00216-013-6874-5] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2012] [Revised: 02/12/2013] [Accepted: 02/26/2013] [Indexed: 10/27/2022]
Abstract
The objective was to investigate the alterations of plasma metabolome profiles to identify exposure and effect markers of dietary fiber intake. Subjects (n = 25) aged 58.6 (1.1) years (mean and SD) with a body mass index of 26.6 (0.5) kg/m(2) were given a high fiber (HF) and a low fiber (LF) diet, in a 5-week randomized controlled crossover intervention. The HF diet consisted of oat bran, rye bran, and sugar beet fiber incorporated into test food products, whereas the LF diet was made of equivalent food products to the HF diet, but without adding fibers. Blood plasma samples were collected at the start and end of each intervention period and analyzed by LC-QTOF/MS. In total, 6 features in positive mode and 14 features in negative mode were significantly different between the HF and the LF diet (p < 0.01, q < 0.05). Two markers, 2,6-dihydroxybenzoic acid and 2-aminophenol sulfate, were increased after HF diet, along with a tentatively identified saponin derived from oat avenacosides. The untargeted metabolomics approach enabled the identification of two new markers of dietary fiber intake in human plasma. Further studies will be needed to verify if these markers could serve as compliance markers of fiber intake.
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Wuensch C, Glueck SM, Gross J, Koszelewski D, Schober M, Faber K. Regioselective enzymatic carboxylation of phenols and hydroxystyrene derivatives. Org Lett 2012; 14:1974-7. [PMID: 22471935 PMCID: PMC3593611 DOI: 10.1021/ol300385k] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The enzymatic carboxylation of phenol and styrene derivatives using (de)carboxylases in carbonate buffer proceeded in a highly regioselective fashion: Benzoic acid (de)carboxylases selectively formed o-hydroxybenzoic acid derivatives, phenolic acid (de)carboxylases selectively acted at the β-carbon atom of styrenes forming (E)-cinnamic acids.
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Affiliation(s)
- Christiane Wuensch
- Austrian Centre of Industrial Biotechnology, University of Graz, Heinrichstrasse 28, A-8010 Graz, Austria
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Uhe A, Hölscher M, Leitner W. Carboxylation of Arene CH Bonds with CO2: A DFT-Based Approach to Catalyst Design. Chemistry 2011; 18:170-7. [DOI: 10.1002/chem.201102785] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2011] [Indexed: 02/05/2023]
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Kirimura K, Yanaso S, Kosaka S, Koyama K, Hattori T, Ishii Y. Production ofp-Aminosalicylic Acid through Enzymatic Kolbe–Schmitt Reaction Catalyzed by Reversible Salicylic Acid Decarboxylase. CHEM LETT 2011. [DOI: 10.1246/cl.2011.206] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Abstract
Dwindling petroleum feedstocks and increased CO(2)-concentrations in the atmosphere currently open the concept of using CO(2) as raw material for the synthesis of well-defined organic compounds. In parallel to recent advances in the chemical CO(2)-fixation, enzymatic (biocatalytic) carboxylation is currently being investigated at an increased pace. On the one hand, this critical review provides a concise overview on highly specific biosynthetic pathways for CO(2)-fixation and, on the other hand, a summary of biodegradation (detoxification) processes involving enzymes which possess relaxed substrate specificities, which allow their application for the regioselective carboxylation of organic substrates to furnish the corresponding carboxylic acids (145 references).
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Affiliation(s)
- Silvia M Glueck
- Research Centre Applied Biocatalysis, University of Graz, Heinrichstrasse 28, A-8010 Graz, Austria
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