51
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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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52
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Bassanini I, Ferrandi EE, Vanoni M, Ottolina G, Riva S, Crotti M, Brenna E, Monti D. Peroxygenase-Catalyzed Enantioselective Sulfoxidations. European J Org Chem 2017. [DOI: 10.1002/ejoc.201701390] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Ivan Bassanini
- Istituto di Chimica del Riconoscimento Molecolare; Consiglio Nazionale delle Ricerche; Via Mario Bianco 9 20131 Milano Italy
- Dipartimento di Chimica; Università degli Studi di Milano; Via Golgi 19 20133 Milano Italy
| | - Erica Elisa Ferrandi
- Istituto di Chimica del Riconoscimento Molecolare; Consiglio Nazionale delle Ricerche; Via Mario Bianco 9 20131 Milano Italy
| | - Marta Vanoni
- Istituto di Chimica del Riconoscimento Molecolare; Consiglio Nazionale delle Ricerche; Via Mario Bianco 9 20131 Milano Italy
| | - Gianluca Ottolina
- Istituto di Chimica del Riconoscimento Molecolare; Consiglio Nazionale delle Ricerche; Via Mario Bianco 9 20131 Milano Italy
| | - Sergio Riva
- Istituto di Chimica del Riconoscimento Molecolare; Consiglio Nazionale delle Ricerche; Via Mario Bianco 9 20131 Milano Italy
| | - Michele Crotti
- Dipartimento di Chimica, Materiali, Ingegneria Chimica; Politecnico di Milano; Via Mancinelli 7 20131 Milano Italy
| | - Elisabetta Brenna
- Dipartimento di Chimica, Materiali, Ingegneria Chimica; Politecnico di Milano; Via Mancinelli 7 20131 Milano Italy
| | - Daniela Monti
- Istituto di Chimica del Riconoscimento Molecolare; Consiglio Nazionale delle Ricerche; Via Mario Bianco 9 20131 Milano Italy
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53
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Amaya JA, Rutland CD, Leschinsky N, Makris TM. A Distal Loop Controls Product Release and Chemo- and Regioselectivity in Cytochrome P450 Decarboxylases. Biochemistry 2017; 57:344-353. [PMID: 29227633 DOI: 10.1021/acs.biochem.7b01065] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Cytochrome P450 OleT utilizes hydrogen peroxide (H2O2) to catalyze the decarboxylation or hydroxylation of fatty acid (FA) substrates. Both reactions are initiated through the abstraction of a substrate hydrogen atom by the high-valent iron-oxo intermediate known as Compound I. Here, we specifically probe the influence of substrate coordination on OleT reaction partitioning through the combined use of fluorescent and electron paramagnetic resonance (EPR)-active FA probes and mutagenesis of a structurally disordered F-G loop that is distal from the heme-iron active site. Both probes are efficiently metabolized by OleT and efficiently trigger the formation of Compound I. Transient fluorescence and EPR reveal a slow product release step, mediated by the F-G loop, that limits OleT turnover. A single-amino acid change or excision of the loop reveals that this region establishes critical interactions to anchor FA substrates in place. The stabilization afforded by the F-G loop is essential for regulating regiospecific C-H abstraction and allowing for efficient decarboxylation to occur. These results highlight a regulatory strategy whereby the fate of activated oxygen species can be controlled at distances far removed from the site of chemistry.
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Affiliation(s)
- José A Amaya
- Department of Chemistry and Biochemistry, University of South Carolina , Columbia, South Carolina 29208, United States
| | - Cooper D Rutland
- Department of Chemistry and Biochemistry, University of South Carolina , Columbia, South Carolina 29208, United States
| | - Nicholas Leschinsky
- Department of Chemistry and Biochemistry, University of South Carolina , Columbia, South Carolina 29208, United States
| | - Thomas M Makris
- Department of Chemistry and Biochemistry, University of South Carolina , Columbia, South Carolina 29208, United States
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54
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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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55
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Selective aerobic oxidation reactions using a combination of photocatalytic water oxidation and enzymatic oxyfunctionalisations. Nat Catal 2017; 1:55-62. [PMID: 29430568 PMCID: PMC5798593 DOI: 10.1038/s41929-017-0001-5] [Citation(s) in RCA: 172] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
Peroxygenases offer attractive means to address challenges in selective oxyfunctionalisation chemistry. Despite their attractiveness, the application of peroxygenases in synthetic chemistry remains challenging due to their facile inactivation by the stoichiometric oxidant (H2O2). Often atom inefficient peroxide generation systems are required, which show little potential for large scale implementation. Here we show that visible light-driven, catalytic water oxidation can be used for in situ generation of H2O2 from water, rendering the peroxygenase catalytically active. In this way the stereoselective oxyfunctionalisation of hydrocarbons can be achieved by simply using the catalytic system, water and visible light.
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56
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Janusz G, Pawlik A, Sulej J, Swiderska-Burek U, Jarosz-Wilkolazka A, Paszczynski A. Lignin degradation: microorganisms, enzymes involved, genomes analysis and evolution. FEMS Microbiol Rev 2017; 41:941-962. [PMID: 29088355 PMCID: PMC5812493 DOI: 10.1093/femsre/fux049] [Citation(s) in RCA: 354] [Impact Index Per Article: 50.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Accepted: 10/12/2017] [Indexed: 12/11/2022] Open
Abstract
Extensive research efforts have been dedicated to describing degradation of wood, which is a complex process; hence, microorganisms have evolved different enzymatic and non-enzymatic strategies to utilize this plentiful plant material. This review describes a number of fungal and bacterial organisms which have developed both competitive and mutualistic strategies for the decomposition of wood and to thrive in different ecological niches. Through the analysis of the enzymatic machinery engaged in wood degradation, it was possible to elucidate different strategies of wood decomposition which often depend on ecological niches inhabited by given organism. Moreover, a detailed description of low molecular weight compounds is presented, which gives these organisms not only an advantage in wood degradation processes, but seems rather to be a new evolutionatory alternative to enzymatic combustion. Through analysis of genomics and secretomic data, it was possible to underline the probable importance of certain wood-degrading enzymes produced by different fungal organisms, potentially giving them advantage in their ecological niches. The paper highlights different fungal strategies of wood degradation, which possibly correlates to the number of genes coding for secretory enzymes. Furthermore, investigation of the evolution of wood-degrading organisms has been described.
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Affiliation(s)
- Grzegorz Janusz
- Department of Biochemistry, Maria Curie-Sklodowska University, Akademicka 19 St., 20-033 Lublin, Poland
| | - Anna Pawlik
- Department of Biochemistry, Maria Curie-Sklodowska University, Akademicka 19 St., 20-033 Lublin, Poland
| | - Justyna Sulej
- Department of Biochemistry, Maria Curie-Sklodowska University, Akademicka 19 St., 20-033 Lublin, Poland
| | - Urszula Swiderska-Burek
- Department of Botany and Mycology, Maria Curie-Sklodowska University, Akademicka 19 St., 20-033 Lublin, Poland
| | - Anna Jarosz-Wilkolazka
- Department of Biochemistry, Maria Curie-Sklodowska University, Akademicka 19 St., 20-033 Lublin, Poland
| | - Andrzej Paszczynski
- School of Food Science, Food Research Center, Room 103, University of Idaho, Moscow, ID 83844, USA
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57
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Hsieh CH, Huang X, Amaya JA, Rutland CD, Keys CL, Groves JT, Austin RN, Makris TM. The Enigmatic P450 Decarboxylase OleT Is Capable of, but Evolved To Frustrate, Oxygen Rebound Chemistry. Biochemistry 2017; 56:3347-3357. [PMID: 28603981 DOI: 10.1021/acs.biochem.7b00338] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
OleT is a cytochrome P450 enzyme that catalyzes the removal of carbon dioxide from variable chain length fatty acids to form 1-alkenes. In this work, we examine the binding and metabolic profile of OleT with shorter chain length (n ≤ 12) fatty acids that can form liquid transportation fuels. Transient kinetics and product analyses confirm that OleT capably activates hydrogen peroxide with shorter substrates to form the high-valent intermediate Compound I and largely performs C-C bond scission. However, the enzyme also produces fatty alcohol side products using the high-valent iron oxo chemistry commonly associated with insertion of oxygen into hydrocarbons. When presented with a short chain fatty acid that can initiate the formation of Compound I, OleT oxidizes the diagnostic probe molecules norcarane and methylcyclopropane in a manner that is reminiscent of reactions of many CYP hydroxylases with radical clock substrates. These data are consistent with a decarboxylation mechanism in which Compound I abstracts a substrate hydrogen atom in the initial step. Positioning of the incipient substrate radical is a crucial element in controlling the efficiency of activated OH rebound.
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Affiliation(s)
- Chun H Hsieh
- Department of Chemistry and Biochemistry, University of South Carolina , Columbia, South Carolina 29208, United States
| | - Xiongyi Huang
- Department of Chemistry, Princeton University , Princeton, New Jersey 08544, United States
| | - José A Amaya
- Department of Chemistry and Biochemistry, University of South Carolina , Columbia, South Carolina 29208, United States
| | - Cooper D Rutland
- Department of Chemistry and Biochemistry, University of South Carolina , Columbia, South Carolina 29208, United States
| | - Carson L Keys
- Department of Chemistry and Biochemistry, University of South Carolina , Columbia, South Carolina 29208, United States
| | - John T Groves
- Department of Chemistry, Princeton University , Princeton, New Jersey 08544, United States
| | - Rachel N Austin
- Department of Chemistry, Barnard College, Columbia University , New York, New York 10027, United States
| | - Thomas M Makris
- Department of Chemistry and Biochemistry, University of South Carolina , Columbia, South Carolina 29208, United States
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58
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Mate DM, Palomino MA, Molina-Espeja P, Martin-Diaz J, Alcalde M. Modification of the peroxygenative:peroxidative activity ratio in the unspecific peroxygenase from Agrocybe aegerita by structure-guided evolution. Protein Eng Des Sel 2017; 30:189-196. [PMID: 28044007 DOI: 10.1093/protein/gzw073] [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: 10/14/2016] [Accepted: 12/12/2016] [Indexed: 11/14/2022] Open
Abstract
Unspecific peroxygenase (UPO) is a heme-thiolate peroxidase capable of performing with high-selectivity C-H oxyfunctionalizations of great interest in organic synthesis through its peroxygenative activity. However, the convergence of such activity with an unwanted peroxidative activity encumbers practical applications. In this study, we have modified the peroxygenative:peroxidative activity ratio (P:p ratio) of UPO from Agrocybe aegerita by structure-guided evolution. Several flexible loops (Glu1-Pro35, Gly103-Asp131, Ser226-Gly243, Gln254-Thr276 and Ty293-Arg327) were selected on the basis on their B-factors and ΔΔG values. The full ensemble of segments (43% of UPO sequence) was subjected to focused evolution by the Mutagenic Organized Recombination Process by Homologous IN vivo Grouping (MORPHING) method in Saccharomyces cerevisiae. Five independent mutant libraries were screened in terms of P:p ratio and thermostability. We identified several variants that harbored substitutions at positions 120 and 320 with a strong enhancement in the P:p ratio albeit at the cost of stability. The most thermostable mutant of this process (S226G with an increased T50 of 2°C) was subjected to further combinatorial saturation mutagenesis on Thr120 and Thr320 yielding a collection of variants with modified P:p ratio and recovered stability. Our results seem to indicate the coexistence of several oxidation sites for peroxidative and peroxygenative activities in UPO.
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Affiliation(s)
- Diana M Mate
- Department of Biocatalysis, Institute of Catalysis, CSIC, Marie Curie 2, 28049 Madrid, Spain
| | - Miguel A Palomino
- Department of Biocatalysis, Institute of Catalysis, CSIC, Marie Curie 2, 28049 Madrid, Spain
| | - Patricia Molina-Espeja
- Department of Biocatalysis, Institute of Catalysis, CSIC, Marie Curie 2, 28049 Madrid, Spain
| | - Javier Martin-Diaz
- Department of Biocatalysis, Institute of Catalysis, CSIC, Marie Curie 2, 28049 Madrid, Spain
| | - Miguel Alcalde
- Department of Biocatalysis, Institute of Catalysis, CSIC, Marie Curie 2, 28049 Madrid, Spain
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59
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Petitjean M. A Fast Algorithm to Compute Conical Pockets in Proteins. Application to the Structural Characterization of γ-Carbonic Anhydrases. Mol Inform 2017; 36. [PMID: 28402608 DOI: 10.1002/minf.201600155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 03/30/2017] [Indexed: 11/12/2022]
Abstract
Some major proteins families, such as carbonic anhydrases (CAs), have a conical cavity at the active site. No algorithm was available to compute conical cavities, so we needed to design one. The fast algorithm we designed let us show on a set of 717 CAs extracted from the PDB database that γ-CAs are characterized by active site cavity cone angles significantly larger than those of α-CAs and β-CAs: the generatrix-axis angles are greater than 60° for the γ-CAs while they are smaller than 50° for the other CAs. Free binaries of the CONICA software implementing the algorithm are available through a software repository at http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html.
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Affiliation(s)
- Michel Petitjean
- Université Paris Diderot, MTi (INSERM UMR-S 973), 35 rue Hélène Brion, F-75013, Paris, France.,Université Paris Diderot, E-pôle de génoinformatique (IJM, CNRS UMR 7592), 15 rue Hélène Brion, F-75013 Paris, France
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60
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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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61
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Li X, He Q, Li H, Gao X, Hu M, Li S, Zhai Q, Jiang Y, Wang X. Bioconversion of non-steroidal anti-inflammatory drugs diclofenac and naproxen by chloroperoxidase. Biochem Eng J 2017. [DOI: 10.1016/j.bej.2016.12.018] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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62
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Shoji O, Watanabe Y. Monooxygenation of Nonnative Substrates Catalyzed by Bacterial Cytochrome P450s Facilitated by Decoy Molecules. CHEM LETT 2017. [DOI: 10.1246/cl.160963] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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63
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Rais D, Zibek S. Biotechnological and Biochemical Utilization of Lignin. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2017; 166:469-518. [PMID: 28540404 DOI: 10.1007/10_2017_6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
This chapter provides an overview of the biosynthesis and structure of lignin. Moreover, examples of the commercial use of lignin and its promising future implementation are briefly described. Many applications are still hampered by the properties of technical lignins. Thus, the major challenge is the conversion of lignins into suitable building blocks or aromatics in order to open up new avenues for the usage of this renewable raw material. This chapter focuses on details about natural lignin degradation by fungi and bacteria, which harbor potential tools for lignin degradation and modification, which might help to develop eco-efficient processes for lignin utilization.
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Affiliation(s)
| | - Susanne Zibek
- Fraunhofer Institute for Interfacial Engineering and Biotechnology, Stuttgart, Germany.
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64
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Zhu D, Zhang P, Xie C, Zhang W, Sun J, Qian WJ, Yang B. Biodegradation of alkaline lignin by Bacillus ligniniphilus L1. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:44. [PMID: 28239416 PMCID: PMC5320714 DOI: 10.1186/s13068-017-0735-y] [Citation(s) in RCA: 92] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Accepted: 02/14/2017] [Indexed: 05/07/2023]
Abstract
BACKGROUND Lignin is the most abundant aromatic biopolymer in the biosphere and it comprises up to 30% of plant biomass. Although lignin is the most recalcitrant component of the plant cell wall, still there are microorganisms able to decompose it or degrade it. Fungi are recognized as the most widely used microbes for lignin degradation. However, bacteria have also been known to be able to utilize lignin as a carbon or energy source. Bacillus ligniniphilus L1 was selected in this study due to its capability to utilize alkaline lignin as a single carbon or energy source and its excellent ability to survive in extreme environments. RESULTS To investigate the aromatic metabolites of strain L1 decomposing alkaline lignin, GC-MS analysis was performed and fifteen single phenol ring aromatic compounds were identified. The dominant absorption peak included phenylacetic acid, 4-hydroxy-benzoicacid, and vanillic acid with the highest proportion of metabolites resulting in 42%. Comparison proteomic analysis was carried out for further study showed that approximately 1447 kinds of proteins were produced, 141 of which were at least twofold up-regulated with alkaline lignin as the single carbon source. The up-regulated proteins contents different categories in the biological functions of protein including lignin degradation, ABC transport system, environmental response factors, protein synthesis, assembly, etc. CONCLUSIONS GC-MS analysis showed that alkaline lignin degradation of strain L1 produced 15 kinds of aromatic compounds. Comparison proteomic data and metabolic analysis showed that to ensure the degradation of lignin and growth of strain L1, multiple aspects of cells metabolism including transporter, environmental response factors, and protein synthesis were enhanced. Based on genome and proteomic analysis, at least four kinds of lignin degradation pathway might be present in strain L1, including a Gentisate pathway, the benzoic acid pathway and the β-ketoadipate pathway. The study provides an important basis for lignin degradation by bacteria.
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Affiliation(s)
- Daochen Zhu
- School of Environment and safty Engineering, Jiangsu University, Zhenjiang, Jiangsu China
- State Key Laboratory of Microbial Culture Collection and Application, Guangdong Institute of Microbiology, Guangzhou, Guangdong China
| | - Peipei Zhang
- School of Environment and safty Engineering, Jiangsu University, Zhenjiang, Jiangsu China
| | - Changxiao Xie
- School of Environment and safty Engineering, Jiangsu University, Zhenjiang, Jiangsu China
| | - Weimin Zhang
- State Key Laboratory of Microbial Culture Collection and Application, Guangdong Institute of Microbiology, Guangzhou, Guangdong China
| | - Jianzhong Sun
- School of Environment and safty Engineering, Jiangsu University, Zhenjiang, Jiangsu China
| | - Wei-Jun Qian
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99352 USA
| | - Bin Yang
- Bioproducts, Sciences and Engineering Laboratory, Department of Biological Systems Engineering, Washington State University, Richland, WA 99354 USA
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65
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Wise CE, Grant JL, Amaya JA, Ratigan SC, Hsieh CH, Manley OM, Makris TM. Divergent mechanisms of iron-containing enzymes for hydrocarbon biosynthesis. J Biol Inorg Chem 2016; 22:221-235. [DOI: 10.1007/s00775-016-1425-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Accepted: 12/09/2016] [Indexed: 12/22/2022]
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66
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Fernández-Fueyo E, Ni Y, Gomez Baraibar A, Alcalde M, van Langen LM, Hollmann F. Towards preparative peroxygenase-catalyzed oxyfunctionalization reactions in organic media. ACTA ACUST UNITED AC 2016. [DOI: 10.1016/j.molcatb.2016.09.013] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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67
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Exploring the catalase activity of unspecific peroxygenases and the mechanism of peroxide-dependent heme destruction. ACTA ACUST UNITED AC 2016. [DOI: 10.1016/j.molcatb.2016.10.014] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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68
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Heterolytic OO bond cleavage: Functional role of Glu113 during bis-Fe(IV) formation in MauG. J Inorg Biochem 2016; 167:60-67. [PMID: 27907864 DOI: 10.1016/j.jinorgbio.2016.11.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Revised: 09/23/2016] [Accepted: 11/08/2016] [Indexed: 01/16/2023]
Abstract
The diheme enzyme MauG utilizes H2O2 to perform oxidative posttranslational modification on a protein substrate. A bis-Fe(IV) species of MauG was previously identified as a key intermediate in this reaction. Heterolytic cleavage of the OO bond of H2O2 drives the formation of the bis-Fe(IV) intermediate. In this work, we tested a hypothesis that a glutamate residue, Glu113 in the distal pocket of the pentacoordinate heme of MauG, facilitates heterolytic OO bond cleavage, thereby leading to bis-Fe(IV) formation. This hypothesis was proposed based on sequence alignment and structural comparison with other H2O2-utilizing hemoenzymes, especially those from the diheme enzyme superfamily that MauG belongs to. Electron paramagnetic resonance (EPR) characterization of the reaction between MauG and H2O2 revealed that mutation of Glu113 inhibited heterolytic OO bond cleavage, in agreement with our hypothesis. This result was further confirmed by the HPLC study in which an analog of H2O2, cumene hydroperoxide, was used to probe the pattern of OO bond cleavage. Together, our data suggest that Glu113 functions as an acid-base catalyst to assist heterolytic OO bond cleavage during the early stage of the catalytic reaction. This work advances our mechanistic understanding of the H2O2-activation process during bis-Fe(IV) formation in MauG.
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69
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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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70
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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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71
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Expanding the substrate scope and reactivity of cytochrome P450 OleT. Biochem Biophys Res Commun 2016; 476:462-466. [DOI: 10.1016/j.bbrc.2016.05.145] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Accepted: 05/27/2016] [Indexed: 12/11/2022]
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72
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Rapid and efficient degradation of bisphenol A by chloroperoxidase from Caldariomyces fumago: product analysis and ecotoxicity evaluation of the degraded solution. Biotechnol Lett 2016; 38:1483-91. [DOI: 10.1007/s10529-016-2137-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Accepted: 05/24/2016] [Indexed: 10/21/2022]
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73
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Bauß A, Langenmaier M, Strittmatter E, Plattner DA, Koslowski T. Thermodynamic Integration Networks and Their Application to Charge Transfer Reactions within the AauDyPI Fungal Peroxidase. J Phys Chem B 2016; 120:4937-44. [DOI: 10.1021/acs.jpcb.6b03327] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Anna Bauß
- Institut
für Physikalische Chemie, Universität Freiburg, Albertstraße
23a, D-79104 Freiburg
im Breisgau, Germany
| | - Michael Langenmaier
- Institut
für Physikalische Chemie, Universität Freiburg, Albertstraße
23a, D-79104 Freiburg
im Breisgau, Germany
| | - Eric Strittmatter
- Institut
für Organische Chemie, Universität Freiburg, Albertstraße
21, D-79104 Freiburg
im Breisgau, Germany
| | - Dietmar A. Plattner
- Institut
für Organische Chemie, Universität Freiburg, Albertstraße
21, D-79104 Freiburg
im Breisgau, Germany
| | - Thorsten Koslowski
- Institut
für Physikalische Chemie, Universität Freiburg, Albertstraße
23a, D-79104 Freiburg
im Breisgau, Germany
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74
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Xu G, Wang BG. Independent Evolution of Six Families of Halogenating Enzymes. PLoS One 2016; 11:e0154619. [PMID: 27153321 PMCID: PMC4859513 DOI: 10.1371/journal.pone.0154619] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2016] [Accepted: 04/17/2016] [Indexed: 11/18/2022] Open
Abstract
Halogenated natural products are widespread in the environment, and the halogen atoms are typically vital to their bioactivities. Thus far, six families of halogenating enzymes have been identified: cofactor-free haloperoxidases (HPO), vanadium-dependent haloperoxidases (V-HPO), heme iron-dependent haloperoxidases (HI-HPO), non-heme iron-dependent halogenases (NI-HG), flavin-dependent halogenases (F-HG), and S-adenosyl-L-methionine (SAM)-dependent halogenases (S-HG). However, these halogenating enzymes with similar biological functions but distinct structures might have evolved independently. Phylogenetic and structural analyses suggest that the HPO, V-HPO, HI-HPO, NI-HG, F-HG, and S-HG enzyme families may have evolutionary relationships to the α/β hydrolases, acid phosphatases, peroxidases, chemotaxis phosphatases, oxidoreductases, and SAM hydroxide adenosyltransferases, respectively. These halogenating enzymes have established sequence homology, structural conservation, and mechanistic features within each family. Understanding the distinct evolutionary history of these halogenating enzymes will provide further insights into the study of their catalytic mechanisms and halogenation specificity.
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Affiliation(s)
- Gangming Xu
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Nanhai Road 7, Qingdao, 266071, People’s Republic of China
- * E-mail:
| | - Bin-Gui Wang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Nanhai Road 7, Qingdao, 266071, People’s Republic of China
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75
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Schmidt-Dannert C. Biocatalytic portfolio of Basidiomycota. Curr Opin Chem Biol 2016; 31:40-9. [PMID: 26812494 DOI: 10.1016/j.cbpa.2016.01.002] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Revised: 01/04/2016] [Accepted: 01/08/2016] [Indexed: 11/16/2022]
Abstract
Basidiomycota fungi have received little attention for applications in biocatalysis and biotechnology and remain greatly understudied despite their importance for carbon recycling, ecosystem functioning and medicinal properties. The steady influx of genome data has facilitated detailed studies aimed at understanding the evolution and function of fungal lignocellulose degradation. These studies and recent explorations into the secondary metabolomes have uncovered large portfolios of enzymes useful for biocatalysis and biosynthesis. This review will provide an overview of the biocatalytic repertoires of Basidiomycota characterized to date with the hope of motivation more research into the chemical toolkits of this diverse group of fungi.
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Affiliation(s)
- Claudia Schmidt-Dannert
- Department of Biochemistry, Molecular Biology & Biophysics, University of Minnesota, 140 Gortner Laboratory, 1479 Gortner Avenue, Saint Paul, MN 55108, USA.
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76
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Molina-Espeja P, Cañellas M, Plou FJ, Hofrichter M, Lucas F, Guallar V, Alcalde M. Synthesis of 1-Naphthol by a Natural Peroxygenase Engineered by Directed Evolution. Chembiochem 2016; 17:341-9. [DOI: 10.1002/cbic.201500493] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Indexed: 11/11/2022]
Affiliation(s)
- Patricia Molina-Espeja
- Department of Biocatalysis; Institute of Catalysis; CSIC; C/Marie Curie n° 2L10 28049 Madrid Spain
| | | | - Francisco J. Plou
- Department of Biocatalysis; Institute of Catalysis; CSIC; C/Marie Curie n° 2L10 28049 Madrid Spain
| | - Martin Hofrichter
- TU Dresden; International Institute Zittau; Department of Bio- and Environmental Sciences; Markt 23 02763 Zittau Germany
| | - Fatima Lucas
- Anaxomics Biotech; Balmes 89 08008 Barcelona Spain
- Joint BSC-CRG-IRB Research Program in Computational Biology; Barcelona Supercomputing Center; Jordi Girona 29 08034 Barcelona Spain
| | - Victor Guallar
- Joint BSC-CRG-IRB Research Program in Computational Biology; Barcelona Supercomputing Center; Jordi Girona 29 08034 Barcelona Spain
- ICREA: Institució Catalana de Recerca i Estudis Avançats; Passeig Lluís Companys 23 08010 Barcelona Spain
| | - Miguel Alcalde
- Department of Biocatalysis; Institute of Catalysis; CSIC; C/Marie Curie n° 2L10 28049 Madrid Spain
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77
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Lucas F, Babot ED, Cañellas M, del Río JC, Kalum L, Ullrich R, Hofrichter M, Guallar V, Martínez AT, Gutiérrez A. Molecular determinants for selective C25-hydroxylation of vitamins D2and D3by fungal peroxygenases. Catal Sci Technol 2016. [DOI: 10.1039/c5cy00427f] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Regioselective hydroxylation of vitamin D byAgrocybe aegeritaandCoprinopsis cinereaperoxygenases was investigated in an experimental and computational study.
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Affiliation(s)
- Fátima Lucas
- Joint BSC-CRG-IRB Research Program in Computational Biology
- Barcelona Supercomputing Center
- E-08034 Barcelona
- Spain
| | - Esteban D. Babot
- Instituto de Recursos Naturales y Agrobiología de Sevilla
- CSIC
- E-41012 Seville
- Spain
| | - Marina Cañellas
- Joint BSC-CRG-IRB Research Program in Computational Biology
- Barcelona Supercomputing Center
- E-08034 Barcelona
- Spain
- Anaxomics Biotech
| | - José C. del Río
- Instituto de Recursos Naturales y Agrobiología de Sevilla
- CSIC
- E-41012 Seville
- Spain
| | | | - René Ullrich
- TU Dresden
- Department of Bio- and Environmental Sciences
- 02763 Zittau
- Germany
| | - Martin Hofrichter
- TU Dresden
- Department of Bio- and Environmental Sciences
- 02763 Zittau
- Germany
| | - Victor Guallar
- Joint BSC-CRG-IRB Research Program in Computational Biology
- Barcelona Supercomputing Center
- E-08034 Barcelona
- Spain
- ICREA
| | | | - Ana Gutiérrez
- Instituto de Recursos Naturales y Agrobiología de Sevilla
- CSIC
- E-41012 Seville
- Spain
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78
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Shoji O, Fujishiro T, Nishio K, Kano Y, Kimoto H, Chien SC, Onoda H, Muramatsu A, Tanaka S, Hori A, Sugimoto H, Shiro Y, Watanabe Y. A substrate-binding-state mimic of H2O2-dependent cytochrome P450 produced by one-point mutagenesis and peroxygenation of non-native substrates. Catal Sci Technol 2016. [DOI: 10.1039/c6cy00630b] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
H2O2-dependent cytochrome P450s that can catalyze monooxygenation of nonnative substrates were constructed by one-point mutagenesis.
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79
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Ni Y, Fernández-Fueyo E, Baraibar AG, Ullrich R, Hofrichter M, Yanase H, Alcalde M, van Berkel WJH, Hollmann F. Peroxygenase-katalysierte Oxyfunktionalisierung angetrieben durch Methanoloxidation. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201507881] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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80
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Ni Y, Fernández-Fueyo E, Baraibar AG, Ullrich R, Hofrichter M, Yanase H, Alcalde M, van Berkel WJH, Hollmann F. Peroxygenase-Catalyzed Oxyfunctionalization Reactions Promoted by the Complete Oxidation of Methanol. Angew Chem Int Ed Engl 2015; 55:798-801. [DOI: 10.1002/anie.201507881] [Citation(s) in RCA: 98] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2015] [Indexed: 11/05/2022]
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81
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Kiebist J, Holla W, Heidrich J, Poraj-Kobielska M, Sandvoss M, Simonis R, Gröbe G, Atzrodt J, Hofrichter M, Scheibner K. One-pot synthesis of human metabolites of SAR548304 by fungal peroxygenases. Bioorg Med Chem 2015; 23:4324-4332. [PMID: 26142319 DOI: 10.1016/j.bmc.2015.06.035] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Revised: 06/03/2015] [Accepted: 06/11/2015] [Indexed: 12/15/2022]
Abstract
Unspecific peroxygenases (UPOs, EC 1.11.2.1) have proved to be stable oxygen-transferring biocatalysts for H2O2-dependent transformation of pharmaceuticals. We have applied UPOs in a drug development program and consider the enzymatic approach in parallel to a conventional chemical synthesis of the human metabolites of the bile acid reabsorption inhibitor SAR548304. Chemical preparation of N,N-di-desmethyl metabolite was realized by a seven-step synthesis starting from a late precursor of SAR548304 and included among others palladium catalysis and laborious chromatographic purification with an overall yield of 27%. The enzymatic approach revealed that the UPO of Marasmius rotula is particularly suitable for selective N-dealkylation of the drug and enabled us to prepare both human metabolites via one-pot conversion with an overall yield of 66% N,N-di-desmethyl metabolite and 49% of N-mono-desmethylated compound in two separated kinetic-controlled reactions.
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Affiliation(s)
- Jan Kiebist
- Enzymtechnology, Faculty of Science, BTU Cottbus-Senftenberg, Großenhainer Str. 57, 01968 Senftenberg, Germany
| | - Wolfgang Holla
- Isotope Chemistry & Metabolite Synthesis, DSAR-DD, Sanofi-Aventis, Industriepark Höchst G876, 65926 Frankfurt am Main, Germany.
| | - Johannes Heidrich
- Isotope Chemistry & Metabolite Synthesis, DSAR-DD, Sanofi-Aventis, Industriepark Höchst G876, 65926 Frankfurt am Main, Germany
| | - Marzena Poraj-Kobielska
- Department of Bio- and Environmental Sciences, TU Dresden-IHI Zittau, Markt 23, 02763 Zittau, Germany
| | - Martin Sandvoss
- Isotope Chemistry & Metabolite Synthesis, DSAR-DD, Sanofi-Aventis, Industriepark Höchst G876, 65926 Frankfurt am Main, Germany
| | - Reiner Simonis
- Isotope Chemistry & Metabolite Synthesis, DSAR-DD, Sanofi-Aventis, Industriepark Höchst G876, 65926 Frankfurt am Main, Germany
| | - Glenn Gröbe
- Enzymtechnology, Faculty of Science, BTU Cottbus-Senftenberg, Großenhainer Str. 57, 01968 Senftenberg, Germany
| | - Jens Atzrodt
- Isotope Chemistry & Metabolite Synthesis, DSAR-DD, Sanofi-Aventis, Industriepark Höchst G876, 65926 Frankfurt am Main, Germany
| | - Martin Hofrichter
- Department of Bio- and Environmental Sciences, TU Dresden-IHI Zittau, Markt 23, 02763 Zittau, Germany
| | - Katrin Scheibner
- Enzymtechnology, Faculty of Science, BTU Cottbus-Senftenberg, Großenhainer Str. 57, 01968 Senftenberg, Germany
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82
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Holtmann D, Fraaije MW, Arends IWCE, Opperman DJ, Hollmann F. The taming of oxygen: biocatalytic oxyfunctionalisations. Chem Commun (Camb) 2015; 50:13180-200. [PMID: 24902635 DOI: 10.1039/c3cc49747j] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The scope and limitations of oxygenases as catalysts for preparative organic synthesis is discussed.
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Affiliation(s)
- Dirk Holtmann
- DECHEMA Research Institute, Theodor-Heuss-Allee 25, 60486 Frankfurt am Main, Germany
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83
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Poraj-Kobielska M, Peter S, Leonhardt S, Ullrich R, Scheibner K, Hofrichter M. Immobilization of unspecific peroxygenases (EC 1.11.2.1) in PVA/PEG gel and hollow fiber modules. Biochem Eng J 2015. [DOI: 10.1016/j.bej.2015.02.037] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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84
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Zámocký M, Hofbauer S, Schaffner I, Gasselhuber B, Nicolussi A, Soudi M, Pirker KF, Furtmüller PG, Obinger C. Independent evolution of four heme peroxidase superfamilies. Arch Biochem Biophys 2015; 574:108-19. [PMID: 25575902 PMCID: PMC4420034 DOI: 10.1016/j.abb.2014.12.025] [Citation(s) in RCA: 151] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Revised: 12/23/2014] [Accepted: 12/24/2014] [Indexed: 01/19/2023]
Abstract
Four heme peroxidase superfamilies (peroxidase-catalase, peroxidase-cyclooxygenase, peroxidase-chlorite dismutase and peroxidase-peroxygenase superfamily) arose independently during evolution, which differ in overall fold, active site architecture and enzymatic activities. The redox cofactor is heme b or posttranslationally modified heme that is ligated by either histidine or cysteine. Heme peroxidases are found in all kingdoms of life and typically catalyze the one- and two-electron oxidation of a myriad of organic and inorganic substrates. In addition to this peroxidatic activity distinct (sub)families show pronounced catalase, cyclooxygenase, chlorite dismutase or peroxygenase activities. Here we describe the phylogeny of these four superfamilies and present the most important sequence signatures and active site architectures. The classification of families is described as well as important turning points in evolution. We show that at least three heme peroxidase superfamilies have ancient prokaryotic roots with several alternative ways of divergent evolution. In later evolutionary steps, they almost always produced highly evolved and specialized clades of peroxidases in eukaryotic kingdoms with a significant portion of such genes involved in coding various fusion proteins with novel physiological functions.
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Affiliation(s)
- Marcel Zámocký
- Department of Chemistry, Division of Biochemistry, VIBT - Vienna Institute of BioTechnology, University of Natural Resources and Life Sciences, Muthgasse 18, A-1190 Vienna, Austria; Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, SK-84551 Bratislava, Slovakia.
| | - Stefan Hofbauer
- Department of Chemistry, Division of Biochemistry, VIBT - Vienna Institute of BioTechnology, University of Natural Resources and Life Sciences, Muthgasse 18, A-1190 Vienna, Austria; Department for Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, A-1030 Vienna, Austria
| | - Irene Schaffner
- Department of Chemistry, Division of Biochemistry, VIBT - Vienna Institute of BioTechnology, University of Natural Resources and Life Sciences, Muthgasse 18, A-1190 Vienna, Austria
| | - Bernhard Gasselhuber
- Department of Chemistry, Division of Biochemistry, VIBT - Vienna Institute of BioTechnology, University of Natural Resources and Life Sciences, Muthgasse 18, A-1190 Vienna, Austria
| | - Andrea Nicolussi
- Department of Chemistry, Division of Biochemistry, VIBT - Vienna Institute of BioTechnology, University of Natural Resources and Life Sciences, Muthgasse 18, A-1190 Vienna, Austria
| | - Monika Soudi
- Department of Chemistry, Division of Biochemistry, VIBT - Vienna Institute of BioTechnology, University of Natural Resources and Life Sciences, Muthgasse 18, A-1190 Vienna, Austria
| | - Katharina F Pirker
- Department of Chemistry, Division of Biochemistry, VIBT - Vienna Institute of BioTechnology, University of Natural Resources and Life Sciences, Muthgasse 18, A-1190 Vienna, Austria
| | - Paul G Furtmüller
- Department of Chemistry, Division of Biochemistry, VIBT - Vienna Institute of BioTechnology, University of Natural Resources and Life Sciences, Muthgasse 18, A-1190 Vienna, Austria
| | - Christian Obinger
- Department of Chemistry, Division of Biochemistry, VIBT - Vienna Institute of BioTechnology, University of Natural Resources and Life Sciences, Muthgasse 18, A-1190 Vienna, Austria
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85
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Steroid hydroxylation by basidiomycete peroxygenases: a combined experimental and computational study. Appl Environ Microbiol 2015; 81:4130-42. [PMID: 25862224 DOI: 10.1128/aem.00660-15] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Accepted: 04/03/2015] [Indexed: 12/14/2022] Open
Abstract
The goal of this study is the selective oxyfunctionalization of steroids under mild and environmentally friendly conditions using fungal enzymes. With this purpose, peroxygenases from three basidiomycete species were tested for the hydroxylation of a variety of steroidal compounds, using H2O2 as the only cosubstrate. Two of them are wild-type enzymes from Agrocybe aegerita and Marasmius rotula, and the third one is a recombinant enzyme from Coprinopsis cinerea. The enzymatic reactions on free and esterified sterols, steroid hydrocarbons, and ketones were monitored by gas chromatography, and the products were identified by mass spectrometry. Hydroxylation at the side chain over the steroidal rings was preferred, with the 25-hydroxyderivatives predominating. Interestingly, antiviral and other biological activities of 25-hydroxycholesterol have been reported recently (M. Blanc et al., Immunity 38:106-118, 2013, http://dx.doi.org/10.1016/j.immuni.2012.11.004). However, hydroxylation in the ring moiety and terminal hydroxylation at the side chain also was observed in some steroids, the former favored by the absence of oxygenated groups at C-3 and by the presence of conjugated double bonds in the rings. To understand the yield and selectivity differences between the different steroids, a computational study was performed using Protein Energy Landscape Exploration (PELE) software for dynamic ligand diffusion. These simulations showed that the active-site geometry and hydrophobicity favors the entrance of the steroid side chain, while the entrance of the ring is energetically penalized. Also, a direct correlation between the conversion rate and the side chain entrance ratio could be established that explains the various reaction yields observed.
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86
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Abstract
A kinetic and spectroscopic characterization of the ferryl intermediate (APO-II) from APO, the heme-thiolate peroxygenase from Agrocybe aegerita, is described. APO-II was generated by reaction of the ferric enzyme with metachloroperoxybenzoic acid in the presence of nitroxyl radicals and detected with the use of rapid-mixing stopped-flow UV-visible (UV-vis) spectroscopy. The nitroxyl radicals served as selective reductants of APO-I, reacting only slowly with APO-II. APO-II displayed a split Soret UV-vis spectrum (370 nm and 428 nm) characteristic of thiolate ligation. Rapid-mixing, pH-jump spectrophotometry revealed a basic pKa of 10.0 for the Fe(IV)-O-H of APO-II, indicating that APO-II is protonated under typical turnover conditions. Kinetic characterization showed that APO-II is unusually reactive toward a panel of benzylic C-H and phenolic substrates, with second-order rate constants for C-H and O-H bond scission in the range of 10-10(7) M(-1)⋅s(-1). Our results demonstrate the important role of the axial cysteine ligand in increasing the proton affinity of the ferryl oxygen of APO intermediates, thus providing additional driving force for C-H and O-H bond scission.
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87
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Linde D, Ruiz-Dueñas FJ, Fernández-Fueyo E, Guallar V, Hammel KE, Pogni R, Martínez AT. Basidiomycete DyPs: Genomic diversity, structural-functional aspects, reaction mechanism and environmental significance. Arch Biochem Biophys 2015; 574:66-74. [PMID: 25637654 DOI: 10.1016/j.abb.2015.01.018] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Revised: 01/15/2015] [Accepted: 01/21/2015] [Indexed: 11/26/2022]
Abstract
The first enzyme with dye-decolorizing peroxidase (DyP) activity was described in 1999 from an arthroconidial culture of the fungus Bjerkandera adusta. However, the first DyP sequence had been deposited three years before, as a peroxidase gene from a culture of an unidentified fungus of the family Polyporaceae (probably Irpex lacteus). Since the first description, fewer than ten basidiomycete DyPs have been purified and characterized, but a large number of sequences are available from genomes. DyPs share a general fold and heme location with chlorite dismutases and other DyP-type related proteins (such as Escherichia coli EfeB), forming the CDE superfamily. Taking into account the lack of an evolutionary relationship with the catalase-peroxidase superfamily, the observed heme pocket similarities must be considered as a convergent type of evolution to provide similar reactivity to the enzyme cofactor. Studies on the Auricularia auricula-judae DyP showed that high-turnover oxidation of anthraquinone type and other DyP substrates occurs via long-range electron transfer from an exposed tryptophan (Trp377, conserved in most basidiomycete DyPs), whose catalytic radical was identified in the H2O2-activated enzyme. The existence of accessory oxidation sites in DyP is suggested by the residual activity observed after site-directed mutagenesis of the above tryptophan. DyP degradation of substituted anthraquinone dyes (such as Reactive Blue 5) most probably proceeds via typical one-electron peroxidase oxidations and product breakdown without a DyP-catalyzed hydrolase reaction. Although various DyPs are able to break down phenolic lignin model dimers, and basidiomycete DyPs also present marginal activity on nonphenolic dimers, a significant contribution to lignin degradation is unlikely because of the low activity on high redox-potential substrates.
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Affiliation(s)
- Dolores Linde
- Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, E-28040 Madrid, Spain
| | | | - Elena Fernández-Fueyo
- Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, E-28040 Madrid, Spain
| | - Victor 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
| | - Kenneth E Hammel
- US Forest Products Laboratory, One Gifford Pinchot Drive, Madison, WI 53726, USA
| | - Rebecca Pogni
- Dept. Biotechnologies, Chemistry and Pharmacy, University of Siena, I-53100 Siena, Italy
| | - Angel T Martínez
- Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, E-28040 Madrid, Spain.
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88
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Hofrichter M, Kellner H, Pecyna MJ, Ullrich R. Fungal Unspecific Peroxygenases: Heme-Thiolate Proteins That Combine Peroxidase and Cytochrome P450 Properties. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2015; 851:341-68. [DOI: 10.1007/978-3-319-16009-2_13] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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89
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Bormann S, Gomez Baraibar A, Ni Y, Holtmann D, Hollmann F. Specific oxyfunctionalisations catalysed by peroxygenases: opportunities, challenges and solutions. Catal Sci Technol 2015. [DOI: 10.1039/c4cy01477d] [Citation(s) in RCA: 96] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Peroxygenases are promising oxyfunctionalisation catalysts for organic synthesis.
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Affiliation(s)
| | - Alvaro Gomez Baraibar
- Delft University of Technology
- Department of Biotechnology
- 2628 BL Delft
- The Netherlands
| | - Yan Ni
- Delft University of Technology
- Department of Biotechnology
- 2628 BL Delft
- The Netherlands
| | - Dirk Holtmann
- DECHEMA Research Institute
- 60486 Frankfurt am Main
- Germany
| | - Frank Hollmann
- Delft University of Technology
- Department of Biotechnology
- 2628 BL Delft
- The Netherlands
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90
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Onoda H, Shoji O, Watanabe Y. Acetate anion-triggered peroxygenation of non-native substrates by wild-type cytochrome P450s. Dalton Trans 2015; 44:15316-23. [DOI: 10.1039/c5dt00797f] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Wild-type cytochrome P450SPα and cytochrome P450BSβ can catalyze the oxidation of non-native substrates by performing the reaction at a high concentration of the acetate anion.
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Affiliation(s)
- Hiroki Onoda
- Department of Chemistry
- Graduate School of Science
- Nagoya University
- Nagoya 464-8602
- Japan
| | - Osami Shoji
- Department of Chemistry
- Graduate School of Science
- Nagoya University
- Nagoya 464-8602
- Japan
| | - Yoshihito Watanabe
- Department of Chemistry
- Graduate School of Science
- Nagoya University
- Nagoya 464-8602
- Japan
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91
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The toolbox of Auricularia auricula-judae dye-decolorizing peroxidase - Identification of three new potential substrate-interaction sites. Arch Biochem Biophys 2014; 574:75-85. [PMID: 25542606 DOI: 10.1016/j.abb.2014.12.016] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Revised: 12/09/2014] [Accepted: 12/13/2014] [Indexed: 11/21/2022]
Abstract
Dye-decolorizing peroxidases (DyPs) such as AauDyPI from the fungus Auricularia auricula-judae are able to oxidize substrates of different kinds and sizes. A crystal structure of an AauDyPI-imidazole complex gives insight into the binding patterns of organic molecules within the heme cavity of a DyP. Several small N-containing heterocyclic aromatics are shown to bind in the AauDyPI heme cavity, hinting to susceptibility of DyPs to azole-based inhibitors similar to cytochromes P450. Imidazole is confirmed as a competitive inhibitor with regard to peroxide binding. In contrast, bulky substrates such as anthraquinone dyes are converted at the enzyme surface. In the crystal structure a substrate analog, 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid (HEPES), binds to a tyrosine-rich hollow harboring Y25, Y147, and Y337. Spin trapping with a nitric oxide donor uncovers Y229 as an additional tyrosine-based radical center in AauDyPI. Multi-frequency EPR spectroscopy further reveals the presence of at least one intermediate tryptophanyl radical center in activated AauDyPI with W377 as the most likely candidate.
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92
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93
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Babot ED, del Río JC, Kalum L, Martínez AT, Gutiérrez A. Regioselective Hydroxylation in the Production of 25-Hydroxyvitamin D byCoprinopsis cinereaPeroxygenase. ChemCatChem 2014. [DOI: 10.1002/cctc.201402795] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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94
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Directed evolution of unspecific peroxygenase from Agrocybe aegerita. Appl Environ Microbiol 2014; 80:3496-507. [PMID: 24682297 DOI: 10.1128/aem.00490-14] [Citation(s) in RCA: 131] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Unspecific peroxygenase (UPO) represents a new type of heme-thiolate enzyme with self-sufficient mono(per)oxygenase activity and many potential applications in organic synthesis. With a view to taking advantage of these properties, we subjected the Agrocybe aegerita UPO1-encoding gene to directed evolution in Saccharomyces cerevisiae. To promote functional expression, several different signal peptides were fused to the mature protein, and the resulting products were tested. Over 9,000 clones were screened using an ad hoc dual-colorimetric assay that assessed both peroxidative and oxygen transfer activities. After 5 generations of directed evolution combined with hybrid approaches, 9 mutations were introduced that resulted in a 3,250-fold total activity improvement with no alteration in protein stability. A breakdown between secretion and catalytic activity was performed by replacing the native signal peptide of the original parental type with that of the evolved mutant; the evolved leader increased functional expression 27-fold, whereas an 18-fold improvement in the kcat/Km value for oxygen transfer activity was obtained. The evolved UPO1 was active and highly stable in the presence of organic cosolvents. Mutations in the hydrophobic core of the signal peptide contributed to enhance functional expression up to 8 mg/liter, while catalytic efficiencies for peroxidative and oxygen transfer reactions were increased by several mutations in the vicinity of the heme access channel. Overall, the directed-evolution platform described is a valuable point of departure for the development of customized UPOs with improved features and for the study of structure-function relationships.
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95
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Hofrichter M, Ullrich R. Oxidations catalyzed by fungal peroxygenases. Curr Opin Chem Biol 2014; 19:116-25. [PMID: 24607599 DOI: 10.1016/j.cbpa.2014.01.015] [Citation(s) in RCA: 170] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2013] [Revised: 01/21/2014] [Accepted: 01/21/2014] [Indexed: 11/28/2022]
Abstract
The enzymatic oxyfunctionalization of organic molecules under physiological conditions has attracted keen interest from the chemical community. Unspecific peroxygenases (EC 1.11.2.1) secreted by fungi represent an intriguing enzyme type that selectively transfers peroxide-borne oxygen with high efficiency to diverse substrates including unactivated hydrocarbons. They are glycosylated heme-thiolate enzymes that form a separate superfamily of heme proteins. Among the catalyzed reactions are hydroxylations, epoxidations, dealkylations, oxidations of organic hetero atoms and inorganic halides as well as one-electron oxidations. The substrate spectrum of fungal peroxygenases and the product patterns show similarities both to cytochrome P450 monooxygenases and classic heme peroxidases. Given that selective oxyfunctionalizations are among the most difficult to realize chemical reactions and that respectively transformed molecules are of general importance in organic and pharmaceutical syntheses, it will be worth developing peroxygenase biocatalysts for industrial applications.
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Affiliation(s)
- Martin Hofrichter
- TU Dresden - International Institute Zittau, Department of Bio- and Environmental Sciences, Markt 23, 02763 Zittau, Germany.
| | - René Ullrich
- TU Dresden - International Institute Zittau, Department of Bio- and Environmental Sciences, Markt 23, 02763 Zittau, Germany
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96
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Shoji O, Watanabe Y. Peroxygenase reactions catalyzed by cytochromes P450. J Biol Inorg Chem 2014; 19:529-39. [DOI: 10.1007/s00775-014-1106-9] [Citation(s) in RCA: 106] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Accepted: 01/07/2014] [Indexed: 11/25/2022]
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