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Huang X, Groves JT. Oxygen Activation and Radical Transformations in Heme Proteins and Metalloporphyrins. Chem Rev 2018; 118:2491-2553. [PMID: 29286645 PMCID: PMC5855008 DOI: 10.1021/acs.chemrev.7b00373] [Citation(s) in RCA: 591] [Impact Index Per Article: 98.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Indexed: 12/20/2022]
Abstract
As a result of the adaptation of life to an aerobic environment, nature has evolved a panoply of metalloproteins for oxidative metabolism and protection against reactive oxygen species. Despite the diverse structures and functions of these proteins, they share common mechanistic grounds. An open-shell transition metal like iron or copper is employed to interact with O2 and its derived intermediates such as hydrogen peroxide to afford a variety of metal-oxygen intermediates. These reactive intermediates, including metal-superoxo, -(hydro)peroxo, and high-valent metal-oxo species, are the basis for the various biological functions of O2-utilizing metalloproteins. Collectively, these processes are called oxygen activation. Much of our understanding of the reactivity of these reactive intermediates has come from the study of heme-containing proteins and related metalloporphyrin compounds. These studies not only have deepened our understanding of various functions of heme proteins, such as O2 storage and transport, degradation of reactive oxygen species, redox signaling, and biological oxygenation, etc., but also have driven the development of bioinorganic chemistry and biomimetic catalysis. In this review, we survey the range of O2 activation processes mediated by heme proteins and model compounds with a focus on recent progress in the characterization and reactivity of important iron-oxygen intermediates. Representative reactions initiated by these reactive intermediates as well as some context from prior decades will also be presented. We will discuss the fundamental mechanistic features of these transformations and delineate the underlying structural and electronic factors that contribute to the spectrum of reactivities that has been observed in nature as well as those that have been invented using these paradigms. Given the recent developments in biocatalysis for non-natural chemistries and the renaissance of radical chemistry in organic synthesis, we envision that new enzymatic and synthetic transformations will emerge based on the radical processes mediated by metalloproteins and their synthetic analogs.
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Affiliation(s)
- Xiongyi Huang
- Department
of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
- Department
of Chemistry, California Institute of Technology, Pasadena, California 91125, United States
| | - John T. Groves
- Department
of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
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52
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Hanano A, Alkara M, Almousally I, Shaban M, Rahman F, Hassan M, Murphy DJ. The Peroxygenase Activity of the Aspergillus flavus Caleosin, AfPXG, Modulates the Biosynthesis of Aflatoxins and Their Trafficking and Extracellular Secretion via Lipid Droplets. Front Microbiol 2018; 9:158. [PMID: 29467750 PMCID: PMC5808235 DOI: 10.3389/fmicb.2018.00158] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 01/23/2018] [Indexed: 11/29/2022] Open
Abstract
Aflatoxins (AF) are highly detrimental to human and animal health. We recently demonstrated that the Aspergillus flavus caleosin, AfPXG, had peroxygenase activity and mediated fungal development and AF accumulation. We now report the characterization of an AfPXG-deficient line using reference strain NRRL3357. The resulting fungal phenotype included a severe decrease in mycelium growth, failure to sporulate, and reduced AF production. Increasing cellular oxidative status by administration of hydrogen peroxide and cumene hydroperoxide did not restore the AfPXG-deficient phenotype, which suggests that AfPXG-deficiency is not directly related to oxidative stress. To investigate possible alternative roles of AfPXG, a gain of function approach was used to overexpress AfPXG, with the reporter gene Gfp, in an AfPXG-deficient line, termed AfPXG+ . The resulting phenotype included elevated numbers of stable lipid droplets (LDs) plus enhanced AF production. Highly purified LDs from AfPXG+ cultures sequestered AF and this ability was positively correlated with overall LD number. Site-specific mutagenesis of AfPXG to delete Histidine 85 (AfPXGHis85), a residue essential for its catalytic activity, or deletion of the putative LD targeting domain (AfPXGD126-140), showed that AfPXG-peroxygenase activity was required for AF biosynthesis and that integration of AF into LDs was required for their export via a LD-dependent pathway. Ectopic expression in fungal cells of the plant LD-associated protein, oleosin, also resulted in both additional LD accumulation and enhanced AF secretion. These results suggest that both fungal LDs and their associated caleosin proteins are intimately involved in the biosynthesis, trafficking, and secretion of AF.
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Affiliation(s)
- Abdulsamie Hanano
- Department of Molecular Biology and Biotechnology, Atomic Energy Commission of Syria, Damascus, Syria
| | - Mari Alkara
- Department of Molecular Biology and Biotechnology, Atomic Energy Commission of Syria, Damascus, Syria
| | - Ibrahem Almousally
- Department of Molecular Biology and Biotechnology, Atomic Energy Commission of Syria, Damascus, Syria
| | - Mouhnad Shaban
- Department of Molecular Biology and Biotechnology, Atomic Energy Commission of Syria, Damascus, Syria
| | - Farzana Rahman
- Genomics and Computational Biology Research Group, University of South Wales, Pontypridd, United Kingdom
| | - Mehedi Hassan
- Genomics and Computational Biology Research Group, University of South Wales, Pontypridd, United Kingdom
| | - Denis J. Murphy
- Genomics and Computational Biology Research Group, University of South Wales, Pontypridd, United Kingdom
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53
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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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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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Karich A, Ullrich R, Scheibner K, Hofrichter M. Fungal Unspecific Peroxygenases Oxidize the Majority of Organic EPA Priority Pollutants. Front Microbiol 2017; 8:1463. [PMID: 28848501 PMCID: PMC5552789 DOI: 10.3389/fmicb.2017.01463] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Accepted: 07/20/2017] [Indexed: 11/18/2022] Open
Abstract
Unspecific peroxygenases (UPOs) are secreted fungal enzymes with promiscuity for oxygen transfer and oxidation reactions. Functionally, they represent hybrids of P450 monooxygenases and heme peroxidases; phylogenetically they belong to the family of heme-thiolate peroxidases. Two UPOs from the basidiomycetous fungi Agrocybe aegerita (AaeUPO) and Marasmius rotula (MroUPO) converted 35 out of 40 compounds listed as EPA priority pollutants, including chlorinated benzenes and their derivatives, halogenated biphenyl ethers, nitroaromatic compounds, polycyclic aromatic hydrocarbons (PAHs) and phthalic acid derivatives. These oxygenations and oxidations resulted in diverse products and—if at all—were limited for three reasons: (i) steric hindrance caused by multiple substitutions or bulkiness of the compound as such (e.g., hexachlorobenzene or large PAHs), (ii) strong inactivation of aromatic rings (e.g., nitrobenzene), and (iii) low water solubility (e.g., complex arenes). The general outcome of our study is that UPOs can be considered as extracellular counterparts of intracellular monooxygenases, both with respect to catalyzed reactions and catalytic versatility. Therefore, they should be taken into consideration as a relevant biocatalytic detoxification and biodegradation tool used by fungi when confronted with toxins, xenobiotics and pollutants in their natural environments.
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Affiliation(s)
- Alexander Karich
- Department of Bio-and Environmental Sciences, Technische Universität Dresden-International Institute ZittauZittau, Germany
| | - René Ullrich
- Department of Bio-and Environmental Sciences, Technische Universität Dresden-International Institute ZittauZittau, Germany
| | - Katrin Scheibner
- Enzyme Technology Unit, Brandenburg University of TechnologyCottbus, Germany
| | - Martin Hofrichter
- Department of Bio-and Environmental Sciences, Technische Universität Dresden-International Institute ZittauZittau, Germany
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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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Onderko EL, Silakov A, Yosca TH, Green MT. Characterization of a selenocysteine-ligated P450 compound I reveals direct link between electron donation and reactivity. Nat Chem 2017. [DOI: 10.1038/nchem.2781] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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59
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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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60
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Yosca TH, Ledray AP, Ngo J, Green MT. A new look at the role of thiolate ligation in cytochrome P450. J Biol Inorg Chem 2017; 22:209-220. [PMID: 28091754 PMCID: PMC5640440 DOI: 10.1007/s00775-016-1430-3] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2016] [Accepted: 12/14/2016] [Indexed: 10/20/2022]
Abstract
Protonated ferryl (or iron(IV)hydroxide) intermediates have been characterized in several thiolate-ligated heme proteins that are known to catalyze C-H bond activation. The basicity of the ferryl intermediates in these species has been proposed to play a critical role in facilitating this chemistry, allowing hydrogen abstraction at reduction potentials below those that would otherwise lead to oxidative degradation of the enzyme. In this contribution, we discuss the events that led to the assignment and characterization of the unusual iron(IV)hydroxide species, highlighting experiments that provided a quantitative measure of the ferryl basicity, the iron(IV)hydroxide pKa. We then turn to the importance of the iron(IV)hydroxide state, presenting a new way of looking at the role of thiolate ligation in these systems.
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Affiliation(s)
- Timothy H Yosca
- Departments of Chemistry & Molecular Biology and Biochemistry, University of California-Irvine, 4134, Natural Sciences 1, Irvine, CA 92697, USA
| | - Aaron P Ledray
- Departments of Chemistry & Molecular Biology and Biochemistry, University of California-Irvine, 4134, Natural Sciences 1, Irvine, CA 92697, USA
| | - Joanna Ngo
- Departments of Chemistry & Molecular Biology and Biochemistry, University of California-Irvine, 4134, Natural Sciences 1, Irvine, CA 92697, USA
| | - Michael T Green
- Departments of Chemistry & Molecular Biology and Biochemistry, University of California-Irvine, 4134, Natural Sciences 1, Irvine, CA 92697, USA.
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61
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Meng L, Li H, Bao M, Sun P. Metabolic pathway for a new strain Pseudomonas synxantha LSH-7': from chemotaxis to uptake of n-hexadecane. Sci Rep 2017; 7:39068. [PMID: 28051099 PMCID: PMC5209730 DOI: 10.1038/srep39068] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 11/17/2016] [Indexed: 11/08/2022] Open
Abstract
Bacteria can use n-hexadecane as a carbon source, but it remains incompletely understood whether n-hexadecane is transformed into metabolic intermediates prior to cellular uptake or not. We newly isolated a strain identified as Pseudomonas synxantha LSH-7' and conducted chemotaxis experiment of this bacterial strain towards n-hexadecane, hexadecanol and hexadecanoic acid with qualitative assays respectively. Furthermore, we described the identification of extracellular alkane hydroxylase and alcohol dehydrogenase activity; acidification of the culture medium; identification of hexadecanoic acid in the culture medium by the GC-MS analysis; and variation concentration of intracellular n-hexadecane and hexadecanoic acid. A detailed analysis of the experimental data revealed the chemotaxis of this bacterial strain towards n-hexadecane instead of its metabolic intermediates. Our results further suggested that only a fraction of total n-hexadecane followed this path, and alkane hydrolase and hexadecanol dehydrogenase were constitutively expressed when grown in the medium of n-hexadecane. Most strikingly, we quantitatively investigated the concentration of n-hexadecane adsorbed by bacterial chemotaxis. Our findings provided an original insight n-hexadecane might be converted to hexadecanoic acid extracellularly before it was taken up across the cell membrane.
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Affiliation(s)
- Long Meng
- Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China, Qingdao 266100, China
- College of Chemistry & Chemical Engineering, Ocean University of China, Qingdao 266100, China
| | - Haoshuai Li
- Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China, Qingdao 266100, China
- College of Chemistry & Chemical Engineering, Ocean University of China, Qingdao 266100, China
| | - Mutai Bao
- Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China, Qingdao 266100, China
- College of Chemistry & Chemical Engineering, Ocean University of China, Qingdao 266100, China
| | - Peiyan Sun
- Key Laboratory of Marine Spill Oil Identification and Damage Assessment Technology, North China Sea Environmental Monitoring Center, State Oceanic Administration, Qingdao 266033, China
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62
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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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63
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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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64
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Electro-enzymatic hydroxylation of ethylbenzene by the evolved unspecific peroxygenase of Agrocybe aegerita. ACTA ACUST UNITED AC 2016. [DOI: 10.1016/j.molcatb.2016.12.008] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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65
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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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66
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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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67
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Tearing down to build up: Metalloenzymes in the biosynthesis lincomycin, hormaomycin and the pyrrolo [1,4]benzodiazepines. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1864:724-737. [DOI: 10.1016/j.bbapap.2016.03.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Revised: 02/24/2016] [Accepted: 03/02/2016] [Indexed: 11/21/2022]
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68
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Soussan L, Pen N, Belleville MP, Marcano JS, Paolucci-Jeanjean D. Alkane biohydroxylation: Interests, constraints and future developments. J Biotechnol 2016; 222:117-42. [DOI: 10.1016/j.jbiotec.2016.02.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Revised: 01/17/2016] [Accepted: 02/02/2016] [Indexed: 01/07/2023]
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69
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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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70
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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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Miyaji A, Miyoshi T, Motokura K, Baba T. Discrimination of the prochiral hydrogens at the C-2 position of n-alkanes by the methane/ammonia monooxygenase family proteins. Org Biomol Chem 2015; 13:8261-70. [PMID: 26138087 DOI: 10.1039/c5ob00640f] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The selectivity of ammonia monooxygenase from Nitrosomonas europaea (AMO-Ne) for the oxidation of C4-C8n-alkanes to the corresponding alcohol isomers was examined to show the ability of AMO-Ne to recognize the n-alkane orientation within the catalytic site. AMO-Ne in whole cells produces 1- and 2-alcohols from C4-C8n-alkanes, and the regioselectivity is dependent on the length of the carbon chain. 2-Alcohols produced from C4-C7n-alkanes were predominantly either the R- or S-enantiomers, while 2-octanol produced from n-octane was racemic. These results indicate that AMO-Ne can discriminate between the prochiral hydrogens at the C-2 position, with the degree of discrimination varying according to the n-alkane. Compared to the particulate methane monooxygenase (pMMO) of Methylococcus capsulatus (Bath) and that of Methylosinus trichosporium OB3b, AMO-Ne showed a distinct ability to discriminate between the orientation of n-butane and n-pentane in the catalytic site.
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Affiliation(s)
- Akimitsu Miyaji
- Department of Environmental Chemistry and Engineering, Tokyo Institute of Technology, 4259 G-1-14 Nagatsuta-cho, Midori-ku, Yokohama 226-8502, Japan.
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73
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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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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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75
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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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76
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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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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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78
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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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79
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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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81
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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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82
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Peter S, Karich A, Ullrich R, Gröbe G, Scheibner K, Hofrichter M. Enzymatic one-pot conversion of cyclohexane into cyclohexanone: Comparison of four fungal peroxygenases. ACTA ACUST UNITED AC 2014. [DOI: 10.1016/j.molcatb.2013.09.016] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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83
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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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84
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von Bühler CJ, Urlacher VB. A novel P450-based biocatalyst for the selective production of chiral 2-alkanols. Chem Commun (Camb) 2014; 50:4089-91. [DOI: 10.1039/c4cc00647j] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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85
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Piontek K, Strittmatter E, Ullrich R, Gröbe G, Pecyna MJ, Kluge M, Scheibner K, Hofrichter M, Plattner DA. Structural basis of substrate conversion in a new aromatic peroxygenase: cytochrome P450 functionality with benefits. J Biol Chem 2013; 288:34767-76. [PMID: 24126915 DOI: 10.1074/jbc.m113.514521] [Citation(s) in RCA: 94] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Aromatic peroxygenases (APOs) represent a unique oxidoreductase sub-subclass of heme proteins with peroxygenase and peroxidase activity and were thus recently assigned a distinct EC classification (EC 1.11.2.1). They catalyze, inter alia, oxyfunctionalization reactions of aromatic and aliphatic hydrocarbons with remarkable regio- and stereoselectivities. When compared with cytochrome P450, APOs appear to be the choice enzymes for oxyfunctionalizations in organic synthesis due to their independence from a cellular environment and their greater chemical versatility. Here, the first two crystal structures of a heavily glycosylated fungal aromatic peroxygenase (AaeAPO) are described. They reveal different pH-dependent ligand binding modes. We model the fitting of various substrates in AaeAPO, illustrating the way the enzyme oxygenates polycyclic aromatic hydrocarbons. Spatial restrictions by a phenylalanine pentad in the active-site environment govern substrate specificity in AaeAPO.
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Affiliation(s)
- Klaus Piontek
- From the Institute of Organic Chemistry, University of Freiburg, Albertstrasse 21, 79104 Freiburg
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86
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Poraj-Kobielska M, Atzrodt J, Holla W, Sandvoss M, Gröbe G, Scheibner K, Hofrichter M. Preparation of labeled human drug metabolites and drug-drug interaction-probes with fungal peroxygenases. J Labelled Comp Radiopharm 2013; 56:513-9. [PMID: 24285530 DOI: 10.1002/jlcr.3103] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2013] [Revised: 06/28/2013] [Accepted: 07/01/2013] [Indexed: 01/15/2023]
Abstract
Enzymatic conversion of a drug can be an efficient alternative for the preparation of a complex metabolite compared with a multi-step chemical synthesis approach. Limitations exist for chemical methods for direct oxygen incorporation into organic molecules often suffering from low yields and unspecific oxidation and also for alternative whole-cell biotransformation processes, which require specific fermentation know-how. Stable oxygen-transferring biocatalysts such as unspecific peroxygenases (UPOs) could be an alternative for the synthesis of human drug metabolites and related stable isotope-labeled analogues. This work shows that UPOs can be used in combination with hydrogen/deuterium exchange for an efficient one-step process for the preparation of 4'-OH-diclofenac-d6. The scope of the reaction was investigated by screening of different peroxygenase subtypes for the transformation of selected deuterium-labeled substrates such as phenacetin-d3 or lidocaine-d3. Experiments with diclofenac-d7 revealed that the deuterium-labeling does not affect the kinetic parameters. By using the latter substrate and H2 (18) O2 as cosubstrate, it was possible to prepare a doubly isotope-labeled metabolite (4'-(18) OH-diclofenac-d6). UPOs offer certain practical advantages compared with P450 enzyme systems in terms of stability and ease of handling. Given these advantages, future work will expand the existing 'monooxygenation toolbox' of different fungal peroxygenases that mimic P450 in vitro reactions.
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Affiliation(s)
- Marzena Poraj-Kobielska
- Department of Biological and Environmental Sciences, TU Dresden - International Institute Zittau, Markt 23, 02763, Zittau, Germany
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87
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Ruiz-Dueñas FJ, Lundell T, Floudas D, Nagy LG, Barrasa JM, Hibbett DS, Martínez AT. Lignin-degrading peroxidases in Polyporales: an evolutionary survey based on 10 sequenced genomes. Mycologia 2013; 105:1428-44. [PMID: 23921235 DOI: 10.3852/13-059] [Citation(s) in RCA: 100] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The genomes of three representative Polyporales (Bjerkandera adusta, Phlebia brevispora and a member of the Ganoderma lucidum complex) were sequenced to expand our knowledge on the diversity of ligninolytic and related peroxidase genes in this Basidiomycota order that includes most wood-rotting fungi. The survey was completed by analyzing the heme-peroxidase genes in the already available genomes of seven more Polyporales species representing the antrodia, gelatoporia, core polyporoid and phlebioid clades. The study confirms the absence of ligninolytic peroxidase genes from the manganese peroxidase (MnP), lignin peroxidase (LiP) and versatile peroxidase (VP) families, in the brown-rot fungal genomes (all of them from the antrodia clade), which include only a limited number of predicted low redox-potential generic peroxidase (GP) genes. When members of the heme-thiolate peroxidase (HTP) and dye-decolorizing peroxidase (DyP) superfamilies (up to a total of 64 genes) also are considered, the newly sequenced B. adusta appears as the Polyporales species with the highest number of peroxidase genes due to the high expansion of both the ligninolytic peroxidase and DyP (super)families. The evolutionary relationships of the 111 genes for class-II peroxidases (from the GP, MnP, VP, LiP families) in the 10 Polyporales genomes is discussed including the existence of different MnP subfamilies and of a large and homogeneous LiP cluster, while different VPs mainly cluster with short MnPs. Finally, ancestral state reconstructions showed that a putative MnP gene, derived from a primitive GP that incorporated the Mn(II)-oxidation site, is the precursor of all the class-II ligninolytic peroxidases. Incorporation of an exposed tryptophan residue involved in oxidative degradation of lignin in a short MnP apparently resulted in evolution of the first VP. One of these ancient VPs might have lost the Mn(II)-oxidation site being at the origin of all the LiP enzymes, which are found only in species of the order Polyporales.
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88
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Wang X, Peter S, Ullrich R, Hofrichter M, Groves JT. Driving Force for Oxygen‐Atom Transfer by Heme‐Thiolate Enzymes. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201302137] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Xiaoshi Wang
- Department of Chemistry, Princeton University, Princeton, NJ 08544 (USA)
| | - Sebastian Peter
- Department of Bio‐ and Environmental Sciences, International Graduate School of Zittau, 02763 Zittau (Germany)
| | - René Ullrich
- Department of Bio‐ and Environmental Sciences, International Graduate School of Zittau, 02763 Zittau (Germany)
| | - Martin Hofrichter
- Department of Bio‐ and Environmental Sciences, International Graduate School of Zittau, 02763 Zittau (Germany)
| | - John T. Groves
- Department of Chemistry, Princeton University, Princeton, NJ 08544 (USA)
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89
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Wang X, Peter S, Ullrich R, Hofrichter M, Groves JT. Driving force for oxygen-atom transfer by heme-thiolate enzymes. Angew Chem Int Ed Engl 2013; 52:9238-41. [PMID: 23825007 DOI: 10.1002/anie.201302137] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2013] [Revised: 04/18/2013] [Indexed: 11/06/2022]
Affiliation(s)
- Xiaoshi Wang
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
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90
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Atzrodt J, Derdau V. Selected scientific topics of the 11th International Isotope Symposium on the Synthesis and Applications of Isotopes and Isotopically Labeled Compounds. J Labelled Comp Radiopharm 2013; 56:408-16. [PMID: 24285513 DOI: 10.1002/jlcr.3096] [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: 05/21/2013] [Revised: 06/19/2013] [Accepted: 06/19/2013] [Indexed: 01/02/2023]
Abstract
This micro-review describes hot topics and new trends in isotope science discussed at the 11th International Isotope Symposium on the Synthesis and Applications of Isotopes and Isotopically Labeled Compounds from a personal perspective.
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Affiliation(s)
- Jens Atzrodt
- Isotope Chemistry & Metabolite Synthesis, DSAR-DD, Sanofi-Aventis Deutschland GmbH, Industriepark Höchst G876, 65926, Frankfurt am Main, Germany
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91
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Müller CA, Akkapurathu B, Winkler T, Staudt S, Hummel W, Gröger H, Schwaneberg U. In VitroDouble Oxidation ofn-Heptane with Direct Cofactor Regeneration. Adv Synth Catal 2013. [DOI: 10.1002/adsc.201300143] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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92
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Trippe KM, Wolpert TJ, Hyman MR, Ciuffetti LM. RNAi silencing of a cytochrome P450 monoxygenase disrupts the ability of a filamentous fungus, Graphium sp., to grow on short-chain gaseous alkanes and ethers. Biodegradation 2013; 25:137-51. [DOI: 10.1007/s10532-013-9646-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2013] [Accepted: 04/27/2013] [Indexed: 10/26/2022]
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93
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Peter S, Kinne M, Ullrich R, Kayser G, Hofrichter M. Epoxidation of linear, branched and cyclic alkenes catalyzed by unspecific peroxygenase. Enzyme Microb Technol 2013; 52:370-6. [DOI: 10.1016/j.enzmictec.2013.02.013] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2012] [Revised: 02/22/2013] [Accepted: 02/25/2013] [Indexed: 10/27/2022]
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94
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Babot ED, del Río JC, Kalum L, Martínez AT, Gutiérrez A. Oxyfunctionalization of aliphatic compounds by a recombinant peroxygenase from
Coprinopsis cinerea. Biotechnol Bioeng 2013; 110:2323-32. [DOI: 10.1002/bit.24904] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2013] [Revised: 03/01/2013] [Accepted: 03/04/2013] [Indexed: 11/09/2022]
Affiliation(s)
- Esteban D. Babot
- Instituto de Recursos Naturales y Agrobiología de SevillaCSICReina Mercedes 10, E‐41012 SevilleSpain
| | - José C. del Río
- Instituto de Recursos Naturales y Agrobiología de SevillaCSICReina Mercedes 10, E‐41012 SevilleSpain
| | | | | | - Ana Gutiérrez
- Instituto de Recursos Naturales y Agrobiología de SevillaCSICReina Mercedes 10, E‐41012 SevilleSpain
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95
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Karich A, Kluge M, Ullrich R, Hofrichter M. Benzene oxygenation and oxidation by the peroxygenase of Agrocybe aegerita. AMB Express 2013; 3:5. [PMID: 23327645 PMCID: PMC3565944 DOI: 10.1186/2191-0855-3-5] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2012] [Accepted: 01/14/2013] [Indexed: 11/10/2022] Open
Abstract
Aromatic peroxygenase (APO) is an extracellular enzyme produced by the agaric basidiomycete Agrocybe aegerita that catalyzes diverse peroxide-dependent oxyfunctionalization reactions. Here we describe the oxygenation of the unactivated aromatic ring of benzene with hydrogen peroxide as co-substrate. The optimum pH of the reaction was around 7 and it proceeded via an initial epoxide intermediate that re-aromatized in aqueous solution to form phenol. Identity of the epoxide intermediate as benzene oxide was proved by a freshly prepared authentic standard using GC-MS and LC-MS analyses. Second and third [per]oxygenation was also observed and resulted in the formation of further hydroxylation and following [per]oxidation products: hydroquinone and p-benzoquinone, catechol and o-benzoquinone as well as 1,2,4-trihydroxybenzene and hydroxy-p-benzoquinone, respectively. Using H218O2 as co-substrate and ascorbic acid as radical scavenger, inhibiting the formation of peroxidation products (e.g., p-benzoquinone), the origin of the oxygen atom incorporated into benzene or phenol was proved to be the peroxide. Apparent enzyme kinetic constants (kcat, Km) for the peroxygenation of benzene were estimated to be around 8 s-1 and 3.6 mM. These results raise the possibility that peroxygenases may be useful for enzymatic syntheses of hydroxylated benzene derivatives under mild conditions.
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Cooper HLR, Mishra G, Huang X, Pender-Cudlip M, Austin RN, Shanklin J, Groves JT. Parallel and competitive pathways for substrate desaturation, hydroxylation, and radical rearrangement by the non-heme diiron hydroxylase AlkB. J Am Chem Soc 2012; 134:20365-75. [PMID: 23157204 PMCID: PMC3531984 DOI: 10.1021/ja3059149] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A purified and highly active form of the non-heme diiron hydroxylase AlkB was investigated using the diagnostic probe substrate norcarane. The reaction afforded C2 (26%) and C3 (43%) hydroxylation and desaturation products (31%). Initial C-H cleavage at C2 led to 7% C2 hydroxylation and 19% 3-hydroxymethylcyclohexene, a rearrangement product characteristic of a radical rearrangement pathway. A deuterated substrate analogue, 3,3,4,4-norcarane-d(4), afforded drastically reduced amounts of C3 alcohol (8%) and desaturation products (5%), while the radical rearranged alcohol was now the major product (65%). This change in product ratios indicates a large kinetic hydrogen isotope effect of ∼20 for both the C-H hydroxylation at C3 and the desaturation pathway, with all of the desaturation originating via hydrogen abstraction at C3 and not C2. The data indicate that AlkB reacts with norcarane via initial C-H hydrogen abstraction from C2 or C3 and that the three pathways, C3 hydroxylation, C3 desaturation, and C2 hydroxylation/radical rearrangement, are parallel and competitive. Thus, the incipient radical at C3 either reacts with the iron-oxo center to form an alcohol or proceeds along the desaturation pathway via a second H-abstraction to afford both 2-norcarene and 3-norcarene. Subsequent reactions of these norcarenes lead to detectable amounts of hydroxylation products and toluene. By contrast, the 2-norcaranyl radical intermediate leads to C2 hydroxylation and the diagnostic radical rearrangement, but this radical apparently does not afford desaturation products. The results indicate that C-H hydroxylation and desaturation follow analogous stepwise reaction channels via carbon radicals that diverge at the product-forming step.
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Affiliation(s)
| | - Girish Mishra
- Department of Biology, Brookhaven National Laboratory, 50 Bell Avenue, Upton, NY 11973
| | - Xiongyi Huang
- Department of Chemistry, Princeton University, Princeton NJ 08544
| | | | | | - John Shanklin
- Department of Biology, Brookhaven National Laboratory, 50 Bell Avenue, Upton, NY 11973
| | - John T. Groves
- Department of Chemistry, Princeton University, Princeton NJ 08544
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Bordeaux M, Galarneau A, Drone J. Catalytic, Mild, and Selective Oxyfunctionalization of Linear Alkanes: Current Challenges. Angew Chem Int Ed Engl 2012; 51:10712-23. [DOI: 10.1002/anie.201203280] [Citation(s) in RCA: 108] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2012] [Indexed: 02/02/2023]
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98
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Bordeaux M, Galarneau A, Drone J. Katalytische, milde und selektive Oxyfunktionalisierung von linearen Alkanen: aktuelle Herausforderungen. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201203280] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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99
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Wang X, Peter S, Kinne M, Hofrichter M, Groves JT. Detection and kinetic characterization of a highly reactive heme-thiolate peroxygenase compound I. J Am Chem Soc 2012; 134:12897-900. [PMID: 22827262 DOI: 10.1021/ja3049223] [Citation(s) in RCA: 90] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The extracellular heme-thiolate peroxygenase from Agrocybe aegerita (AaeAPO) has been shown to hydroxylate alkanes and numerous other substrates using hydrogen peroxide as the terminal oxidant. We describe the kinetics of formation and decomposition of AaeAPO compound I upon its reaction with mCPBA. The UV-vis spectral features of AaeAPO-I (361, 694 nm) are similar to those of chloroperoxidase-I and the recently described cytochrome P450-I. The second-order rate constant for AaeAPO-I formation was 1.0 (±0.4) × 10(7) M(-1) s(-1) at pH 5.0, 4 °C. The relatively slow decomposition rate, 1.4 (±0.03) s(-1), allowed the measurement of its reactivity toward a panel of substrates. The observed rate constants, k2', spanned 5 orders of magnitude and correlated linearly with bond dissociation enthalpies (BDEs) of strong C-H bond substrates with a log k2' vs BDE slope of ∼0.4. However, the hydroxylation rate was insensitive to a C-H BDE below 90 kcal/mol, similar to the behavior of the tert-butoxyl radical. The shape and slope of the Brønsted-Evans-Polanyi plot indicate a symmetrical transition state for the stronger C-H bonds and suggest entropy control of the rate in an early transition state for weaker C-H bonds. The AaeAPO-II Fe(IV)O-H BDE was estimated to be ∼103 kcal/mol. All results support the formation of a highly reactive AaeAPO oxoiron(IV) porphyrin radical cation intermediate that is the active oxygen species in these hydroxylation reactions.
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Affiliation(s)
- Xiaoshi Wang
- Department of Chemistry, Princeton University , Princeton, New Jersey 08544, United States
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