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Tjallinks G, Boverio A, Maric I, Rozeboom H, Arentshorst M, Visser J, Ram AFJ, Mattevi A, Fraaije MW. Structure elucidation and characterization of patulin synthase, insights into the formation of a fungal mycotoxin. FEBS J 2023; 290:5114-5126. [PMID: 37366079 DOI: 10.1111/febs.16804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 04/06/2023] [Accepted: 04/24/2023] [Indexed: 06/28/2023]
Abstract
Patulin synthase (PatE) from Penicillium expansum is a flavin-dependent enzyme that catalyses the last step in the biosynthesis of the mycotoxin patulin. This secondary metabolite is often present in fruit and fruit-derived products, causing postharvest losses. The patE gene was expressed in Aspergillus niger allowing purification and characterization of PatE. This confirmed that PatE is active not only on the proposed patulin precursor ascladiol but also on several aromatic alcohols including 5-hydroxymethylfurfural. By elucidating its crystal structure, details on its catalytic mechanism were revealed. Several aspects of the active site architecture are reminiscent of that of fungal aryl-alcohol oxidases. Yet, PatE is most efficient with ascladiol as substrate confirming its dedicated role in biosynthesis of patulin.
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Affiliation(s)
- Gwen Tjallinks
- Molecular Enzymology, University of Groningen, The Netherlands
- Department of Biology and Biotechnology, University of Pavia, Italy
| | - Alessandro Boverio
- Molecular Enzymology, University of Groningen, The Netherlands
- Department of Biology and Biotechnology, University of Pavia, Italy
| | - Ivana Maric
- Molecular Enzymology, University of Groningen, The Netherlands
| | | | | | - Jaap Visser
- Institute of Biology Leiden, Leiden University, The Netherlands
| | - Arthur F J Ram
- Institute of Biology Leiden, Leiden University, The Netherlands
| | - Andrea Mattevi
- Department of Biology and Biotechnology, University of Pavia, Italy
| | - Marco W Fraaije
- Molecular Enzymology, University of Groningen, The Netherlands
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2
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Dulchavsky M, Mitra R, Wu K, Li J, Boer K, Liu X, Zhang Z, Vasquez C, Clark CT, Funckes K, Shankar K, Bonnet-Zahedi S, Siddiq M, Sepulveda Y, Suhandynata RT, Momper JD, Calabrese AN, George O, Stull F, Bardwell JCA. Directed evolution unlocks oxygen reactivity for a nicotine-degrading flavoenzyme. Nat Chem Biol 2023; 19:1406-1414. [PMID: 37770699 PMCID: PMC10611581 DOI: 10.1038/s41589-023-01426-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 08/23/2023] [Indexed: 09/30/2023]
Abstract
The flavoenzyme nicotine oxidoreductase (NicA2) is a promising injectable treatment to aid in the cessation of smoking, a behavior responsible for one in ten deaths worldwide. NicA2 acts by degrading nicotine in the bloodstream before it reaches the brain. Clinical use of NicA2 is limited by its poor catalytic activity in the absence of its natural electron acceptor CycN. Without CycN, NicA2 is instead oxidized slowly by dioxygen (O2), necessitating unfeasibly large doses in a therapeutic setting. Here, we report a genetic selection strategy that directly links CycN-independent activity of NicA2 to growth of Pseudomonas putida S16. This selection enabled us to evolve NicA2 variants with substantial improvement in their rate of oxidation by O2. The encoded mutations cluster around a putative O2 tunnel, increasing flexibility and accessibility to O2 in this region. These mutations further confer desirable clinical properties. A variant form of NicA2 is tenfold more effective than the wild type at degrading nicotine in the bloodstream of rats.
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Affiliation(s)
- Mark Dulchavsky
- Howard Hughes Medical Institute and Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
- Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, MI, USA
| | - Rishav Mitra
- Howard Hughes Medical Institute and Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Kevin Wu
- Howard Hughes Medical Institute and Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Joshua Li
- Howard Hughes Medical Institute and Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Karli Boer
- Department of Chemistry, Western Michigan University, Kalamazoo, MI, USA
| | - Xiaomeng Liu
- Howard Hughes Medical Institute and Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Zhiyao Zhang
- Department of Chemistry, Western Michigan University, Kalamazoo, MI, USA
| | - Cristian Vasquez
- Department of Chemistry, Western Michigan University, Kalamazoo, MI, USA
| | | | - Kaitrin Funckes
- Department of Chemistry, Western Michigan University, Kalamazoo, MI, USA
| | - Kokila Shankar
- Department of Psychiatry, University of California, San Diego, La Jolla, CA, USA
| | - Selene Bonnet-Zahedi
- Department of Psychiatry, University of California, San Diego, La Jolla, CA, USA
| | - Mohammad Siddiq
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
| | - Yadira Sepulveda
- School of Pharmacy and Pharmaceutical Science, University of California, San Diego, La Jolla, CA, USA
| | - Raymond T Suhandynata
- School of Pharmacy and Pharmaceutical Science, University of California, San Diego, La Jolla, CA, USA
- Department of Pathology, University of California, San Diego, La Jolla, CA, USA
| | - Jeremiah D Momper
- School of Pharmacy and Pharmaceutical Science, University of California, San Diego, La Jolla, CA, USA
| | - Antonio N Calabrese
- Astbury Centre for Structural Molecular Biology, S chool of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Olivier George
- Department of Psychiatry, University of California, San Diego, La Jolla, CA, USA
| | - Frederick Stull
- Department of Chemistry, Western Michigan University, Kalamazoo, MI, USA
| | - James C A Bardwell
- Howard Hughes Medical Institute and Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA.
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3
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Ferreira P, Carro J, Balcells B, Martínez AT, Serrano A. Expanding the Physiological Role of Aryl-Alcohol Flavooxidases as Quinone Reductases. Appl Environ Microbiol 2023; 89:e0184422. [PMID: 37154753 DOI: 10.1128/aem.01844-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023] Open
Abstract
Aryl-alcohol oxidases (AAOs) are members of the glucose-methanol-choline oxidase/dehydrogenase (GMC) superfamily. These extracellular flavoproteins have been described as auxiliary enzymes in the degradation of lignin by several white-rot basidiomycetes. In this context, they oxidize fungal secondary metabolites and lignin-derived compounds using O2 as an electron acceptor, and supply H2O2 to ligninolytic peroxidases. Their substrate specificity, including mechanistic aspects of the oxidation reaction, has been characterized in Pleurotus eryngii AAO, taken as a model enzyme of this GMC superfamily. AAOs show broad reducing-substrate specificity in agreement with their role in lignin degradation, being able to oxidize both nonphenolic and phenolic aryl alcohols (and hydrated aldehydes). In the present work, the AAOs from Pleurotus ostreatus and Bjerkandera adusta were heterologously expressed in Escherichia coli, and their physicochemical properties and oxidizing abilities were compared with those of the well-known recombinant AAO from P. eryngii. In addition, electron acceptors different from O2, such as p-benzoquinone and the artificial redox dye 2,6-Dichlorophenolindophenol, were also studied. Differences in reducing-substrate specificity were found between the AAO enzymes from B. adusta and the two Pleurotus species. Moreover, the three AAOs oxidized aryl alcohols concomitantly with the reduction of p-benzoquinone, with similar or even higher efficiencies than when using their preferred oxidizing-substrate, O2. IMPORTANCE In this work, quinone reductase activity is analyzed in three AAO flavooxidases, whose preferred oxidizing-substrate is O2. The results presented, including reactions in the presence of both oxidizing substrates-benzoquinone and molecular oxygen-suggest that such aryl-alcohol dehydrogenase activity, although less important than its oxidase activity in terms of maximal turnover, may have a physiological role during fungal decay of lignocellulose by the reduction of quinones (and phenoxy radicals) from lignin degradation, preventing repolymerization. Moreover, the resulting hydroquinones would participate in redox-cycling reactions for the production of hydroxyl free radical involved in the oxidative attack of the plant cell-wall. Hydroquinones can also act as mediators for laccases and peroxidases in lignin degradation in the form of semiquinone radicals, as well as activators of lytic polysaccharide monooxygenases in the attack of crystalline cellulose. Moreover, reduction of these, and other phenoxy radicals produced by laccases and peroxidases, promotes lignin degradation by limiting repolymerization reactions. These findings expand the role of AAO in lignin biodegradation.
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Affiliation(s)
- Patricia Ferreira
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Zaragoza, Spain
- Instituto de Biocomputación y Física de Sistemas Complejos, BIFI (GBsC-CSIC Joint Unit), Universidad de Zaragoza, Zaragoza, Spain
| | - Juan Carro
- Centro de Investigaciones Biológicas "Margarita Salas", CSIC, Madrid, Spain
| | - Beatriz Balcells
- Centro de Investigaciones Biológicas "Margarita Salas", CSIC, Madrid, Spain
| | - Angel T Martínez
- Centro de Investigaciones Biológicas "Margarita Salas", CSIC, Madrid, Spain
| | - Ana Serrano
- Centro de Investigaciones Biológicas "Margarita Salas", CSIC, Madrid, Spain
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Hiraka K, Yoshida H, Tsugawa W, Asano R, La Belle JT, Ikebukuro K, Sode K. Structure of lactate oxidase from Enterococcus hirae revealed new aspects of active site loop function: Product-inhibition mechanism and oxygen gatekeeper. Protein Sci 2022; 31:e4434. [PMID: 36173159 PMCID: PMC9490804 DOI: 10.1002/pro.4434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 08/18/2022] [Accepted: 08/24/2022] [Indexed: 11/09/2022]
Abstract
l-Lactate oxidase (LOx) is a flavin mononucleotide (FMN)-dependent triose phosphate isomerase (TIM) barrel fold enzyme that catalyzes the oxidation of l-lactate using oxygen as a primary electron acceptor. Although reductive half-reaction mechanism of LOx has been studied by structure-based kinetic studies, oxidative half-reaction and substrate/product-inhibition mechanisms were yet to be elucidated. In this study, the structure and enzymatic properties of wild-type and mutant LOxs from Enterococcus hirae (EhLOx) were investigated. EhLOx structure showed the common TIM-barrel fold with flexible loop region. Noteworthy observations were that the EhLOx crystal structures prepared by co-crystallization with product, pyruvate, revealed the complex structures with "d-lactate form ligand," which was covalently bonded with a Tyr211 side chain. This observation provided direct evidence to suggest the product-inhibition mode of EhLOx. Moreover, this structure also revealed a flip motion of Met207 side chain, which is located on the flexible loop region as well as Tyr211. Through a saturation mutagenesis study of Met207, one of the mutants Met207Leu showed the drastically decreased oxidase activity but maintained dye-mediated dehydrogenase activity. The structure analysis of EhLOx Met207Leu revealed the absence of flipping in the vicinity of FMN, unlike the wild-type Met207 side chain. Together with the simulation of the oxygen-accessible channel prediction, Met207 may play as an oxygen gatekeeper residue, which contributes oxygen uptake from external enzyme to FMN. Three clades of LOxs are proposed based on the difference of the Met207 position and they have different oxygen migration pathway from external enzyme to active center FMN.
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Affiliation(s)
- Kentaro Hiraka
- Department of Biotechnology and Life Science, Graduate School of EngineeringTokyo University of Agriculture and TechnologyTokyoJapan
- College of Science, Engineering and TechnologyGrand Canyon UniversityPhoenixArizonaUSA
| | - Hiromi Yoshida
- Department of Basic Life Science, Faculty of MedicineKagawa UniversityKagawaJapan
| | - Wakako Tsugawa
- Department of Biotechnology and Life Science, Graduate School of EngineeringTokyo University of Agriculture and TechnologyTokyoJapan
| | - Ryutaro Asano
- Department of Biotechnology and Life Science, Graduate School of EngineeringTokyo University of Agriculture and TechnologyTokyoJapan
| | - Jeffrey T. La Belle
- College of Science, Engineering and TechnologyGrand Canyon UniversityPhoenixArizonaUSA
| | - Kazunori Ikebukuro
- Department of Biotechnology and Life Science, Graduate School of EngineeringTokyo University of Agriculture and TechnologyTokyoJapan
| | - Koji Sode
- Joint Department of Biomedical EngineeringThe University of North Carolina at Chapel Hill and North Carolina State UniversityChapel HillNorth CarolinaUSA
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5
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Sayed M, Gaber Y, Junghus F, Martín EV, Pyo SH, Hatti-Kaul R. Oxidation of 5-hydroxymethylfurfural with a novel aryl alcohol oxidase from Mycobacterium sp. MS1601. Microb Biotechnol 2022; 15:2176-2190. [PMID: 35349220 PMCID: PMC9328741 DOI: 10.1111/1751-7915.14052] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Revised: 03/06/2022] [Accepted: 03/08/2022] [Indexed: 11/30/2022] Open
Abstract
Bio‐based 5‐hydroxymethylfurfural (HMF) serves as an important platform for several chemicals, among which 2,5‐furan dicarboxylic acid (FDCA) has attracted considerable interest as a monomer for the production of polyethylene furanoate (PEF), a potential alternative for fossil‐based polyethylene terephthalate (PET). This study is based on the HMF oxidizing activity shown by Mycobacterium sp. MS 1601 cells and investigation of the enzyme catalysing the oxidation. The Mycobacterium whole cells oxidized the HMF to FDCA (60% yield) and hydroxymethyl furan carboxylic acid (HMFCA). A gene encoding a novel bacterial aryl alcohol oxidase, hereinafter MycspAAO, was identified in the genome and was cloned and expressed in Escherichia coli Bl21 (DE3). The purified MycspAAO displayed activity against several alcohols and aldehydes; 3,5 dimethoxy benzyl alcohol (veratryl alcohol) was the best substrate among those tested followed by HMF. 5‐Hydroxymethylfurfural was converted to 5‐formyl‐2‐furoic acid (FFCA) via diformyl furan (DFF) with optimal activity at pH 8 and 30–40°C. FDCA formation was observed during long reaction time with low HMF concentration. Mutagenesis of several amino acids shaping the active site and evaluation of the variants showed Y444F to have around 3‐fold higher kcat/Km and ~1.7‐fold lower Km with HMF.
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Affiliation(s)
- Mahmoud Sayed
- Division of Biotechnology, Department of Chemistry, Center for Chemistry and Chemical Engineering, Lund University, Lund, SE-22100, Sweden.,Department of Botany and Microbiology, Faculty of Science, South Valley University, Qena, 83523, Egypt
| | - Yasser Gaber
- Department of Microbiology and Immunology, Faculty of Pharmacy, Beni-Suef University, Beni-Suef, 62511, Egypt.,Department of Pharmaceutics and Pharmaceutical Technology, Faculty of Pharmacy, Mutah University, Al-Karak, 61710, Jordan
| | - Fredrik Junghus
- Division of Biotechnology, Department of Chemistry, Center for Chemistry and Chemical Engineering, Lund University, Lund, SE-22100, Sweden
| | - Eric Valdés Martín
- Division of Biotechnology, Department of Chemistry, Center for Chemistry and Chemical Engineering, Lund University, Lund, SE-22100, Sweden
| | - Sang-Hyun Pyo
- Division of Biotechnology, Department of Chemistry, Center for Chemistry and Chemical Engineering, Lund University, Lund, SE-22100, Sweden
| | - Rajni Hatti-Kaul
- Division of Biotechnology, Department of Chemistry, Center for Chemistry and Chemical Engineering, Lund University, Lund, SE-22100, Sweden
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6
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Seo E, Kim M, Park S, Park S, Oh D, Bornscheuer U, Park J. Enzyme Access Tunnel Engineering in Baeyer‐Villiger Monooxygenases to Improve Oxidative Stability and Biocatalyst Performance. Adv Synth Catal 2021. [DOI: 10.1002/adsc.202101044] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Eun‐Ji Seo
- Department of Food Science and Engineering Ewha Womans University Seoul 03760 Republic of Korea
| | - Myeong‐Ju Kim
- Department of Food Science and Engineering Ewha Womans University Seoul 03760 Republic of Korea
| | - So‐Yeon Park
- Department of Food Science and Engineering Ewha Womans University Seoul 03760 Republic of Korea
| | - Seongsoon Park
- Department of Chemistry, Center for NanoBio Applied Technology Sungshin Women's University Seoul 01133 Republic of Korea
| | - Deok‐Kun Oh
- Department of Bioscience and Biotechnology Konkuk University Seoul 05029 Republic of Korea
| | - Uwe Bornscheuer
- Institute of Biochemistry, Department of Biotechnology & Enzyme Catalysis Greifswald University Greifswald 17487 Germany
| | - Jin‐Byung Park
- Department of Food Science and Engineering Ewha Womans University Seoul 03760 Republic of Korea
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7
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Pecularities and applications of aryl-alcohol oxidases from fungi. Appl Microbiol Biotechnol 2021; 105:4111-4126. [PMID: 33997930 PMCID: PMC8140971 DOI: 10.1007/s00253-021-11337-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 05/03/2021] [Accepted: 05/06/2021] [Indexed: 12/16/2022]
Abstract
Abstract Aryl-alcohol oxidases (AAOs) are FAD-containing enzymes that oxidize a broad range of aromatic as well as aliphatic allylic alcohols to aldehydes. Their broad substrate spectrum accompanied by the only need for molecular oxygen as cosubstrate and production of hydrogen peroxide as sole by-product makes these enzymes very promising biocatalysts. AAOs were used in the synthesis of flavors, fragrances, and other high-value-added compounds and building blocks as well as in dye decolorization and pulp biobleaching. Furthermore, AAOs offer a huge potential as efficient suppliers of hydrogen peroxide for peroxidase- and peroxygenase-catalyzed reactions. A prerequisite for application as biocatalysts at larger scale is the production of AAOs in sufficient amounts. Heterologous expression of these predominantly fungal enzymes is, however, quite challenging. This review summarizes different approaches aiming at enhancing heterologous expression of AAOs and gives an update on substrates accepted by these promising enzymes as well as potential fields of their application. Key points • Aryl-alcohol oxidases (AAOs) supply ligninolytic peroxidases with H2O2. • AAOs accept a broad spectrum of aromatic and aliphatic allylic alcohols. • AAOs are potential biocatalysts for the production of high-value-added bio-based chemicals.
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Viñambres M, Espada M, Martínez AT, Serrano A. Screening and Evaluation of New Hydroxymethylfurfural Oxidases for Furandicarboxylic Acid Production. Appl Environ Microbiol 2020; 86:e00842-20. [PMID: 32503910 PMCID: PMC7414962 DOI: 10.1128/aem.00842-20] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 05/31/2020] [Indexed: 11/20/2022] Open
Abstract
The enzymatic production of 2,5-furandicarboxylic acid (FDCA) from 5-hydroxymethylfurfural (HMF) has gained interest in recent years, as FDCA is a renewable precursor of poly(ethylene-2,5-furandicarboxylate) (PEF). 5-Hydroxymethylfurfural oxidases (HMFOs) form a flavoenzyme family with genes annotated in a dozen bacterial species but only one enzyme purified and characterized to date (after heterologous expression of a Methylovorus sp. HMFO gene). This oxidase acts on both furfuryl alcohols and aldehydes and, therefore, is able to catalyze the conversion of HMF into FDCA through 2,5-diformylfuran (DFF) and 2,5-formylfurancarboxylic acid (FFCA), with only the need of oxygen as a cosubstrate. To enlarge the repertoire of HMFO enzymes available, genetic databases were screened for putative HMFO genes, followed by heterologous expression in Escherichia coli After unsuccessful trials with other bacterial HMFO genes, HMFOs from two Pseudomonas species were produced as active soluble enzymes, purified, and characterized. The Methylovorus sp. enzyme was also produced and purified in parallel for comparison. Enzyme stability against temperature, pH, and hydrogen peroxide, three key aspects for application, were evaluated (together with optimal conditions for activity), revealing differences between the three HMFOs. Also, the kinetic parameters for HMF, DFF, and FFCA oxidation were determined, the new HMFOs having higher efficiencies for the oxidation of FFCA, which constitutes the bottleneck in the enzymatic route for FDCA production. These results were used to set up the best conditions for FDCA production by each enzyme, attaining a compromise between optimal activity and half-life under different conditions of operation.IMPORTANCE HMFO is the only enzyme described to date that can catalyze by itself the three consecutive oxidation steps to produce FDCA from HMF. Unfortunately, only one HMFO enzyme is currently available for biotechnological application. This availability is enlarged here by the identification, heterologous production, purification, and characterization of two new HMFOs, one from Pseudomonas nitroreducens and one from an unidentified Pseudomonas species. Compared to the previously known Methylovorus HMFO, the new enzyme from P. nitroreducens exhibits better performance for FDCA production in wider pH and temperature ranges, with higher tolerance for the hydrogen peroxide formed, longer half-life during oxidation, and higher yield and total turnover numbers in long-term conversions under optimized conditions. All these features are relevant properties for the industrial production of FDCA. In summary, gene screening and heterologous expression can facilitate the selection and improvement of HMFO enzymes as biocatalysts for the enzymatic synthesis of renewable building blocks in the production of bioplastics.
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Affiliation(s)
- Mario Viñambres
- Centro de Investigaciones Biológicas Margarita Salas, CSIC, Madrid, Spain
| | - Marta Espada
- Centro de Investigaciones Biológicas Margarita Salas, CSIC, Madrid, Spain
| | - Angel T Martínez
- Centro de Investigaciones Biológicas Margarita Salas, CSIC, Madrid, Spain
| | - Ana Serrano
- Centro de Investigaciones Biológicas Margarita Salas, CSIC, Madrid, Spain
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Abstract
Aryl-alcohol oxidases (AAO) constitute a family of FAD-containing enzymes, included in the glucose-methanol-choline oxidase/dehydrogenase superfamily of proteins. They are commonly found in fungi, where their eco-physiological role is to produce hydrogen peroxide that activates ligninolytic peroxidases in white-rot (lignin-degrading) basidiomycetes or to trigger the Fenton reactions in brown-rot (carbohydrate-degrading) basidiomycetes. These enzymes catalyze the oxidation of a plethora of aromatic, and some aliphatic, polyunsaturated alcohols bearing conjugated primary hydroxyl group. Besides, the enzymes show activity on the hydrated forms of the corresponding aldehydes. Some AAO features, such as the broad range of substrates that it can oxidize (with the only need of molecular oxygen as co-substrate) and its stereoselective mechanism, confer good properties to these enzymes as industrial biocatalysts. In fact, AAO can be used for different biotechnological applications, such as flavor synthesis, secondary alcohol deracemization and oxidation of furfurals for the production of furandicarboxylic acid as a chemical building block. Also, AAO can participate in processes of interest in the wood biorefinery and textile industries as an auxiliary enzyme providing hydrogen peroxide to ligninolytic or dye-decolorizing peroxidases. Both rational design and directed molecular evolution have been employed to engineer AAO for some of the above biotechnological applications.
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Affiliation(s)
- Ana Serrano
- Centro de Investigaciones Biológicas Margarita Salas (CIB), CSIC, Madrid, Spain.
| | - Juan Carro
- Centro de Investigaciones Biológicas Margarita Salas (CIB), CSIC, Madrid, Spain
| | - Angel T Martínez
- Centro de Investigaciones Biológicas Margarita Salas (CIB), CSIC, Madrid, Spain.
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10
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Kadowaki MAS, Higasi PMR, de Godoy MO, de Araújo EA, Godoy AS, Prade RA, Polikarpov I. Enzymatic versatility and thermostability of a new aryl-alcohol oxidase from Thermothelomyces thermophilus M77. Biochim Biophys Acta Gen Subj 2020; 1864:129681. [PMID: 32653619 DOI: 10.1016/j.bbagen.2020.129681] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 06/14/2020] [Accepted: 06/30/2020] [Indexed: 01/23/2023]
Abstract
Background Fungal aryl-alcohol oxidases (AAOx) are extracellular flavoenzymes that belong to glucose-methanol-choline oxidoreductase family and are responsible for the selective conversion of primary aromatic alcohols into aldehydes and aromatic aldehydes to their corresponding acids, with concomitant production of hydrogen peroxide (H2O2) as by-product. The H2O2 can be provided to lignin degradation pathway, a biotechnological property explored in biofuel production. In the thermophilic fungus Thermothelomyces thermophilus (formerly Myceliophthora thermophila), just one AAOx was identified in the exo-proteome. Methods The glycosylated and non-refolded crystal structure of an AAOx from T. thermophilus at 2.6 Å resolution was elucidated by X-ray crystallography combined with small-angle X-ray scattering (SAXS) studies. Moreover, biochemical analyses were carried out to shed light on enzyme substrate specificity and thermostability. Results This flavoenzyme harbors a flavin adenine dinucleotide as a cofactor and is able to oxidize aromatic substrates and 5-HMF. Our results also show that the enzyme has similar oxidation rates for bulky or simple aromatic substrates such as cinnamyl and veratryl alcohols. Moreover, the crystal structure of MtAAOx reveals an open active site, which might explain observed specificity of the enzyme. Conclusions MtAAOx shows previously undescribed structural differences such as a fully accessible catalytic tunnel, heavy glycosylation and Ca2+ binding site providing evidences for thermostability and activity of the enzymes from AA3_2 subfamily. General significance Structural and biochemical analyses of MtAAOx could be important for comprehension of aryl-alcohol oxidases structure-function relationships and provide additional molecular tools to be used in future biotechnological applications.
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Affiliation(s)
- Marco Antonio Seiki Kadowaki
- São Carlos Institute of Physics, University of São Paulo, Av. Trabalhador São-carlense, 400, São Carlos, SP 13566-590, Brazil.
| | - Paula Miwa Rabelo Higasi
- São Carlos Institute of Physics, University of São Paulo, Av. Trabalhador São-carlense, 400, São Carlos, SP 13566-590, Brazil
| | - Mariana Ortiz de Godoy
- São Carlos Institute of Physics, University of São Paulo, Av. Trabalhador São-carlense, 400, São Carlos, SP 13566-590, Brazil
| | - Evandro Ares de Araújo
- São Carlos Institute of Physics, University of São Paulo, Av. Trabalhador São-carlense, 400, São Carlos, SP 13566-590, Brazil
| | - Andre Schutzer Godoy
- São Carlos Institute of Physics, University of São Paulo, Av. Trabalhador São-carlense, 400, São Carlos, SP 13566-590, Brazil
| | - Rolf Alexander Prade
- Departments of Microbiology & Molecular Genetics and Biochemistry & Molecular Biology, Oklahoma State University, OK, USA
| | - Igor Polikarpov
- São Carlos Institute of Physics, University of São Paulo, Av. Trabalhador São-carlense, 400, São Carlos, SP 13566-590, Brazil.
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11
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Viña-Gonzalez J, Alcalde M. Directed evolution of the aryl-alcohol oxidase: Beyond the lab bench. Comput Struct Biotechnol J 2020; 18:1800-1810. [PMID: 32695272 PMCID: PMC7358221 DOI: 10.1016/j.csbj.2020.06.037] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 06/19/2020] [Accepted: 06/20/2020] [Indexed: 11/22/2022] Open
Abstract
Aryl-alcohol oxidase (AAO) is a fungal GMC flavoprotein secreted by white-rot fungi that supplies H2O2 to the ligninolytic consortium. This enzyme can oxidize a wide array of aromatic alcohols in a highly enantioselective manner, an important trait in organic synthesis. The best strategy to adapt AAO to industrial needs is to engineer its properties by directed evolution, aided by computational analysis. The aim of this review is to describe the strategies and challenges we faced when undertaking laboratory evolution of AAO. After a comprehensive introduction into the structure of AAO, its function and potential applications, the different directed evolution enterprises designed to express the enzyme in an active and soluble form in yeast are described, as well as those to unlock new activities involving the oxidation of secondary aromatic alcohols and the synthesis of furandicarboxylic acids.
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Affiliation(s)
- Javier Viña-Gonzalez
- Department of Biocatalysis, Institute of Catalysis, CSIC, Cantoblanco, 28049 Madrid, Spain
| | - Miguel Alcalde
- Department of Biocatalysis, Institute of Catalysis, CSIC, Cantoblanco, 28049 Madrid, Spain
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12
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Alteration of Electron Acceptor Preferences in the Oxidative Half-Reaction of Flavin-Dependent Oxidases and Dehydrogenases. Int J Mol Sci 2020; 21:ijms21113797. [PMID: 32471202 PMCID: PMC7312611 DOI: 10.3390/ijms21113797] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 05/22/2020] [Accepted: 05/24/2020] [Indexed: 11/30/2022] Open
Abstract
In this review, recent progress in the engineering of the oxidative half-reaction of flavin-dependent oxidases and dehydrogenases is discussed, considering their current and future applications in bioelectrochemical studies, such as for the development of biosensors and biofuel cells. There have been two approaches in the studies of oxidative half-reaction: engineering of the oxidative half-reaction with oxygen, and engineering of the preference for artificial electron acceptors. The challenges for engineering oxidative half-reactions with oxygen are further categorized into the following approaches: (1) mutation to the putative residues that compose the cavity where oxygen may be located, (2) investigation of the vicinities where the reaction with oxygen may take place, and (3) investigation of possible oxygen access routes to the isoalloxazine ring. Among these approaches, introducing a mutation at the oxygen access route to the isoalloxazine ring represents the most versatile and effective strategy. Studies to engineer the preference of artificial electron acceptors are categorized into three different approaches: (1) engineering of the charge at the residues around the substrate entrance, (2) engineering of a cavity in the vicinity of flavin, and (3) decreasing the glycosylation degree of enzymes. Among these approaches, altering the charge in the vicinity where the electron acceptor may be accessed will be most relevant.
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13
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Song JW, Seo JH, Oh DK, Bornscheuer UT, Park JB. Design and engineering of whole-cell biocatalytic cascades for the valorization of fatty acids. Catal Sci Technol 2020. [DOI: 10.1039/c9cy01802f] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
This review presents the key factors to construct a productive whole-cell biocatalytic cascade exemplified for the biotransformation of renewable fatty acids.
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Affiliation(s)
- Ji-Won Song
- Department of Food Science and Engineering
- Ewha Womans University
- Seoul 03760
- Republic of Korea
| | - Joo-Hyun Seo
- Department of Bio and Fermentation Convergence Technology
- Kookmin University
- Seoul 02707
- Republic of Korea
| | - Doek-Kun Oh
- Department of Bioscience and Biotechnology
- Konkuk University
- Seoul 143-701
- Republic of Korea
| | - Uwe T. Bornscheuer
- Institute of Biochemistry
- Department of Biotechnology & Enzyme Catalysis
- Greifswald University
- 17487 Greifswald
- Germany
| | - Jin-Byung Park
- Department of Food Science and Engineering
- Ewha Womans University
- Seoul 03760
- Republic of Korea
- Institute of Molecular Microbiology and Biosystems Engineering
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14
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Gandomkar S, Jost E, Loidolt D, Swoboda A, Pickl M, Elaily W, Daniel B, Fraaije MW, Macheroux P, Kroutil W. Biocatalytic Enantioselective Oxidation of Sec-Allylic Alcohols with Flavin-Dependent Oxidases. Adv Synth Catal 2019; 361:5264-5271. [PMID: 31894182 PMCID: PMC6919931 DOI: 10.1002/adsc.201900921] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 09/26/2019] [Indexed: 01/17/2023]
Abstract
The oxidation of allylic alcohols is challenging to perform in a chemo- as well as stereo-selective fashion at the expense of molecular oxygen using conventional chemical protocols. Here, we report the identification of a library of flavin-dependent oxidases including variants of the berberine bridge enzyme (BBE) analogue from Arabidopsis thaliana (AtBBE15) and the 5-(hydroxymethyl)furfural oxidase (HMFO) and its variants (V465T, V465S, V465T/W466H and V367R/W466F) for the enantioselective oxidation of sec-allylic alcohols. While primary and benzylic alcohols as well as certain sugars are well known to be transformed by flavin-dependent oxidases, sec-allylic alcohols have not been studied yet except in a single report. The model substrates investigated were oxidized enantioselectively in a kinetic resolution with an E-value of up to >200. For instance HMFO V465S/T oxidized the (S)-enantiomer of (E)-oct-3-en-2-ol (1 a) and (E)-4-phenylbut-3-en-2-ol with E>200 giving the remaining (R)-alcohol with ee>99% at 50% conversion. The enantioselectivity could be decreased if required by medium engineering by the addition of cosolvents (e. g. dimethyl sulfoxide).
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Affiliation(s)
- Somayyeh Gandomkar
- Institute of Chemistry, NAWI Graz, BioTechMed GrazUniversity of GrazHeinrichstr. 288010GrazAustria
| | - Etta Jost
- Institute of Chemistry, NAWI Graz, BioTechMed GrazUniversity of GrazHeinrichstr. 288010GrazAustria
| | - Doris Loidolt
- Institute of Chemistry, NAWI Graz, BioTechMed GrazUniversity of GrazHeinrichstr. 288010GrazAustria
| | - Alexander Swoboda
- Institute of Chemistry, NAWI Graz, BioTechMed GrazUniversity of GrazHeinrichstr. 288010GrazAustria
| | - Mathias Pickl
- Institute of Chemistry, NAWI Graz, BioTechMed GrazUniversity of GrazHeinrichstr. 288010GrazAustria
| | - Wael Elaily
- Institute of BiochemistryGraz University of TechnologyPetersgasse 12/II8010GrazAustria
- Chemistry of Natural & Microbial Products DepartmentNational Research Centre33 El Buhouth St12622CairoEgypt
| | - Bastian Daniel
- Institute of BiochemistryGraz University of TechnologyPetersgasse 12/II8010GrazAustria
- Austrian Centre of Industrial Biotechnology, c/o Institute of Molecular BiosciencesUniversity of GrazHumboldtstraße 508010GrazAustria
| | - Marco W. Fraaije
- Molecular Enzymology GroupUniversity of GroningenNijenborgh 49747AGGroningenThe Netherlands
| | - Peter Macheroux
- Institute of BiochemistryGraz University of TechnologyPetersgasse 12/II8010GrazAustria
| | - Wolfgang Kroutil
- Institute of Chemistry, NAWI Graz, BioTechMed GrazUniversity of GrazHeinrichstr. 288010GrazAustria
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15
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Serrano A, Sancho F, Viña-González J, Carro J, Alcalde M, Guallar V, Martínez AT. Switching the substrate preference of fungal aryl-alcohol oxidase: towards stereoselective oxidation of secondary benzyl alcohols. Catal Sci Technol 2019. [DOI: 10.1039/c8cy02447b] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Using PELE computational simulations the ability to deracemize secondary benzylic alcohols was introduced (by I500M/F501W double mutation) in stereoselective AAO.
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Affiliation(s)
- Ana Serrano
- Centro de Investigaciones Biológicas
- CSIC
- E-28040 Madrid
- Spain
| | - Ferran Sancho
- Barcelona Supercomputing Center
- E-08034 Barcelona
- Spain
| | | | - Juan Carro
- Centro de Investigaciones Biológicas
- CSIC
- E-28040 Madrid
- Spain
| | - Miguel Alcalde
- Department of Biocatalysis
- Institute of Catalysis
- CSIC
- Madrid
- Spain
| | - Victor Guallar
- Barcelona Supercomputing Center
- E-08034 Barcelona
- Spain
- ICREA
- Barcelona
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16
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Carro J, Amengual-Rigo P, Sancho F, Medina M, Guallar V, Ferreira P, Martínez AT. Multiple implications of an active site phenylalanine in the catalysis of aryl-alcohol oxidase. Sci Rep 2018; 8:8121. [PMID: 29802285 PMCID: PMC5970180 DOI: 10.1038/s41598-018-26445-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Accepted: 05/11/2018] [Indexed: 01/15/2023] Open
Abstract
Aryl-alcohol oxidase (AAO) has demonstrated to be an enzyme with a bright future ahead due to its biotechnological potential in deracemisation of chiral compounds, production of bioplastic precursors and other reactions of interest. Expanding our understanding on the AAO reaction mechanisms, through the investigation of its structure-function relationships, is crucial for its exploitation as an industrial biocatalyst. In this regard, previous computational studies suggested an active role for AAO Phe397 at the active-site entrance. This residue is located in a loop that partially covers the access to the cofactor forming a bottleneck together with two other aromatic residues. Kinetic and affinity spectroscopic studies, complemented with computational simulations using the recently developed adaptive-PELE technology, reveal that the Phe397 residue is important for product release and to help the substrates attain a catalytically relevant position within the active-site cavity. Moreover, removal of aromaticity at the 397 position impairs the oxygen-reduction activity of the enzyme. Experimental and computational findings agree very well in the timing of product release from AAO, and the simulations help to understand the experimental results. This highlights the potential of adaptive-PELE to provide answers to the questions raised by the empirical results in the study of enzyme mechanisms.
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Affiliation(s)
- Juan Carro
- Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, E-28040, Madrid, Spain
| | - Pep Amengual-Rigo
- Barcelona Supercomputing Center, Jordi Girona 31, E-08034, Barcelona, Spain
| | - Ferran Sancho
- Barcelona Supercomputing Center, Jordi Girona 31, E-08034, Barcelona, Spain
| | - Milagros Medina
- Department of Biochemistry and Cellular and Molecular Biology, and BIFI, University of Zaragoza, E-50009, Zaragoza, Spain
| | - Victor Guallar
- Barcelona Supercomputing Center, Jordi Girona 31, E-08034, Barcelona, Spain. .,ICREA, Passeig Lluís Companys 23, E-08010, Barcelona, Spain.
| | - Patricia Ferreira
- Department of Biochemistry and Cellular and Molecular Biology, and BIFI, University of Zaragoza, E-50009, Zaragoza, Spain.
| | - Angel T Martínez
- Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, E-28040, Madrid, Spain.
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17
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Carro J, Ferreira P, Martínez AT, Gadda G. Stepwise Hydrogen Atom and Proton Transfers in Dioxygen Reduction by Aryl-Alcohol Oxidase. Biochemistry 2018; 57:1790-1797. [DOI: 10.1021/acs.biochem.8b00106] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Juan Carro
- Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, E-28040 Madrid, Spain
| | - Patricia Ferreira
- Departament of Biochemistry and Cellular and Molecular Biology and Institute for Biocomputation and Physics of Complex Systems (BIFI), University of Zaragoza, E-50009 Zaragoza, Spain
| | - Angel T. Martínez
- Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, E-28040 Madrid, Spain
| | - Giovanni Gadda
- Department of Chemistry, Department of Biology, Center for Biotechnology and Drug Design, and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia 30302-3965, United States
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18
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Kinetic Resolution of sec
-Thiols by Enantioselective Oxidation with Rationally Engineered 5-(Hydroxymethyl)furfural Oxidase. Angew Chem Int Ed Engl 2018; 57:2864-2868. [DOI: 10.1002/anie.201713189] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 01/20/2018] [Indexed: 11/07/2022]
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19
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Pickl M, Swoboda A, Romero E, Winkler CK, Binda C, Mattevi A, Faber K, Fraaije MW. Kinetic Resolution ofsec-Thiols by Enantioselective Oxidation with Rationally Engineered 5-(Hydroxymethyl)furfural Oxidase. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201713189] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Mathias Pickl
- Department of Chemistry; University of Graz; Heinrichstrasse 28 8010 Graz Austria
| | - Alexander Swoboda
- Department of Chemistry; University of Graz; Heinrichstrasse 28 8010 Graz Austria
| | - Elvira Romero
- Department of Biotechnology; University of Groningen; Nijenborgh 4 9747AG Groningen The Netherlands
| | - Christoph K. Winkler
- Department of Chemistry; University of Graz; Heinrichstrasse 28 8010 Graz Austria
- Austrian Centre of Industrial Biotechnology (ACIB GmbH); c/o Heinrichstrasse 28 8010 Graz Austria
| | - Claudia Binda
- Department of Biology and Biotechnology “Lazzaro Spallanzani”; University of Pavia; Via Ferrata 9 27100 Pavia Italy
| | - Andrea Mattevi
- Department of Biology and Biotechnology “Lazzaro Spallanzani”; University of Pavia; Via Ferrata 9 27100 Pavia Italy
| | - Kurt Faber
- Department of Chemistry; University of Graz; Heinrichstrasse 28 8010 Graz Austria
| | - Marco W. Fraaije
- Department of Biotechnology; University of Groningen; Nijenborgh 4 9747AG Groningen The Netherlands
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20
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Romero E, Gómez Castellanos JR, Gadda G, Fraaije MW, Mattevi A. Same Substrate, Many Reactions: Oxygen Activation in Flavoenzymes. Chem Rev 2018; 118:1742-1769. [DOI: 10.1021/acs.chemrev.7b00650] [Citation(s) in RCA: 216] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Elvira Romero
- Molecular Enzymology Group, University of Groningen, Nijenborgh 4, 9747AG Groningen, The Netherlands
| | - J. Rubén Gómez Castellanos
- Department of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia, Via Ferrata 9, 27100 Pavia, Italy
| | - Giovanni Gadda
- Departments of Chemistry and Biology, Center for Diagnostics and Therapeutics, and Center for Biotechnology and Drug Design, Georgia State University, Atlanta, Georgia 30302-3965, United States
| | - Marco W. Fraaije
- Molecular Enzymology Group, University of Groningen, Nijenborgh 4, 9747AG Groningen, The Netherlands
| | - Andrea Mattevi
- Department of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia, Via Ferrata 9, 27100 Pavia, Italy
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21
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Activities of Secreted Aryl Alcohol Quinone Oxidoreductases from Pycnoporus cinnabarinus Provide Insights into Fungal Degradation of Plant Biomass. Appl Environ Microbiol 2016; 82:2411-2423. [PMID: 26873317 DOI: 10.1128/aem.03761-15] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Accepted: 02/08/2016] [Indexed: 11/20/2022] Open
Abstract
Auxiliary activities family 3 subfamily 2 (AA3_2) from the CAZy database comprises various functions related to ligninolytic enzymes, such as fungal aryl alcohol oxidases (AAO) and glucose oxidases, both of which are flavoenzymes. The recent study of the Pycnoporus cinnabarinus CIRM BRFM 137 genome combined with its secretome revealed that four AA3_2 enzymes are secreted during biomass degradation. One of these AA3_2 enzymes, scf184803.g17, has recently been produced heterologously in Aspergillus niger Based on the enzyme's activity and specificity, it was assigned to the glucose dehydrogenases (PcinnabarinusGDH [PcGDH]). Here, we analyze the distribution of the other three AA3_2 enzymes (scf185002.g8, scf184611.g7, and scf184746.g13) to assess their putative functions. These proteins showed the highest homology with aryl alcohol oxidase from Pleurotus eryngii Biochemical characterization demonstrated that they were also flavoenzymes harboring flavin adenine dinucleotide (FAD) as a cofactor and able to oxidize a wide variety of phenolic and nonphenolic aryl alcohols and one aliphatic polyunsaturated primary alcohol. Though presenting homology with fungal AAOs, these enzymes exhibited greater efficiency in reducing electron acceptors (quinones and one artificial acceptor) than molecular oxygen and so were defined as aryl-alcohol:quinone oxidoreductases (AAQOs) with two enzymes possessing residual oxidase activity (PcAAQO2 and PcAAQO3). Structural comparison of PcAAQO homology models with P. eryngii AAO demonstrated a wider substrate access channel connecting the active-site cavity to the solvent, explaining the absence of activity with molecular oxygen. Finally, the ability of PcAAQOs to reduce radical intermediates generated by laccase from P. cinnabarinus was demonstrated, shedding light on the ligninolytic system of this fungus.
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22
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Salvi F, Rodriguez I, Hamelberg D, Gadda G. Role of F357 as an Oxygen Gate in the Oxidative Half-Reaction of Choline Oxidase. Biochemistry 2016; 55:1473-84. [PMID: 26907558 DOI: 10.1021/acs.biochem.5b01356] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Choline oxidase from Arthrobacter globiformis catalyzes the oxidation of choline to glycine betaine by using oxygen as an electron acceptor. A partially rate limiting isomerization of the reduced wild-type enzyme during the reaction with oxygen was previously detected using solvent viscosity effects. In this study, we hypothesized that the side chains of M62 and F357, located at the entrance to the active site of choline oxidase, may be related to the slow isomerization detected. We engineered a double-variant enzyme M62A/F357A. The kinetic characterization of the double-variant enzyme showed a lack of the isomerization detected in wild-type choline oxidase, and a lack of saturation with an oxygen concentration as high as 1 mM, while most other kinetic parameters were similar to those of wild-type choline oxidase. The kinetic characterization of the single-variant enzymes established that only the side chain of F357 plays a role in the isomerization of choline oxidase in the oxidative half-reaction. Molecular dynamics studies suggest that the slow isomerization related to F357 is possibly due to the participation of the phenyl ring in a newly proposed gating mechanism for a narrow tunnel, assumed to regulate the access of oxygen to the reduced cofactor.
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Affiliation(s)
- Francesca Salvi
- Department of Chemistry, ‡Department of Biology, §Center for Biotechnology and Drug Design, and ∥Center for Diagnostics and Therapeutics, Georgia State University , Atlanta, Georgia 30302, United States
| | - Isela Rodriguez
- Department of Chemistry, ‡Department of Biology, §Center for Biotechnology and Drug Design, and ∥Center for Diagnostics and Therapeutics, Georgia State University , Atlanta, Georgia 30302, United States
| | - Donald Hamelberg
- Department of Chemistry, ‡Department of Biology, §Center for Biotechnology and Drug Design, and ∥Center for Diagnostics and Therapeutics, Georgia State University , Atlanta, Georgia 30302, United States
| | - Giovanni Gadda
- Department of Chemistry, ‡Department of Biology, §Center for Biotechnology and Drug Design, and ∥Center for Diagnostics and Therapeutics, Georgia State University , Atlanta, Georgia 30302, United States
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23
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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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24
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Kameshwar AKS, Qin W. Lignin Degrading Fungal Enzymes. PRODUCTION OF BIOFUELS AND CHEMICALS FROM LIGNIN 2016. [DOI: 10.1007/978-981-10-1965-4_4] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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25
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Focused Directed Evolution of Aryl-Alcohol Oxidase in Saccharomyces cerevisiae by Using Chimeric Signal Peptides. Appl Environ Microbiol 2015; 81:6451-62. [PMID: 26162870 DOI: 10.1128/aem.01966-15] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Accepted: 07/03/2015] [Indexed: 01/16/2023] Open
Abstract
Aryl-alcohol oxidase (AAO) is an extracellular flavoprotein that supplies ligninolytic peroxidases with H2O2 during natural wood decay. With a broad substrate specificity and highly stereoselective reaction mechanism, AAO is an attractive candidate for studies into organic synthesis and synthetic biology, and yet the lack of suitable heterologous expression systems has precluded its engineering by directed evolution. In this study, the native signal sequence of AAO from Pleurotus eryngii was replaced by those of the mating α-factor and the K1 killer toxin, as well as different chimeras of both prepro-leaders in order to drive secretion in Saccharomyces cerevisiae. The secretion of these AAO constructs increased in the following order: preproα-AAO > preαproK-AAO > preKproα-AAO > preproK-AAO. The chimeric preαproK-AAO was subjected to focused-directed evolution with the aid of a dual screening assay based on the Fenton reaction. Random mutagenesis and DNA recombination was concentrated on two protein segments (Met[α1]-Val109 and Phe392-Gln566), and an array of improved variants was identified, among which the FX7 mutant (harboring the H91N mutation) showed a dramatic 96-fold improvement in total activity with secretion levels of 2 mg/liter. Analysis of the N-terminal sequence of the FX7 variant confirmed the correct processing of the preαproK hybrid peptide by the KEX2 protease. FX7 showed higher stability in terms of pH and temperature, whereas the pH activity profiles and the kinetic parameters were maintained. The Asn91 lies in the flavin attachment loop motif, and it is a highly conserved residue in all members of the GMC superfamily, except for P. eryngii and P. pulmonarius AAO. The in vitro involution of the enzyme by restoring the consensus ancestor Asn91 promoted AAO expression and stability.
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26
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Pickl M, Fuchs M, Glueck SM, Faber K. The substrate tolerance of alcohol oxidases. Appl Microbiol Biotechnol 2015; 99:6617-42. [PMID: 26153139 PMCID: PMC4513209 DOI: 10.1007/s00253-015-6699-6] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Revised: 05/10/2015] [Accepted: 05/15/2015] [Indexed: 11/29/2022]
Abstract
Alcohols are a rich source of compounds from renewable sources, but they have to be activated in order to allow the modification of their carbon backbone. The latter can be achieved via oxidation to the corresponding aldehydes or ketones. As an alternative to (thermodynamically disfavoured) nicotinamide-dependent alcohol dehydrogenases, alcohol oxidases make use of molecular oxygen but their application is under-represented in synthetic biotransformations. In this review, the mechanism of copper-containing and flavoprotein alcohol oxidases is discussed in view of their ability to accept electronically activated or non-activated alcohols and their propensity towards over-oxidation of aldehydes yielding carboxylic acids. In order to facilitate the selection of the optimal enzyme for a given biocatalytic application, the substrate tolerance of alcohol oxidases is compiled and discussed: Substrates are classified into groups (non-activated prim- and sec-alcohols; activated allylic, cinnamic and benzylic alcohols; hydroxy acids; sugar alcohols; nucleotide alcohols; sterols) together with suitable alcohol oxidases, their microbial source, relative activities and (stereo)selectivities.
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Affiliation(s)
- Mathias Pickl
- Department of Chemistry, Organic & Bioorganic Chemistry, University of Graz, Heinrichstrasse 28, A-8010, Graz, Austria
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27
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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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Ferreira P, Hernández-Ortega A, Lucas F, Carro J, Herguedas B, Borrelli KW, Guallar V, Martínez AT, Medina M. Aromatic stacking interactions govern catalysis in aryl-alcohol oxidase. FEBS J 2015; 282:3091-106. [PMID: 25639975 DOI: 10.1111/febs.13221] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Revised: 01/10/2015] [Accepted: 01/28/2015] [Indexed: 01/05/2023]
Abstract
Aryl-alcohol oxidase (AAO, EC 1.1.3.7) generates H2 O2 for lignin degradation at the expense of benzylic and other π system-containing primary alcohols, which are oxidized to the corresponding aldehydes. Ligand diffusion studies on Pleurotus eryngii AAO showed a T-shaped stacking interaction between the Tyr92 side chain and the alcohol substrate at the catalytically competent position for concerted hydride and proton transfers. Bi-substrate kinetics analysis revealed that reactions with 3-chloro- or 3-fluorobenzyl alcohols (halogen substituents) proceed via a ping-pong mechanism. However, mono- and dimethoxylated substituents (in 4-methoxybenzyl and 3,4-dimethoxybenzyl alcohols) altered the mechanism and a ternary complex was formed. Electron-withdrawing substituents resulted in lower quantum mechanics stacking energies between aldehyde and the tyrosine side chain, contributing to product release, in agreement with the ping-pong mechanism observed in 3-chloro- and 3-fluorobenzyl alcohol kinetics analysis. In contrast, the higher stacking energies when electron donor substituents are present result in reaction of O2 with the flavin through a ternary complex, in agreement with the kinetics of methoxylated alcohols. The contribution of Tyr92 to the AAO reaction mechanism was investigated by calculation of stacking interaction energies and site-directed mutagenesis. Replacement of Tyr92 by phenylalanine does not alter the AAO kinetic constants (on 4-methoxybenzyl alcohol), most probably because the stacking interaction is still possible. However, introduction of a tryptophan residue at this position strongly reduced the affinity for the substrate (i.e. the pre-steady state Kd and steady-state Km increase by 150-fold and 75-fold, respectively), and therefore the steady-state catalytic efficiency, suggesting that proper stacking is impossible with this bulky residue. The above results confirm the role of Tyr92 in substrate binding, thus governing the kinetic mechanism in AAO.
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Affiliation(s)
- Patricia Ferreira
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, and Instituto de Biocomputación y Física de Sistemas Complejos, Zaragoza, Spain
| | - Aitor Hernández-Ortega
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Fátima Lucas
- Joint Barcelona Supercomputing Center-Centre for Genomic Regulation-Institute for Research in Biomedicine Research Program in Computational Biology, Barcelona Supercomputing Center, Barcelona, Spain
| | - Juan Carro
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Beatriz Herguedas
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, and Instituto de Biocomputación y Física de Sistemas Complejos, Zaragoza, Spain
| | - Kenneth W Borrelli
- Joint Barcelona Supercomputing Center-Centre for Genomic Regulation-Institute for Research in Biomedicine Research Program in Computational Biology, Barcelona Supercomputing Center, Barcelona, Spain
| | - Victor Guallar
- Joint Barcelona Supercomputing Center-Centre for Genomic Regulation-Institute for Research in Biomedicine Research Program in Computational Biology, Barcelona Supercomputing Center, Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
| | - Angel T Martínez
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Milagros Medina
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, and Instituto de Biocomputación y Física de Sistemas Complejos, Zaragoza, Spain
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Carro J, Ferreira P, Rodríguez L, Prieto A, Serrano A, Balcells B, Ardá A, Jiménez‐Barbero J, Gutiérrez A, Ullrich R, Hofrichter M, Martínez AT. 5‐hydroxymethylfurfural conversion by fungal aryl‐alcohol oxidase and unspecific peroxygenase. FEBS J 2015; 282:3218-29. [DOI: 10.1111/febs.13177] [Citation(s) in RCA: 112] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Revised: 12/05/2014] [Accepted: 12/10/2014] [Indexed: 01/11/2023]
Affiliation(s)
- Juan Carro
- Centro de Investigaciones Biológicas Consejo Superior de Investigaciones Científicas Madrid Spain
| | - Patricia Ferreira
- Facultad de Ciencias and Instituto de Biocomputación y Física de Sistemas Complejos Zaragoza Spain
| | - Leonor Rodríguez
- Centro de Investigaciones Biológicas Consejo Superior de Investigaciones Científicas Madrid Spain
| | - Alicia Prieto
- Centro de Investigaciones Biológicas Consejo Superior de Investigaciones Científicas Madrid Spain
| | - Ana Serrano
- Centro de Investigaciones Biológicas Consejo Superior de Investigaciones Científicas Madrid Spain
| | - Beatriz Balcells
- Centro de Investigaciones Biológicas Consejo Superior de Investigaciones Científicas Madrid Spain
| | - Ana Ardá
- Centro de Investigaciones Biológicas Consejo Superior de Investigaciones Científicas Madrid Spain
| | - Jesús Jiménez‐Barbero
- Centro de Investigaciones Biológicas Consejo Superior de Investigaciones Científicas Madrid Spain
| | - Ana Gutiérrez
- Instituto de Recursos Naturales y Agrobiología de Sevilla Consejo Superior de Investigaciones Científicas Seville Spain
| | - René Ullrich
- Department of Bio‐ and Environmental Sciences International Institute of Zittau Germany
| | - Martin Hofrichter
- Department of Bio‐ and Environmental Sciences International Institute of Zittau Germany
| | - Angel T. Martínez
- Centro de Investigaciones Biológicas Consejo Superior de Investigaciones Científicas Madrid Spain
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Brugger D, Krondorfer I, Shelswell C, Huber-Dittes B, Haltrich D, Peterbauer CK. Engineering pyranose 2-oxidase for modified oxygen reactivity. PLoS One 2014; 9:e109242. [PMID: 25296188 PMCID: PMC4190269 DOI: 10.1371/journal.pone.0109242] [Citation(s) in RCA: 13] [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: 06/04/2014] [Accepted: 07/12/2014] [Indexed: 01/15/2023] Open
Abstract
Pyranose 2-oxidase (POx), a member of the GMC family of flavoproteins, catalyzes the regioselective oxidation of aldopyranoses at position C2 to the corresponding 2-ketoaldoses. During the first half-reaction, FAD is reduced to FADH2 and reoxidized in the second half-reaction by reducing molecular oxygen to H2O2. Alternative electron acceptors including quinones, radicals or chelated metal ions show significant and in some cases even higher activity. While oxygen as cheap and abundantly available electron acceptor is favored for many processes, reduced oxygen reactivity is desirable for some applications such as in biosensors/biofuel cells because of reduced oxidative damages to the biocatalyst from concomitant H2O2 production as well as reduced electron "leakage" to oxygen. The reactivity of flavoproteins with oxygen is of considerable scientific interest, and the determinants of oxygen activation and reactivity are the subject of numerous studies. We applied site-saturation mutagenesis on a set of eleven amino acids around the active site based on the crystal structure of the enzyme. Using microtiter plate screening assays with peroxidase/2,2'-azino-bis(3-ethylbenzthiazoline-6-sulphonic acid) and 2,6-dichlorophenolindophenol, variants of POx with decreased oxidase activity and maintained dehydrogenase activity were identified. Variants T166R, Q448H, L545C, L547R and N593C were characterized with respect to their apparent steady-state constants with oxygen and the alternative electron acceptors DCPIP, 1,4-benzoquinone and ferricenium ion, and the effect of the mutations was rationalized based on structural properties.
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Affiliation(s)
- Dagmar Brugger
- Food Biotechnology Laboratory, Department of Food Sciences and Technology, BOKU - University of Natural Resources and Life Sciences, Vienna, Austria
| | - Iris Krondorfer
- Food Biotechnology Laboratory, Department of Food Sciences and Technology, BOKU - University of Natural Resources and Life Sciences, Vienna, Austria
| | - Christopher Shelswell
- Food Biotechnology Laboratory, Department of Food Sciences and Technology, BOKU - University of Natural Resources and Life Sciences, Vienna, Austria
| | - Benjamin Huber-Dittes
- Food Biotechnology Laboratory, Department of Food Sciences and Technology, BOKU - University of Natural Resources and Life Sciences, Vienna, Austria
| | - Dietmar Haltrich
- Food Biotechnology Laboratory, Department of Food Sciences and Technology, BOKU - University of Natural Resources and Life Sciences, Vienna, Austria
| | - Clemens K. Peterbauer
- Food Biotechnology Laboratory, Department of Food Sciences and Technology, BOKU - University of Natural Resources and Life Sciences, Vienna, Austria
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31
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Bucci A, Abrams CF. Oxygen Pathways and Allostery in Monomeric Sarcosine Oxidase via Single-Sweep Free-Energy Reconstruction. J Chem Theory Comput 2014; 10:2668-2676. [PMID: 25061440 PMCID: PMC4095932 DOI: 10.1021/ct500088z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2014] [Indexed: 01/12/2023]
Abstract
Monomeric sarcosine oxidase (MSOX) is a flavoprotein D-amino acid oxidase with reported sarcosine and oxygen activation sites on the re and si faces of the flavin ring, respectively. O2 transport routes to the catalytic interior are not well understood and are difficult to ascertain solely from MSOX crystal structures. A composite free-energy method known as single-sweep is used to map and thermodynamically characterize oxygen sites and routes leading to the catalytically active Lys265 from the protein surface. The result is a network of pathways and free energies within MSOX illustrating that oxygen can access two free-energy minima on the re face of the reduced flavin from four separate solvent portals. No such minimum is observed on the si face. The pathways are geometrically similar for three major states of the enzyme: (1) apo with a closed flavin cleft, (2) apo with an open flavin cleft, and (3) inhibitor-bound with a closed flavin cleft. Interestingly, free energies along these transport pathways display significantly deeper minima when the substrate-mimicking inhibitor 2-furoic acid is bound at the sarcosine site, even at locations far from this site. This suggests a substrate-dependent allosteric modulation of the kinetics of O2 transport from the solvent to the active site.
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Affiliation(s)
- Anthony Bucci
- Dept. Chemical and Biological
Engineering, Drexel University, Philadelphia, Pennsylvania 19104, United States
| | - Cameron F. Abrams
- Dept. Chemical and Biological
Engineering, Drexel University, Philadelphia, Pennsylvania 19104, United States
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32
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Aldonolactone oxidoreductases. Methods Mol Biol 2014; 1146:95-111. [PMID: 24764090 DOI: 10.1007/978-1-4939-0452-5_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/21/2023]
Abstract
Vitamin C is a widely used vitamin. Here we review the occurrence and properties of aldonolactone oxidoreductases, an important group of flavoenzymes responsible for the ultimate production of vitamin C and its analogs in animals, plants, and single-cell organisms.
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Chakraborty M, Goel M, Chinnadayyala SR, Dahiya UR, Ghosh SS, Goswami P. Molecular characterization and expression of a novel alcohol oxidase from Aspergillus terreus MTCC6324. PLoS One 2014; 9:e95368. [PMID: 24752075 PMCID: PMC3994049 DOI: 10.1371/journal.pone.0095368] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Accepted: 03/26/2014] [Indexed: 11/28/2022] Open
Abstract
The alcohol oxidase (AOx) cDNA from Aspergillus terreus MTCC6324 with an open reading frame (ORF) of 2001 bp was constructed from n-hexadecane induced cells and expressed in Escherichia coli with a yield of ∼4.2 mg protein g−1 wet cell. The deduced amino acid sequences of recombinant rAOx showed maximum structural homology with the chain B of aryl AOx from Pleurotus eryngii. A functionally active AOx was achieved by incubating the apo-AOx with flavin adenine dinucleotide (FAD) for ∼80 h at 16°C and pH 9.0. The isoelectric point and mass of the apo-AOx were found to be 6.5±0.1 and ∼74 kDa, respectively. Circular dichroism data of the rAOx confirmed its ordered structure. Docking studies with an ab-initio protein model demonstrated the presence of a conserved FAD binding domain with an active substrate binding site. The rAOx was specific for aryl alcohols and the order of its substrate preference was 4-methoxybenzyl alcohol >3-methoxybenzyl alcohol>3, 4-dimethoxybenzyl alcohol > benzyl alcohol. A significantly high aggregation to ∼1000 nm (diameter) and catalytic efficiency (kcat/Km) of 7829.5 min−1 mM−1 for 4-methoxybenzyl alcohol was also demonstrated for rAOx. The results infer the novelty of the AOx and its potential biocatalytic application.
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Affiliation(s)
- Mitun Chakraborty
- Department of Biotechnology, Indian Institute of Technology Guwahati, Assam, India
| | - Manish Goel
- Department of Biotechnology, Indian Institute of Technology Guwahati, Assam, India
| | | | - Ujjwal Ranjan Dahiya
- Department of Biotechnology, Indian Institute of Technology Guwahati, Assam, India
| | - Siddhartha Sankar Ghosh
- Department of Biotechnology, Indian Institute of Technology Guwahati, Assam, India
- * E-mail: (SSG); (PG)
| | - Pranab Goswami
- Department of Biotechnology, Indian Institute of Technology Guwahati, Assam, India
- * E-mail: (SSG); (PG)
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34
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Krondorfer I, Lipp K, Brugger D, Staudigl P, Sygmund C, Haltrich D, Peterbauer CK. Engineering of pyranose dehydrogenase for increased oxygen reactivity. PLoS One 2014; 9:e91145. [PMID: 24614932 PMCID: PMC3948749 DOI: 10.1371/journal.pone.0091145] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Accepted: 02/07/2014] [Indexed: 11/22/2022] Open
Abstract
Pyranose dehydrogenase (PDH), a member of the GMC family of flavoproteins, shows a very broad sugar substrate specificity but is limited to a narrow range of electron acceptors and reacts extremely slowly with dioxygen as acceptor. The use of substituted quinones or (organo)metals as electron acceptors is undesirable for many production processes, especially of food ingredients. To improve the oxygen reactivity, site-saturation mutagenesis libraries of twelve amino acids around the active site of Agaricus meleagris PDH were expressed in Saccharomyces cerevisiae. We established high-throughput screening assays for oxygen reactivity and standard dehydrogenase activity using an indirect Amplex Red/horseradish peroxidase and a DCIP/D-glucose based approach. The low number of active clones confirmed the catalytic role of H512 and H556. Only one position was found to display increased oxygen reactivity. Histidine 103, carrying the covalently linked FAD cofactor in the wild-type, was substituted by tyrosine, phenylalanine, tryptophan and methionine. Variant H103Y was produced in Pichia pastoris and characterized and revealed a five-fold increase of the oxygen reactivity.
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Affiliation(s)
- Iris Krondorfer
- Food Biotechnology Laboratory, Department of Food Science and Technology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Katharina Lipp
- Food Biotechnology Laboratory, Department of Food Science and Technology, University of Natural Resources and Life Sciences, Vienna, Austria
- University of Applied Sciences Wiener Neustadt – Campus Tulln, Tulln, Austria
| | - Dagmar Brugger
- Food Biotechnology Laboratory, Department of Food Science and Technology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Petra Staudigl
- Food Biotechnology Laboratory, Department of Food Science and Technology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Christoph Sygmund
- Food Biotechnology Laboratory, Department of Food Science and Technology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Dietmar Haltrich
- Food Biotechnology Laboratory, Department of Food Science and Technology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Clemens K. Peterbauer
- Food Biotechnology Laboratory, Department of Food Science and Technology, University of Natural Resources and Life Sciences, Vienna, Austria
- * E-mail:
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35
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Rohr CO, Levin LN, Mentaberry AN, Wirth SA. A first insight into Pycnoporus sanguineus BAFC 2126 transcriptome. PLoS One 2013; 8:e81033. [PMID: 24312521 PMCID: PMC3846667 DOI: 10.1371/journal.pone.0081033] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2013] [Accepted: 10/09/2013] [Indexed: 12/12/2022] Open
Abstract
Fungi of the genus Pycnoporus are white-rot basidiomycetes widely studied because of their ability to synthesize high added-value compounds and enzymes of industrial interest. Here we report the sequencing, assembly and analysis of the transcriptome of Pycnoporus sanguineus BAFC 2126 grown at stationary phase, in media supplemented with copper sulfate. Using the 454 pyrosequencing platform we obtained a total of 226,336 reads (88,779,843 bases) that were filtered and de novo assembled to generate a reference transcriptome of 7,303 transcripts. Putative functions were assigned for 4,732 transcripts by searching similarities of six-frame translated sequences against a customized protein database and by the presence of conserved protein domains. Through the analysis of translated sequences we identified transcripts encoding 178 putative carbohydrate active enzymes, including representatives of 15 families with roles in lignocellulose degradation. Furthermore, we found many transcripts encoding enzymes related to lignin hydrolysis and modification, including laccases and peroxidases, as well as GMC oxidoreductases, copper radical oxidases and other enzymes involved in the generation of extracellular hydrogen peroxide and iron homeostasis. Finally, we identified the transcripts encoding all of the enzymes involved in terpenoid backbone biosynthesis pathway, various terpene synthases related to the biosynthesis of sesquiterpenoids and triterpenoids precursors, and also cytochrome P450 monooxygenases, glutathione S-transferases and epoxide hydrolases with potential functions in the biodegradation of xenobiotics and the enantioselective biosynthesis of biologically active drugs. To our knowledge this is the first report of a transcriptome of genus Pycnoporus and a resource for future molecular studies in P. sanguineus.
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Affiliation(s)
- Cristian O. Rohr
- Instituto de Ecología, Genética y Evolución, Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad de Buenos Aires, Buenos Aires, Argentina
| | - Laura N. Levin
- Laboratorio de Micología Experimental, Departamento de Biodiversidad y Biología Experimental, Universidad de Buenos Aires, Ciudad de Buenos Aires, Buenos Aires, Argentina
| | - Alejandro N. Mentaberry
- Laboratorio de Agrobiotecnología, Universidad de Buenos Aires, Ciudad de Buenos Aires, Buenos Aires, Argentina
| | - Sonia A. Wirth
- Laboratorio de Agrobiotecnología, Universidad de Buenos Aires, Ciudad de Buenos Aires, Buenos Aires, Argentina
- * E-mail:
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36
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An overview on alcohol oxidases and their potential applications. Appl Microbiol Biotechnol 2013; 97:4259-75. [DOI: 10.1007/s00253-013-4842-9] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2012] [Revised: 03/06/2013] [Accepted: 03/07/2013] [Indexed: 10/27/2022]
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37
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Lucas MF, Guallar V. Single vs. multiple ligand pathways in globins: a computational view. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:1739-43. [PMID: 23388390 DOI: 10.1016/j.bbapap.2013.01.035] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2012] [Revised: 01/25/2013] [Accepted: 01/28/2013] [Indexed: 11/30/2022]
Abstract
Diatomic ligand migration in globins has been the subject of numerous studies. Still, a consensus picture for the ligand entrance is not clear, with a growing concern among experimental researchers that computational simulations always show multiple pathways for any globin. Modeling non-biased ligand entrance from conventional molecular dynamics techniques, however, has shown to be difficult (and expensive). Here we use our Monte Carlo methodology, capable of freely mapping ligand diffusion and the description of rare events, to two well-studied systems: myoglobin and the mini-hemoglobin from the sea worm Cerebratulus lacteus. Our results clearly show that the simulations are specific to the system providing a different trend in the entrance pathway, as expected from experiments. While Mb presents multiple entrance pathways, populating the well-known xenon cavities, in CerHb the ligand enters the protein only by one apolar channel. Most of the trajectories (64%) visiting myoglobin's active site though, are gated by the distal histidine. Such detailed information, accessible through the state of the art algorithms in PELE, is computationally inexpensive and available to all non-profit researchers. This article is part of a Special Issue entitled: Oxygen Binding and Sensing Proteins.
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Affiliation(s)
- M Fátima Lucas
- Joint BSC-IRB Research Program in Computational Biology, Barcelona Supercomputing Center, Barcelona, Spain
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38
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Tan TC, Spadiut O, Wongnate T, Sucharitakul J, Krondorfer I, Sygmund C, Haltrich D, Chaiyen P, Peterbauer CK, Divne C. The 1.6 Å crystal structure of pyranose dehydrogenase from Agaricus meleagris rationalizes substrate specificity and reveals a flavin intermediate. PLoS One 2013; 8:e53567. [PMID: 23326459 PMCID: PMC3541233 DOI: 10.1371/journal.pone.0053567] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2012] [Accepted: 11/29/2012] [Indexed: 11/18/2022] Open
Abstract
Pyranose dehydrogenases (PDHs) are extracellular flavin-dependent oxidoreductases secreted by litter-decomposing fungi with a role in natural recycling of plant matter. All major monosaccharides in lignocellulose are oxidized by PDH at comparable yields and efficiencies. Oxidation takes place as single-oxidation or sequential double-oxidation reactions of the carbohydrates, resulting in sugar derivatives oxidized primarily at C2, C3 or C2/3 with the concomitant reduction of the flavin. A suitable electron acceptor then reoxidizes the reduced flavin. Whereas oxygen is a poor electron acceptor for PDH, several alternative acceptors, e.g., quinone compounds, naturally present during lignocellulose degradation, can be used. We have determined the 1.6-Å crystal structure of PDH from Agaricus meleagris. Interestingly, the flavin ring in PDH is modified by a covalent mono- or di-atomic species at the C(4a) position. Under normal conditions, PDH is not oxidized by oxygen; however, the related enzyme pyranose 2-oxidase (P2O) activates oxygen by a mechanism that proceeds via a covalent flavin C(4a)-hydroperoxide intermediate. Although the flavin C(4a) adduct is common in monooxygenases, it is unusual for flavoprotein oxidases, and it has been proposed that formation of the intermediate would be unfavorable in these oxidases. Thus, the flavin adduct in PDH not only shows that the adduct can be favorably accommodated in the active site, but also provides important details regarding the structural, spatial and physicochemical requirements for formation of this flavin intermediate in related oxidases. Extensive in silico modeling of carbohydrates in the PDH active site allowed us to rationalize the previously reported patterns of substrate specificity and regioselectivity. To evaluate the regioselectivity of D-glucose oxidation, reduction experiments were performed using fluorinated glucose. PDH was rapidly reduced by 3-fluorinated glucose, which has the C2 position accessible for oxidation, whereas 2-fluorinated glucose performed poorly (C3 accessible), indicating that the glucose C2 position is the primary site of attack.
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Affiliation(s)
- Tien Chye Tan
- School of Biotechnology, KTH Royal Institute of Technology, Stockholm, Sweden
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Oliver Spadiut
- School of Biotechnology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Thanyaporn Wongnate
- Department of Biochemistry and Center of Excellence in Protein Structure and Function, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Jeerus Sucharitakul
- Department of Biochemistry, Faculty of Dentistry, Chulalongkorn University, Bangkok, Thailand
| | - Iris Krondorfer
- Food Biotechnology Laboratory, BOKU University of Natural Resources and Life Sciences, Vienna, Austria
| | - Christoph Sygmund
- Food Biotechnology Laboratory, BOKU University of Natural Resources and Life Sciences, Vienna, Austria
| | - Dietmar Haltrich
- Food Biotechnology Laboratory, BOKU University of Natural Resources and Life Sciences, Vienna, Austria
| | - Pimchai Chaiyen
- Department of Biochemistry and Center of Excellence in Protein Structure and Function, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Clemens K. Peterbauer
- Food Biotechnology Laboratory, BOKU University of Natural Resources and Life Sciences, Vienna, Austria
| | - Christina Divne
- School of Biotechnology, KTH Royal Institute of Technology, Stockholm, Sweden
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- * E-mail:
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39
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Chaiyen P, Fraaije MW, Mattevi A. The enigmatic reaction of flavins with oxygen. Trends Biochem Sci 2012; 37:373-80. [DOI: 10.1016/j.tibs.2012.06.005] [Citation(s) in RCA: 150] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2012] [Revised: 06/19/2012] [Accepted: 06/28/2012] [Indexed: 10/28/2022]
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40
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Hernández-Ortega A, Lucas F, Ferreira P, Medina M, Guallar V, Martínez AT. Role of Active Site Histidines in the Two Half-Reactions of the Aryl-Alcohol Oxidase Catalytic Cycle. Biochemistry 2012; 51:6595-608. [DOI: 10.1021/bi300505z] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | - Fátima Lucas
- Joint BSC-IRB
Research Program
in Computational Biology, Barcelona Supercomputing Center, Jordi Girona 29, E-08034 Barcelona, Spain
| | - Patricia Ferreira
- Department of Biochemistry and
Molecular and Cellular Biology and Institute of Biocomputation and
Physics of Complex Systems, University of Zaragoza, E-50009 Zaragoza, Spain
| | - Milagros Medina
- Department of Biochemistry and
Molecular and Cellular Biology and Institute of Biocomputation and
Physics of Complex Systems, University of Zaragoza, E-50009 Zaragoza, Spain
| | - Victor Guallar
- Joint BSC-IRB
Research Program
in Computational Biology, Barcelona Supercomputing Center, Jordi Girona 29, E-08034 Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluís Companys 23, E-08010 Barcelona, Spain
| | - Angel T. Martínez
- Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, E-28040
Madrid, Spain
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41
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Hernández-Ortega A, Ferreira P, Merino P, Medina M, Guallar V, Martínez AT. Stereoselective Hydride Transfer by Aryl-Alcohol Oxidase, a Member of the GMC Superfamily. Chembiochem 2012; 13:427-35. [PMID: 22271643 DOI: 10.1002/cbic.201100709] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2011] [Indexed: 11/06/2022]
Affiliation(s)
- Aitor Hernández-Ortega
- Centro de Investigaciones Biológicas (CIB), Consejo Superior de Investigaciones Científicas (CSIC), Ramiro de Maeztu 9, 28040 Madrid, Spain
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Fungal aryl-alcohol oxidase: a peroxide-producing flavoenzyme involved in lignin degradation. Appl Microbiol Biotechnol 2012; 93:1395-410. [DOI: 10.1007/s00253-011-3836-8] [Citation(s) in RCA: 121] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2011] [Revised: 12/06/2011] [Accepted: 12/09/2011] [Indexed: 11/30/2022]
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