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Scocozza M, Vieyra F, Battaglini F, Martins LO, Murgida DH. Electrochemical Actuation of a DyP Peroxidase: A Facile Method for Drastic Improvement of the Catalytic Performance. ACS Catal 2023; 13:7437-7449. [PMID: 37288089 PMCID: PMC10243304 DOI: 10.1021/acscatal.3c01530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 04/20/2023] [Indexed: 06/09/2023]
Abstract
Dye decolorizing peroxidases (DyP) have attracted interest for applications such as dye-containing wastewater remediation and biomass processing. So far, efforts to improve operational pH ranges, activities, and stabilities have focused on site-directed mutagenesis and directed evolution strategies. Here, we show that the performance of the DyP from Bacillus subtilis can be drastically boosted without the need for complex molecular biology procedures by simply activating the enzyme electrochemically in the absence of externally added H2O2. Under these conditions, the enzyme shows specific activities toward a variety of chemically different substrates that are significantly higher than in its canonical operation. Moreover, it presents much broader pH activity profiles with the maxima shifted toward neutral to alkaline. We also show that the enzyme can be successfully immobilized on biocompatible electrodes. When actuated electrochemically, the enzymatic electrodes have two orders of magnitude higher turnover numbers than with the standard H2O2-dependent operation and preserve about 30% of the initial electrocatalytic activity after 5 days of operation-storage cycles.
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Affiliation(s)
- Magalí
F. Scocozza
- Departamento
de Química Inorgánica, Analítica y Química
Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires C1428EGA, Argentina
- Instituto
de Química Física de Los Materiales, Medio Ambiente
y Energía (INQUIMAE), CONICET-Universidad
de Buenos Aires, Buenos Aires C1428EGA, Argentina
| | - Francisco Vieyra
- Departamento
de Química Inorgánica, Analítica y Química
Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires C1428EGA, Argentina
- Instituto
de Química Física de Los Materiales, Medio Ambiente
y Energía (INQUIMAE), CONICET-Universidad
de Buenos Aires, Buenos Aires C1428EGA, Argentina
| | - Fernando Battaglini
- Departamento
de Química Inorgánica, Analítica y Química
Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires C1428EGA, Argentina
- Instituto
de Química Física de Los Materiales, Medio Ambiente
y Energía (INQUIMAE), CONICET-Universidad
de Buenos Aires, Buenos Aires C1428EGA, Argentina
| | - Ligia O. Martins
- Instituto
de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras 2780-157, Portugal
| | - Daniel H. Murgida
- Departamento
de Química Inorgánica, Analítica y Química
Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires C1428EGA, Argentina
- Instituto
de Química Física de Los Materiales, Medio Ambiente
y Energía (INQUIMAE), CONICET-Universidad
de Buenos Aires, Buenos Aires C1428EGA, Argentina
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2
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Nys K, Pfanzagl V, Roefs J, Obinger C, Van Doorslaer S. In Vitro Heme Coordination of a Dye-Decolorizing Peroxidase-The Interplay of Key Amino Acids, pH, Buffer and Glycerol. Int J Mol Sci 2021; 22:ijms22189849. [PMID: 34576013 PMCID: PMC8468270 DOI: 10.3390/ijms22189849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 08/31/2021] [Accepted: 09/03/2021] [Indexed: 11/17/2022] Open
Abstract
Dye-decolorizing peroxidases (DyPs) have gained interest for their ability to oxidize anthraquinone-derived dyes and lignin model compounds. Spectroscopic techniques, such as electron paramagnetic resonance and optical absorption spectroscopy, provide main tools to study how the enzymatic function is linked to the heme-pocket architecture, provided the experimental conditions are carefully chosen. Here, these techniques are used to investigate the effect of active site perturbations on the structure of ferric P-class DyP from Klebsiella pneumoniae (KpDyP) and three variants of the main distal residues (D143A, R232A and D143A/R232A). Arg-232 is found to be important for maintaining the heme distal architecture and essential to facilitate an alkaline transition. The latter is promoted in absence of Asp-143. Furthermore, the non-innocent effect of the buffer choice and addition of the cryoprotectant glycerol is shown. However, while unavoidable or indiscriminate experimental conditions are pitfalls, careful comparison of the effects of different exogenous molecules on the electronic structure and spin state of the heme iron contains information about the inherent flexibility of the heme pocket. The interplay between structural flexibility, key amino acids, pH, temperature, buffer and glycerol during in vitro spectroscopic studies is discussed with respect to the poor peroxidase activity of bacterial P-class DyPs.
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Affiliation(s)
- Kevin Nys
- BIMEF Laboratory, Department of Chemistry, University of Antwerp, 2610 Antwerp, Belgium; (K.N.); (J.R.)
| | - Vera Pfanzagl
- Division of Biochemistry, Department of Chemistry, BOKU—University of Natural Resources and Life Sciences, 1190 Vienna, Austria; (V.P.); (C.O.)
| | - Jeroen Roefs
- BIMEF Laboratory, Department of Chemistry, University of Antwerp, 2610 Antwerp, Belgium; (K.N.); (J.R.)
| | - Christian Obinger
- Division of Biochemistry, Department of Chemistry, BOKU—University of Natural Resources and Life Sciences, 1190 Vienna, Austria; (V.P.); (C.O.)
| | - Sabine Van Doorslaer
- BIMEF Laboratory, Department of Chemistry, University of Antwerp, 2610 Antwerp, Belgium; (K.N.); (J.R.)
- Correspondence: ; Tel.: +32-3-265-2461
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Rai A, Klare JP, Reinke PYA, Englmaier F, Fohrer J, Fedorov R, Taft MH, Chizhov I, Curth U, Plettenburg O, Manstein DJ. Structural and Biochemical Characterization of a Dye-Decolorizing Peroxidase from Dictyostelium discoideum. Int J Mol Sci 2021; 22:ijms22126265. [PMID: 34200865 PMCID: PMC8230527 DOI: 10.3390/ijms22126265] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Revised: 05/29/2021] [Accepted: 06/05/2021] [Indexed: 12/23/2022] Open
Abstract
A novel cytoplasmic dye-decolorizing peroxidase from Dictyostelium discoideum was investigated that oxidizes anthraquinone dyes, lignin model compounds, and general peroxidase substrates such as ABTS efficiently. Unlike related enzymes, an aspartate residue replaces the first glycine of the conserved GXXDG motif in Dictyostelium DyPA. In solution, Dictyostelium DyPA exists as a stable dimer with the side chain of Asp146 contributing to the stabilization of the dimer interface by extending the hydrogen bond network connecting two monomers. To gain mechanistic insights, we solved the Dictyostelium DyPA structures in the absence of substrate as well as in the presence of potassium cyanide and veratryl alcohol to 1.7, 1.85, and 1.6 Å resolution, respectively. The active site of Dictyostelium DyPA has a hexa-coordinated heme iron with a histidine residue at the proximal axial position and either an activated oxygen or CN- molecule at the distal axial position. Asp149 is in an optimal conformation to accept a proton from H2O2 during the formation of compound I. Two potential distal solvent channels and a conserved shallow pocket leading to the heme molecule were found in Dictyostelium DyPA. Further, we identified two substrate-binding pockets per monomer in Dictyostelium DyPA at the dimer interface. Long-range electron transfer pathways associated with a hydrogen-bonding network that connects the substrate-binding sites with the heme moiety are described.
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Affiliation(s)
- Amrita Rai
- Institute for Biophysical Chemistry, Hannover Medical School, Fritz Hartmann Centre for Medical Research Carl Neuberg Str. 1, D-30625 Hannover, Germany; (A.R.); (P.Y.A.R.); (M.H.T.); (I.C.); (U.C.)
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, D-44227 Dortmund, Germany
| | - Johann P. Klare
- Department of Physics, University of Osnabrueck, Barbarastrasse 7, D-49076 Osnabrück, Germany;
| | - Patrick Y. A. Reinke
- Institute for Biophysical Chemistry, Hannover Medical School, Fritz Hartmann Centre for Medical Research Carl Neuberg Str. 1, D-30625 Hannover, Germany; (A.R.); (P.Y.A.R.); (M.H.T.); (I.C.); (U.C.)
- Division for Structural Biochemistry, Hannover Medical School, Carl Neuberg Str. 1, D-30625 Hannover, Germany;
- Center for Free-Electron Laser Science, German Electron Synchrotron (DESY), Notkestr. 85, D-22607 Hamburg, Germany
| | - Felix Englmaier
- Institute of Medicinal Chemistry, Helmholtz Zentrum München (GmbH), German Research Center for Environmental Health, Ingolstädter Landstraße 1, D-85764 Neuherberg, Germany; (F.E.); (O.P.)
- Center of Biomolecular Drug Research (BMWZ), Institute of Organic Chemistry, Leibniz University Hannover, Schneiderberg 1b, D-30167 Hannover, Germany;
| | - Jörg Fohrer
- Center of Biomolecular Drug Research (BMWZ), Institute of Organic Chemistry, Leibniz University Hannover, Schneiderberg 1b, D-30167 Hannover, Germany;
- NMR Department of the Department of Chemistry, Technical University Darmstadt, Clemens Schöpf Institute for Organic Chemistry and Biochemistry, Alarich-Weiss-Strasse 4, D-64287 Darmstadt, Germany
| | - Roman Fedorov
- Division for Structural Biochemistry, Hannover Medical School, Carl Neuberg Str. 1, D-30625 Hannover, Germany;
| | - Manuel H. Taft
- Institute for Biophysical Chemistry, Hannover Medical School, Fritz Hartmann Centre for Medical Research Carl Neuberg Str. 1, D-30625 Hannover, Germany; (A.R.); (P.Y.A.R.); (M.H.T.); (I.C.); (U.C.)
| | - Igor Chizhov
- Institute for Biophysical Chemistry, Hannover Medical School, Fritz Hartmann Centre for Medical Research Carl Neuberg Str. 1, D-30625 Hannover, Germany; (A.R.); (P.Y.A.R.); (M.H.T.); (I.C.); (U.C.)
- Division for Structural Biochemistry, Hannover Medical School, Carl Neuberg Str. 1, D-30625 Hannover, Germany;
| | - Ute Curth
- Institute for Biophysical Chemistry, Hannover Medical School, Fritz Hartmann Centre for Medical Research Carl Neuberg Str. 1, D-30625 Hannover, Germany; (A.R.); (P.Y.A.R.); (M.H.T.); (I.C.); (U.C.)
- Division for Structural Biochemistry, Hannover Medical School, Carl Neuberg Str. 1, D-30625 Hannover, Germany;
| | - Oliver Plettenburg
- Institute of Medicinal Chemistry, Helmholtz Zentrum München (GmbH), German Research Center for Environmental Health, Ingolstädter Landstraße 1, D-85764 Neuherberg, Germany; (F.E.); (O.P.)
- Center of Biomolecular Drug Research (BMWZ), Institute of Organic Chemistry, Leibniz University Hannover, Schneiderberg 1b, D-30167 Hannover, Germany;
| | - Dietmar J. Manstein
- Institute for Biophysical Chemistry, Hannover Medical School, Fritz Hartmann Centre for Medical Research Carl Neuberg Str. 1, D-30625 Hannover, Germany; (A.R.); (P.Y.A.R.); (M.H.T.); (I.C.); (U.C.)
- Division for Structural Biochemistry, Hannover Medical School, Carl Neuberg Str. 1, D-30625 Hannover, Germany;
- RESiST, Cluster of Excellence 2155, Medizinische Hochschule Hannover, D-30625 Hannover, Germany
- Correspondence: ; Tel.: +49-511-5323700
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Abstract
The beginnings of redox biology are recalled with special emphasis on formation, metabolism and function of reactive oxygen and nitrogen species in mammalian systems. The review covers the early history of heme peroxidases and the metabolism of hydrogen peroxide, the discovery of selenium as integral part of glutathione peroxidases, which expanded the scope of the field to other hydroperoxides including lipid hydroperoxides, the discovery of superoxide dismutases and superoxide radicals in biological systems and their role in host defense, tissue damage, metabolic regulation and signaling, the identification of the endothelial-derived relaxing factor as the nitrogen monoxide radical (more commonly named nitric oxide) and its physiological and pathological implications. The article highlights the perception of hydrogen peroxide and other hydroperoxides as signaling molecules, which marks the beginning of the flourishing fields of redox regulation and redox signaling. Final comments describe the development of the redox language. In the 18th and 19th century, it was highly individualized and hard to translate into modern terminology. In the 20th century, the redox language co-developed with the chemical terminology and became clearer. More recently, the introduction and inflationary use of poorly defined terms has unfortunately impaired the understanding of redox events in biological systems.
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Affiliation(s)
- Leopold Flohé
- Dipartimento di Medicina Molecolare, Università degli Studi di Padova, v.le G. Colombo 3, 35121 Padova, Italy;
- Departamento de Bioquímica, Universidad de la República, Avda. General Flores 2125, 11800 Montevideo, Uruguay
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5
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Bathish B, Paumann-Page M, Paton LN, Kettle AJ, Winterbourn CC. Peroxidasin mediates bromination of tyrosine residues in the extracellular matrix. J Biol Chem 2020; 295:12697-12705. [PMID: 32675287 DOI: 10.1074/jbc.ra120.014504] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 07/05/2020] [Indexed: 01/09/2023] Open
Abstract
Peroxidasin is a heme peroxidase that oxidizes bromide to hypobromous acid (HOBr), a powerful oxidant that promotes the formation of the sulfilimine crosslink in collagen IV in basement membranes. We investigated whether HOBr released by peroxidasin leads to other oxidative modifications of proteins, particularly bromination of tyrosine residues, in peroxidasin-expressing PFHR9 cells. Using stable isotope dilution LC-MS/MS, we detected the formation of 3-bromotyrosine, a specific biomarker of HOBr-mediated protein modification. The level of 3-bromotyrosine in extracellular matrix proteins from normally cultured cells was 1.1 mmol/mol tyrosine and decreased significantly in the presence of the peroxidasin inhibitor, phloroglucinol. A negligible amount of 3-bromotyrosine was detected in peroxidasin-knockout cells. 3-Bromotyrosine formed both during cell growth in culture and in the isolated decellularized extracellular matrix when embedded peroxidasin was supplied with hydrogen peroxide and bromide. The level of 3-bromotyrosine was significantly higher in extracellular matrix than intracellular proteins, although a low amount was detected intracellularly. 3-Bromotyrosine levels increased with higher bromide concentrations and decreased in the presence of physiological concentrations of thiocyanate and urate. However, these peroxidase substrates showed moderate to minimal inhibition of collagen IV crosslinking. Our findings provide evidence that peroxidasin promotes the formation of 3-bromotyrosine in proteins. They show that HOBr produced by peroxidasin is selective for, but not limited to, the crosslinking of collagen IV. Based on our findings, the use of 3-bromotyrosine as a specific biomarker of oxidative damage by HOBr warrants further investigation in clinical conditions linked to high peroxidasin expression.
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Affiliation(s)
- Boushra Bathish
- Centre for Free Radical Research, Department of Pathology and Biomedical Science, University of Otago Christchurch, Christchurch, New Zealand
| | - Martina Paumann-Page
- Centre for Free Radical Research, Department of Pathology and Biomedical Science, University of Otago Christchurch, Christchurch, New Zealand
| | - Louise N Paton
- Centre for Free Radical Research, Department of Pathology and Biomedical Science, University of Otago Christchurch, Christchurch, New Zealand
| | - Anthony J Kettle
- Centre for Free Radical Research, Department of Pathology and Biomedical Science, University of Otago Christchurch, Christchurch, New Zealand
| | - Christine C Winterbourn
- Centre for Free Radical Research, Department of Pathology and Biomedical Science, University of Otago Christchurch, Christchurch, New Zealand
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Schmitz LM, Rosenthal K, Lütz S. Recent advances in heme biocatalysis engineering. Biotechnol Bioeng 2019; 116:3469-3475. [PMID: 31483477 DOI: 10.1002/bit.27156] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 07/17/2019] [Accepted: 08/29/2019] [Indexed: 01/13/2023]
Abstract
Heme enzymes have the potential to be widely used as biocatalysts due to their capability to perform a vast variety of oxidation reactions. In spite of their versatility, the application of heme enzymes was long time-limited for the industry due to their low activity and stability in large scale processes. The identification of novel natural biocatalysts and recent advances in protein engineering have led to new reactions with a high application potential. The latest creation of a serine-ligated mutant of BM3 showed an efficient transfer of reactive carbenes into C═C bonds of olefins reaching total turnover numbers of more than 60,000 and product titers of up to 27 g/L-1 . This prominent example shows that heme enzymes are becoming competitive to chemical syntheses while being already advantageous in terms of high yield, regioselectivity, stereoselectivity and environmentally friendly reaction conditions. Advances in reactor concepts and the influencing parameters on reaction performance are also under investigation resulting in improved productivities and increased stability of the heme biocatalytic systems. In this mini review, we briefly present the latest advancements in the field of heme enzymes towards increased reaction scope and applicability.
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Affiliation(s)
- Lisa Marie Schmitz
- Department of Biochemical and Chemical Engineering, TU Dortmund University, Dortmund, Germany
| | - Katrin Rosenthal
- Department of Biochemical and Chemical Engineering, TU Dortmund University, Dortmund, Germany
| | - Stephan Lütz
- Department of Biochemical and Chemical Engineering, TU Dortmund University, Dortmund, Germany
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Lazzarotto F, Turchetto-Zolet AC, Margis-Pinheiro M. Revisiting the Non-Animal Peroxidase Superfamily. Trends Plant Sci 2015; 20:807-813. [PMID: 26463217 DOI: 10.1016/j.tplants.2015.08.005] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Revised: 08/04/2015] [Accepted: 08/12/2015] [Indexed: 06/05/2023]
Abstract
Peroxidases reduce peroxide through substrate oxidation in order to alleviate oxidative stress in aerobic organisms. Since the initial description of the non-animal peroxidase superfamily, great effort has been made to characterize this large and heterogeneous group of proteins. Next generation sequencing data have permitted an in-depth study of the molecular evolution of this superfamily and allowed us to perform a phylogenetic reconstruction. Through this analysis, we identified two additional class I members and, here, we discuss the similarities and differences among members of this class. Our results provide new insights into the organization of these antioxidant enzymes, allowing us to propose a new model for the emergence and evolution of this superfamily.
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Affiliation(s)
- Fernanda Lazzarotto
- Programa de Pós-Graduação em Genética e Biologia Molecular, Departamento de Genética, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, RS, Brazil
| | - Andreia Carina Turchetto-Zolet
- Programa de Pós-Graduação em Genética e Biologia Molecular, Departamento de Genética, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, RS, Brazil
| | - Márcia Margis-Pinheiro
- Programa de Pós-Graduação em Genética e Biologia Molecular, Departamento de Genética, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, RS, Brazil.
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Yadav RSS, Patel VK, Yadav KDS, Sharma JK, Singh NP. Lignin peroxidases of some indigenous ligninolytic fungi: secretion and enzymatic characteristics. Indian J Microbiol 2010; 50:132-8. [PMID: 22815586 PMCID: PMC3396419 DOI: 10.1007/s12088-010-0073-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2008] [Accepted: 08/14/2008] [Indexed: 10/18/2022] Open
Abstract
Secretion and enzymatic characteristics of lignin peroxidases from Gloeophyllum sepiarium MTCC 1170, Cladosporium herbarum MTCC 346, Lenzites betulina MTCC 1183, Daedalea flavida MTCC 145, Hexagonia teruis MTCC 1119 and Coirolopsis floccosa MTCC 1177 ligninolytic fungal strains have been reported. Secretion of lignin peroxidase by these ligninolytic fungal strains have been found to be in the range of 0.86 to 3.0 enzyme unit per ml of the culture medium. The enzymatic characteristics like K(m), pH and temperature optima of all the lignin peroxidases of the above fungal strains have been determined using veratryl alcohol and H(2)O(2) as the variable substrates. The K(m) values using veratryl alcohol as the substrate were found to be 65.0 μM, 58.5 μM, 63.0 μM, 54.5 μM, 54.6 μM and 61.0 μM respectively. The K(m) values using H(2)O(2) as the substrate were found to be 88.0 μM, 86.0 μM, 71.0 μM, 67.0 μM, 80.0 μM and 78.0 μM respectively. The pH optima values for lignin peroxidases of the above ligninolytic fungal strains were found to be 2.5, 2.4, 2.4, 2.25, 2.5 and 2.8 respectively, where as the temperature optima values were 25°C, 24°C, 25°C, 23°C, 24°C and 25°C respectively.
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Affiliation(s)
- R. S. S. Yadav
- />Department of Chemistry, D.D.U. Gorakhpur University, Gorakhpur, 273 009 India
| | - V. K. Patel
- />Department of Chemistry, D.D.U. Gorakhpur University, Gorakhpur, 273 009 India
| | - K. D. S. Yadav
- />Department of Chemistry, D.D.U. Gorakhpur University, Gorakhpur, 273 009 India
| | - J. K. Sharma
- />Department of Chemistry, Udai Pratap College, Varansi, 221 002 India
| | - N. P. Singh
- />Department of Chemistry, Udai Pratap College, Varansi, 221 002 India
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