1
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Pupart H, Lukk T, Väljamäe P. Dye-decolorizing peroxidase of Thermobifida halotolerance displays complex kinetics with both substrate inhibition and apparent positive cooperativity. Arch Biochem Biophys 2024; 754:109931. [PMID: 38382807 DOI: 10.1016/j.abb.2024.109931] [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: 11/27/2023] [Revised: 02/15/2024] [Accepted: 02/16/2024] [Indexed: 02/23/2024]
Abstract
Dye-decolorizing peroxidases (DyPs) have been intensively investigated for the purpose of industrial dye decolourization and lignin degradation. Unfortunately, the characterization of these peroxidases is hampered by their non-Michaelis-Menten kinetics, exemplified by substrate inhibition and/or positive cooperativity. Although often observed, the underlying mechanisms behind the unusual kinetics of DyPs are poorly understood. Here we studied the kinetics of the oxidation of 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS), hydroquinones, and anthraquinone dyes by DyP from the bacterium Thermobifida halotolerans (ThDyP) and solved its crystal structure. We also provide rate equations for different kinetic mechanisms explaining the complex kinetics of heme peroxidases. Kinetic studies along with the analysis of the structure of ThDyP suggest that the substrate inhibition is caused by the non-productive binding of ABTS to the enzyme resting state. Strong irreversible inactivation of ThDyP by H2O2 in the absence of ABTS suggests that the substrate inhibition by H2O2 may be caused by the non-productive binding of H2O2 to compound I. Positive cooperativity was observed only with the oxidation of ABTS but not with the two electron-donating substrates. Although the conventional mechanism of cooperativity cannot be excluded, we propose that the oxidation of ABTS assumes the simultaneous binding of two ABTS molecules to reduce compound I to the enzyme resting state, and this causes the apparent positive cooperativity.
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Affiliation(s)
- Hegne Pupart
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Akadeemia tee 15, 12618, Tallinn, Estonia.
| | - Tiit Lukk
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Akadeemia tee 15, 12618, Tallinn, Estonia.
| | - Priit Väljamäe
- Institute of Molecular and Cell Biology, University of Tartu, Riia 23b-202, 51010, Tartu, Estonia.
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2
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Mangini V, Rosini E, Caliandro R, Mangiatordi GF, Delre P, Sciancalepore AG, Pollegioni L, Haidukowski M, Mazzorana M, Sumarah MW, Renaud JB, Flaig R, Mulè G, Belviso BD, Loi M. DypB peroxidase for aflatoxin removal: New insights into the toxin degradation process. CHEMOSPHERE 2024; 349:140826. [PMID: 38040262 DOI: 10.1016/j.chemosphere.2023.140826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 11/24/2023] [Accepted: 11/26/2023] [Indexed: 12/03/2023]
Abstract
Aflatoxin B1 (AFB1) is one of the most potent carcinogens and a widespread food and feed contaminant. As for other toxins, many efforts are devoted to find efficient and environmentally-friendly methods to degrade AFB1, such as enzymatic treatments, thus improving the safety of food and feed products. In this regard, the dye decolorizing peroxidase of type B (DypB) can efficiently degrade AFB1. The molecular mechanism, which is required to drive protein optimization in view of the usage of DypB as a mycotoxin reduction agent in large scale application, is unknown. Here, we focused on the role of four DypB residues in the degradation of AFB1 by alanine-scanning (residues 156, 215, 239 and 246), which were identified from biochemical assays to be kinetically relevant for the degradation. As a result of DypB degradation, AFB1 is converted into four products. Interestingly, the relative abundancy of these products depends on the replaced residues. Molecular dynamics simulations were used to investigate the role of these residues in the binding step between protein and manganese, a metal ion which is expected to be involved in the degradation process. We found that the size of the haem pocket as well as conformational changes in the protein structure could play a role in determining the kinetics of AFB1 removal and, consequently, guide the process towards specific degradation products.
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Affiliation(s)
- V Mangini
- Istituto di Cristallografia, Consiglio Nazionale delle Ricerche, Via Amendola 122/o, Bari, 70126, Italy
| | - E Rosini
- Department of Biotechnology and Life Sciences, University of Insubria, Via J. H. Dunant 3, Varese, 21100, Italy
| | - R Caliandro
- Istituto di Cristallografia, Consiglio Nazionale delle Ricerche, Via Amendola 122/o, Bari, 70126, Italy
| | - G F Mangiatordi
- Istituto di Cristallografia, Consiglio Nazionale delle Ricerche, Via Amendola 122/o, Bari, 70126, Italy
| | - P Delre
- Istituto di Cristallografia, Consiglio Nazionale delle Ricerche, Via Amendola 122/o, Bari, 70126, Italy
| | - A G Sciancalepore
- Istituto di Cristallografia, Consiglio Nazionale delle Ricerche, Via Amendola 122/o, Bari, 70126, Italy
| | - L Pollegioni
- Department of Biotechnology and Life Sciences, University of Insubria, Via J. H. Dunant 3, Varese, 21100, Italy
| | - M Haidukowski
- Istituto di Scienze delle Produzioni Alimentari, Consiglio Nazionale delle Ricerche, Via Amendola 122/o, Bari, 70126, Italy
| | - M Mazzorana
- Diamond Light Source Ltd., Diamond House, Harwell Science & Innovation Campus, Didcot, OX11 0DE, UK; Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, OX11 0FA, UK
| | - M W Sumarah
- London Research and Development Centre, Agriculture and Agri-Food Canada, 1391 Sandford Street London, Ontario, Canada, N5V4T3
| | - J B Renaud
- London Research and Development Centre, Agriculture and Agri-Food Canada, 1391 Sandford Street London, Ontario, Canada, N5V4T3
| | - R Flaig
- Diamond Light Source Ltd., Diamond House, Harwell Science & Innovation Campus, Didcot, OX11 0DE, UK; Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, OX11 0FA, UK
| | - G Mulè
- Istituto di Scienze delle Produzioni Alimentari, Consiglio Nazionale delle Ricerche, Via Amendola 122/o, Bari, 70126, Italy.
| | - B D Belviso
- Istituto di Cristallografia, Consiglio Nazionale delle Ricerche, Via Amendola 122/o, Bari, 70126, Italy.
| | - M Loi
- Istituto di Scienze delle Produzioni Alimentari, Consiglio Nazionale delle Ricerche, Via Amendola 122/o, Bari, 70126, Italy
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3
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Pupart H, Vastšjonok D, Lukk T, Väljamäe P. Dye-Decolorizing Peroxidase of Streptomyces coelicolor ( ScDyPB) Exists as a Dynamic Mixture of Kinetically Different Oligomers. ACS OMEGA 2024; 9:3866-3876. [PMID: 38284010 PMCID: PMC10809370 DOI: 10.1021/acsomega.3c07963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 12/19/2023] [Accepted: 12/21/2023] [Indexed: 01/30/2024]
Abstract
Dye-decolorizing peroxidases (DyPs) are heme-dependent enzymes that catalyze the oxidation of various substrates including environmental pollutants such as azo dyes and also lignin. DyPs often display complex non-Michaelis-Menten kinetics with substrate inhibition or positive cooperativity. Here, we performed in-depth kinetic characterization of the DyP of the bacterium Streptomyces coelicolor (ScDyPB). The activity of ScDyPB was found to be dependent on its concentration in the working stock used to initiate the reactions as well as on the pH of the working stock. Furthermore, the above-listed conditions had different effects on the oxidation of 2,2'-azino-di(3-ethyl-benzothiazoline-6-sulfonic acid) (ABTS) and methylhydroquinone, suggesting that different mechanisms are used in the oxidation of these substrates. The kinetics of the oxidation of ABTS were best described by the model whereby ScDyPB exists as a mixture of two kinetically different enzyme forms. Both forms obey the ping-pong kinetic mechanism, but one form is substrate-inhibited by the ABTS, whereas the other is not. Gel filtration chromatography and dynamic light scattering analyses revealed that ScDyPB exists as a complex mixture of molecules with different sizes. We propose that ScDyPB populations with low and high degrees of oligomerization have different kinetic properties. Such enzyme oligomerization-dependent modulation of the kinetic properties adds further dimension to the complexity of the kinetics of DyPs but also suggests novel possibilities for the regulation of their catalytic activity.
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Affiliation(s)
- Hegne Pupart
- Department
of Chemistry and Biotechnology, Tallinn
University of Technology, 15 Akadeemia tee, Tallinn 12618, Estonia
| | - Darja Vastšjonok
- Institute
of Molecular and Cell Biology, University
of Tartu, Riia 23b-202, Tartu 51010, Estonia
| | - Tiit Lukk
- Department
of Chemistry and Biotechnology, Tallinn
University of Technology, 15 Akadeemia tee, Tallinn 12618, Estonia
| | - Priit Väljamäe
- Institute
of Molecular and Cell Biology, University
of Tartu, Riia 23b-202, Tartu 51010, Estonia
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4
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Dhankhar P, Dalal V, Sharma AK, Kumar P. Structural insights at acidic pH of dye-decolorizing peroxidase from Bacillus subtilis. Proteins 2023; 91:508-517. [PMID: 36345957 DOI: 10.1002/prot.26444] [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: 06/09/2022] [Revised: 10/17/2022] [Accepted: 11/03/2022] [Indexed: 11/10/2022]
Abstract
Dye-decolorizing peroxidases (DyPs), a type of heme-containing oxidoreductase enzymes, catalyze the peroxide-dependent oxidation of various industrial dyes as well as lignin and lignin model compounds. In our previous work, we have recently reported the crystal structures of class A-type DyP from Bacillus subtilis at pH 7.0 (BsDyP7), exposing the location of three binding sites for small substrates and high redox-potential substrates. The biochemical studies revealed the optimum acidic pH for enzyme activity. In the present study, the crystal structure of BsDyP at acidic pH (BsDyP4) reveals two-monomer units stabilized by intermolecular salt bridges and a hydrogen bond network in a homo-dimeric unit. Based on the monomeric structural comparison of BsDyP4 and BsDyP7, minor differences were observed in the loop regions, that is, LI (Ala64-Gln71), LII (Glu96-Lys108), LIII (Pro117-Leu124), and LIV (Leu295-Asp303). Despite these differences, BsDyP4 adopts similar heme architecture as well as three substrate-binding sites to BsDyP7. In BsDyP4, a shift in Asp187, heme pocket residue discloses the plausible reason for optimal acidic pH for BsDyP activity. This study provides insight into the structural changes in BsDyP at acidic pH, where BsDyP is biologically active.
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Affiliation(s)
- Poonam Dhankhar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, India
| | - Vikram Dalal
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, India
| | - Ashwani Kumar Sharma
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, India
| | - Pravindra Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, India
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5
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Dhankhar P, Dalal V, Singh V, Sharma AK, Kumar P. Structure of dye-decolorizing peroxidase from Bacillus subtilis in complex with veratryl alcohol. Int J Biol Macromol 2021; 193:601-608. [PMID: 34687768 DOI: 10.1016/j.ijbiomac.2021.10.100] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 10/04/2021] [Accepted: 10/14/2021] [Indexed: 11/17/2022]
Abstract
Dye-decolorizing peroxidases (DyPs) are heme-containing peroxidases, which have promising application in biodegradation of phenolic lignin compounds and in detoxification of dyes. In this study, the crystal structure of BsDyP- veratryl alcohol (VA) complex delves deep into the binding of small substrate molecules within the DyP heme cavity. The biochemical analysis shows that BsDyP oxidizes the VA with a turnover number of 0.065 s-1, followed by the oxidation of 2,6-dimethoxyphenol (DMP) and guaiacol with a comparable turnover number (kcat) of 0.07 s-1 and 0.07 s-1, respectively. Moreover, biophysical and computational studies reveal the comparable binding affinity of substrates to BsDyP and produce lower-energy stable BsDyP-ligand(s) complexes. All together with our previous findings, we are providing a complete structural description of substrate-binding sites in DyP. The structural insight of BsDyP helps to modulate its engineering to enhance the activity towards the oxidation of a wide range of substrates.
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Affiliation(s)
- Poonam Dhankhar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, 247667, India
| | - Vikram Dalal
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, 247667, India
| | - Vishakha Singh
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, 247667, India
| | - Ashwani Kumar Sharma
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, 247667, India
| | - Pravindra Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, 247667, India.
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6
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Rodrigues CF, Borges PT, Scocozza MF, Silva D, Taborda A, Brissos V, Frazão C, Martins LO. Loops around the Heme Pocket Have a Critical Role in the Function and Stability of BsDyP from Bacillus subtilis. Int J Mol Sci 2021; 22:ijms221910862. [PMID: 34639208 PMCID: PMC8509576 DOI: 10.3390/ijms221910862] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 10/01/2021] [Accepted: 10/05/2021] [Indexed: 11/27/2022] Open
Abstract
Bacillus subtilis BsDyP belongs to class I of the dye-decolorizing peroxidase (DyP) family of enzymes and is an interesting biocatalyst due to its high redox potential, broad substrate spectrum and thermostability. This work reports the optimization of BsDyP using directed evolution for improved oxidation of 2,6-dimethoxyphenol, a model lignin-derived phenolic. After three rounds of evolution, one variant was identified displaying 7-fold higher catalytic rates and higher production yields as compared to the wild-type enzyme. The analysis of X-ray structures of the wild type and the evolved variant showed that the heme pocket is delimited by three long conserved loop regions and a small α helix where, incidentally, the mutations were inserted in the course of evolution. One loop in the proximal side of the heme pocket becomes more flexible in the evolved variant and the size of the active site cavity is increased, as well as the width of its mouth, resulting in an enhanced exposure of the heme to solvent. These conformational changes have a positive functional role in facilitating electron transfer from the substrate to the enzyme. However, they concomitantly resulted in decreasing the enzyme’s overall stability by 2 kcal mol−1, indicating a trade-off between functionality and stability. Furthermore, the evolved variant exhibited slightly reduced thermal stability compared to the wild type. The obtained data indicate that understanding the role of loops close to the heme pocket in the catalysis and stability of DyPs is critical for the development of new and more powerful biocatalysts: loops can be modulated for tuning important DyP properties such as activity, specificity and stability.
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Affiliation(s)
- Carolina F. Rodrigues
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av da República, 2780-157 Oeiras, Portugal; (C.F.R.); (P.T.B.); (D.S.); (A.T.); (V.B.); (C.F.)
| | - Patrícia T. Borges
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av da República, 2780-157 Oeiras, Portugal; (C.F.R.); (P.T.B.); (D.S.); (A.T.); (V.B.); (C.F.)
| | - Magali F. Scocozza
- Instituto de Química Física de los Materiales, Medio Ambiente y Energia (INQUIMAE), CONICET—Universidad de Buenos Aires, Buenos Aires 148EHA, Argentina;
| | - Diogo Silva
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av da República, 2780-157 Oeiras, Portugal; (C.F.R.); (P.T.B.); (D.S.); (A.T.); (V.B.); (C.F.)
| | - André Taborda
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av da República, 2780-157 Oeiras, Portugal; (C.F.R.); (P.T.B.); (D.S.); (A.T.); (V.B.); (C.F.)
| | - Vânia Brissos
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av da República, 2780-157 Oeiras, Portugal; (C.F.R.); (P.T.B.); (D.S.); (A.T.); (V.B.); (C.F.)
| | - Carlos Frazão
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av da República, 2780-157 Oeiras, Portugal; (C.F.R.); (P.T.B.); (D.S.); (A.T.); (V.B.); (C.F.)
| | - Lígia O. Martins
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av da República, 2780-157 Oeiras, Portugal; (C.F.R.); (P.T.B.); (D.S.); (A.T.); (V.B.); (C.F.)
- Correspondence:
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7
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Kimani V, Ullrich R, Büttner E, Herzog R, Kellner H, Jehmlich N, Hofrichter M, Liers C. First Dye-Decolorizing Peroxidase from an Ascomycetous Fungus Secreted by Xylaria grammica. Biomolecules 2021; 11:biom11091391. [PMID: 34572604 PMCID: PMC8469222 DOI: 10.3390/biom11091391] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Revised: 09/16/2021] [Accepted: 09/17/2021] [Indexed: 11/29/2022] Open
Abstract
Background: Fungal DyP-type peroxidases have so far been described exclusively for basidiomycetes. Moreover, peroxidases from ascomycetes that oxidize Mn2+ ions are yet not known. Methods: We describe here the physicochemical, biocatalytic, and molecular characterization of a DyP-type peroxidase (DyP, EC 1.11.1.19) from an ascomycetous fungus. Results: The enzyme oxidizes classic peroxidase substrates such as 2,6-DMP but also veratryl alcohol and notably Mn2+ to Mn3+ ions, suggesting a physiological function of this DyP in lignin modification. The KM value (49 µM) indicates that Mn2+ ions bind with high affinity to the XgrDyP protein but their subsequent oxidation into reactive Mn3+ proceeds with moderate efficiency compared to MnPs and VPs. Mn2+ oxidation was most effective at an acidic pH (between 4.0 and 5.0) and a hypothetical surface exposed an Mn2+ binding site comprising three acidic amino acids (two aspartates and one glutamate) could be localized within the hypothetical XgrDyP structure. The oxidation of Mn2+ ions is seemingly supported by four aromatic amino acids that mediate an electron transfer from the surface to the heme center. Conclusions: Our findings shed new light on the possible involvement of DyP-type peroxidases in lignocellulose degradation, especially by fungi that lack prototypical ligninolytic class II peroxidases.
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Affiliation(s)
- Virginia Kimani
- Unit of Environmental Biotechnology, International Institute Zittau, Dresden University of Technology, Markt 23, 02763 Zittau, Germany; (V.K.); (R.U.); (E.B.); (R.H.); (H.K.); (M.H.)
- Kenya Industrial Research and Development Institute, Nairobi P.O. Box 30650-00100, Kenya
| | - René Ullrich
- Unit of Environmental Biotechnology, International Institute Zittau, Dresden University of Technology, Markt 23, 02763 Zittau, Germany; (V.K.); (R.U.); (E.B.); (R.H.); (H.K.); (M.H.)
| | - Enrico Büttner
- Unit of Environmental Biotechnology, International Institute Zittau, Dresden University of Technology, Markt 23, 02763 Zittau, Germany; (V.K.); (R.U.); (E.B.); (R.H.); (H.K.); (M.H.)
| | - Robert Herzog
- Unit of Environmental Biotechnology, International Institute Zittau, Dresden University of Technology, Markt 23, 02763 Zittau, Germany; (V.K.); (R.U.); (E.B.); (R.H.); (H.K.); (M.H.)
| | - Harald Kellner
- Unit of Environmental Biotechnology, International Institute Zittau, Dresden University of Technology, Markt 23, 02763 Zittau, Germany; (V.K.); (R.U.); (E.B.); (R.H.); (H.K.); (M.H.)
| | - Nico Jehmlich
- Helmholtz-Centre for Environmental Research–UFZ, Department of Molecular System Biology, 04318 Leipzig, Germany;
| | - Martin Hofrichter
- Unit of Environmental Biotechnology, International Institute Zittau, Dresden University of Technology, Markt 23, 02763 Zittau, Germany; (V.K.); (R.U.); (E.B.); (R.H.); (H.K.); (M.H.)
| | - Christiane Liers
- Unit of Environmental Biotechnology, International Institute Zittau, Dresden University of Technology, Markt 23, 02763 Zittau, Germany; (V.K.); (R.U.); (E.B.); (R.H.); (H.K.); (M.H.)
- Correspondence: ; Tel.: +49-3583-6124154
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8
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Characterization of Class V DyP-Type Peroxidase SaDyP1 from Streptomyces avermitilis and Evaluation of SaDyPs Expression in Mycelium. Int J Mol Sci 2021; 22:ijms22168683. [PMID: 34445389 PMCID: PMC8395514 DOI: 10.3390/ijms22168683] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 07/31/2021] [Accepted: 08/09/2021] [Indexed: 11/17/2022] Open
Abstract
DyP-type peroxidases are a family of heme peroxidases named for their ability to degrade persistent anthraquinone dyes. DyP-type peroxidases are subclassified into three classes: classes P, I and V. Based on its genome sequence, Streptomyces avermitilis, eubacteria, has two genes presumed to encode class V DyP-type peroxidases and two class I genes. We have previously shown that ectopically expressed SaDyP2, a member of class V, indeed has the characteristics of a DyP-type peroxidase. In this study, we analyzed SaDyP1, a member of the same class V as SaDyP2. SaDyP1 showed high amino acid sequence identity to SaDyP2, retaining a conserved GXXDG motif and catalytic aspartate. SaDyP1 degraded anthraquinone dyes, which are specific substrates of DyP-type peroxidases but not azo dyes. In addition to such substrate specificity, SaDyP1 showed other features of DyP-type peroxidases, such as low optimal pH. Furthermore, immunoblotting using an anti-SaDyP2 polyclonal antibody revealed that SaDyP1 and/or SaDyP2 is expressed in mycelia of wild-type S. avermitilis.
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9
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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: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [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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10
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Li L, Wang T, Chen T, Huang W, Zhang Y, Jia R, He C. Revealing two important tryptophan residues with completely different roles in a dye-decolorizing peroxidase from Irpex lacteus F17. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:128. [PMID: 34059116 PMCID: PMC8165797 DOI: 10.1186/s13068-021-01978-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 05/19/2021] [Indexed: 05/07/2023]
Abstract
BACKGROUND Dye-decolorizing peroxidases (DyPs) represent a novel family of heme peroxidases that use H2O2 as the final electron acceptor to catalyze the oxidation of various organic compounds. A DyP from Irpex lacteus F17 (Il-DyP4, corresponding to GenBank MG209114), obtained by heterologous expression, exhibits a high catalytic efficiency for phenolic compounds and a strong decolorizing ability toward various synthetic dyes. However, the enzyme structure and the catalytic residues involved in substrate oxidation remain poorly understood. RESULTS Here, we obtained a high-resolution structure (2.0 Å, PDB: 7D8M) of Il‑DyP4 with α-helices, anti-parallel β-sheets and one ferric heme cofactor sandwiched between two domains. The crystal structure of Il‑DyP4 revealed two heme access channels leading from the enzyme molecular surface to its heme region, and also showed four conserved amino acid residues forming the pocket for the conversion of hydrogen peroxide into the water molecule. In addition, we found that Trp264 and Trp380, were two important residues with different roles in Il‑DyP4, by using site-directed mutagenesis and an electron paramagnetic resonance (EPR) study. Trp264 is a noncatalytic residue that mainly is used for maintaining the normal spatial conformation of the heme region and the high-spin state of heme Fe3+ of Il‑DyP4, while Trp380 serves as the surface-exposed radical-forming residue that is closely related to the oxidation of substrates including not only bulky dyes, but also simple phenols. CONCLUSIONS This study is important for better understanding the catalytic properties of fungal DyPs and their structure-function relationships.
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Affiliation(s)
- Liuqing Li
- School of Life Science, Economic and Technology Development Zone, Anhui University, 111 jiulong Road, Hefei, Anhui, PR China, 230601
- Anhui Key Laboratory of Modern Biomanufacturing, Anhui University, Hefei, Anhui Province, China
| | - Tao Wang
- School of Life Science, Economic and Technology Development Zone, Anhui University, 111 jiulong Road, Hefei, Anhui, PR China, 230601
- Anhui Key Laboratory of Modern Biomanufacturing, Anhui University, Hefei, Anhui Province, China
| | - Taohua Chen
- School of Life Science, Economic and Technology Development Zone, Anhui University, 111 jiulong Road, Hefei, Anhui, PR China, 230601
- Anhui Key Laboratory of Modern Biomanufacturing, Anhui University, Hefei, Anhui Province, China
| | - Wenhan Huang
- School of Life Science, Economic and Technology Development Zone, Anhui University, 111 jiulong Road, Hefei, Anhui, PR China, 230601
- Anhui Key Laboratory of Modern Biomanufacturing, Anhui University, Hefei, Anhui Province, China
| | - Yinliang Zhang
- School of Life Science, Economic and Technology Development Zone, Anhui University, 111 jiulong Road, Hefei, Anhui, PR China, 230601
- Anhui Key Laboratory of Modern Biomanufacturing, Anhui University, Hefei, Anhui Province, China
| | - Rong Jia
- School of Life Science, Economic and Technology Development Zone, Anhui University, 111 jiulong Road, Hefei, Anhui, PR China, 230601.
- Anhui Key Laboratory of Modern Biomanufacturing, Anhui University, Hefei, Anhui Province, China.
| | - Chao He
- School of Life Science, Economic and Technology Development Zone, Anhui University, 111 jiulong Road, Hefei, Anhui, PR China, 230601.
- Anhui Key Laboratory of Modern Biomanufacturing, Anhui University, Hefei, Anhui Province, China.
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11
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Sugano Y, Yoshida T. DyP-Type Peroxidases: Recent Advances and Perspectives. Int J Mol Sci 2021; 22:5556. [PMID: 34074047 PMCID: PMC8197335 DOI: 10.3390/ijms22115556] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 05/17/2021] [Accepted: 05/18/2021] [Indexed: 12/16/2022] Open
Abstract
In this review, we chart the major milestones in the research progress on the DyP-type peroxidase family over the past decade. Though mainly distributed among bacteria and fungi, this family actually exhibits more widespread diversity. Advanced tertiary structural analyses have revealed common and different features among members of this family. Notably, the catalytic cycle for the peroxidase activity of DyP-type peroxidases appears to be different from that of other ubiquitous heme peroxidases. DyP-type peroxidases have also been reported to possess activities in addition to peroxidase function, including hydrolase or oxidase activity. They also show various cellular distributions, functioning not only inside cells but also outside of cells. Some are also cargo proteins of encapsulin. Unique, noteworthy functions include a key role in life-cycle switching in Streptomyces and the operation of an iron transport system in Staphylococcus aureus, Bacillus subtilis and Escherichia coli. We also present several probable physiological roles of DyP-type peroxidases that reflect the widespread distribution and function of these enzymes. Lignin degradation is the most common function attributed to DyP-type peroxidases, but their activity is not high compared with that of standard lignin-degrading enzymes. From an environmental standpoint, degradation of natural antifungal anthraquinone compounds is a specific focus of DyP-type peroxidase research. Considered in its totality, the DyP-type peroxidase family offers a rich source of diverse and attractive materials for research scientists.
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Affiliation(s)
- Yasushi Sugano
- Department of Chemical and Biological Sciences, Faculty of Science, Japan Women’s University, Tokyo 112-8681, Japan;
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12
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Falade AO, Ekundayo TC. Emerging biotechnological potentials of DyP-type peroxidases in remediation of lignin wastes and phenolic pollutants: a global assessment (2007-2019). Lett Appl Microbiol 2020; 72:13-23. [PMID: 32974921 DOI: 10.1111/lam.13392] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 09/03/2020] [Accepted: 09/10/2020] [Indexed: 12/15/2022]
Abstract
Dye decolourizing peroxidase (DyP) is an emerging biocatalyst with enormous bioremediation and biotechnological potentials. This study examined the global trend of research related to DyP through a bibliometric analysis. The search term 'dye decolourizing peroxidase' or 'DyP-type peroxidase' was used to retrieve published articles between 2007 and 2019 from the Web of Science (WoS) and Scopus databases. A total of 62 articles were published within the period, with an annual growth rate of 17·6%. The highest research output was observed in 2015, which accounted for about 13% of the total output in 12 years. Germany published the highest number of articles (n = 10, 16·1%) with a total citation of 478. However, the lowest number of published articles among the top 10 countries was observed in India and Korea (n = 2, 3·2%). Research collaboration was low (collaboration index = 4·08). In addition to dye decolourizing peroxidase(s) and DyP-type peroxidase(s) (n = 33, 53·23%), the top authors keywords and research focus included lignin and lignin degradation (n = 10, 16·1 %). More so, peroxidase (n = 59, 95·2%), amino acid sequence (n = 27, 46·8%), lignin (n = 24, 38·7%) and metabolism (n = 23, 37·1%) were highly represented in keywords-plus. The most common conceptual framework from this study include characterization, lignin degradation and environmental proteomics. Apart from the inherent efficient dye-decolourizing properties, this study showed that DyP has emerging biotechnological potentials in lignin degradation and remediation of phenolic environmental pollutants, which at the moment are under explored globally.
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Affiliation(s)
- A O Falade
- Department of Biochemistry, University of Medical Sciences, Ondo, Ondo State, Nigeria
| | - T C Ekundayo
- Department of Biological Sciences, University of Medical Sciences, Ondo, Ondo State, Nigeria
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13
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Dhankhar P, Dalal V, Mahto JK, Gurjar BR, Tomar S, Sharma AK, Kumar P. Characterization of dye-decolorizing peroxidase from Bacillus subtilis. Arch Biochem Biophys 2020; 693:108590. [DOI: 10.1016/j.abb.2020.108590] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 09/14/2020] [Accepted: 09/16/2020] [Indexed: 12/25/2022]
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14
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Catucci G, Valetti F, Sadeghi SJ, Gilardi G. Biochemical features of dye‐decolorizing peroxidases: Current impact on lignin degradation. Biotechnol Appl Biochem 2020; 67:751-759. [DOI: 10.1002/bab.2015] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 08/26/2020] [Indexed: 12/21/2022]
Affiliation(s)
- Gianluca Catucci
- Department of Life Sciences and Systems Biology University of Torino Torino 10123 Italy
| | - Francesca Valetti
- Department of Life Sciences and Systems Biology University of Torino Torino 10123 Italy
| | - Sheila J. Sadeghi
- Department of Life Sciences and Systems Biology University of Torino Torino 10123 Italy
| | - Gianfranco Gilardi
- Department of Life Sciences and Systems Biology University of Torino Torino 10123 Italy
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15
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Routoula E, Patwardhan SV. Degradation of Anthraquinone Dyes from Effluents: A Review Focusing on Enzymatic Dye Degradation with Industrial Potential. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:647-664. [PMID: 31913605 DOI: 10.1021/acs.est.9b03737] [Citation(s) in RCA: 172] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Up to 84 000 tons of dye can be lost in water, and 90 million tons of water are attributed annually to dye production and their application, mainly in the textile and leather industry, making the dyestuff industry responsible for up to 20% of the industrial water pollution. The majority of dyes industrially used today are aromatic compounds with complex, reinforced structures, with anthraquinone dyes being the second largest produced in terms of volume. Despite the progress on decolorization and degradation of azo dyes, very little attention has been given to anthraquinone dyes. Anthraquinone dyes pose a serious environmental problem as their reinforced structure makes them difficult to degrade naturally. Existing methods of decolorization might be effective but are neither efficient nor practical due to extended time, space, and cost requirements. Attention should be given to the emerging routes for dye decolorization via the enzymatic action of oxidoreductases, which have already a strong presence in various other bioremediation applications. This review will discusses the presence of anthraquinone dyes in the effluents and ways for their remediation from dyehouse effluents, focusing on enzymatic processes.
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Affiliation(s)
- Eleni Routoula
- Department of Chemical and Biological Engineering , University of Sheffield Mappin Street , Sheffield , United Kingdom , S1 3JD
| | - Siddharth V Patwardhan
- Department of Chemical and Biological Engineering , University of Sheffield Mappin Street , Sheffield , United Kingdom , S1 3JD
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16
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Linde D, Ayuso-Fernández I, Ruiz-Dueñas FJ, Martínez AT. Different fungal peroxidases oxidize nitrophenols at a surface catalytic tryptophan. Arch Biochem Biophys 2019; 668:23-28. [PMID: 31095936 DOI: 10.1016/j.abb.2019.05.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 04/30/2019] [Accepted: 05/11/2019] [Indexed: 10/26/2022]
Abstract
Dye-decolorizing peroxidase (DyP) from Auricularia auricula-judae and versatile peroxidase (VP) from Pleurotus eryngii oxidize the three mononitrophenol isomers. Both enzymes have been overexpressed in Escherichia coli and in vitro activated. Despite their very different three-dimensional structures, the nitrophenol oxidation site is located at a solvent-exposed aromatic residue in both DyP (Trp377) and VP (Trp164), as revealed by liquid chromatography coupled to mass spectrometry and kinetic analyses of nitrophenol oxidation by the native enzymes and their tryptophan-less variants (the latter showing 10-60 fold lower catalytic efficiencies).
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Affiliation(s)
- Dolores Linde
- Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, E-28040, Madrid, Spain
| | - Iván Ayuso-Fernández
- Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, E-28040, Madrid, 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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Chaplin AK, Chicano TM, Hampshire BV, Wilson MT, Hough MA, Svistunenko DA, Worrall JAR. An Aromatic Dyad Motif in Dye Decolourising Peroxidases Has Implications for Free Radical Formation and Catalysis. Chemistry 2019; 25:6141-6153. [PMID: 30945782 DOI: 10.1002/chem.201806290] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Indexed: 01/27/2023]
Abstract
Dye decolouring peroxidases (DyPs) are the most recent class of heme peroxidase to be discovered. On reacting with H2 O2 , DyPs form a high-valent iron(IV)-oxo species and a porphyrin radical (Compound I) followed by stepwise oxidation of an organic substrate. In the absence of substrate, the ferryl species decays to form transient protein-bound radicals on redox active amino acids. Identification of radical sites in DyPs has implications for their oxidative mechanism with substrate. Using a DyP from Streptomyces lividans, referred to as DtpA, which displays low reactivity towards synthetic dyes, activation with H2 O2 was explored. A Compound I EPR spectrum was detected, which in the absence of substrate decays to a protein-bound radical EPR signal. Using a newly developed version of the Tyrosyl Radical Spectra Simulation Algorithm, the radical EPR signal was shown to arise from a pristine tyrosyl radical and not a mixed Trp/Tyr radical that has been widely reported in DyP members exhibiting high activity with synthetic dyes. The radical site was identified as Tyr374, with kinetic studies inferring that although Tyr374 is not on the electron-transfer pathway from the dye RB19, its replacement with a Phe does severely compromise activity with other organic substrates. These findings hint at the possibility that alternative electron-transfer pathways for substrate oxidation are operative within the DyP family. In this context, a role for a highly conserved aromatic dyad motif is discussed.
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Affiliation(s)
- Amanda K Chaplin
- Present address: Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Tadeo Moreno Chicano
- Present address: Department of Molecular Mechanisms, Max Planck Institute for Medical Research, Jahnstraße 29, 69120, Heidelberg, Germany
| | - Bethany V Hampshire
- Present address: Department of Physics, University of Warwick, Coventry, CV4 7AL, UK
| | - Michael T Wilson
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK
| | - Michael A Hough
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK
| | - Dimitri A Svistunenko
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK
| | - Jonathan A R Worrall
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK
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18
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Ramirez-Escudero M, Molina-Espeja P, Gomez de Santos P, Hofrichter M, Sanz-Aparicio J, Alcalde M. Structural Insights into the Substrate Promiscuity of a Laboratory-Evolved Peroxygenase. ACS Chem Biol 2018; 13:3259-3268. [PMID: 30376293 DOI: 10.1021/acschembio.8b00500] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Because of their minimal requirements, substrate promiscuity and product selectivity, fungal peroxygenases are now considered to be the jewel in the crown of C-H oxyfunctionalization biocatalysts. In this work, the crystal structure of the first laboratory-evolved peroxygenase expressed by yeast was determined at a resolution of 1.5 Å. Notable differences were detected between the evolved and native peroxygenase from Agrocybe aegerita, including the presence of a full N-terminus and a broader heme access channel due to the mutations that accumulated through directed evolution. Further mutagenesis and soaking experiments with a palette of peroxygenative and peroxidative substrates suggested dynamic trafficking through the heme channel as the main driving force for the exceptional substrate promiscuity of peroxygenase. Accordingly, this study provides the first structural evidence at an atomic level regarding the mode of substrate binding for this versatile biocatalyst, which is discussed within a biological and chemical context.
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Affiliation(s)
- Mercedes Ramirez-Escudero
- Department of Crystallography & Structural Biology, Institute of Physical Chemistry “Rocasolano”, CSIC, 28006 Madrid, Spain
| | | | | | - Martin Hofrichter
- Department of Bio- and Environmental Sciences, TU Dresden, International Institute Zittau, Mark 23, 02763 Zittau, Germany
| | - Julia Sanz-Aparicio
- Department of Crystallography & Structural Biology, Institute of Physical Chemistry “Rocasolano”, CSIC, 28006 Madrid, Spain
| | - Miguel Alcalde
- Department of Biocatalysis, Institute of Catalysis, CSIC, 28049 Madrid, Spain
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19
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Reina R, García-Sánchez M, Liers C, García-Romera I, Aranda E. An Overview of Fungal Applications in the Valorization of Lignocellulosic Agricultural By-Products: The Case of Two-Phase Olive Mill Wastes. Fungal Biol 2018. [DOI: 10.1007/978-3-319-77386-5_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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20
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Shrestha R, Huang G, Meekins DA, Geisbrecht BV, Li P. Mechanistic Insights into Dye-Decolorizing Peroxidase Revealed by Solvent Isotope and Viscosity Effects. ACS Catal 2017; 7:6352-6364. [PMID: 29308295 PMCID: PMC5751952 DOI: 10.1021/acscatal.7b01861] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Dye-decolorizing peroxidases (DyPs) are a family of H2O2-dependent heme peroxidases, which have shown potential applications in lignin degradation and valorization. However, the DyP kinetic mechanism remains underexplored. Using structural biology and solvent isotope (sKIE) and viscosity effects, many mechanistic characteristics have been uncovered for the B-class ElDyP from Enterobacter lignolyticus. Its structure revealed that a water molecule acts as the sixth axial ligand with two channels at diameters of ~3.0 and 8.0 Å leading to the heme center. A conformational change of ERS* to ERS, which have identical spectral characteristics, was proposed as the final step in DyPs' bisubstrate Ping-Pong mechanism. This step is also the rate-determining step in ABTS oxidation. The normal KIE of wild-type ElDyP with D2O2 at pH 3.5 suggested that cmpd 0 deprotonation by the distal aspartate is rate-limiting in the formation of cmpd I, which is more reactive under acidic pH than under neutral or alkaline pH. The viscosity effects and other biochemical methods implied that the reducing substrate binds with cmpd I instead of the free enzyme. The significant inverse sKIEs of kcat/KM and kERS* suggested that the aquo release in DyPs is mechanistically important and may explain the enzyme's adoption of two-electron reduction for cmpd I. The distal aspartate is catalytically more important than the distal arginine and plays key roles in determining DyPs' acidic pH optimum. The kinetic mechanism of D143H-ElDyP was also briefly studied. The results obtained will pave the way for future protein engineering to improve DyPs' lignolytic activity.
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Affiliation(s)
- Ruben Shrestha
- Department of Chemistry, Kansas State University, Manhattan, KS, 66506, USA
| | - Gaochao Huang
- Department of Chemistry, Kansas State University, Manhattan, KS, 66506, USA
| | - David A. Meekins
- Department of Chemistry, Kansas State University, Manhattan, KS, 66506, USA
| | - Brian V. Geisbrecht
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS, 66506, USA
| | - Ping Li
- Department of Chemistry, Kansas State University, Manhattan, KS, 66506, USA
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21
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Lauber C, Schwarz T, Nguyen QK, Lorenz P, Lochnit G, Zorn H. Identification, heterologous expression and characterization of a dye-decolorizing peroxidase of Pleurotus sapidus. AMB Express 2017; 7:164. [PMID: 28831735 PMCID: PMC5567573 DOI: 10.1186/s13568-017-0463-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2017] [Accepted: 08/17/2017] [Indexed: 11/10/2022] Open
Abstract
The coding sequence of a peroxidase from the secretome of Pleurotus sapidus was cloned from a cDNA library. Bioinformatic analyses revealed an open reading frame of 1551 bp corresponding to a primary translation product of 516 amino acids. The DyP-type peroxidase was heterologously produced in Trichoderma reesei with an activity of 55,000 U L-1. The enzyme was purified from the culture supernatant, biochemically characterized and the kinetic parameters were determined. The enzyme has an N-terminal signal peptide composed of 62 amino acids. Analysis by Blue Native PAGE and activity staining with ABTS, as well as gel filtration chromatography showed the native dimeric state of the enzyme (115 kDa). Analysis of the substrate range revealed that the recombinant enzyme catalyzes, in addition to the conversion of some classic peroxidase substrates such as 2,2'-azino-bis(3-ethylthiazoline-6-sulfonate) and substituted phenols like 2,6-dimethoxyphenol, also the decolorization of the anthraquinonic dye Reactive Blue 5. The enzyme also catalyzes bleaching of natural colorants such as β-carotene and annatto. Surprisingly, β-carotene was transformed in the presence and absence of H2O2 by rPsaDyP, however enzyme activity was increased by the addition of H2O2. This indicates that the rPsaDyP has an oxidase function in addition to a peroxidase activity. As a consequence of the high affinity to the characteristic substrate Reactive Blue 5 the rPsaDyP belongs functionally to the dyp-type peroxidase family.
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22
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Brissos V, Tavares D, Sousa AC, Robalo MP, Martins LO. Engineering a Bacterial DyP-Type Peroxidase for Enhanced Oxidation of Lignin-Related Phenolics at Alkaline pH. ACS Catal 2017. [DOI: 10.1021/acscatal.6b03331] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Vânia Brissos
- Instituto
de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av da República, 2780-157 Oeiras, Portugal
| | - Diogo Tavares
- Instituto
de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av da República, 2780-157 Oeiras, Portugal
| | - Ana Catarina Sousa
- Área
Departamental de Engenharia Química, ISEL-Instituto Superior de Engenharia de Lisboa, Instituto Politécnico de Lisboa, R. Conselheiro Emídio Navarro, 1, 1959-007 Lisboa, Portugal
- Centro
de Química Estrutural, Complexo I, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal
| | - Maria Paula Robalo
- Área
Departamental de Engenharia Química, ISEL-Instituto Superior de Engenharia de Lisboa, Instituto Politécnico de Lisboa, R. Conselheiro Emídio Navarro, 1, 1959-007 Lisboa, Portugal
- Centro
de Química Estrutural, Complexo I, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal
| | - Lígia O. Martins
- Instituto
de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av da República, 2780-157 Oeiras, Portugal
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Huang G, Shrestha R, Jia K, Geisbrecht BV, Li P. Enantioselective Synthesis of Dilignol Model Compounds and Their Stereodiscrimination Study with a Dye-Decolorizing Peroxidase. Org Lett 2017; 19:1820-1823. [PMID: 28326791 DOI: 10.1021/acs.orglett.7b00587] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A four-step enantioselective approach was developed to synthesize anti (1R,2S)-1a and (1S,2R)-1b containing a β-O-4 linkage in good yields. A significant difference was observed for the apparent binding affinities of four stereospecific lignin model compounds with TcDyP by surface plasmon resonance, which was not translated into a significant difference in enzyme activities. The discrepancy may be attributed to the conformational change involving a loop widely present in DyPs upon H2O2 binding.
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Affiliation(s)
- Gaochao Huang
- Department of Chemistry and ‡Department of Biochemistry and Molecular Biophysics, Kansas State University , Manhattan, Kansas 66506, United States
| | - Ruben Shrestha
- Department of Chemistry and ‡Department of Biochemistry and Molecular Biophysics, Kansas State University , Manhattan, Kansas 66506, United States
| | - Kaimin Jia
- Department of Chemistry and ‡Department of Biochemistry and Molecular Biophysics, Kansas State University , Manhattan, Kansas 66506, United States
| | - Brian V Geisbrecht
- Department of Chemistry and ‡Department of Biochemistry and Molecular Biophysics, Kansas State University , Manhattan, Kansas 66506, United States
| | - Ping Li
- Department of Chemistry and ‡Department of Biochemistry and Molecular Biophysics, Kansas State University , Manhattan, Kansas 66506, United States
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Sugawara K, Nishihashi Y, Narioka T, Yoshida T, Morita M, Sugano Y. Characterization of a novel DyP-type peroxidase from Streptomyces avermitilis. J Biosci Bioeng 2017; 123:425-430. [PMID: 28089379 DOI: 10.1016/j.jbiosc.2016.12.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 12/01/2016] [Indexed: 01/20/2023]
Abstract
DyP-type peroxidases are a heme peroxidase family with unique properties whose members are widely distributed from prokaryotes to eukaryotes. DyP-type peroxidases are subdivided into class P, I and V based on structure-based sequence alignment. Class V enzymes possess degradation activities for anthraquinone dyes, and include extra sequences compared with class P and I. Class V enzymes are mainly found in fungi, with only two such proteins, AnaPX and DyP2, reported in bacteria. Here, we heterologously expressed, purified and biochemically characterized SaDyP2 protein, predicted to belong to class V. SaDyP2 was purified as a ∼50 kDa enzyme containing a heme cofactor and was found to oxidize the typical peroxidase substrates, ABTS and DMP. SaDyP2 was generally thermostable and exhibited a lower optimal pH, a feature typical of DyP-type peroxidases. It also degraded anthraquinone dyes, a specific substrate of DyP-type peroxidases, although the kcat for SaDyP2 was lower than that for other class V enzymes. The Km value of SaDyP2 for anthraquinone dye was similar to that of other enzymes of this class. Homology modeling revealed that the structure of SaDyP2 best fit that of class V enzymes.
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Affiliation(s)
- Kanako Sugawara
- Department of Chemical and Biological Sciences, Faculty of Science, Japan Women's University, 2-8-1 Mejirodai, Bunkyo-Ku, Tokyo 112-8681, Japan
| | - Yuriko Nishihashi
- Department of Chemical and Biological Sciences, Faculty of Science, Japan Women's University, 2-8-1 Mejirodai, Bunkyo-Ku, Tokyo 112-8681, Japan
| | - Tomomi Narioka
- Department of Chemical and Biological Sciences, Faculty of Science, Japan Women's University, 2-8-1 Mejirodai, Bunkyo-Ku, Tokyo 112-8681, Japan
| | - Toru Yoshida
- Department of Bioresource and Environmental Sciences, Faculty of Life Sciences, Kyoto Sangyo University, Kamigamo-Motoyama, Kyoto 603-8555, Japan
| | - Mifumi Morita
- Environmental Chemistry and Engineering, Interdisciplinary Graduate School of Science and Engineering, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226-8503, Japan
| | - Yasushi Sugano
- Department of Chemical and Biological Sciences, Faculty of Science, Japan Women's University, 2-8-1 Mejirodai, Bunkyo-Ku, Tokyo 112-8681, Japan.
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25
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de Gonzalo G, Colpa DI, Habib MH, Fraaije MW. Bacterial enzymes involved in lignin degradation. J Biotechnol 2016; 236:110-9. [DOI: 10.1016/j.jbiotec.2016.08.011] [Citation(s) in RCA: 315] [Impact Index Per Article: 39.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Accepted: 08/16/2016] [Indexed: 01/01/2023]
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Yoshida T, Ogola HJO, Amano Y, Hisabori T, Ashida H, Sawa Y, Tsuge H, Sugano Y. Anabaena sp. DyP-type peroxidase is a tetramer consisting of two asymmetric dimers. Proteins 2015; 84:31-42. [PMID: 26492416 DOI: 10.1002/prot.24952] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Revised: 10/01/2015] [Accepted: 10/11/2015] [Indexed: 11/10/2022]
Abstract
DyP-type peroxidases are a newly discovered family of heme peroxidases distributed from prokaryotes to eukaryotes. Recently, using a structure-based sequence alignment, we proposed the new classes, P, I and V, as substitutes for classes A, B, C, and D [Arch Biochem Biophys 2015;574:49-55]. Although many class V enzymes from eukaryotes have been characterized, only two from prokaryotes have been reported. Here, we show the crystal structure of one of these two enzymes, Anabaena sp. DyP-type peroxidase (AnaPX). AnaPX is tetramer formed from Cys224-Cys224 disulfide-linked dimers. The tetramer of wild-type AnaPX was stable at all salt concentrations tested. In contrast, the C224A mutant showed salt concentration-dependent oligomeric states: in 600 mM NaCl, it maintained a tetrameric structure, whereas in the absence of salt, it dissociated into monomers, leading to a reduction in thermostability. Although the tetramer exhibits non-crystallographic, 2-fold symmetry in the asymmetric unit, two subunits forming the Cys224-Cys224 disulfide-linked dimer are related by 165° rotation. This asymmetry creates an opening to cavities facing the inside of the tetramer, providing a pathway for hydrogen peroxide access. Finally, a phylogenetic analysis using structure-based sequence alignments showed that class V enzymes from prokaryotes, including AnaPX, are phylogenetically closely related to class V enzymes from eukaryotes.
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Affiliation(s)
- Toru Yoshida
- Department of Bioresource and Environmental Sciences, Faculty of Life Sciences, Kyoto Sangyo University, Kamigamo-Motoyama, Kyoto, 603-8555, Japan
| | - Henry Joseph Oduor Ogola
- School of Agricultural and Food Sciences, Jaramogi Oginga Odinga University of Science and Technology, Bondo, Kenya
| | - Yoshimi Amano
- Chemical Resources Laboratory, Tokyo Institute of Technology, Nagatsuta 4259-R1-8, Midori-Ku, Yokohama, 226-8503, Japan
| | - Toru Hisabori
- Chemical Resources Laboratory, Tokyo Institute of Technology, Nagatsuta 4259-R1-8, Midori-Ku, Yokohama, 226-8503, Japan
| | - Hiroyuki Ashida
- Department of Molecular and Functional Genomics, Interdisciplinary Center for Science Research, Shimane University, Nishikawatsu 1060, Matsue, Shimane, 690-8504, Japan
| | - Yoshihiro Sawa
- Department of Life Science and Biotechnology, Faculty of Life and Environmental Science, Shimane University, Matsue, Shimane, 690-8504, Japan
| | - Hideaki Tsuge
- Department of Bioresource and Environmental Sciences, Faculty of Life Sciences, Kyoto Sangyo University, Kamigamo-Motoyama, Kyoto, 603-8555, Japan
| | - Yasushi Sugano
- Department of Chemical and Biological Sciences, Faculty of Science, Japan Women's University, 2-8-1 Mejirodai, Bunkyo-Ku, Tokyo, 112-8681, Japan
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Baratto MC, Sinicropi A, Linde D, Sáez-Jiménez V, Sorace L, Ruiz-Duenas FJ, Martinez AT, Basosi R, Pogni R. Redox-Active Sites in Auricularia auricula-judae Dye-Decolorizing Peroxidase and Several Directed Variants: A Multifrequency EPR Study. J Phys Chem B 2015; 119:13583-92. [PMID: 26120933 DOI: 10.1021/acs.jpcb.5b02961] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Peroxide-activated Auricularia auricula-judae dye-decolorizing peroxidase (DyP) forms a mixed Trp377 and Tyr337 radical, the former being responsible for oxidation of the typical DyP substrates (Linde et al. Biochem. J., 2015, 466, 253-262); however, a pure tryptophanyl radical EPR signal is detected at pH 7 (where the enzyme is inactive), in contrast with the mixed signal observed at pH for optimum activity, pH 3. On the contrary, the presence of a second tyrosine radical (at Tyr147) is deduced by a multifrequency EPR study of a variety of simple and double-directed variants (including substitution of the above and other tryptophan and tyrosine residues) at different freezing times after their activation by H2O2 (at pH 3). This points out that subsidiary long-range electron-transfer pathways enter into operation when the main pathway(s) is removed by directed mutagenesis, with catalytic efficiencies progressively decreasing. Finally, self-reduction of the Trp377 neutral radical is observed when reaction time (before freezing) is increased in the absence of reducing substrates (from 10 to 60 s). Interestingly, the tryptophanyl radical is stable in the Y147S/Y337S variant, indicating that these two tyrosine residues are involved in the self-reduction reaction.
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Affiliation(s)
- Maria Camilla Baratto
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena , I-53100 Siena, Italy
| | - Adalgisa Sinicropi
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena , I-53100 Siena, Italy
| | - Dolores Linde
- Centro de Investigaciones Biológicas, CSIC , Ramiro de Maeztu 9, E-28040 Madrid, Spain
| | - Verónica Sáez-Jiménez
- Centro de Investigaciones Biológicas, CSIC , Ramiro de Maeztu 9, E-28040 Madrid, Spain
| | - Lorenzo Sorace
- Department of Chemistry, "Ugo Schiff" and INSTM RU, University of Florence , 50019 Sesto Fiorentino, Florence, Italy
| | | | - Angel T Martinez
- Centro de Investigaciones Biológicas, CSIC , Ramiro de Maeztu 9, E-28040 Madrid, Spain
| | - Riccardo Basosi
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena , I-53100 Siena, Italy
| | - Rebecca Pogni
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena , I-53100 Siena, Italy
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Celis AI, DuBois JL. Substrate, product, and cofactor: The extraordinarily flexible relationship between the CDE superfamily and heme. Arch Biochem Biophys 2015; 574:3-17. [PMID: 25778630 PMCID: PMC4414885 DOI: 10.1016/j.abb.2015.03.004] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Revised: 03/06/2015] [Accepted: 03/08/2015] [Indexed: 12/21/2022]
Abstract
PFam Clan 0032, also known as the CDE superfamily, is a diverse group of at least 20 protein families sharing a common α,β-barrel domain. Of these, six different groups bind heme inside the barrel's interior, using it alternately as a cofactor, substrate, or product. Focusing on these six, an integrated picture of structure, sequence, taxonomy, and mechanism is presented here, detailing how a single structural motif might be able to mediate such an array of functions with one of nature's most important small molecules.
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Affiliation(s)
- Arianna I Celis
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, United States
| | - Jennifer L DuBois
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, United States.
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Fernández-Fueyo E, Linde D, Almendral D, López-Lucendo MF, Ruiz-Dueñas FJ, Martínez AT. Description of the first fungal dye-decolorizing peroxidase oxidizing manganese(II). Appl Microbiol Biotechnol 2015; 99:8927-42. [PMID: 25967658 PMCID: PMC4619462 DOI: 10.1007/s00253-015-6665-3] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Revised: 04/24/2015] [Accepted: 04/29/2015] [Indexed: 12/29/2022]
Abstract
Two phylogenetically divergent genes of the new family of dye-decolorizing peroxidases (DyPs) were found during comparison of the four DyP genes identified in the Pleurotus ostreatus genome with over 200 DyP genes from other basidiomycete genomes. The heterologously expressed enzymes (Pleos-DyP1 and Pleos-DyP4, following the genome nomenclature) efficiently oxidize anthraquinoid dyes (such as Reactive Blue 19), which are characteristic DyP substrates, as well as low redox-potential dyes (such as 2,2-azinobis-(3-ethylbenzothiazoline-6-sulfonic acid)) and substituted phenols. However, only Pleos-DyP4 oxidizes the high redox-potential dye Reactive Black 5, at the same time that it displays high thermal and pH stability. Unexpectedly, both enzymes also oxidize Mn2+ to Mn3+, albeit with very different catalytic efficiencies. Pleos-DyP4 presents a Mn2+ turnover (56 s−1) nearly in the same order of the two other Mn2+-oxidizing peroxidase families identified in the P. ostreatus genome: manganese peroxidases (100 s−1 average turnover) and versatile peroxidases (145 s−1 average turnover), whose genes were also heterologously expressed. Oxidation of Mn2+ has been reported for an Amycolatopsis DyP (24 s−1) and claimed for other bacterial DyPs, albeit with lower activities, but this is the first time that Mn2+ oxidation is reported for a fungal DyP. Interestingly, Pleos-DyP4 (together with ligninolytic peroxidases) is detected in the secretome of P. ostreatus grown on different lignocellulosic substrates. It is suggested that generation of Mn3+ oxidizers plays a role in the P. ostreatus white-rot lifestyle since three different families of Mn2+-oxidizing peroxidase genes are present in its genome being expressed during lignocellulose degradation.
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Affiliation(s)
- Elena Fernández-Fueyo
- Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, E-28040, Madrid, Spain
| | - Dolores Linde
- Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, E-28040, Madrid, Spain
| | - David Almendral
- Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, E-28040, Madrid, Spain
| | - María F López-Lucendo
- Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, E-28040, Madrid, Spain
| | | | - Angel T Martínez
- Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, E-28040, Madrid, Spain.
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30
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Catalytic surface radical in dye-decolorizing peroxidase: a computational, spectroscopic and site-directed mutagenesis study. Biochem J 2015; 466:253-62. [PMID: 25495127 PMCID: PMC4357238 DOI: 10.1042/bj20141211] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Dye-decolorizing peroxidase (DyP) of Auricularia auricula-judae has been expressed in Escherichia coli as a representative of a new DyP family, and subjected to mutagenic, spectroscopic, crystallographic and computational studies. The crystal structure of DyP shows a buried haem cofactor, and surface tryptophan and tyrosine residues potentially involved in long-range electron transfer from bulky dyes. Simulations using PELE (Protein Energy Landscape Exploration) software provided several binding-energy optima for the anthraquinone-type RB19 (Reactive Blue 19) near the above aromatic residues and the haem access-channel. Subsequent QM/MM (quantum mechanics/molecular mechanics) calculations showed a higher tendency of Trp-377 than other exposed haem-neighbouring residues to harbour a catalytic protein radical, and identified the electron-transfer pathway. The existence of such a radical in H₂O₂-activated DyP was shown by low-temperature EPR, being identified as a mixed tryptophanyl/tyrosyl radical in multifrequency experiments. The signal was dominated by the Trp-377 neutral radical contribution, which disappeared in the W377S variant, and included a tyrosyl contribution assigned to Tyr-337 after analysing the W377S spectra. Kinetics of substrate oxidation by DyP suggests the existence of high- and low-turnover sites. The high-turnover site for oxidation of RB19 (k(cat) > 200 s⁻¹) and other DyP substrates was assigned to Trp-377 since it was absent from the W377S variant. The low-turnover site/s (RB19 k(cat) ~20 s⁻¹) could correspond to the haem access-channel, since activity was decreased when the haem channel was occluded by the G169L mutation. If a tyrosine residue is also involved, it will be different from Tyr-337 since all activities are largely unaffected in the Y337S variant.
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Büttner E, Ullrich R, Strittmatter E, Piontek K, Plattner DA, Hofrichter M, Liers C. Oxidation and nitration of mononitrophenols by a DyP-type peroxidase. Arch Biochem Biophys 2015; 574:86-92. [PMID: 25796533 DOI: 10.1016/j.abb.2015.03.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Revised: 02/23/2015] [Accepted: 03/02/2015] [Indexed: 10/23/2022]
Abstract
Substantial conversion of nitrophenols, typical high-redox potential phenolic substrates, by heme peroxidases has only been reported for lignin peroxidase (LiP) so far. But also a dye-decolorizing peroxidase of Auricularia auricula-judae (AauDyP) was found to be capable of acting on (i) ortho-nitrophenol (oNP), (ii) meta-nitrophenol (mNP) and (iii) para-nitrophenol (pNP). The pH dependency for pNP oxidation showed an optimum at pH 4.5, which is typical for phenol conversion by DyPs and other heme peroxidases. In the case of oNP and pNP conversion, dinitrophenols (2,4-DNP and 2,6-DNP) were identified as products and for pNP additionally p-benzoquinone. Moreover, indications were found for the formation of random polymerization products originating from initially formed phenoxy radical intermediates. Nitration was examined using (15)N-labeled pNP and Na(14)NO2 as an additional source of nitro-groups. Products were identified by HPLC-MS, and mass-to-charge ratios were evaluated to clarify the origin of nitro-groups. The additional nitrogen in DNPs formed during enzymatic conversion was found to originate both from (15)N-pNP and (14)NO2Na. Based on these results, a hypothetical reaction scheme and a catalytically responsible confine of the enzyme's active site are postulated.
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Affiliation(s)
- Enrico Büttner
- TU Dresden, International Institute Zittau, Markt 23, 02763 Zittau, Germany
| | - René Ullrich
- TU Dresden, International Institute Zittau, Markt 23, 02763 Zittau, Germany
| | - Eric Strittmatter
- University of Freiburg, Institute of Organic Chemistry, Albertstrasse 21, 79104 Freiburg, Germany
| | - Klaus Piontek
- University of Freiburg, Institute of Organic Chemistry, Albertstrasse 21, 79104 Freiburg, Germany
| | - Dietmar A Plattner
- University of Freiburg, Institute of Organic Chemistry, Albertstrasse 21, 79104 Freiburg, Germany
| | - Martin Hofrichter
- TU Dresden, International Institute Zittau, Markt 23, 02763 Zittau, Germany
| | - Christiane Liers
- TU Dresden, International Institute Zittau, Markt 23, 02763 Zittau, Germany.
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The multihued palette of dye-decolorizing peroxidases. Arch Biochem Biophys 2015; 574:56-65. [PMID: 25743546 DOI: 10.1016/j.abb.2015.01.014] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Revised: 01/11/2015] [Accepted: 01/16/2015] [Indexed: 12/31/2022]
Abstract
Dye-decolorizing peroxidases (DyPs; EC 1.11.1.19) are heme enzymes that comprise a family of the dimeric α+β barrel structural superfamily of proteins. The first DyP, identified relatively recently in the fungus Bjerkandera adusta, was characterized for its ability to catalyze the decolorization of anthraquinone-based industrial dyes. These enzymes are now known to be present in all three domains of life, but do not appear to occur in plants or animals. They are involved in a range of physiological processes, although in many cases their roles remain unknown. This has not prevented the development of their biocatalytic potential, which includes the transformation of lignin. This review highlights the functional diversity of DyPs in the light of phylogenetic, structural and biochemical data. The phylogenetic analysis reveals the existence of at least five classes of DyPs. Their potential physiological roles are discussed based in part on synteny analyses. Finally, the considerable biotechnological potential of DyPs is summarized.
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A dye-decolorizing peroxidase from Bacillus subtilis exhibiting substrate-dependent optimum temperature for dyes and β-ether lignin dimer. Sci Rep 2015; 5:8245. [PMID: 25650125 PMCID: PMC4316163 DOI: 10.1038/srep08245] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Accepted: 12/19/2014] [Indexed: 11/17/2022] Open
Abstract
In the biorefinery using lignocellulosic biomass as feedstock, pretreatment to breakdown or loosen lignin is important step and various approaches have been conducted. For biological pretreatment, we screened Bacillus subtilis KCTC2023 as a potential lignin-degrading bacterium based on veratryl alcohol (VA) oxidation test and the putative heme-containing dye-decolorizing peroxidase was found in the genome of B. subtilis KCTC2023. The peroxidase from B. subtilis KCTC2023 (BsDyP) was capable of oxidizing various substrates and atypically exhibits substrate-dependent optimum temperature: 30°C for dyes (Reactive Blue19 and Reactive Black5) and 50°C for high redox potential substrates (2,2′-azino-bis(3-ethylbenzothiazoline-6-sulphonic acid [ABTS], VA, and veratryl glycerol-β-guaiacyl ether [VGE]) over +1.0 V vs. normal hydrogen electrode. At 50°C, optimum temperature for high redox potential substrates, BsDyP not only showed the highest VA oxidation activity (0.13 Umg−1) among the previously reported bacterial peroxidases but also successfully achieved VGE decomposition by cleaving Cα-Cβ bond in the absence of any oxidative mediator with a specific activity of 0.086 Umg−1 and a conversion rate of 53.5%. Based on our results, BsDyP was identified as the first bacterial peroxidase capable of oxidizing high redox potential lignin-related model compounds, especially VGE, revealing a previously unknown versatility of lignin degrading biocatalyst in nature.
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Yoshida T, Sugano Y. A structural and functional perspective of DyP-type peroxidase family. Arch Biochem Biophys 2015; 574:49-55. [PMID: 25655348 DOI: 10.1016/j.abb.2015.01.022] [Citation(s) in RCA: 95] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2014] [Revised: 01/23/2015] [Accepted: 01/26/2015] [Indexed: 11/26/2022]
Abstract
Dye-decolorizing peroxidase from the basidiomycete Bjerkandera adusta Dec 1 (DyP) is a heme peroxidase. This name reflects its ability to degrade several anthraquinone dyes. The substrate specificity, the amino acid sequence, and the tertiary structure of DyP are different from those of the other heme peroxidase (super)families. Therefore, many proteins showing the similar amino acid sequences to that of DyP are called DyP-type peroxidase which is a new family of heme peroxidase identified in 2007. In fact, all structures of this family show a similar structure fold. However, this family includes many proteins whose amino acid sequence identity to DyP is lower than 15% and/or whose catalytic efficiency (kcat/Km) is a few orders of magnitude less than that of DyP. A protein showing an activity different from peroxidase activity (dechelatase activity) has been also reported. In addition, the precise physiological roles of DyP-type peroxidases are unknown. These facts raise a question of whether calling this family DyP-type peroxidase is suitable. Here, we review the differences and similarities of structure and function among this family and propose the reasonable new classification of DyP-type peroxidase family, that is, class P, I and V. In this contribution, we discuss the adequacy of this family name.
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Affiliation(s)
- Toru Yoshida
- Department of Bioresource and Environmental Sciences, Faculty of Life Sciences, Kyoto Sangyo University, Kamigamo-Motoyama, Kita-ku, Kyoto 603-8555, Japan
| | - Yasushi Sugano
- Department of Chemical and Biological Sciences, Faculty of Science, Japan Women's University, 2-8-1 Mejirodai, Bunkyo-ku, Tokyo 112-8681, Japan.
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Linde D, Ruiz-Dueñas FJ, Fernández-Fueyo E, Guallar V, Hammel KE, Pogni R, Martínez AT. Basidiomycete DyPs: Genomic diversity, structural-functional aspects, reaction mechanism and environmental significance. Arch Biochem Biophys 2015; 574:66-74. [PMID: 25637654 DOI: 10.1016/j.abb.2015.01.018] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Revised: 01/15/2015] [Accepted: 01/21/2015] [Indexed: 11/26/2022]
Abstract
The first enzyme with dye-decolorizing peroxidase (DyP) activity was described in 1999 from an arthroconidial culture of the fungus Bjerkandera adusta. However, the first DyP sequence had been deposited three years before, as a peroxidase gene from a culture of an unidentified fungus of the family Polyporaceae (probably Irpex lacteus). Since the first description, fewer than ten basidiomycete DyPs have been purified and characterized, but a large number of sequences are available from genomes. DyPs share a general fold and heme location with chlorite dismutases and other DyP-type related proteins (such as Escherichia coli EfeB), forming the CDE superfamily. Taking into account the lack of an evolutionary relationship with the catalase-peroxidase superfamily, the observed heme pocket similarities must be considered as a convergent type of evolution to provide similar reactivity to the enzyme cofactor. Studies on the Auricularia auricula-judae DyP showed that high-turnover oxidation of anthraquinone type and other DyP substrates occurs via long-range electron transfer from an exposed tryptophan (Trp377, conserved in most basidiomycete DyPs), whose catalytic radical was identified in the H2O2-activated enzyme. The existence of accessory oxidation sites in DyP is suggested by the residual activity observed after site-directed mutagenesis of the above tryptophan. DyP degradation of substituted anthraquinone dyes (such as Reactive Blue 5) most probably proceeds via typical one-electron peroxidase oxidations and product breakdown without a DyP-catalyzed hydrolase reaction. Although various DyPs are able to break down phenolic lignin model dimers, and basidiomycete DyPs also present marginal activity on nonphenolic dimers, a significant contribution to lignin degradation is unlikely because of the low activity on high redox-potential substrates.
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Affiliation(s)
- Dolores Linde
- Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, E-28040 Madrid, Spain
| | | | - Elena Fernández-Fueyo
- Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, E-28040 Madrid, Spain
| | - Victor Guallar
- Joint BSC-CRG-IRB Research Program in Computational Biology, Barcelona Supercomputing Center, Jordi Girona 29, E-08034 Barcelona, Spain; ICREA, Passeig Lluís Companys 23, E-08010 Barcelona, Spain
| | - Kenneth E Hammel
- US Forest Products Laboratory, One Gifford Pinchot Drive, Madison, WI 53726, USA
| | - Rebecca Pogni
- Dept. Biotechnologies, Chemistry and Pharmacy, University of Siena, I-53100 Siena, Italy
| | - Angel T Martínez
- Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, E-28040 Madrid, Spain.
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36
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Mendes S, Catarino T, Silveira C, Todorovic S, Martins LO. The catalytic mechanism of A-type dye-decolourising peroxidase BsDyP: neither aspartate nor arginine is individually essential for peroxidase activity. Catal Sci Technol 2015. [DOI: 10.1039/c5cy00478k] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
BsDyP from Bacillus subtilis belongs to the new dye-decolourising peroxidase (DyP) family. Here, we use transient kinetics to provide details on the catalytic cycle of BsDyP.
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Affiliation(s)
- S. Mendes
- Instituto de Tecnologia Química e Biológica António Xavier
- Universidade Nova de Lisboa
- Portugal
| | - T. Catarino
- Instituto de Tecnologia Química e Biológica António Xavier
- Universidade Nova de Lisboa
- Portugal
- Departamento de Química
- Faculdade de Ciências e Tecnologia
| | - C. Silveira
- Instituto de Tecnologia Química e Biológica António Xavier
- Universidade Nova de Lisboa
- Portugal
| | - S. Todorovic
- Instituto de Tecnologia Química e Biológica António Xavier
- Universidade Nova de Lisboa
- Portugal
| | - L. O. Martins
- Instituto de Tecnologia Química e Biológica António Xavier
- Universidade Nova de Lisboa
- Portugal
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Heterologous expression and physicochemical characterization of a fungal dye-decolorizing peroxidase from Auricularia auricula-judae. Protein Expr Purif 2014; 103:28-37. [PMID: 25153532 DOI: 10.1016/j.pep.2014.08.007] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Revised: 08/07/2014] [Accepted: 08/10/2014] [Indexed: 11/21/2022]
Abstract
An efficient heterologous expression system for Auricularia auricula-judae dye-decolorizing peroxidase (DyP) has been constructed. DNA coding for the mature protein sequence was cloned into the pET23a vector and expressed in Escherichia coli BL21(DE3)pLysS. Recombinant DyP was obtained in high yield as inclusion bodies, and different parameters for its in vitro activation were optimized with a refolding yield of ∼8.5% of the E. coli-expressed DyP. Then, a single chromatographic step allowed the recovery of 17% of the refolded DyP as pure enzyme (1.5mg per liter of culture). The thermal stabilities of wild DyP from A. auricula-judae and recombinant DyP from E. coli expression were similar up to 60°C, but the former was more stable in the 62-70°C range. Stabilities against pH and H2O2 were also measured, and a remarkably high stability at extreme pH values (from pH 2 to 12) was observed. The kinetic constants of recombinant DyP for the oxidation of different substrates were determined and, when compared with those of wild DyP, no important differences were ascertained. Both enzymes showed high affinity for Reactive Blue 19 (anthraquinone dye), Reactive Black 5 (azo dye), 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) and 2,6-dimethoxyphenol, with similar acidic pH optima and oxidative stabilities. Oxidation of veratryl alcohol and a nonphenolic lignin model dimer were confirmed, although as minor enzymatic activities. Interestingly, two sets of kinetic constants could be obtained for the oxidation of Reactive Blue 19 and other substrates, suggesting the existence of more than one oxidation site in this new peroxidase family.
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