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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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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3
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Kalkan Ö, Kantamneni S, Brings L, Han H, Bean R, Mancuso AP, Koua FHM. Heterologous expression, purification and structural features of native Dictyostelium discoideum dye-decolorizing peroxidase bound to a natively incorporated heme. Front Chem 2023; 11:1220543. [PMID: 37593106 PMCID: PMC10427876 DOI: 10.3389/fchem.2023.1220543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 07/20/2023] [Indexed: 08/19/2023] Open
Abstract
The Dictyostelium discoideum dye-decolorizing peroxidase (DdDyP) is a newly discovered peroxidase, which belongs to a unique class of heme peroxidase family that lacks homology to the known members of plant peroxidase superfamily. DdDyP catalyzes the H2O2-dependent oxidation of a wide-spectrum of substrates ranging from polycyclic dyes to lignin biomass, holding promise for potential industrial and biotechnological applications. To study the molecular mechanism of DdDyP, highly pure and functional protein with a natively incorporated heme is required, however, obtaining a functional DyP-type peroxidase with a natively bound heme is challenging and often requires addition of expensive biosynthesis precursors. Alternatively, a heme in vitro reconstitution approach followed by a chromatographic purification step to remove the excess heme is often used. Here, we show that expressing the DdDyP peroxidase in ×2 YT enriched medium at low temperature (20°C), without adding heme supplement or biosynthetic precursors, allows for a correct native incorporation of heme into the apo-protein, giving rise to a stable protein with a strong Soret peak at 402 nm. Further, we crystallized and determined the native structure of DdDyP at a resolution of 1.95 Å, which verifies the correct heme binding and its geometry. The structural analysis also reveals a binding of two water molecules at the distal site of heme plane bridging the catalytic residues (Arg239 and Asp149) of the GXXDG motif to the heme-Fe(III) via hydrogen bonds. Our results provide new insights into the geometry of native DdDyP active site and its implication on DyP catalysis.
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Affiliation(s)
- Özlem Kalkan
- European XFEL GmbH, Schenefeld, Schleswig-Holstein, Germany
- Department of Molecular Biology and Genetics, Faculty of Science, Istanbul University, Istanbul, Türkiye
| | | | - Lea Brings
- European XFEL GmbH, Schenefeld, Schleswig-Holstein, Germany
| | - Huijong Han
- European XFEL GmbH, Schenefeld, Schleswig-Holstein, Germany
| | - Richard Bean
- European XFEL GmbH, Schenefeld, Schleswig-Holstein, Germany
| | - Adrian P. Mancuso
- European XFEL GmbH, Schenefeld, Schleswig-Holstein, Germany
- La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, Australia
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, United Kingdom
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4
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Silva D, Rodrigues F, Lorena C, Borges PT, Martins LO. Biocatalysis for biorefineries: The case of dye-decolorizing peroxidases. Biotechnol Adv 2023; 65:108153. [PMID: 37044267 DOI: 10.1016/j.biotechadv.2023.108153] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 04/06/2023] [Accepted: 04/09/2023] [Indexed: 04/14/2023]
Abstract
Dye-decolorizing Peroxidases (DyPs) are heme-containing enzymes in fungi and bacteria that catalyze the reduction of hydrogen peroxide to water with concomitant oxidation of various substrates, including anthraquinone dyes, lignin-related phenolic and non-phenolic compounds, and metal ions. Investigation of DyPs has shed new light on peroxidases, one of the most extensively studied families of oxidoreductases; still, details of their microbial physiological role and catalytic mechanisms remain to be fully disclosed. They display a distinctive ferredoxin-like fold encompassing anti-parallel β-sheets and α-helices, and long conserved loops surround the heme pocket with a role in catalysis and stability. A tunnel routes H2O2 to the heme pocket, whereas binding sites for the reducing substrates are in cavities near the heme or close to distal aromatic residues at the surface. Variations in reactions, the role of catalytic residues, and mechanisms were observed among different classes of DyP. They were hypothetically related to the presence or absence of distal H2O molecules in the heme pocket. The engineering of DyPs for improved properties directed their biotechnological applications, primarily centered on treating textile effluents and degradation of other hazardous pollutants, to fields such as biosensors and valorization of lignin, the most abundant renewable aromatic polymer. In this review, we track recent research contributions that furthered our understanding of the activity, stability, and structural properties of DyPs and their biotechnological applications. Overall, the study of DyP-type peroxidases has significant implications for environmental sustainability and the development of new bio-based products and materials with improved end-of-life options via biodegradation and chemical recyclability, fostering the transition to a sustainable bio-based industry in the circular economy realm.
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Affiliation(s)
- Diogo Silva
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - F Rodrigues
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Constança Lorena
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Patrícia T Borges
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Av. da República, 2780-157 Oeiras, 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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5
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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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6
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Yang L, He W, Yun Y, Gao Y, Zhu Z, Teng M, Liang Z, Niu L. Defining A Global Map of Functional Group-based 3D Ligand-binding Motifs. GENOMICS, PROTEOMICS & BIOINFORMATICS 2022; 20:765-779. [PMID: 35288344 PMCID: PMC9881048 DOI: 10.1016/j.gpb.2021.08.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 06/30/2021] [Accepted: 09/27/2021] [Indexed: 01/31/2023]
Abstract
Uncovering conserved 3D protein-ligand binding patterns on the basis of functional groups (FGs) shared by a variety of small molecules can greatly expand our knowledge of protein-ligand interactions. Despite that conserved binding patterns for a few commonly used FGs have been reported in the literature, large-scale identification and evaluation of FG-based 3D binding motifs are still lacking. Here, we propose a computational method, Automatic FG-based Three-dimensional Motif Extractor (AFTME), for automatic mapping of 3D motifs to different FGs of a specific ligand. Applying our method to 233 naturally-occurring ligands, we define 481 FG-binding motifs that are highly conserved across different ligand-binding pockets. Systematic analysis further reveals four main classes of binding motifs corresponding to distinct sets of FGs. Combinations of FG-binding motifs facilitate the binding of proteins to a wide spectrum of ligands with various binding affinities. Finally, we show that our FG-motif map can be used to nominate FGs that potentially bind to specific drug targets, thus providing useful insights and guidance for rational design of small-molecule drugs.
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Affiliation(s)
- Liu Yang
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China; Division of Molecular and Cellular Biophysics, Hefei National Laboratory for Physical Sciences at the Microscale, Hefei 230026, China
| | - Wei He
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China; Division of Molecular and Cellular Biophysics, Hefei National Laboratory for Physical Sciences at the Microscale, Hefei 230026, China.
| | - Yuehui Yun
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China; Division of Molecular and Cellular Biophysics, Hefei National Laboratory for Physical Sciences at the Microscale, Hefei 230026, China
| | - Yongxiang Gao
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China; Division of Molecular and Cellular Biophysics, Hefei National Laboratory for Physical Sciences at the Microscale, Hefei 230026, China
| | - Zhongliang Zhu
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China; Division of Molecular and Cellular Biophysics, Hefei National Laboratory for Physical Sciences at the Microscale, Hefei 230026, China
| | - Maikun Teng
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China; Division of Molecular and Cellular Biophysics, Hefei National Laboratory for Physical Sciences at the Microscale, Hefei 230026, China
| | - Zhi Liang
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China; Division of Molecular and Cellular Biophysics, Hefei National Laboratory for Physical Sciences at the Microscale, Hefei 230026, China.
| | - Liwen Niu
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China; Division of Molecular and Cellular Biophysics, Hefei National Laboratory for Physical Sciences at the Microscale, Hefei 230026, China.
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7
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Borges PT, Silva D, Silva TF, Brissos V, Cañellas M, Lucas MF, Masgrau L, Melo EP, Machuqueiro M, Frazão C, Martins LO. Unveiling molecular details behind improved activity at neutral to alkaline pH of an engineered DyP-type peroxidase. Comput Struct Biotechnol J 2022; 20:3899-3910. [PMID: 35950185 PMCID: PMC9334217 DOI: 10.1016/j.csbj.2022.07.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 07/18/2022] [Accepted: 07/18/2022] [Indexed: 01/21/2023] Open
Abstract
DyP-type peroxidases (DyPs) are microbial enzymes that catalyze the oxidation of a wide range of substrates, including synthetic dyes, lignin-derived compounds, and metals, such as Mn2+ and Fe2+, and have enormous biotechnological potential in biorefineries. However, many questions on the molecular basis of enzyme function and stability remain unanswered. In this work, high-resolution structures of PpDyP wild-type and two engineered variants (6E10 and 29E4) generated by directed evolution were obtained. The X-ray crystal structures revealed the typical ferredoxin-like folds, with three heme access pathways, two tunnels, and one cavity, limited by three long loops including catalytic residues. Variant 6E10 displays significantly increased loops' flexibility that favors function over stability: despite the considerably higher catalytic efficiency, this variant shows poorer protein stability compared to wild-type and 29E4 variants. Constant-pH MD simulations revealed a more positively charged microenvironment near the heme pocket of variant 6E10, particularly in the neutral to alkaline pH range. This microenvironment affects enzyme activity by modulating the pK a of essential residues in the heme vicinity and should account for variant 6E10 improved activity at pH 7-8 compared to the wild-type and 29E4 that show optimal enzymatic activity close to pH 4. Our findings shed light on the structure-function relationships of DyPs at the molecular level, including their pH-dependent conformational plasticity. These are essential for understanding and engineering the catalytic properties of DyPs for future biotechnological applications.
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Affiliation(s)
- Patrícia T. Borges
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Diogo Silva
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Tomás F.D. Silva
- BioISI – Biosystems & Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Vânia Brissos
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Marina Cañellas
- Zymvol Biomodeling, Carrer Roc Boronat, 117, 08018 Barcelona, Spain
| | | | - Laura Masgrau
- Zymvol Biomodeling, Carrer Roc Boronat, 117, 08018 Barcelona, Spain,Department of Chemistry, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Eduardo P. Melo
- Centro de Ciências do Mar, Universidade do Algarve, 8005-139 Faro, Portugal
| | - Miguel Machuqueiro
- BioISI – Biosystems & Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Carlos Frazão
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Lígia O. Martins
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Av. da República, 2780-157 Oeiras, Portugal,Corresponding author.
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8
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Lučić M, Wilson MT, Svistunenko DA, Owen RL, Hough MA, Worrall JAR. Aspartate or arginine? Validated redox state X-ray structures elucidate mechanistic subtleties of Fe IV = O formation in bacterial dye-decolorizing peroxidases. J Biol Inorg Chem 2021; 26:743-761. [PMID: 34477969 PMCID: PMC8463360 DOI: 10.1007/s00775-021-01896-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 08/23/2021] [Indexed: 11/26/2022]
Abstract
Structure determination of proteins and enzymes by X-ray crystallography remains the most widely used approach to complement functional and mechanistic studies. Capturing the structures of intact redox states in metalloenzymes is critical for assigning the chemistry carried out by the metal in the catalytic cycle. Unfortunately, X-rays interact with protein crystals to generate solvated photoelectrons that can reduce redox active metals and hence change the coordination geometry and the coupled protein structure. Approaches to mitigate such site-specific radiation damage continue to be developed, but nevertheless application of such approaches to metalloenzymes in combination with mechanistic studies are often overlooked. In this review, we summarize our recent structural and kinetic studies on a set of three heme peroxidases found in the bacterium Streptomyces lividans that each belong to the dye decolourizing peroxidase (DyP) superfamily. Kinetically, each of these DyPs has a distinct reactivity with hydrogen peroxide. Through a combination of low dose synchrotron X-ray crystallography and zero dose serial femtosecond X-ray crystallography using an X-ray free electron laser (XFEL), high-resolution structures with unambiguous redox state assignment of the ferric and ferryl (FeIV = O) heme species have been obtained. Experiments using stopped-flow kinetics, solvent-isotope exchange and site-directed mutagenesis with this set of redox state validated DyP structures have provided the first comprehensive kinetic and structural framework for how DyPs can modulate their distal heme pocket Asp/Arg dyad to use either the Asp or the Arg to facilitate proton transfer and rate enhancement of peroxide heterolysis.
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Affiliation(s)
- Marina Lučić
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK
| | - Michael T Wilson
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK
| | - Dimitri A Svistunenko
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK
| | - Robin L Owen
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, OX11 0DE, Oxfordshire, UK
| | - Michael A Hough
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK
| | - Jonathan A R Worrall
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK.
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9
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Dye Decoloring Peroxidase Structure, Catalytic Properties and Applications: Current Advancement and Futurity. Catalysts 2021. [DOI: 10.3390/catal11080955] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Dye decoloring peroxidases (DyPs) were named after their high efficiency to decolorize and degrade a wide range of dyes. DyPs are a type of heme peroxidase and are quite different from known heme peroxidases in terms of amino acid sequences, protein structure, catalytic residues, and physical and chemical properties. DyPs oxidize polycyclic dyes and phenolic compounds. Thus they find high application potentials in dealing with environmental problems. The structure and catalytic characteristics of DyPs of different families from the amino acid sequence, protein structure, and enzymatic properties, and analyzes the high-efficiency degradation ability of some DyPs in dye and lignin degradation, which vary greatly among DyPs classes. In addition, application prospects of DyPs in biomedicine and other fields are also discussed briefly. At the same time, the research strategy based on genetic engineering and synthetic biology in improving the stability and catalytic activity of DyPs are summarized along with the important industrial applications of DyPs and associated challenges. Moreover, according to the current research findings, bringing DyPs to the industrial level may require improving the catalytic efficiency of DyP, increasing production, and enhancing alkali resistance and toxicity.
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10
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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] [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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11
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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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12
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Alsadik A, Athamneh K, Yousef AF, Shah I, Ashraf SS. Efficient Degradation of 2-Mercaptobenzothiazole and Other Emerging Pollutants by Recombinant Bacterial Dye-Decolorizing Peroxidases. Biomolecules 2021; 11:biom11050656. [PMID: 33946934 PMCID: PMC8146892 DOI: 10.3390/biom11050656] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 04/24/2021] [Accepted: 04/25/2021] [Indexed: 01/11/2023] Open
Abstract
In recent years, concerns are being raised about the potential harmful effects of emerging pollutants (EPs) on human and aquatic lives. Extensive research is being conducted on developing efficient remediation strategies to target this new class of toxic pollutants. Studies focused on biological (enzyme-based) methods have shown potential as greener and possibly more economical alternatives to other treatment approaches, such as chemical methods. The current study focused on the use of recombinantly produced novel bacterial peroxidases, namely dye-decolorizing peroxidases (DyPs), to study their effectiveness in degrading a number of diverse EPs. In this context, a sensitive bioanalytical Liquid chromatography-tandem mass spectrometry (LCMSMS)-based method was developed to simultaneously detect a mixture of 31 EPs and to examine their degradability by a panel of seven different recombinant bacterial DyPs (rDyPs). We show that up to 9 of the 31 tested EPs could be degraded by at least one of the DyPs tested. The results also indicated that not all rDyPs behaved similarly in their abilities to degrade EPs, as some rDyPs (such as SviDyP and CboDyP) showed a promising potential to degrade EPs while others (such as ScDyP) were almost ineffective. Additionally, the role of redox mediators for effective emerging pollutant degradation by rDyPs was also examined, which showed dramatic improvement in the DyP-mediated degradation of five different EPs. Detailed analysis of 2-mercaptobenzothiazole degradation by SviDyP showed that six distinct breakdown products were generated. The present study showed for the first time that recombinant bacterial DyPs can be used for wastewater remediation by degrading a range of different EPs.
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Affiliation(s)
- Aya Alsadik
- Department of Chemistry, College of Arts and Sciences, Khalifa University of Science and Technology, Abu Dhabi P.O. Box 127788, United Arab Emirates; (A.A.); (K.A.); (A.F.Y.)
| | - Khawlah Athamneh
- Department of Chemistry, College of Arts and Sciences, Khalifa University of Science and Technology, Abu Dhabi P.O. Box 127788, United Arab Emirates; (A.A.); (K.A.); (A.F.Y.)
| | - Ahmed F. Yousef
- Department of Chemistry, College of Arts and Sciences, Khalifa University of Science and Technology, Abu Dhabi P.O. Box 127788, United Arab Emirates; (A.A.); (K.A.); (A.F.Y.)
- Center for Membranes and Advanced Water Technology (CMAT), Khalifa University of Science and Technology, Abu Dhabi P.O. Box 127788, United Arab Emirates
| | - Iltaf Shah
- Department of Chemistry, College of Sciences, UAE University, Al Ain P.O. Box 15551, United Arab Emirates;
| | - Syed Salman Ashraf
- Department of Chemistry, College of Arts and Sciences, Khalifa University of Science and Technology, Abu Dhabi P.O. Box 127788, United Arab Emirates; (A.A.); (K.A.); (A.F.Y.)
- Center for Biotechnology (BTC), Khalifa University of Science and Technology, Abu Dhabi P.O. Box 127788, United Arab Emirates
- Correspondence: ; Tel.: +971-503126075
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13
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Tang Y, Mu A, Zhang Y, Zhou S, Wang W, Lai Y, Zhou X, Liu F, Yang X, Gong H, Wang Q, Rao Z. Cryo-EM structure of Mycobacterium smegmatis DyP-loaded encapsulin. Proc Natl Acad Sci U S A 2021; 118:e2025658118. [PMID: 33853951 PMCID: PMC8072242 DOI: 10.1073/pnas.2025658118] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Encapsulins containing dye-decolorizing peroxidase (DyP)-type peroxidases are ubiquitous among prokaryotes, protecting cells against oxidative stress. However, little is known about how they interact and function. Here, we have isolated a native cargo-packaging encapsulin from Mycobacterium smegmatis and determined its complete high-resolution structure by cryogenic electron microscopy (cryo-EM). This encapsulin comprises an icosahedral shell and a dodecameric DyP cargo. The dodecameric DyP consists of two hexamers with a twofold axis of symmetry and stretches across the interior of the encapsulin. Our results reveal that the encapsulin shell plays a role in stabilizing the dodecameric DyP. Furthermore, we have proposed a potential mechanism for removing the hydrogen peroxide based on the structural features. Our study also suggests that the DyP is the primary cargo protein of mycobacterial encapsulins and is a potential target for antituberculosis drug discovery.
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Affiliation(s)
- Yanting Tang
- State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, 300353 Tianjin, China
| | - An Mu
- National Laboratory of Biomacromolecules, Chinese Academy of Sciences Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 100101 Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, 100049 Beijing, China
| | - Yuying Zhang
- State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, 300353 Tianjin, China
| | - Shan Zhou
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Nankai University, 300071 Tianjin, China
| | - Weiwei Wang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 201210 Shanghai, China
- School of Life Science and Technology, ShanghaiTech University, 201210 Shanghai, China
| | - Yuezheng Lai
- State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, 300353 Tianjin, China
| | - Xiaoting Zhou
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 201210 Shanghai, China
- School of Life Science and Technology, ShanghaiTech University, 201210 Shanghai, China
| | - Fengjiang Liu
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 201210 Shanghai, China
- School of Life Science and Technology, ShanghaiTech University, 201210 Shanghai, China
| | - Xiuna Yang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 201210 Shanghai, China
- School of Life Science and Technology, ShanghaiTech University, 201210 Shanghai, China
| | - Hongri Gong
- State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, 300353 Tianjin, China;
| | - Quan Wang
- National Laboratory of Biomacromolecules, Chinese Academy of Sciences Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 100101 Beijing, China;
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 201210 Shanghai, China
- School of Life Science and Technology, ShanghaiTech University, 201210 Shanghai, China
| | - Zihe Rao
- State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, 300353 Tianjin, China
- National Laboratory of Biomacromolecules, Chinese Academy of Sciences Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 100101 Beijing, China
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Nankai University, 300071 Tianjin, China
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 201210 Shanghai, China
- School of Life Science and Technology, ShanghaiTech University, 201210 Shanghai, China
- Laboratory of Structural Biology, Tsinghua University, 100084 Beijing, China
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14
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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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15
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Kirykowicz AM, Woodward JD. Shotgun EM of mycobacterial protein complexes during stationary phase stress. Curr Res Struct Biol 2020; 2:204-212. [PMID: 34235480 PMCID: PMC8244302 DOI: 10.1016/j.crstbi.2020.09.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Revised: 09/08/2020] [Accepted: 09/11/2020] [Indexed: 10/27/2022] Open
Abstract
There is little structural information about the protein complexes conferring resistance in Mycobacterium tuberculosis (Mtb) to anti-microbial oxygen and nitrogen radicals in the phagolysosome. Here, we expose the model Mycobacterium, Mycobacterium smegmatis, to simulated oxidative-stress conditions and apply a shotgun EM method for the structural detection of the resulting protein assemblies. We identified: glutamine synthetase I, essential for Mtb virulence; bacterioferritin A, critical for Mtb iron regulation; aspartyl aminopeptidase M18, a protease; and encapsulin, which produces a cage-like structure to enclose cargo proteins. After further investigation, we found that encapsulin carries dye-decolourising peroxidase, a protein antioxidant, as its primary cargo under the conditions tested.
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Affiliation(s)
- Angela M. Kirykowicz
- Department of Biochemistry, University of Cambridge, Sanger Building, Tennis Court Road, Cambridge, CB2 1GA, UK
- Division of Medical Biochemistry and Structural Biology, Department of Integrative Biomedical Sciences, University of Cape Town, Anzio Road, Observatory, 7925, Cape Town, South Africa
| | - Jeremy D. Woodward
- Division of Medical Biochemistry and Structural Biology, Department of Integrative Biomedical Sciences, University of Cape Town, Anzio Road, Observatory, 7925, Cape Town, South Africa
- Structural Biology Research Unit, University of Cape Town, South Africa
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16
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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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17
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Understanding molecular enzymology of porphyrin-binding α + β barrel proteins - One fold, multiple functions. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2020; 1869:140536. [PMID: 32891739 PMCID: PMC7611857 DOI: 10.1016/j.bbapap.2020.140536] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 08/26/2020] [Accepted: 09/02/2020] [Indexed: 11/24/2022]
Abstract
There is a high functional diversity within the structural superfamily of porphyrin-binding dimeric α + β barrel proteins. In this review we aim to analyze structural constraints of chlorite dismutases, dye-decolorizing peroxidases and coproheme decarboxylases in detail. We identify regions of structural variations within the highly conserved fold, which are most likely crucial for functional specificities. The loop linking the two ferredoxin-like domains within one subunit can be of different sequence lengths and can adopt various structural conformations, consequently defining the shape of the substrate channels and the respective active site architectures. The redox cofactor, heme b or coproheme, is oriented differently in either of the analyzed enzymes. By thoroughly dissecting available structures and discussing all available results in the context of the respective functional mechanisms of each of these redox-active enzymes, we highlight unsolved mechanistic questions in order to spark future research in this field.
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18
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Silveira CM, Moe E, Fraaije M, Martins LO, Todorovic S. Resonance Raman view of the active site architecture in bacterial DyP-type peroxidases. RSC Adv 2020; 10:11095-11104. [PMID: 35495352 PMCID: PMC9050505 DOI: 10.1039/d0ra00950d] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 03/11/2020] [Indexed: 11/21/2022] Open
Abstract
Dye decolorizing peroxidases (DyPs) are novel haem-containing peroxidases, which are structurally unrelated to classical peroxidases. They lack the highly conserved distal histidine that acts as an acid-base catalyst in the catalytic reaction of classical peroxidases, which implies distinct mechanistic properties. Despite the remarkable catalytic properties and recognized potential for biotechnology applications, the knowledge of DyP's structural features in solution, which govern the reactivity and catalysis, is lagging behind. Resonance Raman (RR) spectroscopy can reveal fine details of the active site structure in hemoproteins, reporting on the oxidation and spin state and coordination of the haem cofactor. We provide an overview of the haem binding pocket architecture of the enzymes from A, B and C DyP subfamilies, in the light of those established for classical peroxidases and search for subfamily specific features among DyPs. RR demonstrates that multiple spin populations typically co-exist in DyPs, like in the case of classical peroxidases. The haem spin/coordination state is strongly pH dependent and correlates well with the respective catalytic properties of DyPs. Unlike in the case of classical peroxidases, a surprisingly high abundance of catalytically incompetent low spin population is observed in several DyPs, and tentatively related to the alternative physiological function of these enzymes. The molecular details of active sites of DyPs, elucidated by RR spectroscopy, can furthermore guide approaches for biotechnological exploitation of these promising biocatalysts.
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Affiliation(s)
- Célia M Silveira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa Av. da República 2780-157 Oeiras Portugal
| | - Elin Moe
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa Av. da República 2780-157 Oeiras Portugal
| | - Marco Fraaije
- Molecular Enzymology, University of Groningen Nijenborgh 4 9747AG Groningen The Netherlands
| | - Lígia O Martins
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa Av. da República 2780-157 Oeiras Portugal
| | - Smilja Todorovic
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa Av. da República 2780-157 Oeiras Portugal
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19
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Chauhan PS. Role of various bacterial enzymes in complete depolymerization of lignin: A review. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2020. [DOI: 10.1016/j.bcab.2020.101498] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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20
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Chan JC, Paice M, Zhang X. Enzymatic Oxidation of Lignin: Challenges and Barriers Toward Practical Applications. ChemCatChem 2019. [DOI: 10.1002/cctc.201901480] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Jou C. Chan
- Voiland School of Chemical Engineering and Bioengineering Washington State University 2710 Crimson Way Richland WA-99354 USA
| | - Michael Paice
- FPInnovations Pulp Paper & Bioproducts 2665 East Mall Vancouver BC V6T 1Z4 Canada
| | - Xiao Zhang
- Voiland School of Chemical Engineering and Bioengineering Washington State University 2710 Crimson Way Richland WA-99354 USA
- Pacific Northwest National Laboratory 520 Battelle Boulevard P.O. Box 999, MSIN P8-60 Richland WA-99352 USA
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21
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Pernil R, Schleiff E. Metalloproteins in the Biology of Heterocysts. Life (Basel) 2019; 9:E32. [PMID: 30987221 PMCID: PMC6616624 DOI: 10.3390/life9020032] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 03/18/2019] [Accepted: 03/28/2019] [Indexed: 12/15/2022] Open
Abstract
Cyanobacteria are photoautotrophic microorganisms present in almost all ecologically niches on Earth. They exist as single-cell or filamentous forms and the latter often contain specialized cells for N₂ fixation known as heterocysts. Heterocysts arise from photosynthetic active vegetative cells by multiple morphological and physiological rearrangements including the absence of O₂ evolution and CO₂ fixation. The key function of this cell type is carried out by the metalloprotein complex known as nitrogenase. Additionally, many other important processes in heterocysts also depend on metalloproteins. This leads to a high metal demand exceeding the one of other bacteria in content and concentration during heterocyst development and in mature heterocysts. This review provides an overview on the current knowledge of the transition metals and metalloproteins required by heterocysts in heterocyst-forming cyanobacteria. It discusses the molecular, physiological, and physicochemical properties of metalloproteins involved in N₂ fixation, H₂ metabolism, electron transport chains, oxidative stress management, storage, energy metabolism, and metabolic networks in the diazotrophic filament. This provides a detailed and comprehensive picture on the heterocyst demands for Fe, Cu, Mo, Ni, Mn, V, and Zn as cofactors for metalloproteins and highlights the importance of such metalloproteins for the biology of cyanobacterial heterocysts.
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Affiliation(s)
- Rafael Pernil
- Institute for Molecular Biosciences, Goethe University Frankfurt, Max-von-Laue-Straβe 9, 60438 Frankfurt am Main, Germany.
| | - Enrico Schleiff
- Institute for Molecular Biosciences, Goethe University Frankfurt, Max-von-Laue-Straβe 9, 60438 Frankfurt am Main, Germany.
- Frankfurt Institute for Advanced Studies, Ruth-Moufang-Straße 1, 60438 Frankfurt am Main, Germany.
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue-Straβe 15, 60438 Frankfurt am Main, Germany.
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22
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Yang C, Yue F, Cui Y, Xu Y, Shan Y, Liu B, Zhou Y, Lü X. Biodegradation of lignin by Pseudomonas sp. Q18 and the characterization of a novel bacterial DyP-type peroxidase. J Ind Microbiol Biotechnol 2018; 45:913-927. [PMID: 30051274 DOI: 10.1007/s10295-018-2064-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Accepted: 07/23/2018] [Indexed: 11/25/2022]
Abstract
Lignin valorization can be obtained through cleavage of selected bonds by microbial enzymes, in which lignin is segregated from cellulose and hemicellulose and abundant phenolic compounds can be provided. In this study, Pseudomonas sp. Q18, previously isolated from rotten wood in China, was used to degrade alkali lignin and raw lignocellulosic material. Gel-permeation chromatography, field-emission scanning electron microscope, and GC-MS were combined to investigate the degradation process. The GC-MS results revealed that the quantities of aromatic compounds with phenol ring from lignin increased significantly after incubation with Pseudomonas sp. Q18, which indicated the degradation of lignin. According to the lignin-derived metabolite analysis, it was proposed that a DyP-type peroxidase (PmDyP) might exist in strain Q18. Thereafter, the gene of PmDyP was cloned and expressed, after which the recombinant PmDyP was purified and the enzymatic kinetics of PmDyP were assayed. According to results, PmDyP showed promising characteristics for lignocellulosic biodegradation in biorefinery.
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Affiliation(s)
- Chenxian Yang
- College of Food Science and Engineering, Northwest A&F University, Yangling District, Xianyang, 712100, Shaanxi Province, China
| | - Fangfang Yue
- College of Food Science and Engineering, Northwest A&F University, Yangling District, Xianyang, 712100, Shaanxi Province, China
| | - Yanlong Cui
- College of Food Science and Engineering, Northwest A&F University, Yangling District, Xianyang, 712100, Shaanxi Province, China
| | - Yuanmei Xu
- College of Food Science and Engineering, Northwest A&F University, Yangling District, Xianyang, 712100, Shaanxi Province, China
| | - Yuanyuan Shan
- College of Food Science and Engineering, Northwest A&F University, Yangling District, Xianyang, 712100, Shaanxi Province, China
| | - Bianfang Liu
- College of Food Science and Engineering, Northwest A&F University, Yangling District, Xianyang, 712100, Shaanxi Province, China
| | - Yuan Zhou
- College of Food Science and Engineering, Northwest A&F University, Yangling District, Xianyang, 712100, Shaanxi Province, China
| | - Xin Lü
- College of Food Science and Engineering, Northwest A&F University, Yangling District, Xianyang, 712100, Shaanxi Province, China.
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23
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Nichols RJ, Cassidy-Amstutz C, Chaijarasphong T, Savage DF. Encapsulins: molecular biology of the shell. Crit Rev Biochem Mol Biol 2017. [DOI: 10.1080/10409238.2017.1337709] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Robert J. Nichols
- Department of Molecular and Cell Biology, UC Berkeley, Berkeley, CA, USA
| | | | | | - David F. Savage
- Department of Molecular and Cell Biology, UC Berkeley, Berkeley, CA, USA
- Department of Chemistry, UC Berkeley, Berkeley, CA, USA
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Liu X, Yuan Z, Wang J, Cui Y, Liu S, Ma Y, Gu L, Xu S. Crystal structure and biochemical features of dye-decolorizing peroxidase YfeX from Escherichia coli O157 Asp 143 and Arg 232 play divergent roles toward different substrates. Biochem Biophys Res Commun 2017; 484:40-44. [PMID: 28109884 DOI: 10.1016/j.bbrc.2017.01.081] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2017] [Accepted: 01/17/2017] [Indexed: 01/06/2023]
Abstract
YfeX from Escherichia coli O157 is a bacterial dye-decolorizing peroxidase that represents both dye-decoloring activity and typical peroxidase activity. We reported the crystal structure of YfeX bound to heme at 2.09 Å resolution. The YfeX monomer resembles a ferredoxin-like fold and contains two domains. The three conserved residues surrounding the heme group are His215, Asp143 and Arg232. His215 functions as the proximal axial ligand of the heme iron atom. Biochemical data show that the catalytic significance of the conserved Asp143 and Arg232 depends on the substrate types and that YfeX may adopt various catalytic mechanisms toward divergent substrates. In addition, it is observed that an access tunnel spans from the protein molecular surface to the heme distal region, it serves as the passageway for the entrance and binding of the H2O2.
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Affiliation(s)
- Xiuhua Liu
- College of Life Sciences, Hebei University, Baoding, 071002, China.
| | - Zenglin Yuan
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, 250100, China
| | - Jiaxu Wang
- College of Life Sciences, Hebei University, Baoding, 071002, China
| | - Yaqi Cui
- College of Life Sciences, Hebei University, Baoding, 071002, China
| | - Shuang Liu
- College of Life Sciences, Hebei University, Baoding, 071002, China
| | - Yinliang Ma
- College of Life Sciences, Hebei University, Baoding, 071002, China
| | - Lichuan Gu
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, 250100, China
| | - Sujuan Xu
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, 250100, China.
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25
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Acharya G, Kaur G, Subramanian S. Evolutionary relationships between heme-binding ferredoxin α + β barrels. BMC Bioinformatics 2016; 17:168. [PMID: 27089923 PMCID: PMC4835899 DOI: 10.1186/s12859-016-1033-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Accepted: 04/12/2016] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND The α + β barrel superfamily of the ferredoxin-like fold consists of a functionally diverse group of evolutionarily related proteins. The barrel architecture of these proteins is formed by either homo-/hetero-dimerization or duplication and fusion of ferredoxin-like domains. Several members of this superfamily bind heme in order to carry out their functions. RESULTS We analyze the heme-binding sites in these proteins as well as their barrel topologies. Our comparative structural analysis of these heme-binding barrels reveals two distinct modes of packing of the ferredoxin-like domains to constitute the α + β barrel, which is typified by the Type-1/IsdG-like and Type-2/OxdA-like proteins, respectively. We examine the heme-binding pockets and explore the versatility of the α + β barrels ability to accommodate heme or heme-related moieties, such as siroheme, in at least three different sites, namely, the mode seen in IsdG/OxdA, Cld/DyP/EfeB/HemQ and siroheme decarboxylase barrels. CONCLUSIONS Our study offers insights into the plausible evolutionary relationships between the two distinct barrel packing topologies and relate the observed heme-binding sites to these topologies.
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Affiliation(s)
- Giriraj Acharya
- CSIR-Institute of Microbial Technology (IMTECH), Sector 39-A, Chandigarh, India
| | - Gurmeet Kaur
- CSIR-Institute of Microbial Technology (IMTECH), Sector 39-A, Chandigarh, India
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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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27
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Uchida T, Sasaki M, Tanaka Y, Ishimori K. A Dye-Decolorizing Peroxidase from Vibrio cholerae. Biochemistry 2015; 54:6610-21. [PMID: 26431465 DOI: 10.1021/acs.biochem.5b00952] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The dye-decolorizing peroxidase (DyP) protein from Vibrio cholerae (VcDyP) was expressed in Escherichia coli, and its DyP activity was assayed by monitoring degradation of a typical anthraquinone dye, reactive blue 19 (RB19). Its kinetic activity was obtained by fitting the data to the Michaelis-Menten equation, giving kcat and Km values of 1.3 ± 0.3 s(-1) and 50 ± 20 μM, respectively, which are comparable to those of other DyP enzymes. The enzymatic activity of VcDyP was highest at pH 4. A mutational study showed that two distal residues, Asp144 and Arg230, which are conserved in a DyP family, are essential for the DyP reaction. The crystal structure and resonance Raman spectra of VcDyP indicate the transfer of a radical from heme to the protein surface, which was supported by the formation of the intermolecular covalent bond in the reaction with H2O2. To identify the radical site, each of nine tyrosine or two tryptophan residues was substituted. It was clarified that Tyr129 and Tyr235 are in the active site of the dye degradation reaction at lower pH, while Tyr109 and Tyr133 are the sites of an intermolecular covalent bond at higher pH. VcDyP degrades RB19 at lower pH, while it loses activity under neutral or alkaline conditions because of a change in the radical transfer pathway. This finding suggests the presence of a pH-dependent switch of the radical transfer pathway, probably including His178. Although the physiological function of the DyP reaction is unclear, our findings suggest that VcDyP enhances the DyP activity to survive only when it is placed under a severe condition such as being in gastric acid.
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Affiliation(s)
- Takeshi Uchida
- Department of Chemistry, Faculty of Science, Hokkaido University , Sapporo 060-0810, Japan.,Graduate School of Chemical Sciences and Engineering, Hokkaido University , Sapporo 060-0810, Japan
| | - Miho Sasaki
- Graduate School of Chemical Sciences and Engineering, Hokkaido University , Sapporo 060-0810, Japan
| | - Yoshikazu Tanaka
- Faculty of Advanced Life Science, Hokkaido University , Sapporo 060-0808, Japan
| | - Koichiro Ishimori
- Department of Chemistry, Faculty of Science, Hokkaido University , Sapporo 060-0810, Japan.,Graduate School of Chemical Sciences and Engineering, Hokkaido University , Sapporo 060-0810, Japan
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28
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Ramzi AB, Hyeon JE, Han SO. Improved catalytic activities of a dye-decolorizing peroxidase (DyP) by overexpression of ALA and heme biosynthesis genes in Escherichia coli. Process Biochem 2015. [DOI: 10.1016/j.procbio.2015.05.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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29
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Ebihara A, Manzoku M, Fukui K, Shimada A, Morita R, Masui R, Kuramitsu S. Roles of Mn-catalase and a possible heme peroxidase homologue in protection from oxidative stress in Thermus thermophilus. Extremophiles 2015; 19:775-85. [PMID: 25997395 DOI: 10.1007/s00792-015-0753-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Accepted: 04/26/2015] [Indexed: 10/23/2022]
Abstract
Hydrogen peroxide (H2O2) produces hydroxyl radicals that directly attack a variety of biomolecules and cause severe cellular dysfunction. An extremely thermophilic bacterium, Thermus thermophilus HB8, possesses at least three enzymes that can scavenge H2O2: manganese-containing catalase (TTHA0122, MnCAT), a possible peroxiredoxin homologue (TTHA1300), and a possible heme peroxidase (HPX) homologue (TTHA1714). To investigate the roles of these proteins, we attempted to disrupt each of these genes in T. thermophilus HB8. Although we were able to completely disrupt ttha1300, we were unable to completely delete ttha0122 and ttha1714 because of polyploidy. Quantitative real-time PCR showed that, compared to the wild type, 31 % of ttha0122 and 11 % of ttha1714 remained in the ∆ttha0122 and ∆ttha1714 disruption mutants, respectively. Mutants with reduced levels of ttha0122 or ttha1714 exhibited a significant increase in spontaneous mutation frequency. ∆ttha1714 grew slower than the wild type under normal conditions. ∆ttha0122 grew very poorly after exposure to H2O2. Moreover, ∆ttha0122 did not show H2O2-scavenging activity, whereas ∆ttha1300 and ∆ttha1714 scavenged H2O2, a property similar to that exhibited by the wild type. MnCAT purified from T. thermophilus HB8 cells scavenged H2O2 in vitro. The recombinant form of the possible HPX homologue, reconstituted with hemin, showed peroxidase activity with H2O2 as an oxidant substrate. Based on these results, we propose that not only MnCAT but also the possible HPX homologue is involved in protecting the cell from oxidative stress in T. thermophilus.
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Affiliation(s)
- Akio Ebihara
- Faculty of Applied Biological Sciences, Gifu University, 1-1 Yanagido, Gifu, 501-1193, Japan,
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30
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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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31
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Hofbauer S, Hagmüller A, Schaffner I, Mlynek G, Krutzler M, Stadlmayr G, Pirker KF, Obinger C, Daims H, Djinović-Carugo K, Furtmüller PG. Structure and heme-binding properties of HemQ (chlorite dismutase-like protein) from Listeria monocytogenes. Arch Biochem Biophys 2015; 574:36-48. [PMID: 25602700 PMCID: PMC4420033 DOI: 10.1016/j.abb.2015.01.010] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Revised: 01/07/2015] [Accepted: 01/09/2015] [Indexed: 11/17/2022]
Abstract
Chlorite dismutase-like proteins are structurally closely related to functional chlorite dismutases which are heme b-dependent oxidoreductases capable of reducing chlorite to chloride with simultaneous production of dioxygen. Chlorite dismutase-like proteins are incapable of performing this reaction and their biological role is still under discussion. Recently, members of this large protein family were shown to be involved in heme biosynthesis in Gram-positive bacteria, and thus the protein was renamed HemQ in these organisms. In the present work the structural and heme binding properties of the chlorite dismutase-like protein from the Gram-positive pathogen Listeria monocytogenes (LmCld) were analyzed in order to evaluate its potential role as a regulatory heme sensing protein. The homopentameric crystal structure (2.0Å) shows high similarity to chlorite-degrading chlorite dismutases with an important difference in the structure of the putative substrate and heme entrance channel. In solution LmCld is a stable hexamer able to bind the low-spin ligand cyanide. Heme binding is reversible with KD-values determined to be 7.2μM (circular dichroism spectroscopy) and 16.8μM (isothermal titration calorimetry) at pH 7.0. Both acidic and alkaline conditions promote heme release. Presented biochemical and structural data reveal that the chlorite dismutase-like protein from L. monocytogenes could act as a potential regulatory heme sensing and storage protein within heme biosynthesis.
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Affiliation(s)
- Stefan Hofbauer
- Department of Chemistry, Division of Biochemistry, BOKU - University of Natural Resources and Life Sciences, Muthgasse 18, A-1190 Vienna, Austria; Department for Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, A-1030 Vienna, Austria
| | - Andreas Hagmüller
- Department for Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, A-1030 Vienna, Austria
| | - Irene Schaffner
- Department of Chemistry, Division of Biochemistry, BOKU - University of Natural Resources and Life Sciences, Muthgasse 18, A-1190 Vienna, Austria
| | - Georg Mlynek
- Department for Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, A-1030 Vienna, Austria
| | - Michael Krutzler
- Department of Chemistry, Division of Biochemistry, BOKU - University of Natural Resources and Life Sciences, Muthgasse 18, A-1190 Vienna, Austria; Department for Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, A-1030 Vienna, Austria
| | - Gerhard Stadlmayr
- Department of Chemistry, Division of Biochemistry, BOKU - University of Natural Resources and Life Sciences, Muthgasse 18, A-1190 Vienna, Austria
| | - Katharina F Pirker
- Department of Chemistry, Division of Biochemistry, BOKU - University of Natural Resources and Life Sciences, Muthgasse 18, A-1190 Vienna, Austria
| | - Christian Obinger
- Department of Chemistry, Division of Biochemistry, BOKU - University of Natural Resources and Life Sciences, Muthgasse 18, A-1190 Vienna, Austria
| | - Holger Daims
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, A-1090 Vienna, Austria
| | - Kristina Djinović-Carugo
- Department for Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, A-1030 Vienna, Austria; Department of Biochemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, 1000 Ljubljana, Slovenia.
| | - Paul G Furtmüller
- Department of Chemistry, Division of Biochemistry, BOKU - University of Natural Resources and Life Sciences, Muthgasse 18, A-1190 Vienna, Austria.
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32
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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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33
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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: 62] [Impact Index Per Article: 6.9] [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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34
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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: 94] [Impact Index Per Article: 10.4] [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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35
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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: 60] [Impact Index Per Article: 6.7] [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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Characterisation of Dyp-type peroxidases from Pseudomonas fluorescens Pf-5: Oxidation of Mn(II) and polymeric lignin by Dyp1B. Arch Biochem Biophys 2015; 574:93-8. [PMID: 25558792 DOI: 10.1016/j.abb.2014.12.022] [Citation(s) in RCA: 95] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Revised: 12/19/2014] [Accepted: 12/22/2014] [Indexed: 11/24/2022]
Abstract
Members of the DyP family of peroxidases in Gram-positive bacteria have recently been shown to oxidise Mn(II) and lignin model compounds. Gram-negative pseudomonads, which also show activity for lignin oxidation, also contain dyp-type peroxidase genes. Pseudomonas fluorescens Pf-5 contains three dyp-type peroxidases (35, 40 and 55kDa), each of which has been overexpressed in Escherichia coli, purified, and characterised. Each of the three enzymes shows activity for oxidation of phenol substrates, but the 35kDa Dyp1B enzyme also shows activity for oxidation of Mn(II) and Kraft lignin. Treatment of powdered lignocellulose with Dyp1B in the presence of Mn(II) and hydrogen peroxide leads to the release of a low molecular weight lignin fragment, which has been identified by mass spectrometry as a β-aryl ether lignin dimer containing one G unit and one H unit bearing a benzylic ketone. A mechanism for release of this fragment from lignin oxidation is proposed.
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37
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Lee S, J. Mitchell R. Perspectives on the use of transcriptomics to advance biofuels. AIMS BIOENGINEERING 2015. [DOI: 10.3934/bioeng.2015.4.487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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38
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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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39
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Yu W, Liu W, Huang H, Zheng F, Wang X, Wu Y, Li K, Xie X, Jin Y. Application of a novel alkali-tolerant thermostable DyP-type peroxidase from Saccharomonospora viridis DSM 43017 in biobleaching of eucalyptus kraft pulp. PLoS One 2014; 9:e110319. [PMID: 25333297 PMCID: PMC4204856 DOI: 10.1371/journal.pone.0110319] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Accepted: 09/12/2014] [Indexed: 11/19/2022] Open
Abstract
Saccharomonospora viridis is a thermophilic actinomycete that may have biotechnological applications because of its dye decolorizing activity, though the enzymatic oxidative system responsible for this activity remains elusive. Bioinformatic analysis revealed a DyP-type peroxidase gene in the genome of S. viridis DSM 43017 with sequence similarity to peroxidase from dye-decolorizing microbes. This gene, svidyp, consists of 1,215 bp encoding a polypeptide of 404 amino acids. The gene encoding SviDyP was cloned, heterologously expressed in Escherichia coli, and then purified. The recombinant protein could efficiently decolorize several triarylmethane dyes, anthraquinonic and azo dyes under neutral to alkaline conditions. The optimum pH and temperature for SviDyP was pH 7.0 and 70°C, respectively. Compared with other DyP-type peroxidases, SviDyP was more active at high temperatures, retaining>63% of its maximum activity at 50-80°C. It also showed broad pH adaptability (>35% activity at pH 4.0-9.0) and alkali-tolerance (>80% activity after incubation at pH 5-10 for 1 h at 37°C), and was highly thermostable (>60% activity after incubation at 70°C for 2 h at pH 7.0). SviDyP had an accelerated action during the biobleaching of eucalyptus kraft pulp, resulting in a 21.8% reduction in kappa number and an increase of 2.98% (ISO) in brightness. These favorable properties make SviDyP peroxidase a promising enzyme for use in the pulp and paper industries.
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Affiliation(s)
- Wangning Yu
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, PR China
| | - Weina Liu
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, PR China
| | - Huoqing Huang
- Feed Research Institute Chinese Academy of Agricultural Sciences, Beijing, PR China
| | - Fei Zheng
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, PR China
| | - Xiaoyu Wang
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, PR China
| | - Yuying Wu
- College of Materials Science and Technology, Beijing Forestry University, Beijing, PR China
| | - Kangjia Li
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, PR China
| | - Xiangming Xie
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, PR China
| | - Yi Jin
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, PR China
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40
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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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41
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Rai A, Fedorov R, Manstein DJ. Expression, purification and crystallization of a dye-decolourizing peroxidase from Dictyostelium discoideum. Acta Crystallogr F Struct Biol Commun 2014; 70:252-5. [PMID: 24637768 PMCID: PMC3936452 DOI: 10.1107/s2053230x14000545] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2013] [Accepted: 01/09/2014] [Indexed: 11/10/2022] Open
Abstract
Dye-decolourizing peroxidases are haem-containing peroxidases with broad substrate specificity. Using H2O2 as an electron acceptor, they efficiently decolourize various dyes that are of industrial and environmental relevance, such as anthraquninone- and azo-based dyes. In this study, the dye-decolourizing peroxidase DdDyP from Dictyostelium discoideum was overexpressed in Escherichia coli strain Rosetta(DE3)pLysS, purified and crystallized using the vapour-diffusion method. A native crystal diffracted to 1.65 Å resolution and belonged to space group P4(1)2(1)2, with unit-cell parameters a = b = 141.03, c = 95.56 Å, α = β = γ = 90°. The asymmetric unit contains two molecules.
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Affiliation(s)
- Amrita Rai
- Institute for Biophysical Chemistry, Medizinische Hochschule Hannover, Carl-Neuberg-Strasse 1, 30625 Hannover, Germany
| | - Roman Fedorov
- Institute for Biophysical Chemistry, Medizinische Hochschule Hannover, Carl-Neuberg-Strasse 1, 30625 Hannover, Germany
| | - Dietmar J. Manstein
- Institute for Biophysical Chemistry, Medizinische Hochschule Hannover, Carl-Neuberg-Strasse 1, 30625 Hannover, Germany
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42
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Colpa DI, Fraaije MW, van Bloois E. DyP-type peroxidases: a promising and versatile class of enzymes. ACTA ACUST UNITED AC 2014; 41:1-7. [DOI: 10.1007/s10295-013-1371-6] [Citation(s) in RCA: 102] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2013] [Accepted: 10/17/2013] [Indexed: 10/26/2022]
Abstract
Abstract
DyP peroxidases comprise a novel superfamily of heme-containing peroxidases, which is unrelated to the superfamilies of plant and animal peroxidases. These enzymes have so far been identified in the genomes of fungi, bacteria, as well as archaea, although their physiological function is still unclear. DyPs are bifunctional enzymes displaying not only oxidative activity but also hydrolytic activity. Moreover, these enzymes are able to oxidize a variety of organic compounds of which some are poorly converted by established peroxidases, including dyes, β-carotene, and aromatic sulfides. Interestingly, accumulating evidence shows that microbial DyP peroxidases play a key role in the degradation of lignin. Owing to their unique properties, these enzymes are potentially interesting for a variety of biocatalytic applications. In this review, we deal with the biochemical and structural features of DyP-type peroxidases as well as their promising biotechnological potential.
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Affiliation(s)
- Dana I Colpa
- grid.4830.f 0000000404071981 Laboratory of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute University of Groningen Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Marco W Fraaije
- grid.4830.f 0000000404071981 Laboratory of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute University of Groningen Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Edwin van Bloois
- grid.4830.f 0000000404071981 Laboratory of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute University of Groningen Nijenborgh 4 9747 AG Groningen The Netherlands
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43
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Radical formation on a conserved tyrosine residue is crucial for DyP activity. Arch Biochem Biophys 2013; 537:161-7. [PMID: 23876237 DOI: 10.1016/j.abb.2013.07.007] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2013] [Revised: 06/08/2013] [Accepted: 07/05/2013] [Indexed: 11/23/2022]
Abstract
Dye-decolorizing peroxidases (DyPs) are able to cleave bulky anthraquinone dyes. The recently published crystal structure of AauDyPI reveals that a direct oxidation in the distal heme cavity can be excluded for most DyP substrates. It is shown that a surface-exposed tyrosine residue acts as a substrate interaction site for bulky substrates. This amino acid is conserved in eucaryotic DyPs but is missing in the structurally related chlorite dismutases (Clds). Dye-decolorizing peroxidases of procaryotic origin equally possess a conserved tyrosine in the same region of the polypeptide albeit not at the homologous position.
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44
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New dye-decolorizing peroxidases from Bacillus subtilis and Pseudomonas putida MET94: towards biotechnological applications. Appl Microbiol Biotechnol 2013; 98:2053-65. [DOI: 10.1007/s00253-013-5041-4] [Citation(s) in RCA: 105] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2013] [Revised: 06/04/2013] [Accepted: 06/07/2013] [Indexed: 11/27/2022]
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45
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Sezer M, Santos A, Kielb P, Pinto T, Martins LO, Todorovic S. Distinct structural and redox properties of the heme active site in bacterial dye decolorizing peroxidase-type peroxidases from two subfamilies: resonance Raman and electrochemical study. Biochemistry 2013; 52:3074-84. [PMID: 23560556 DOI: 10.1021/bi301630a] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Spectroscopic data of dye decolorizing peroxidases (DyPs) from Bacillus subtilis (BsDyP), an A subfamily member, and Pseudomonas putida (PpDyP), a B subfamily enzyme, reveal distinct heme coordination patterns of the respective active sites. In solution, both enzymes show a heterogeneous spin population, with the six-coordinated low-spin state being the most populated in the former and the five-coordinated quantum mechanically mixed-spin state in the latter. We ascribe the poor catalytic activity of BsDyP to the presence of a catalytically incompetent six-coordinated low-spin population. The spin populations of the two DyPs are sensitively dependent on the pH, temperature, and physical, i.e., solution versus crystal versus immobilized, state of the enzymes. We observe a redox potential for the Fe(2+)/Fe(3+) couple in BsDyP (-40 mV) at pH 7.6 substantially more positive than those reported for the majority of other peroxidases, including PpDyP (-260 mV). Furthermore, we evaluate the potential of the studied enzymes for biotechnological applications on the basis of electrochemical and spectroelectrochemical data.
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Affiliation(s)
- Murat Sezer
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da Republica, 2780-157 Oeiras, Portugal
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46
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Brown ME, Barros T, Chang MCY. Identification and characterization of a multifunctional dye peroxidase from a lignin-reactive bacterium. ACS Chem Biol 2012; 7:2074-81. [PMID: 23054399 DOI: 10.1021/cb300383y] [Citation(s) in RCA: 143] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Plant biomass represents a renewable feedstock that has not yet been fully tapped because of the difficulty in accessing the carbon in its structural biopolymers. Lignin is an especially challenging substrate, but select microbes have evolved complex systems of enzymes for its breakdown through a radical-mediated oxidation process. Fungal systems are well-characterized for their ability to depolymerize lignin, but the ability of bacteria to react with this substrate remains elusive. We have therefore focused on elucidating strategies used by lignin-reactive soil bacteria and describing their oxidative enzyme systems. We now report the identification and characterization of an unusual C-type dye-decolorizing peroxidase from Amycolatopsis sp. 75iv2 (DyP2), which belongs to a family of heme peroxidases reported to be involved in bacterial lignin degradation. Biochemical studies indicate that DyP2 has novel function for this family, with versatile and high activity both as a peroxidase and Mn peroxidase (k(cat)/K(M) ≈ 10(5)-10(6) M(-1) s(-1)). It also has a Mn-dependent oxidase mode of action that expands its substrate scope. Crystallographic studies of DyP2 at 2.25 Å resolution show the existence of a Mn binding pocket and support its key role in catalysis.
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Affiliation(s)
- Margaret E. Brown
- Department
of Chemistry, ‡Department of Molecular and Cell Biology, and §Howard Hughes Medical Institute, University of California, Berkeley,
California 94720-1460, United States
| | - Tiago Barros
- Department
of Chemistry, ‡Department of Molecular and Cell Biology, and §Howard Hughes Medical Institute, University of California, Berkeley,
California 94720-1460, United States
| | - Michelle C. Y. Chang
- Department
of Chemistry, ‡Department of Molecular and Cell Biology, and §Howard Hughes Medical Institute, University of California, Berkeley,
California 94720-1460, United States
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47
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Strittmatter E, Liers C, Ullrich R, Wachter S, Hofrichter M, Plattner DA, Piontek K. First crystal structure of a fungal high-redox potential dye-decolorizing peroxidase: substrate interaction sites and long-range electron transfer. J Biol Chem 2012; 288:4095-102. [PMID: 23235158 DOI: 10.1074/jbc.m112.400176] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Dye-decolorizing peroxidases (DyPs) belong to the large group of heme peroxidases. They utilize hydrogen peroxide to catalyze oxidations of various organic compounds. AauDyPI from Auricularia auricula-judae (fungi) was crystallized, and its crystal structure was determined at 2.1 Å resolution. The mostly helical structure also shows a β-sheet motif typical for DyPs and Cld (chlorite dismutase)-related structures and includes the complete polypeptide chain. At the distal side of the heme molecule, a flexible aspartate residue (Asp-168) plays a key role in catalysis. It guides incoming hydrogen peroxide toward the heme iron and mediates proton rearrangement in the process of Compound I formation. Afterward, its side chain changes its conformation, now pointing toward the protein backbone. We propose an extended functionality of Asp-168, which acts like a gatekeeper by altering the width of the heme cavity access channel. Chemical modifications of potentially redox-active amino acids show that a tyrosine is involved in substrate interaction. Using spin-trapping experiments, a transient radical on the surface-exposed Tyr-337 was identified as the oxidation site for bulky substrates. A possible long-range electron transfer pathway from the surface of the enzyme to the redox cofactor (heme) is discussed.
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Affiliation(s)
- Eric Strittmatter
- Institute of Organic Chemistry, University of Freiburg, Albertstrasse 21, 79104 Freiburg, Germany
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48
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Yoshida T, Tsuge H, Hisabori T, Sugano Y. Crystal structures of dye-decolorizing peroxidase with ascorbic acid and 2,6-dimethoxyphenol. FEBS Lett 2012; 586:4351-6. [PMID: 23159941 DOI: 10.1016/j.febslet.2012.10.049] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2012] [Revised: 10/19/2012] [Accepted: 10/26/2012] [Indexed: 11/27/2022]
Abstract
The structure of dye-decolorizing peroxidase (DyP)-type peroxidase differs from that of other peroxidase families, indicating that DyP-type peroxidases have a different reaction mechanism. We have determined the crystal structures of DyP with ascorbic acid and 2,6-dimethoxyphenol at 1.5 and 1.4Å, respectively. The common binding site for both substrates was located at the entrance of the second cavity leading from the DyP molecular surface to heme. This resulted in a hydrogen bond network connection between each substrate and the heme distal side. This network consisted of water molecules occupying the second cavity, heme 6-propionate, Arg329, and Asn313. This network is consistent with the proton transfer pathway from substrate to DyP.
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Affiliation(s)
- Toru Yoshida
- Chemical Resources Laboratory, Tokyo Institute of Technology, R1-8, 4259 Nagatsuta, Yokohama 226-8503, Japan
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49
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Hofbauer S, Bellei M, Sündermann A, Pirker KF, Hagmüller A, Mlynek G, Kostan J, Daims H, Furtmüller PG, Djinović-Carugo K, Oostenbrink C, Battistuzzi G, Obinger C. Redox thermodynamics of high-spin and low-spin forms of chlorite dismutases with diverse subunit and oligomeric structures. Biochemistry 2012; 51:9501-12. [PMID: 23126649 PMCID: PMC3557923 DOI: 10.1021/bi3013033] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
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Chlorite dismutases (Clds) are heme b-containing
oxidoreductases that convert chlorite to chloride and dioxygen. In
this work, the thermodynamics of the one-electron reduction of the
ferric high-spin forms and of the six-coordinate low-spin cyanide
adducts of the enzymes from Nitrobacter winogradskyi (NwCld) and Candidatus “Nitrospira defluvii”
(NdCld) were determined through spectroelectrochemical experiments.
These proteins belong to two phylogenetically separated lineages that
differ in subunit (21.5 and 26 kDa, respectively) and oligomeric (dimeric
and pentameric, respectively) structure but exhibit similar chlorite
degradation activity. The E°′ values
for free and cyanide-bound proteins were determined to be −119
and −397 mV for NwCld and −113 and −404 mV for
NdCld, respectively (pH 7.0, 25 °C). Variable-temperature spectroelectrochemical
experiments revealed that the oxidized state of both proteins is enthalpically
stabilized. Molecular dynamics simulations suggest that changes in
the protein structure are negligible, whereas solvent reorganization
is mainly responsible for the increase in entropy during the redox
reaction. Obtained data are discussed with respect to the known structures
of the two Clds and the proposed reaction mechanism.
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Affiliation(s)
- Stefan Hofbauer
- Department of Chemistry, Division of Biochemistry, VIBT-Vienna Institute of BioTechnology, BOKU-University of Natural Resources and Life Sciences, A-1190 Vienna, Austria
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50
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Singh R, Grigg JC, Armstrong Z, Murphy MEP, Eltis LD. Distal heme pocket residues of B-type dye-decolorizing peroxidase: arginine but not aspartate is essential for peroxidase activity. J Biol Chem 2012; 287:10623-10630. [PMID: 22308037 DOI: 10.1074/jbc.m111.332171] [Citation(s) in RCA: 77] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
DypB from Rhodococcus jostii RHA1 is a bacterial dye-decolorizing peroxidase (DyP) that oxidizes lignin and Mn(II). Three residues interact with the iron-bound solvent species in ferric DypB: Asn-246 and the conserved Asp-153 and Arg-244. Substitution of either Asp-153 or Asn-246 with alanine minimally affected the second order rate constant for Compound I formation (k(1) ∼ 10(5) M(-1)s(-1)) and the specificity constant (k(cat)/K(m)) for H(2)O(2). Even in the D153A/N246A double variant, these values were reduced less than 30-fold. However, these substitutions dramatically reduced the stability of Compound I (t(1/2) ∼ 0.13 s) as compared with the wild-type enzyme (540 s). By contrast, substitution of Arg-244 with leucine abolished the peroxidase activity, and heme iron of the variant showed a pH-dependent transition from high spin (pH 5) to low spin (pH 8.5). Two variants were designed to mimic the plant peroxidase active site: D153H, which was more than an order of magnitude less reactive with H(2)O(2), and N246H, which had no detectable peroxidase activity. X-ray crystallographic studies revealed that structural changes in the variants are confined to the distal heme environment. The data establish an essential role for Arg-244 in Compound I formation in DypB, possibly through charge stabilization and proton transfer. The principle roles of Asp-153 and Asn-246 appear to be in modulating the subsequent reactivity of Compound I. These results expand the range of residues known to catalyze Compound I formation in heme peroxidases.
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Affiliation(s)
- Rahul Singh
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Jason C Grigg
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Zachary Armstrong
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Michael E P Murphy
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Lindsay D Eltis
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada.
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