1
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Lučić M, Allport T, Clarke TA, Williams LJ, Wilson MT, Chaplin AK, Worrall JAR. The oligomeric states of dye-decolorizing peroxidases from Streptomyces lividans and their implications for mechanism of substrate oxidation. Protein Sci 2024; 33:e5073. [PMID: 38864770 PMCID: PMC11168072 DOI: 10.1002/pro.5073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 05/18/2024] [Accepted: 05/25/2024] [Indexed: 06/13/2024]
Abstract
A common evolutionary mechanism in biology to drive function is protein oligomerization. In prokaryotes, the symmetrical assembly of repeating protein units to form homomers is widespread, yet consideration in vitro of whether such assemblies have functional or mechanistic consequences is often overlooked. Dye-decolorizing peroxidases (DyPs) are one such example, where their dimeric α + β barrel units can form various oligomeric states, but the oligomer influence, if any, on mechanism and function has received little attention. In this work, we have explored the oligomeric state of three DyPs found in Streptomyces lividans, each with very different mechanistic behaviors in their reactions with hydrogen peroxide and organic substrates. Using analytical ultracentrifugation, we reveal that except for one of the A-type DyPs where only a single sedimenting species is detected, oligomer states ranging from homodimers to dodecamers are prevalent in solution. Using cryo-EM on preparations of the B-type DyP, we determined a 3.02 Å resolution structure of a hexamer assembly that corresponds to the dominant oligomeric state in solution as determined by analytical ultracentrifugation. Furthermore, cryo-EM data detected sub-populations of higher-order oligomers, with one of these formed by an arrangement of two B-type DyP hexamers to give a dodecamer assembly. Our solution and structural insights of these oligomer states provide a new framework to consider previous mechanistic studies of these DyP members and are discussed in terms of long-range electron transfer for substrate oxidation and in the "storage" of oxidizable equivalents on the heme until a two-electron donor is available.
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Affiliation(s)
- Marina Lučić
- School of Life SciencesUniversity of EssexColchesterUK
| | - Thomas Allport
- Leicester Institute for Structural and Chemical Biology, Department of Molecular and Cell BiologyUniversity of LeicesterLeicesterUK
| | | | | | | | - Amanda K. Chaplin
- Leicester Institute for Structural and Chemical Biology, Department of Molecular and Cell BiologyUniversity of LeicesterLeicesterUK
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2
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Hermann E, Rodrigues CF, Martins LO, Peterbauer C, Oostenbrink C. Engineering A-type Dye-Decolorizing Peroxidases by Modification of a Conserved Glutamate Residue. Chembiochem 2024; 25:e202300872. [PMID: 38376941 DOI: 10.1002/cbic.202300872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 02/08/2024] [Accepted: 02/20/2024] [Indexed: 02/21/2024]
Abstract
Dye-decolorizing peroxidases (DyPs) are recently identified microbial enzymes that have been used in several Biotechnology applications from wastewater treatment to lignin valorization. However, their properties and mechanism of action still have many open questions. Their heme-containing active site is buried by three conserved flexible loops with a putative role in modulating substrate access and enzyme catalysis. Here, we investigated the role of a conserved glutamate residue in stabilizing interactions in loop 2 of A-type DyPs. First, we did site saturation mutagenesis of this residue, replacing it with all possible amino acids in bacterial DyPs from Bacillus subtilis (BsDyP) and from Kitasatospora aureofaciens (KaDyP1), the latter being characterized here for the first time. We screened the resulting libraries of variants for activity towards ABTS and identified variants with increased catalytic efficiency. The selected variants were purified and characterized for activity and stability. We furthermore used Molecular Dynamics simulations to rationalize the increased catalytic efficiency and found that the main reason is the electron channeling becoming easier from surface-exposed tryptophans. Based on our findings, we also propose that this glutamate could work as a pH switch in the wild-type enzyme, preventing intracellular damage.
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Affiliation(s)
- Enikö Hermann
- Institute of Food Technology, Department of Food Science and Technology, University of Natural Resources and Life Sciences, Vienna, Muthgasse 11, 1190, Vienna, Austria
- Institute for Molecular Modeling and Simulation, Department of Material Science and Life Sciences, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190, Vienna, Austria
| | - Carolina F Rodrigues
- 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
| | - Clemens Peterbauer
- Institute of Food Technology, Department of Food Science and Technology, University of Natural Resources and Life Sciences, Vienna, Muthgasse 11, 1190, Vienna, Austria
| | - Chris Oostenbrink
- Institute for Molecular Modeling and Simulation, Department of Material Science and Life Sciences, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190, Vienna, Austria
- Christian Doppler Laboratory for Molecular Informatics in the Biosciences, University of Natural Resources and Life Sciences, Vienna, Austria
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3
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Lučić M, Wilson MT, Pullin J, Hough MA, Svistunenko DA, Worrall JAR. New insights into controlling radical migration pathways in heme enzymes gained from the study of a dye-decolorising peroxidase. Chem Sci 2023; 14:12518-12534. [PMID: 38020392 PMCID: PMC10646903 DOI: 10.1039/d3sc04453j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 10/06/2023] [Indexed: 12/01/2023] Open
Abstract
In heme enzymes, such as members of the dye-decolorising peroxidase (DyP) family, the formation of the highly oxidising catalytic Fe(iv)-oxo intermediates following reaction with hydrogen peroxide can lead to free radical migration (hole hopping) from the heme to form cationic tyrosine and/or tryptophan radicals. These species are highly oxidising (∼1 V vs. NHE) and under certain circumstances can catalyse the oxidation of organic substrates. Factors that govern which specific tyrosine or tryptophan the free radical migrates to in heme enzymes are not well understood, although in the case of tyrosyl radical formation the nearby proximity of a proton acceptor is a recognised facilitating factor. By using an A-type member of the DyP family (DtpAa) as an exemplar, we combine protein engineering, X-ray crystallography, hole-hopping calculations, EPR spectroscopy and kinetic modelling to provide compelling new insights into the control of radical migration pathways following reaction of the heme with hydrogen peroxide. We demonstrate that the presence of a tryptophan/tyrosine dyad motif displaying a T-shaped orientation of aromatic rings on the proximal side of the heme dominates the radical migration landscape in wild-type DtpAa and continues to do so following the rational engineering into DtpAa of a previously identified radical migration pathway in an A-type homolog on the distal side of the heme. Only on disrupting the proximal dyad, through removal of an oxygen atom, does the radical migration pathway then switch to the engineered distal pathway to form the desired tyrosyl radical. Implications for protein design and biocatalysis are discussed.
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Affiliation(s)
- Marina Lučić
- School of Life Sciences, University of Essex Wivenhoe Park Colchester Essex CO4 3SQ UK
| | - Michael T Wilson
- School of Life Sciences, University of Essex Wivenhoe Park Colchester Essex CO4 3SQ UK
| | - Jacob Pullin
- School of Life Sciences, University of Essex Wivenhoe Park Colchester Essex CO4 3SQ UK
| | - Michael A Hough
- School of Life Sciences, University of Essex Wivenhoe Park Colchester Essex CO4 3SQ UK
- Diamond Light Source, Harwell Science and Innovation Campus Didcot Oxfordshire OX11 0DE UK
| | - Dimitri A Svistunenko
- School of Life Sciences, University of Essex Wivenhoe Park Colchester Essex CO4 3SQ UK
| | - Jonathan A R Worrall
- School of Life Sciences, University of Essex Wivenhoe Park Colchester Essex CO4 3SQ UK
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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: 8] [Impact Index Per Article: 8.0] [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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Gray HB, Winkler JR. Functional and protective hole hopping in metalloenzymes. Chem Sci 2021; 12:13988-14003. [PMID: 34760183 PMCID: PMC8565380 DOI: 10.1039/d1sc04286f] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 09/20/2021] [Indexed: 01/19/2023] Open
Abstract
Electrons can tunnel through proteins in microseconds with a modest release of free energy over distances in the 15 to 20 Å range. To span greater distances, or to move faster, multiple charge transfers (hops) are required. When one of the reactants is a strong oxidant, it is convenient to consider the movement of a positively charged "hole" in a direction opposite to that of the electron. Hole hopping along chains of tryptophan (Trp) and tyrosine (Tyr) residues is a critical function in several metalloenzymes that generate high-potential intermediates by reactions with O2 or H2O2, or by activation with visible light. Examination of the protein structural database revealed that Tyr/Trp chains are common protein structural elements, particularly among enzymes that react with O2 and H2O2. In many cases these chains may serve a protective role in metalloenzymes by deactivating high-potential reactive intermediates formed in uncoupled catalytic turnover.
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Affiliation(s)
- Harry B Gray
- Beckman Institute, California Institute of Technology 1200 E California Boulevard Pasadena CA 19925 USA
| | - Jay R Winkler
- Beckman Institute, California Institute of Technology 1200 E California Boulevard Pasadena CA 19925 USA
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6
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Rodrigues CF, Borges PT, Scocozza MF, Silva D, Taborda A, Brissos V, Frazão C, Martins LO. Loops around the Heme Pocket Have a Critical Role in the Function and Stability of BsDyP from Bacillus subtilis. Int J Mol Sci 2021; 22:ijms221910862. [PMID: 34639208 PMCID: PMC8509576 DOI: 10.3390/ijms221910862] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 10/01/2021] [Accepted: 10/05/2021] [Indexed: 11/27/2022] Open
Abstract
Bacillus subtilis BsDyP belongs to class I of the dye-decolorizing peroxidase (DyP) family of enzymes and is an interesting biocatalyst due to its high redox potential, broad substrate spectrum and thermostability. This work reports the optimization of BsDyP using directed evolution for improved oxidation of 2,6-dimethoxyphenol, a model lignin-derived phenolic. After three rounds of evolution, one variant was identified displaying 7-fold higher catalytic rates and higher production yields as compared to the wild-type enzyme. The analysis of X-ray structures of the wild type and the evolved variant showed that the heme pocket is delimited by three long conserved loop regions and a small α helix where, incidentally, the mutations were inserted in the course of evolution. One loop in the proximal side of the heme pocket becomes more flexible in the evolved variant and the size of the active site cavity is increased, as well as the width of its mouth, resulting in an enhanced exposure of the heme to solvent. These conformational changes have a positive functional role in facilitating electron transfer from the substrate to the enzyme. However, they concomitantly resulted in decreasing the enzyme’s overall stability by 2 kcal mol−1, indicating a trade-off between functionality and stability. Furthermore, the evolved variant exhibited slightly reduced thermal stability compared to the wild type. The obtained data indicate that understanding the role of loops close to the heme pocket in the catalysis and stability of DyPs is critical for the development of new and more powerful biocatalysts: loops can be modulated for tuning important DyP properties such as activity, specificity and stability.
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Affiliation(s)
- Carolina F. Rodrigues
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av da República, 2780-157 Oeiras, Portugal; (C.F.R.); (P.T.B.); (D.S.); (A.T.); (V.B.); (C.F.)
| | - Patrícia T. Borges
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av da República, 2780-157 Oeiras, Portugal; (C.F.R.); (P.T.B.); (D.S.); (A.T.); (V.B.); (C.F.)
| | - Magali F. Scocozza
- Instituto de Química Física de los Materiales, Medio Ambiente y Energia (INQUIMAE), CONICET—Universidad de Buenos Aires, Buenos Aires 148EHA, Argentina;
| | - Diogo Silva
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av da República, 2780-157 Oeiras, Portugal; (C.F.R.); (P.T.B.); (D.S.); (A.T.); (V.B.); (C.F.)
| | - André Taborda
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av da República, 2780-157 Oeiras, Portugal; (C.F.R.); (P.T.B.); (D.S.); (A.T.); (V.B.); (C.F.)
| | - Vânia Brissos
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av da República, 2780-157 Oeiras, Portugal; (C.F.R.); (P.T.B.); (D.S.); (A.T.); (V.B.); (C.F.)
| | - Carlos Frazão
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av da República, 2780-157 Oeiras, Portugal; (C.F.R.); (P.T.B.); (D.S.); (A.T.); (V.B.); (C.F.)
| | - Lígia O. Martins
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av da República, 2780-157 Oeiras, Portugal; (C.F.R.); (P.T.B.); (D.S.); (A.T.); (V.B.); (C.F.)
- Correspondence:
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7
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Nys K, Furtmüller PG, Obinger C, Van Doorslaer S, Pfanzagl V. On the Track of Long-Range Electron Transfer in B-Type Dye-Decolorizing Peroxidases: Identification of a Tyrosyl Radical by Computational Prediction and Electron Paramagnetic Resonance Spectroscopy. Biochemistry 2021; 60:1226-1241. [PMID: 33784066 PMCID: PMC8154254 DOI: 10.1021/acs.biochem.1c00129] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 03/24/2021] [Indexed: 11/29/2022]
Abstract
The catalytic activity of dye-decolorizing peroxidases (DyPs) toward bulky substrates, including anthraquinone dyes, phenolic lignin model compounds, or 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS), is in strong contrast to their sterically restrictive active site. In two of the three known subfamilies (A- and C/D-type DyPs), catalytic protein radicals at surface-exposed sites, which are connected to the heme cofactor by electron transfer path(s), have been identified. So far in B-type DyPs, there has been no evidence for protein radical formation after activation by hydrogen peroxide. Interestingly, B-type Klebsiella pneumoniae dye-decolorizing peroxidase (KpDyP) displays a persistent organic radical in the resting state composed of two species that can be distinguished by W-band electron spin echo electron paramagnetic resonance (EPR) spectroscopy. Here, on the basis of a comprehensive mutational and EPR study of computationally predicted tyrosine and tryptophan variants of KpDyP, we demonstrate the formation of tyrosyl radicals (Y247 and Y92) and a radical-stabilizing Y-W dyad between Y247 and W18 in KpDyP, which are unique to enterobacterial B-type DyPs. Y247 is connected to Y92 by a hydrogen bonding network, is solvent accessible in simulations, and is involved in ABTS oxidation. This suggests the existence of long-range electron path(s) in B-type DyPs. The mechanistic and physiological relevance of the reaction mechanism of B-type DyPs is discussed.
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Affiliation(s)
- Kevin Nys
- BIMEF
Laboratory, Department of Chemistry, University
of Antwerp, 2610 Antwerp, Belgium
| | - Paul Georg Furtmüller
- Department
of Chemistry, Institute of Biochemistry,
BOKU-University of Natural Resources and Life Sciences, 1190 Vienna, Austria
| | - Christian Obinger
- Department
of Chemistry, Institute of Biochemistry,
BOKU-University of Natural Resources and Life Sciences, 1190 Vienna, Austria
| | - Sabine Van Doorslaer
- BIMEF
Laboratory, Department of Chemistry, University
of Antwerp, 2610 Antwerp, Belgium
| | - Vera Pfanzagl
- Department
of Chemistry, Institute of Biochemistry,
BOKU-University of Natural Resources and Life Sciences, 1190 Vienna, Austria
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8
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Uchida T, Omura I, Umetsu S, Ishimori K. Radical transfer but not heme distal residues is essential for pH dependence of dye-decolorizing activity of peroxidase from Vibrio cholerae. J Inorg Biochem 2021; 219:111422. [PMID: 33756393 DOI: 10.1016/j.jinorgbio.2021.111422] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 02/02/2021] [Accepted: 03/07/2021] [Indexed: 02/08/2023]
Abstract
Dye-decolorizing peroxidase (DyP) is a heme-containing enzyme that catalyzes the degradation of anthraquinone dyes. A main feature of DyP is the acidic optimal pH for dye-decolorizing activity. In this study, we constructed several mutant DyP enzymes from Vibrio cholerae (VcDyP), with a view to identifying the decisive factor of the low pH preference of DyP. Initially, distal Asp144, a conserved residue, was replaced with His, which led to significant loss of dye-decolorizing activity. Introduction of His into a position slightly distant from heme resulted in restoration of activity but no shift in optimal pH, indicating that distal residues do not contribute to the pH dependence of catalytic activity. His178, an essential residue for dye decolorization, is located near heme and forms hydrogen bonds with Asp138 and Thr278. While Trp and Tyr mutants of His178 were inactive, the Phe mutant displayed ~35% activity of wild-type VcDyP, indicating that this position is a potential radical transfer route from heme to the active site on the protein surface. The Thr278Val mutant displayed similar enzymatic properties as WT VcDyP, whereas the Asp138Val mutant displayed significantly increased activity at pH 6.5. On the basis of these findings, we propose that neither distal amino acid residues, including Asp144, nor hydrogen bonds between His178 and Thr278 are responsible while the hydrogen bond between His178 and Asp138 plays a key role in the pH dependence of activity.
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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 060-8628, Japan.
| | - Issei Omura
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo 060-8628, Japan
| | - Sayaka Umetsu
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo 060-8628, 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 060-8628, Japan
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9
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Sánchez-Alejandro F, Baratto MC, Basosi R, Graeve O, Vazquez-Duhalt R. Addition of new catalytic sites on the surface of versatile peroxidase for enhancement of LRET catalysis. Enzyme Microb Technol 2019; 131:109429. [PMID: 31615668 DOI: 10.1016/j.enzmictec.2019.109429] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 08/21/2019] [Accepted: 09/10/2019] [Indexed: 11/19/2022]
Abstract
Versatile peroxidase (VP) from Bjerkandera adusta is an enzyme able to oxidize bulky and high-redox substrates trough a Long-Range Electron Transfer (LRET) pathway. In this study, the introduction of radical-forming aromatic amino acids by chemical modification of the protein surface was performed, and the catalytic implications of these additional surface active-sites on the oxidation of 2,6-dimethylphenol, Mn2+ and Remazol Brilliant Blue R (RBBR) were determined. These three different substrates are oxidized in different active-sites of enzyme molecule, of which the high redox RBBR the only one that is transformed by an external radical formed on the protein surface. Both catalytic constants kcat and KM were significantly affected by the chemical modifications. Tryptophan- and tyrosine-modified VP showed higher catalytic transformation than the unmodified enzyme for RBBR, while the Mn2+ oxidation was significantly reduced by all chemical modifications. Electron Paramagnetic Resonance studies demonstrated the formation of additional protein-based radicals after the chemical modification with radical-forming amino acids. In addition, the catalytic rate of the LRET-mediated transformation showed a good correlation with the ionization energy of the additional amino acid on the protein surface.
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Affiliation(s)
- Flor Sánchez-Alejandro
- Centro de Nanociencias y Nanotecnología, Universidad Nacional Autónoma de México, Ensenada, Baja California, Mexico
| | - Maria Camilla Baratto
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Siena, Italy
| | - Riccardo Basosi
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Siena, Italy
| | - Olivia Graeve
- Department of Mechanical and Aerospace Engineering, University of California San Diego, La Jolla, CA, USA
| | - Rafael Vazquez-Duhalt
- Centro de Nanociencias y Nanotecnología, Universidad Nacional Autónoma de México, Ensenada, Baja California, Mexico.
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10
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Lin Y. Rational design of heme enzymes for biodegradation of pollutants toward a green future. Biotechnol Appl Biochem 2019; 67:484-494. [DOI: 10.1002/bab.1788] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Accepted: 06/06/2019] [Indexed: 12/28/2022]
Affiliation(s)
- Ying‐Wu Lin
- School of Chemistry and Chemical Engineering University of South China Hengyang People's Republic of China
- Laboratory of Protein Structure and Function University of South China Hengyang People's Republic of China
- Hunan Key Laboratory for the Design and Application of Actinide Complexes University of South China Hengyang People's Republic of China
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11
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Pfanzagl V, Nys K, Bellei M, Michlits H, Mlynek G, Battistuzzi G, Djinovic-Carugo K, Van Doorslaer S, Furtmüller PG, Hofbauer S, Obinger C. Roles of distal aspartate and arginine of B-class dye-decolorizing peroxidase in heterolytic hydrogen peroxide cleavage. J Biol Chem 2018; 293:14823-14838. [PMID: 30072383 PMCID: PMC6153280 DOI: 10.1074/jbc.ra118.004773] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 07/26/2018] [Indexed: 11/06/2022] Open
Abstract
Dye-decolorizing peroxidases (DyPs) represent the most recently classified hydrogen peroxide-dependent heme peroxidase family. Although widely distributed with more than 5000 annotated genes and hailed for their biotechnological potential, detailed biochemical characterization of their reaction mechanism remains limited. Here, we present the high-resolution crystal structures of WT B-class DyP from the pathogenic bacterium Klebsiella pneumoniae (KpDyP) (1.6 Å) and the variants D143A (1.3 Å), R232A (1.9 Å), and D143A/R232A (1.1 Å). We demonstrate the impact of elimination of the DyP-typical, distal residues Asp-143 and Arg-232 on (i) the spectral and redox properties, (ii) the kinetics of heterolytic cleavage of hydrogen peroxide, (iii) the formation of the low-spin cyanide complex, and (iv) the stability and reactivity of an oxoiron(IV)porphyrin π-cation radical (Compound I). Structural and functional studies reveal that the distal aspartate is responsible for deprotonation of H2O2 and for the poor oxidation capacity of Compound I. Elimination of the distal arginine promotes a collapse of the distal heme cavity, including blocking of one access channel and a conformational change of the catalytic aspartate. We also provide evidence of formation of an oxoiron(IV)-type Compound II in KpDyP with absorbance maxima at 418, 527, and 553 nm. In summary, a reaction mechanism of the peroxidase cycle of B-class DyPs is proposed. Our observations challenge the idea that peroxidase activity toward conventional aromatic substrates is related to the physiological roles of B-class DyPs.
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Affiliation(s)
- Vera Pfanzagl
- From the Department of Chemistry, Division of Biochemistry, BOKU-University of Natural Resources and Life Sciences, 1190 Vienna, Austria
| | - Kevin Nys
- the Department of Physics, University of Antwerp, 2610 Wilrijk, Belgium
| | | | - Hanna Michlits
- From the Department of Chemistry, Division of Biochemistry, BOKU-University of Natural Resources and Life Sciences, 1190 Vienna, Austria
| | - Georg Mlynek
- the Department for Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, 1030 Vienna, Austria
| | - Gianantonio Battistuzzi
- Chemistry and Geology, University of Modena and Reggio Emilia, via Campi 103, 41125 Modena, Italy, and
| | - Kristina Djinovic-Carugo
- the Department for Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, 1030 Vienna, Austria
| | | | - Paul G Furtmüller
- From the Department of Chemistry, Division of Biochemistry, BOKU-University of Natural Resources and Life Sciences, 1190 Vienna, Austria
| | - Stefan Hofbauer
- From the Department of Chemistry, Division of Biochemistry, BOKU-University of Natural Resources and Life Sciences, 1190 Vienna, Austria
| | - Christian Obinger
- From the Department of Chemistry, Division of Biochemistry, BOKU-University of Natural Resources and Life Sciences, 1190 Vienna, Austria,
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12
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Fernández-Fueyo E, Davó-Siguero I, Almendral D, Linde D, Baratto MC, Pogni R, Romero A, Guallar V, Martínez AT. Description of a Non-Canonical Mn(II)-Oxidation Site in Peroxidases. ACS Catal 2018. [DOI: 10.1021/acscatal.8b02306] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Elena Fernández-Fueyo
- Centro de Investigaciones Biológicas, Consejo Superior
de Investigaciones Cientı́ficas (CSIC), E-28006 Madrid, Spain
| | - Irene Davó-Siguero
- Centro de Investigaciones Biológicas, Consejo Superior
de Investigaciones Cientı́ficas (CSIC), E-28006 Madrid, Spain
| | - David Almendral
- Centro de Investigaciones Biológicas, Consejo Superior
de Investigaciones Cientı́ficas (CSIC), E-28006 Madrid, Spain
| | - Dolores Linde
- Centro de Investigaciones Biológicas, Consejo Superior
de Investigaciones Cientı́ficas (CSIC), E-28006 Madrid, Spain
| | - Maria Camilla Baratto
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, I-53100 Siena, Italy
- Consorzio per lo Sviluppo dei Sistemi a Grande Interfase (CSGI), 50019 Florence, Italy
| | - Rebecca Pogni
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, I-53100 Siena, Italy
- Consorzio per lo Sviluppo dei Sistemi a Grande Interfase (CSGI), 50019 Florence, Italy
| | - Antonio Romero
- Centro de Investigaciones Biológicas, Consejo Superior
de Investigaciones Cientı́ficas (CSIC), E-28006 Madrid, Spain
| | - Victor Guallar
- Barcelona Supercomputing Center, E-08034 Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avancats (ICREA), E-08010 Barcelona, Spain
| | - Angel T. Martínez
- Centro de Investigaciones Biológicas, Consejo Superior
de Investigaciones Cientı́ficas (CSIC), E-28006 Madrid, Spain
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13
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Martínez AT, Ruiz-Dueñas FJ, Camarero S, Serrano A, Linde D, Lund H, Vind J, Tovborg M, Herold-Majumdar OM, Hofrichter M, Liers C, Ullrich R, Scheibner K, Sannia G, Piscitelli A, Pezzella C, Sener ME, Kılıç S, van Berkel WJ, Guallar V, Lucas MF, Zuhse R, Ludwig R, Hollmann F, Fernández-Fueyo E, Record E, Faulds CB, Tortajada M, Winckelmann I, Rasmussen JA, Gelo-Pujic M, Gutiérrez A, del Río JC, Rencoret J, Alcalde M. Oxidoreductases on their way to industrial biotransformations. Biotechnol Adv 2017. [DOI: 10.1016/j.biotechadv.2017.06.003] [Citation(s) in RCA: 130] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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14
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Khatoon N, Jamal A, Ali MI. Polymeric pollutant biodegradation through microbial oxidoreductase: A better strategy to safe environment. Int J Biol Macromol 2017. [PMID: 28648638 DOI: 10.1016/j.ijbiomac.2017.06.047] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
The detoxification of xenobiotic organic compounds by various microorganisms through oxidative coupling is facilitated with oxidoreductases. With the help of energy yielding biochemical reactions, these microbes extract energy for their metabolic pathway. They promote the transfer of electrons from a reduced organic substrate to another chemical compound. During such oxidation-reduction reactions, the toxic polymeric substance is finally oxidized into harmless compounds. Enzymatic bioremediation of toxic organic pollutant is a very effective strategy in complex environmental conditions. Oxidoreductases enzymes have a significant potential for the bioremediation of the xenobiotic compounds. Various electron donor complex polymeric substrates containing Phenol and aromatic amines are oxidized by peroxidase in the presence of H2O2 while O2 in the case of dioxygenase. This review attempts to present relevant information on the peroxidases and dioxygenase from various microbial isolates involved in the biodegradation of a wide range of pollutants.
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Affiliation(s)
- Nazia Khatoon
- Environmental Microbiology Laboratory, Department of Microbiology, Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Asif Jamal
- Environmental Microbiology Laboratory, Department of Microbiology, Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Muhammad Ishtiaq Ali
- Environmental Microbiology Laboratory, Department of Microbiology, Quaid-i-Azam University, Islamabad, 45320, Pakistan.
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15
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Brissos V, Tavares D, Sousa AC, Robalo MP, Martins LO. Engineering a Bacterial DyP-Type Peroxidase for Enhanced Oxidation of Lignin-Related Phenolics at Alkaline pH. ACS Catal 2017. [DOI: 10.1021/acscatal.6b03331] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Vânia Brissos
- Instituto
de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av da República, 2780-157 Oeiras, Portugal
| | - Diogo Tavares
- Instituto
de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av da República, 2780-157 Oeiras, Portugal
| | - Ana Catarina Sousa
- Área
Departamental de Engenharia Química, ISEL-Instituto Superior de Engenharia de Lisboa, Instituto Politécnico de Lisboa, R. Conselheiro Emídio Navarro, 1, 1959-007 Lisboa, Portugal
- Centro
de Química Estrutural, Complexo I, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal
| | - Maria Paula Robalo
- Área
Departamental de Engenharia Química, ISEL-Instituto Superior de Engenharia de Lisboa, Instituto Politécnico de Lisboa, R. Conselheiro Emídio Navarro, 1, 1959-007 Lisboa, Portugal
- Centro
de Química Estrutural, Complexo I, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal
| | - Lígia O. Martins
- Instituto
de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av da República, 2780-157 Oeiras, Portugal
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16
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Shrestha R, Chen X, Ramyar KX, Hayati Z, Carlson EA, Bossmann SH, Song L, Geisbrecht BV, Li P. Identification of Surface-Exposed Protein Radicals and A Substrate Oxidation Site in A-Class Dye-Decolorizing Peroxidase from Thermomonospora curvata. ACS Catal 2016; 6:8036-8047. [PMID: 29308294 DOI: 10.1021/acscatal.6b01952] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Dye-decolorizing peroxidases (DyPs) are a family of heme peroxidases, in which a catalytic distal aspartate is involved in H2O2 activation to catalyze oxidations in acidic conditions. They have received much attention due to their potential applications in lignin compound degradation and biofuel production from biomass. However, the mode of oxidation in bacterial DyPs remains unknown. We have recently reported that the bacterial TcDyP from Thermomonospora curvata is among the most active DyPs and shows activity toward phenolic lignin model compounds (J. Biol. Chem.2015, 290, 23447). Based on the X-ray crystal structure solved at 1.75 Å, sigmoidal steady-state kinetics with Reactive Blue 19 (RB19), and formation of compound II-like product in the absence of reducing substrates observed with stopped-flow spectroscopy and electron paramagnetic resonance (EPR), we hypothesized that the TcDyP catalyzes oxidation of large-size substrates via multiple surface-exposed protein radicals. Among 7 tryptophans and 3 tyrosines in TcDyP consisting of 376 residues for the matured protein, W263, W376, and Y332 were identified as surface-exposed protein radicals. Only the W263 was also characterized as one of surface-exposed oxidation sites. SDS-PAGE and size-exclusion chromatography demonstrated that W376 represents an off-pathway destination for electron transfer, resulting in the crosslinking of proteins in the absence of substrates. Mutation of W376 improved compound I stability and overall catalytic efficiency toward RB19. While Y332 is highly conserved across all four classes of DyPs, its catalytic function in A-class TcDyP is minimal possibly due to its extremely small solvent accessible areas. Identification of surface-exposed protein radicals and substrate oxidation sites is important for understanding DyP mechanism and modulating its catalytic functions for improved activity on phenolic lignin.
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Affiliation(s)
| | | | | | - Zahra Hayati
- National
High Magnetic Field Laboratory, Florida State University, Tallahassee, Florida 32310, United States
| | | | | | - Likai Song
- National
High Magnetic Field Laboratory, Florida State University, Tallahassee, Florida 32310, United States
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