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University of Groningen Exploring (Per)Oxidases As Biocatalysts for the Synthesis of Valuable Aromatic Compounds Habib, Mohamed

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University of Groningen Exploring (Per)Oxidases As Biocatalysts for the Synthesis of Valuable Aromatic Compounds Habib, Mohamed University of Groningen Exploring (per)oxidases as biocatalysts for the synthesis of valuable aromatic compounds Habib, Mohamed H M DOI: 10.33612/diss.109693881 IMPORTANT NOTE: You are advised to consult the publisher's version (publisher's PDF) if you wish to cite from it. Please check the document version below. Document Version Publisher's PDF, also known as Version of record Publication date: 2020 Link to publication in University of Groningen/UMCG research database Citation for published version (APA): Habib, M. H. M. (2020). Exploring (per)oxidases as biocatalysts for the synthesis of valuable aromatic compounds. University of Groningen. https://doi.org/10.33612/diss.109693881 Copyright Other than for strictly personal use, it is not permitted to download or to forward/distribute the text or part of it without the consent of the author(s) and/or copyright holder(s), unless the work is under an open content license (like Creative Commons). The publication may also be distributed here under the terms of Article 25fa of the Dutch Copyright Act, indicated by the “Taverne” license. More information can be found on the University of Groningen website: https://www.rug.nl/library/open-access/self-archiving-pure/taverne- amendment. Take-down policy If you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediately and investigate your claim. Downloaded from the University of Groningen/UMCG research database (Pure): http://www.rug.nl/research/portal. For technical reasons the number of authors shown on this cover page is limited to 10 maximum. Download date: 06-10-2021 Exploring (per)oxidases as biocatalysts for the synthesis of valuable aromatic compounds Exploring (per)oxidases as biocatalysts for the synthesis of valuable aromatic compounds PhD thesis The research described in this thesis was carried out in the department of Molecular to obtain the degree of PhD at the Enzymology of the Groningen Biomolecular Sciences and Biotechnology Institute University of Groningen according to the requirements of the Graduate School of Science, Faculty of on the authority of the Mathematics and Natural Sciences, University of Groningen, The Netherlands. Rector Magnificus Prof. C. Wijmenga Mohamed Habib received funding from the Cultural Affairs and Missions Sector, and in accordance with Ministry of Higher Education in Egypt. the decision by the College of Deans. Cover design: Mohamed Habib and Nina Lindhout This thesis will be defended in public on Printed by: Ipskamp Drukkers B.V. Monday, January 20, 2020 at 12:45 pm hours ISBN:ISBN (printed version): 978-94-034-2334-0 ISBN:ISBN (electronic version): 978-94-034-2335-7 by Copyright © Mohamed Habib 2020, Groningen, The Netherlands. All rights reserved. No part of this thesis may be reproduced, stored in a retrieval system, or transmitted in any form or by any means without prior permission of the Mohamed Habib author. born on 8 April 1987 in Riyadh, Saudi Arabia Exploring (per)oxidases as biocatalysts for the synthesis of valuable aromatic compounds PhD thesis The research described in this thesis was carried out in the department of Molecular to obtain the degree of PhD at the Enzymology of the Groningen Biomolecular Sciences and Biotechnology Institute University of Groningen according to the requirements of the Graduate School of Science, Faculty of on the authority of the Mathematics and Natural Sciences, University of Groningen, The Netherlands. Rector Magnificus Prof. C. Wijmenga Mohamed Habib received funding from the Cultural Affairs and Missions Sector, and in accordance with Ministry of Higher Education in Egypt. the decision by the College of Deans. Cover design: Mohamed Habib and Nina Lindhout This thesis will be defended in public on Printed by: Monday, January 20, 2020 at 12:45 pm hours ISBN: ISBN: by Copyright © Mohamed Habib 2020, Groningen, The Netherlands. All rights reserved. No part of this thesis may be reproduced, stored in a retrieval system, or transmitted in any form or by any means without prior permission of the Mohamed Habib author. born on 8 April 1987 in Riyadh, Saudi Arabia Supervisors Table of Contents Chapter I General introduction: Oxidases and peroxidases and their roles in biocatalysis 7 Prof. M.W. Fraaije Prof. D.B. Janssen Chapter II Bacterial enzymes involved in lignin degradation 26 Chapter III A biocatalytic one pot approach for the preparation of lignin oligomers using an oxidase/peroxidase cascade enzyme system 51 ‐ Assessment Committee Chapter IV The biocatalytic synthesis of syringaresinol from 2,6-dimethoxy-4-allylphenol in one-pot using a tailored oxidase/peroxidase system 70 Prof. W.J.H. van Berkel Chapter V Characterization of a new DyP-peroxidase from the alkaliphilic cellulomonad, Prof. G. Maglia Cellulomonas bogoriensis 82 Prof. F. Hollmann Chapter VI Expression and characterization of a resurrected DyP-type peroxidase 100 Summary, Conclusion and Future Outlook 120 Nederlandse Samenvatting 126 Curriculum vitae 131 Acknowledgements 132 Supervisors Table of Contents Chapter I General introduction: Oxidases and peroxidases and their roles in biocatalysis 76 Prof. M.W. Fraaije Prof. D.B. Janssen Chapter II Bacterial enzymes involved in lignin degradation 2426 Chapter III A biocatalytic one pot approach for the preparation of lignin oligomers using an oxidase/peroxidase cascade enzyme system 4851 ‐ Assessment Committee Chapter IV The biocatalytic synthesis of syringaresinol from 2,6-dimethoxy-4-allylphenol in one-pot using a tailored oxidase/peroxidase system 6670 Prof. W.J.H. van Berkel Chapter V Characterization of a new DyP-peroxidase from the alkaliphilic cellulomonad, Prof. G. Maglia Cellulomonas bogoriensis 7882 Prof. F. Hollmann Chapter VI Expression and characterization of a resurrected DyP-type peroxidase 10096 Summary, Conclusion and Future Outlook 116120 Nederlandse Samenvatting 122126 Curriculum vitae 128131 Acknowledgements 129132 1 General introduction: Oxidases and peroxidases and their roles in biocatalysis Mohamed Habib and Marco W. Fraaije 1 Oxidases and peroxidases and their roles in biocatalysis Chapter I 1.1 Introduction redox enzymes is shown in Table 1. Redox enzymes have found numerous 1.1.1 Background applications which include: textile and food processing, synthesis and modification 1.1.1.1 Redox enzymes of polymers, oxidative degradation of pollutants, (asymmetric) synthesis of fine In redox reactions, electron transfer takes place from one reactant to another. In chemicals and pharmaceuticals, and as part of biosensors for a variety of analytical [3,4] synthetic chemistry, these reactions often require harsh conditions (e.g. elevated and clinical applications. temperatures and high pressure) and proceed with low chemo-, regio- and enantioselectivity. A large number of enzymes on the other hand are capable of performing redox reactions with an astonishing high degree of selectivity. These biological catalysts typically require cofactors for catalysis because the building blocks of proteins, amino acids, are not well suited for redox chemistry. Only in some rare cases, redox enzymes perform catalysis without any cofactor [1,2]. Not only redox enzymes, but also many other enzymes rely on cofactors: it is estimated that about half of all enzymes depend on one or more cofactors. Cofactors come in many flavors, ranging from metal ions to highly complex molecules such as vitamin B12 and prenylated FMN (Figure 1). They enable enzymes to catalyze a plethora of reactions that would simply be impossible without a cofactor. The importance of cofactors in nature can also be deduced from the dedicated, complex and energy-consuming biosynthetic pathways of many cofactors. Cofactors can be classified into two cofactor types: prosthetic groups and coenzymes. Prosthetic groups are cofactors that are tightly, sometimes even covalently, bound. A well-known example is the heme cofactor bound in hemoglobin. Coenzymes are cofactors that are loosely bound to the target enzymes and which dissociate upon being converted, to be used by another coenzyme- dependent enzyme. Well-known examples are the NAD(P)+-dependent alcohol dehydrogenases. When considering enzymes as biocatalysts, a dependency on coenzymes presents a challenge as it will require an approach that will recycle the coenzyme. This is not the case when dealing with enzymes that contain a prosthetic group which can be regarded as an integral part of the biocatalyst. Redox enzymes, also named oxidoreductases, typically use cofactors to facilitate the transfer of electrons. While there are numerous redox enzymes known, there is a limited set of redox cofactors available in nature used by these enzymes. Some redox cofactors are rather limited in the type of redox reaction that they can support. For example, nicotinamide cofactors (NAD+ or NADP+) solely enable oxidation and reduction reactions by the transfer of a hydride. There are also cofactors that are used for different types of redox reactions. For example, flavin cofactors (FAD or FMN) facilitate oxidation by hydride transfer but can also support electron transfer, oxygenations, halogenations and other types of reactions. All redox enzymes belong Figure 1. Structural formulas of some cofactors: vitamin B12, prenylated to the EC (Enzyme Commission) class I. According to the EC classification, FMN, FAD, and heme. oxidoreductases can be subclassified into 22 different subclasses, dependent on the type of reaction and substrate(s). A more general classification
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