Biocatalysis Based on Heme Peroxidases
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Biocatalysis Based on Heme Peroxidases . Eduardo Torres l Marcela Ayala Editors Biocatalysis Based on Heme Peroxidases Peroxidases as Potential Industrial Biocatalysts Editors Dr. Eduardo Torres Dr. Marcela Ayala Beneme´rita Universidad Universidad Nacional Auto´noma Auto´noma de Puebla de Me´xico Centro de Quı´mica Instituto de Biotecnologı´a Ciudad Universitaria Av. Universidad, Col. Chamilpa 2001 72570 Puebla 62210 Cuernavaca, Morelos Me´xico Me´xico [email protected] [email protected] ISBN 978-3-642-12626-0 e-ISBN 978-3-642-12627-7 DOI 10.1007/978-3-642-12627-7 Springer Heidelberg Dordrecht London New York Library of Congress Control Number: 2010932759 # Springer-Verlag Berlin Heidelberg 2010 This work is subject to copyright. All rights are reserved, whether the whole or part of the material is concerned, specifically the rights of translation, reprinting, reuse of illustrations, recitation, broadcasting, reproduction on microfilm or in any other way, and storage in data banks. Duplication of this publication or parts thereof is permitted only under the provisions of the German Copyright Law of September 9, 1965, in its current version, and permission for use must always be obtained from Springer. Violations are liable to prosecution under the German Copyright Law. The use of general descriptive names, registered names, trademarks, etc. in this publication does not imply, even in the absence of a specific statement, that such names are exempt from the relevant protective laws and regulations and therefore free for general use. Cover design: WMXDesign GmbH, Heidelberg, Germany Printed on acid-free paper Springer is part of Springer Science+Business Media (www.springer.com) Preface The last systematic description of heme peroxidases was published in 1999 by Brian Dunford, from the University of Alberta in Canada. The book Heme perox- idases covers discussion on three-dimensional structure, reaction mechanism, kinetics, and spectral properties of representative enzymes from bacterial, plant, fungal, and animal origin. Since 1999, vast information on basic but also applied aspects of heme peroxidases has been generated. We believe fusion of these two aspects will benefit research of those dedicated to development of biocatalytic process. The aim of this book is to present recent advances on basic aspects such as evolution, structure–function relation, and catalytic mechanism, as well as applied aspects, such as bioreactor and protein engineering, in order to provide the tools for rational design of enhanced biocatalysts and biocatalytic processes. The book does not include an exhaustive listing of references but rather a selected collection to enrich discussion and to allow envisioning future directions for research. This book is organized in three parts. In Part I, current knowledge of structure and mechanism of peroxidases is covered. From the molecular phylogeny, going through the influence of structural factors over oxidative ability to the molecular mechanism of catalysis, the authors intend to provide an understanding of perox- idases at the molecular level. The understanding of the fundamental behavior of peroxidases will allow further adequation, design, and/or optimization of peroxi- dase-based catalysis to a particular process. In Part II, research on potential applications of peroxidases in several fields is presented and discussed. New processes for the fine chemicals industry, creation of new materials with novel properties, and biotransformation of compounds found in polluted water and soil are the topics included in this part. Finally, Part III presents the challenges that must be overcome in order to develop commercially feasible peroxidase-based industrial processes. As discussed in Chap.1, lowering the cost of the biocatalyst is essential; thus, low cost production and increased stability is discussed in this part. A compendium of useful information on peroxidases is to be found at the end of v vi Preface the book, containing from biochemical properties such as molecular weight and isoelectric point to spectroscopic properties and kinetic data. We would like to thank all the recognized experts that participated as authors in this book. We are also indebted to Prof. Michael A. Pickard, emeritus professor from the University of Alberta, who dedicated all his professional life to the study of peroxidases, and who made significant contributions in the areas of microbial metabolism and fungal enzymes, particularly with chloroperoxidase from Caldar- iomyces fumago, for helpful discussion and editorial assistance. Puebla/Cuernavaca, 2010 Marcela Ayala Eduardo Torres Contents 1 Introduction ............................................................... 1 Marcela Ayala and Eduardo Torres Part I Molecular and Structural Aspects of Peroxidases 2 Molecular Phylogeny of Heme Peroxidases ............................. 7 Marcel Za´mocky´ and Christian Obinger 3 Structural and Functional Features of Peroxidases with a Potential as Industrial Biocatalysts ............................. 37 Francisco J. Ruiz-Duen˜as and Angel T. Martı´nez 4 Redox Potential of Peroxidases ......................................... 61 Marcela Ayala 5 Catalytic Mechanisms of Heme Peroxidases ........................... 79 Paul R. Ortiz de Montellano Part II Prospective Usage of Peroxidases in Industry 6 Potential Applications of Peroxidases in the Fine Chemical Industries ................................................................ 111 Luigi Casella, Enrico Monzani, and Stefania Nicolis 7 Grafting of Functional Molecules: Insights into Peroxidase-Derived Materials .................................... 155 Gibson S. Nyanhongo, Endry Nugroho Prasetyo, Tukayi Kudanga, and Georg Guebitz vii viii Contents 8 Applications and Prospective of Peroxidase Biocatalysis in the Environmental Field ............................................. 179 Cristina Torres-Duarte and Rafael Vazquez-Duhalt Part III Challenges in the Application of Peroxidases 9 Enzyme Technology of Peroxidases: Immobilization, Chemical and Genetic Modification .............................................. 209 Adriana Longoria, Raunel Tinoco, and Eduardo Torres 10 Reactor Engineering .................................................... 245 Juan M. Lema, Carmen Lo´pez, Gemma Eibes, Roberto Taboada-Puig, M. Teresa Moreira, and Gumersindo Feijoo 11 Deactivation of Hemeperoxidases by Hydrogen Peroxide: Focus on Compound III ............................................... 291 Brenda Valderrama 12 Heterologous Expression of Peroxidases .............................. 315 Sandra de Weert and B. Christien Lokman 13 A Compendium of Bio–Physical–Chemical Properties of Peroxidases ........................................................... 335 Humberto Garcia-Arellano Index .......................................................................... 353 Contributors Marcela Ayala Instituto de Biotecnologı´a, UNAM. Av. Universidad 2001, Chamilpa, 62210 Cuernavaca, Morelos, Me´xico, [email protected] Luigi Casella Dipartimento di Chimica Generale, Universita` di Pavia, Via Taramelli 12, 27100 Pavia, Italy, [email protected] Sandra de Weert Institute of Biology Leiden, Leiden University, Sylviusweg 72, 2333BE Leiden, The Netherlands, [email protected] Gemma Eibes Department of Chemical Engineering, School of Engineering, University of Santiago de Compostela, Santiago de Compostela E-15782, Spain Gumersindo Feijoo Department of Chemical Engineering, School of Engineering, University of Santiago de Compostela, Santiago de Compostela E-15782, Spain Humberto Garcia-Arellano Departamento de I Ingenierı´a Quı´mica y Bioquı´mica, Instituto Tecnolo´gico de Veracruz, Calz. M.A. De Quevedo 2779, C.P. 91860 Veracruz, Mexico, [email protected] Georg Guebitz Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12/1, A-8010 Graz, Austria Tukayi Kudanga Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12/1, A-8010 Graz, Austria Juan M. Lema Department of Chemical Engineering, School of Engineering, University of Santiago de Compostela, Santiago de Compostela E-15782, Spain, [email protected] ix x Contributors B. Christien Lokman HAN BioCentre, Laan van Scheut 2, 6525 EM Nijmegen, The Netherlands, [email protected] Carmen Lo´pez Department of Chemical Engineering, School of Engineering, University of Santiago de Compostela, Santiago de Compostela E-15782, Spain Adriana Longoria Instituto de Biotecnologı´a, UNAM. Av. Universidad 2001. Col. Chamilpa, Cuernavaca 62210, Morelos, Me´xico, [email protected] Angel T. Martı´nez Centro de Investigaciones Biolo´gicas, CSIC, Ramiro de Maeztu 9, E-28040 Madrid, Spain Enrico Monzani Dipartimento di Chimica, Generale Universita` di Pavia, Via Taramelli 12, 27100 Pavia, Italy, [email protected] M. Teresa Moreira Department of Chemical Engineering, School of Engineering, University of Santiago de Compostela, Santiago de Compostela E-15782, Spain Stefania Nicolis Dipartimento di Chimica Generale, Universita` di Pavia, Via Taramelli 12, 27100 Pavia, Italy, [email protected] Gibson S. Nyanhongo Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12/1, A-8010 Graz, Austria Christian Obinger Metalloprotein Research Group, Division of Biochemistry, Department of Chemistry, University of Natural Resources and Applied Life Sciences, Muthgasse 18, A-1190 Vienna, Austria Paul R. Ortiz de Montellano Department of Pharmaceutical Chemistry, University