Table Of ContentHeme Peroxidases
RSC Metallobiology Series
Editor-in-Chief:
Professor C. David Garner, University of Nottingham, UK
Series Editors:
Professor Hongzhe Sun, University of Hong Kong, China
Professor Anthony Wedd, University of Melbourne, Australia
Editorial Advisors:
Professor Alison Butler, University of California Santa Barbara, USA
Professor Stefano L. Ciurli, University of Bologna, Italy
Titles in the Series:
1: Mechanisms and Metal Involvement in Neurodegenerative Diseases
2: Binding, Transport and Storage of Metal Ions in Biological Cells
3: 2-Oxoglutarate-Dependent Oxygenases
4: Heme Peroxidases
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Heme Peroxidases
Edited by
Emma Raven
University of Leicester, Leicester, UK
Email: [email protected]
and
Brian Dunford
University of Alberta, Edmonton, Canada
Email: [email protected]
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PrintISBN:978-1-84973-911-5
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Preface
In about 2012, Brian Dunford and Emma Raven agreed, in principle, to
produce a book on heme peroxidases—a conceptually simple task.
Acunningplanwassoondevised,andeventuallyexecuted.Theobjectivewas
to produce updates to Dunford’s earlier two peroxidase texts1,2 by bringing
togetheracollectionofresearchcontributionsallfocusedonvariousaspects
ofhemeperoxidasesandexamined,forthemostpart,throughtheprismof
heme protein structure and mechanism.
Unfortunately, the scientific literature is hardly ever neat and tidy. To a
noviceoreventoanexperiencedhack,theperoxidaseliteraturecanbeatthe
same time frightening and frustrating—if one digs hard enough for long
enoughthengood,badanduglywillbeunearthed.Theaimofthisbookisto
helpthereaderinsummarizingthistrulyvastbodyofinformation.Wehave
presentedthebookthematically.This,itwasdecided,wouldbethesimplest
and most informative way of weaving the complexity of material together.
There are sections on the Structure and Reactivity of Heme Peroxidases (Paul
Ortiz de Montellano, Tom Poulos, Emma Raven, Giulietta Smulevich, Brian
Dunford and Oliver Einsle), on Catalase Peroxidases (Peter Loewen and
Christian Obinger), on Models of Peroxidase Structure and Mechanism
(Hiroshi Fujii, John Dawson/Stefan Franzen), on Mammalian Peroxidases
(Larry Marnett, Tony Kettle/Christine Wintertbourn) and on Industrial and
Biomedical Applications (Eduardo Torres/Marcela Ayala, Tim Bugg). A sad
omission is a chapter on thyroid peroxidase. The passing of the late Alvin
Taurog left a void that we found we could not fill.
RowanFrameandtheRoyalSocietyofChemistryofficeinCambridgehave
been a pleasure to work with throughout, and our book would never have
madeitoutofthestartingblockswithouttheirunwaveringsupport.Butno
amount of professional assistance from publishers can prepare editors for
the many agonies associated with a project of this scale. Our blood, sweat
RSCMetallobiologySeriesNo.4
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vi Preface
andtearswillforeverbeindeliblyingrainedonthepages.Wethankeveryone
else who helped us; especially those unnamed reviewers, some of whom
worked for us at very short notice to make sure things were up to snuff.
This book was made possible, in part, by financial assistance from The
Daiwa Foundation and the RSC Travel Grants Scheme.
We hope it was all worth it and that you, the reader, find what you were
looking for. We know that we have not been able to cover everything. So if
the information that you seek is missing, or (worse) incorrect, then please
accept our deepest apologies and be greatly reassured that, accordingly to
established timescales, it will only be a ten year wait before a new edition
appears.
Emma Raven
Leicester, England
Brian Dunford
Edmonton, Canada
References
1. H. B. Dunford, Heme Peroxidases, John Wiley, Chichester, 1999.
2. H. B. Dunford, Peroxidases and Catalases: Biochemistry, Biophysics, Bio-
technology and Physiology, John Wiley, Chichester, 2nd edn, 2010.
Contents
Author Biographies xv
Section 1 Structure and Reactivity of Heme Peroxidases
Chapter 1 Self-processing of Peroxidases 3
Paul R. Ortiz de Montellano
1.1 Introduction 3
1.2 Protein Modifications 4
1.2.1 Lignin Peroxidases 4
1.2.2 KatG Peroxidases 7
1.3 Heme–Protein Crosslinking 10
1.3.1 Mammalian Peroxidase Ester Links 10
1.3.2 Bacterial Peroxidase Ester Links 13
1.3.3 MPO Methionine–Vinyl Crosslink 14
1.3.4 Model Reactions 15
1.3.5 Role of Methionine–Vinyl Crosslink 20
1.3.6 Role of Ester Crosslinks 22
1.4 Conclusions 24
References 25
Chapter 2 Cytochrome c Peroxidase–Cytochrome c Complexes 31
Thomas L. Poulos
2.1 Initial Studies 31
2.2 CCP–cytc Structure 32
2.3 One Site or Two? 36
2.4 Electron Transfer 38
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2.5 The CCP Trp Radical 40
2.6 Other CCPs 42
2.7 LmP–cytc Crystal Structure 42
2.8 Summary and Conclusion 43
References 44
Chapter 3 Understanding the Reactivity and Interactions of
Peroxidases with Substrates 47
Hanna Kwon, Peter C. E. Moody and Emma L. Raven
3.1 Introduction and Early Studies 47
3.2 DevelopmentofaFrameworkforSubstrateBinding
across the Peroxidase Family 48
3.3 Binding of Mn(II) to Peroxidases 50
3.4 Binding of Ascorbate to Peroxidases 52
3.5 Binding of Hydroxamic Acids to Peroxidases 52
3.6 Binding of Isoniazid to Peroxidases 53
3.7 Binding of Guaiacol and Other Phenolic Substrates
to Peroxidases 54
3.8 Summary 56
References 56
Chapter 4 Structural and Functional Properties of Heme-containing
Peroxidases: a Resonance Raman Perspective for the
Superfamily of Plant, Fungal and Bacterial Peroxidases 61
Giulietta Smulevich, Barry D. Howes and Enrica Droghetti
4.1 Introduction 61
4.2 Superfamily of Plant, Fungal and Bacterial
Peroxidases 63
4.3 AnOverviewofthe ResonanceRamanSpectroscopy
of Heme Proteins 65
4.3.1 Coordination and Spin States of Heme
Proteins 67
4.4 Distal Fe–Ligand Modes as a Probe of Heme Cavity
Structure 67
4.4.1 The Hydroxo Ligand 68
4.4.2 The Fluoride Ligand 69
4.4.3 The CO Ligand 71
4.5 The Proximal Iron–Histidine Stretching Mode:
a Sensitive Probe of Proximal Properties 74
4.5.1 Status of the Fe-proximal Histidine Bond in
Peroxidases 74
Contents ix
4.6 Effect of Mutation 77
4.6.1 Proximal Mutation-induced Effects in the
Distal Cavity 77
4.6.2 Distal Mutation-induced Effects in the
Proximal Cavity 80
4.6.3 ControlofWaterBindingbyDistalMutation 86
4.7 Raman Microscopy Combined with X-ray
Crystallography 87
4.8 Conclusions 91
Acknowledgements 91
References 91
Chapter 5 Heme Peroxidase Kinetics 99
H. Brian Dunford
5.1 Introduction 99
5.2 Kinetics: from the Steady State to Transient State 100
5.3 Oxidation States Six to Two 102
5.4 Mechanism of Compound I Formation 104
5.5 Neutron Diffraction Experiments on Yeast
Cytochrome c Peroxidase 107
5.6 Mechanism of Compound I Reduction 108
5.6.1 Two-electron Reductions of Compound I 108
5.7 Mechanism of Compound II Reduction 109
5.8 Steady State Reactions 109
References 110
Chapter 6 Multiheme Peroxidases 113
AntonBrausemann,JulianSeidel,AnjaWu¨standOliverEinsle
6.1 Biological Significance 113
6.2 Structural Information 114
6.2.1 ArchitectureofBacterialDihemePeroxidases 114
6.2.2 Redox-dependent Structural Changes in
bCCPs 116
6.3 The Mechanism of Peroxide Reduction 118
6.3.1 Reductive Activation of the Enzyme 118
6.3.2 Interaction with the Physiological Electron
Donor 120
6.3.3 The Critical Oxoferryl Intermediate 121
6.4 Related Multiheme Cytochromes 121
6.4.1 Novel Members of the bCCP Family 121
6.4.2 MauG 122
x Contents
6.4.3 Triheme CCPs 124
6.4.4 RoxA 125
6.5 Further Aspects of the bCCP Family 126
Acknowledgements 127
References 127
Section 2 Catalase Peroxidases
Chapter 7 Catalase-peroxidase (KatG) Structure and Function 135
Ignacio Fita, Xavi Carpena and Peter C. Loewen
7.1 Introduction 135
7.2 Features of the KatG Structure 136
7.2.1 Core Structure 136
7.2.2 Disorder in the N-terminal Region 139
7.2.3 Heme Environment 140
7.2.4 Access to the Heme 141
7.2.5 Tryptophan Content 143
7.2.6 Met-Tyr-Trp Crosslinked Adduct and Mobile
Arginine 143
7.2.7 PerhydroxyModificationoftheMYWAdduct 144
7.3 INH and NAD1 Binding to KatG 146
7.4 Structural Implications for the Catalytic
Mechanism 149
References 152
Chapter 8 Mechanistic Aspects of Catalase-peroxidase 156
Bernhard Gasselhuber, Christa Jakopitsch, Marcel Za´mock´y,
Paul G. Furtmu¨ller and Christian Obinger
8.1 Phylogenetic Distribution 156
8.2 Functional and Structural Peculiarities of KatG 159
8.3 The Pseudocatalase Activity of KatG 165
8.4 The Peroxidase Activity of KatG 171
8.5 Catalase versus Peroxidase Activity 174
Abbreviations 175
References 176
Section 3 Models of Peroxidase Structure and Mechanism
Chapter 9 Model Complexes of Heme Peroxidases 183
Hiroshi Fujii
9.1 Introduction 183
9.2 Model Complexes of the Ferric Resting State 185
