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Molybdenum and Tungsten Enzymes

Molybdenum and Tungsten Enzymes

Russ Hille | Carola Schulzke | Martin L Kirk

(2016)

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Book Details

Abstract

There has been enormous progress in our understanding of molybdenum and tungsten enzymes and relevant inorganic complexes of molybdenum and tungsten over the past twenty years. This set of three books provides a timely and comprehensive overview of the field and documents the latest research.
The first volume in the set focusses on the enzymes themselves, and discusses active sites and substrate channels of relevant proteins. The book begins with an introductory overview of the whole field. Chapters are contributed by world leaders and topics covered include pyranopterin cofactor biosynthesis and incorporation of the mature cofactor into apoprotein. Subsequent volumes cover the bioinorganic chemistry relevant to these enzymes and the full range of spectroscopic and theoretical methods that are used to investigate their physical and electronic structure and function.
This text will be a valuable reference to workers both inside and outside the field, including graduate students and young investigators interested in developing new research programs in this area.


This book is edited by Professor Russ Hille (University of California, Riverside), Professor Carola Schulzke (University of Greifswald) and Professor Martin Kirk (University of New Mexico) who have over 275 publications ad over 65 years of experience between them in the field. Their complementary expertise in molybdenum containing enzymes, bioinorganic chemistry and the physical inorganic chemistry of molybdenum complexes and enzymes, respectively, allow the authoritative and comprehensive coverage demonstrated in this book.


Table of Contents

Section Title Page Action Price
Cover Cover
Molybdenum and Tungsten Enzymes Biochemistry i
Preface v
Dedication vii
Contents ix
Chapter 1 - Molybdenum and Tungsten-Containing Enzymes: An Overview 1
1.1 Introduction 1
1.2 Living with Molybdenum and Tungsten 2
1.2.1 The Nitrogen-to-Molybdenum Bio-to-Inorganic Bridge Hypothesis 6
1.3 Chemistry Relevant to Molybdenum and Tungsten Biochemistry 9
1.4 Molybdenum- and Tungsten-Containing Enzymes 15
1.4.1 The Xanthine Oxidase Family 17
1.4.2 The Sulfite Oxidase Family 25
1.4.3 The Dimethylsulfoxide Reductase Family 32
1.4.4 The Tungstoenzymes Family 43
1.4.5 The Nitrogenases 49
1.4.6 A Novel Heterometallic Cluster Containing Molybdenum Found in Biology 52
1.5 Outlook 52
Abbreviations 53
Acknowledgements 54
References 54
Chapter 2 - Abundance, Ubiquity and Evolution of Molybdoenzymes 81
2.1 Introduction 81
2.2 Molybdate Uptake and Molybdenum Cofactor Biosynthesis 83
2.3 Classification of Molybdoenzymes 85
2.4 Occurrence and Evolution of Molybdenum Utilization and Molybdoenzymes 88
2.4.1 Occurrence of Molybdenum Transport and Moco Biosynthesis Pathway Genes 88
2.4.2 Distribution and Phylogeny of Molybdoenzymes 90
2.4.3 Factors that May Affect Evolution of Mo Utilization and Molybdoenzymes 92
2.5 Concluding Remarks 93
Acknowledgements 94
References 94
Chapter 3 - Molybdenum Cofactor Biosynthesis 100
3.1 Introduction 100
3.2 Formation of cPMP from 5′GTP 104
3.3 Formation of MPT by Sulfur Insertion into cPMP 105
3.4 Insertion of Molybdate into MPT 108
3.5 Further Modification of Moco 109
3.5.1 Formation of bis-MGD 109
3.5.2 The Formation of the MCD Cofactor 109
3.5.3 Moco Sulfuration in Eukaryotes 110
3.6 Trafficking of Moco in the Cell 110
3.7 Conclusions 111
Acknowledgements 111
References 111
Chapter 4 - Bacterial Molybdoenzymes: Chaperones, Assembly and Insertion 117
4.1 Introduction 117
4.2 The Essential Role of Dedicated Chaperones for Molybdoenzyme Assembly 118
4.2.1 Chaperones are Required for the Biogenesis of Cognate Molybdoenzymes 118
4.2.2 Structural Constraints of Molybdoenzymes 120
4.2.3 The Identification of Chaperones Dedicated to Specific Molybdoenzymes 120
4.3 The TorD Family of Moco-Binding Chaperones 122
4.3.1 Subfamily Organization of the TorD-Like Chaperones 122
4.3.2 Structural Features of TorD-Like Chaperones 124
4.3.3 Mechanism of Molybdoenzyme Maturation Dependent on TorD-Like Chaperones 125
4.3.3.1 Maturation of TorA, a Soluble Monomeric Molybdoenzyme 125
4.3.3.2 Maturation of Complex Membrane-Associated Molybdoenzymes 127
4.3.3.3 bis-MGD Enzymes Can Acquire Other Accessory Proteins 128
4.3.3.4 Systems Without a Dedicated Chaperone 129
4.4 The Maturation of Formate Dehydrogenases 129
4.5 The Step of Moco Sulfuration for Enzymes of the Xanthine Oxidase Family 133
4.6 Conclusions 136
Funding 136
Acknowledgements 136
References 137
Chapter 5 - The Prokaryotic Mo/W-bisPGD Enzymes Family 143
5.1 Introduction 143
5.2 Reactivity and Substrate Specificity 146
5.2.1 Role of the Mo/W Ligands 149
5.2.2 Role of Amino Acids in the Immediate Environment of the Mo/W Atom 151
5.2.3 Role of the Pterins 152
5.2.4 What Can We Learn from Phylogenetic Analysis of the Mo-bisPGD Superfamily 153
5.3 Molecular Variation of the Mo/W-bisPGD Enzymes 155
5.3.1 The Catalytic Subunit 155
5.3.2 The Electron Transfer Subunit 158
5.3.2.1 Archetypal Subunit 158
5.3.2.2 “Exotic” Subunits 159
5.3.3 The Electron Entry/Exit Subunit 160
5.3.3.1 b-Type Cytochromes 160
5.3.3.2 The NrfD-Type Subunits 161
5.3.3.3 c-Type Cytochromes 161
5.3.3.4 The HydA Subunit in the Hydrogen-Dependent Carbon Dioxide Reductase System 162
5.3.3.5 The NapGH Component 162
5.4 Metabolic Chains Involving Mo/W-bisPGD Enzymes 163
5.4.1 Enzymes Involved in the Nitrogen Cycle 164
5.4.1.1 Nas and Nitrogen Assimilation 165
5.4.1.2 Nar and Nitrate Respiration 166
nNar and cNar.The first step of the bacterial denitrification pathway, catalyzed by the cytoplasmically oriented membrane-bound ... 166
pNar.Several archaeal denitrifiers (e.g. several Haloarchaea sp.244–247) possess a Nar complex that shows two main differences a... 169
5.4.1.3 Nap and Respiration or Dissipation of Excess Reductant 170
5.4.1.4 Nxr and Nitrification or Anammox 171
5.4.2 Enzymes Involved in the Sulfur Cycle 172
5.4.3 Enzymes Involved in the Carbon Cycle 174
5.5 Concluding Remarks 176
Acknowledgements 177
References 177
Chapter 6 - Enzymes of the Xanthine Oxidase Family 192
6.1 Introduction 192
6.2 An Overview of Enzymes from the Xanthine Oxidase Family 195
6.3 Xanthine Oxidoreductases from Eukaryotes and Bacteria 200
6.3.1 The Crystal Structure of Bovine XOR 202
6.3.2 The Xanthine Oxidase/Dehydrogenase Enigma 202
6.3.3 The Physiological Role of Xanthine Oxidoreductase in Mammals 205
6.3.4 The Bacterial XDH from Rhodobacter capsulatus 206
6.3.5 The Mechanism of Substrate Conversion at the XOR Active Site 208
6.3.6 Medical Relevance of XOR 211
6.4 Aldehyde Oxidases 213
6.4.1 The Mammalian Aldehyde Oxidases 214
6.4.1.1 Gene Structure and Expression 214
6.4.1.2 Substrates of Mammalian Aldehyde Oxidases 216
6.4.1.3 Single Nucleotide Polymorphisms 217
6.4.1.4 The Crystal Structure of mAOX3 217
6.4.1.5 Catalytic Mechanism 219
6.4.1.6 The FAD Site 221
6.4.2 Bacterial Aldehyde Oxidoreductases 222
6.4.2.1 The Aldehyde Oxidoreductase MOP from Desulfovibrio gigas 222
6.4.2.2 Quinoline 2-Oxidoreductase from Pseudomonas putida 86 224
6.4.3 Unusual Bacterial Enzymes of the XO Family with Unique Features 226
6.4.3.1 Reversing the Reaction Mechanism in 4-Hydroxybenzoyl-CoA-Reductase 226
6.4.3.2 A Selenide Ligand at the Active Site of Nicotinate Dehydrogenase 227
6.4.3.3 The Only Binuclear Molybdenum Enzyme: Copper and Molybdenum at the Active Site of CODH 229
6.5 Conclusions 231
Acknowledgements 231
References 232
Chapter 7 - The Sulfite Oxidase Family of Molybdenum Enzymes 240
7.1 Introduction 240
7.2 Phylogenetic Structure of the SO Enzyme Family 241
7.3 SO Family Enzymes from Different Types of Organisms 246
7.3.1 SO Family Enzymes from Bacteria 246
7.3.1.1 The cd_02107 Group: YedY and Related Enzymes 246
7.3.1.2 The cd_02108 Group of Enzymes 247
7.3.1.3 SO Family Proteins from Archaea and Proteobacteria (cd_02109) 248
7.3.1.4 The Bacterial Enzymes of the “Moco-dimer” Group – Bacterial Sulfite and Sulfur Dehydrogenases 249
7.3.1.5 The Bacterial SoxCD Proteins (cd_02113) 250
7.3.1.6 The Bacterial “SorA”-type Sulfite Dehydrogenases (cd_02114) 251
7.3.1.7 Other Bacterial Sulfite Oxidizing Enzymes (cd_02110) 252
7.3.2 SO Family Enzymes from Vertebrates 255
7.3.2.1 Maturation of Mammalian SO 256
7.3.2.2 Catalytic Cycle in Vertebrate SO 256
7.3.2.3 SO Deficiency 258
7.3.3 SO Family Enzymes from Plants 261
7.3.3.1 Nitrate Reductase 261
7.3.3.2 SO in Plants 262
7.4 General Aspects of Catalysis in SO Family Enzymes 263
7.4.1 Sulfite Oxidizing Enzymes 263
7.4.2 Nitrite Reduction by SO and Other Mo Enzymes 266
7.5 Concluding Remarks 267
Acknowledgements 268
References 268
Chapter 8 - Nitrogenase Mechanism: Electron and Proton Accumulation and N2 Reduction 274
8.1 Introduction 274
8.2 Electron Transfer and ATP Hydrolysis in Nitrogenase 276
8.2.1 Docking of Fe Protein to the MoFe Protein 276
8.2.2 Electron Transfer Events 277
8.2.3 ATP and Nitrogenase 279
8.2.4 Negative Cooperativity in the Electron Transfer/ATP Hydrolysis Cycle 281
8.3 On the Mechanism of N2 Reduction 282
8.3.1 E4: The “Janus Intermediate” 284
8.3.2 “Dueling” N2 Reduction Pathways 285
8.3.3 Nitrite and Hydroxylamine as Nitrogenase Substrates: Mechanistic Implications for the Pathway of N2 Reduction 287
8.3.4 Mechanistic Convergence and its Implications 287
8.3.5 Evolution of One H2 per N2 Reduced in Nitrogen Fixation is Obligatory 289
8.3.5.1 Hydride Protonation (hp) Mechanism 290
8.3.5.2 Reductive Elimination (re) Mechanism 290
8.3.6 First Experimental Test of the re Mechanism 291
8.3.7 Second Experimental Test of re: Identification of the Key E4(2N2H) Catalytic Intermediate 291
8.4 Summary and Prospects 293
Acknowledgements 294
References 294
Chapter 9 - Biosynthesis of the M-Cluster of Mo-Nitrogenase 297
9.1 Introduction 297
9.2 M-Cluster Assembly 299
9.2.1 Overview 299
9.2.2 Formation of a Precursor to the M-Cluster 299
9.2.3 Maturation of the Precursor into an M-Cluster 306
Acknowledgements 310
References 310
Chapter 10 - Tungsten-Containing Enzymes 313
10.1 Introduction 313
10.2 General Properties of Tungstoenzymes 314
10.2.1 Tungsten-Based Enzymology: State of the Art 314
10.2.2 Tungsto-Pterin Prosthetic-Group: Nomenclature Issues 315
10.2.3 Tungstoenzymes Come in Two Families 317
10.2.4 Reactions Catalyzed by Tungstoenzymes 319
10.3 Specific Properties of AOR-Family Tungstoenzymes 321
10.3.1 Aldehyde Oxidoreductases 321
10.3.1.1 Substrate Specificity 322
10.3.1.2 Reaction Mechanism 323
10.3.2 Benzoyl-CoA Reductase 326
10.4 Specific Properties of DMSOR-Family Tungstoenzyme 328
10.4.1 Formate Dehydrogenase 328
10.4.2 Formylmethanofuran Dehydrogenase 329
10.4.3 DMSO Reductase 331
10.4.4 Nitrate Reductase 332
10.4.5 Acetylene Hydratase 332
10.5 Tungsten Metallomics 333
10.6 Why Tungsten 335
References 337
Subject Index 343