HANDBOOK of FLAVOPROTEINS Volume 1 Oxidases, Dehydrogenases and Related Systems

Russ Hille, Susan Miller, Bruce Palfey (Eds.) HANDBOOK OF FLAVOPROTEINS Volume 1 Oxidases, Dehydrogenases and Related Systems

With contrib. by Donald Becker, Claudia Binda, Eduardo Ceccarelli, Pimchai Chaiyen, Antonio J. Costa Filho, Bastian Daniel, Corinna Dully, Dale Edmondson, Paul Fitzpatrick, Giovanni Gadda, Sandro Ghisla, Niels Henrik Gregersen, Hisashi Hemmi, Rikke Katrine Jentoft Olsen, Jung-Ja Kim, Peter Macheroux, Andrea Mattevi, Milagros Medina, Maria Cristina Nonato, Steven Rokita, Marilyn Schuman Jorns, John J. Tanner, Colin Thorpe, Shiao-Chun Tu, Maria A. Vanoni, Silvia Wallner, Thanyaporn Wongnate

ff Comprehensive treatment of the flavoenzymes ff From basic oxidation-reduction and electron transfer chemistry and enzyme biology to modern biotechnological applications of flavoproteins ff Extensive color figures

The dynamic field of flavin and flavoprotein biochemistry has seen rapid advancement in recent years. This comprehensive two volume set provi- des an overview of all aspects of contemporary research in this important class of enzymes. Topics treated include flavoproteins involved in energy generation, signal transduction and electron transfer (including respiration); oxygen activation by flavoproteins; the biology and biochemistry of complex flavoproteins; flavin and flavoprotein photochemistry/photophysics as well as biotechnological applications of flavoproteins. Recent developments in this field include new structures (including those of large membrane-integral 372 pp., 150 fig. electron transfer complexes containing FMN or FAD), elucidation of the role Hc. of flavoproteins in cell signalling pathways (including both phototaxis and RRP € 149.95 / *US$ 210.00 the circadian cycle) and important new insights into the reaction mechanisms ISBN 978-3-11-026842-3 of flavin-containing enzymes. This volume focussing on oxidases, dehyd- eBook RRP € 149.95 / *US$ 210.00 rogenases and related systems is an essential reference for all researchers ISBN 978-3-11-026891-1 in biochemistry, chemistry, photochemistry and photophysics working on Print + eBook flavoenzymes. RRP € 229.00 / *US$ 321.00 ISBN 978-3-11-026892-8

Date of publication December 2012 Russ Hille, University of California, Riverside, CA, USA; Susan Miller, University of California, San Francisco, CA, USA; Bruce Palfey, University Language English of Michigan, Ann Arbor, MI, USA. Subjects Chemistry  Chemistry, General Biology  Biotechnology Biochemistry  Biochemistry, General Biochemistry  Molecular Biology, Molecu- lar Genetics

*For orders placed in North America. Prices are subject to change. Prices do not include postage and handling. 02 / 13 Table of contents

Preface ...... vii

1 Berberine bridge enzyme and the family of bicovalent ﬂ avoenzymes ...... 1 1.1 Introduction ...... 1 1.2 The paradigm of bicovalent ﬂ avoenzymes: Berberine bridge enzyme (BBE) from Eschscholzia californica ...... 7 1.3 The family of BBE-like enzymes in the plant kingdom: how many and what for? ...... 11 1.4 The occurrence of BBE-like enzymes in fungi ...... 20 1.5 BBE-like enzymes in bacteria: oxidative power for the biosynthesis of antibiotics ...... 22 1.6 Conclusions ...... 24 1.7 Acknowledgments ...... 24 1.8 References ...... 24

2 PutA and proline metabolism ...... 31 2.1 Importance of proline metabolism ...... 31 2.2 Proline utilization A (PutA) proteins ...... 33 2.3 Three-dimensional structures of PutA and PutA domains ...... 36 2.3.1 Structures of the catalytic domains of PutA...... 36 2.3.2 Crystal structure of a minimalist PutA ...... 38 2.3.3 Solution structure of a trifunctional PutA and the role of the CTD ...... 40 2.4 Reaction kinetics of PutA ...... 40 2.4.1 Proline:ubiquinone oxidoreductase activity ...... 41 2.4.2 Substrate channeling ...... 43 2.5 DNA and membrane binding of trifunctional PutA ...... 45 2.5.1 DNA binding ...... 45 2.5.2 Membrane association ...... 47 2.6 PutA functional switching...... 49 2.6.1 Redox-linked global conformational changes ...... 49 2.6.2 Local structural changes near the ﬂ avin ...... 50 2.6.3 Residues important for functional switching ...... 51 2.7 Conclusions and future research directions ...... 52 2.8 Acknowledgements ...... 53 2.9 References ...... 53

3 Flavoenzymes involved in non-redox reactions...... 57 3.1 Introduction ...... 57 3.2 Flavoenzymes for which ﬂ avin cofactors likely play redox-based catalytic roles ...... 58

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3.2.1 Chorismate synthase ...... 58 3.2.2 4-Hydroxybutyryl-CoA dehydratase ...... 60 3.2.3 Polyunsaturated fatty acid isomerase ...... 62 3.2.4 4’-Phosphopantothenoylcysteine decarboxylase ...... 62 3.2.5 Other examples ...... 65 3.3 Flavoenzymes for which ﬂ avin cofactors likely play non-redox catalytic roles ...... 66 3.3.1 Type 2 isopentenyl diphosphate isomerase ...... 66 3.3.2 UDP-galactopyranose mutase ...... 68 3.4 Flavoenzymes for which ﬂ avin cofactors play uncertain, but probably catalytic roles ...... 69 3.4.1 Lycopene cyclase ...... 70 3.4.2 Carotene cis-trans isomerase ...... 70 3.4.3 Fatty acid hydratase ...... 72 3.4.4 2-Haloacrylate hydratase ...... 72 3.5 Conclusions ...... 72 3.6 References ...... 73

4 Enzymes of FMN and FAD Metabolism ...... 79 4.1 Introduction ...... 79 4.2 Enzymes involved in the production of FMN and FAD in different organisms ...... 80 4.3 FMN and FAD metabolism in yeasts and mammals ...... 83 4.4 FMN and FAD metabolism in bacteria depends on a bifunctional enzyme ...... 88 4.5 FMN and FAD metabolism in plants...... 91 4.6 Conclusions and future research directions ...... 93 4.7 Acknowledgments ...... 95 4.8 References ...... 95 4.9 Abbreviations ...... 99

5 Mechanisms of bacterial luciferase and related fl avin reductases ...... 101 5.1 Introduction ...... 101 5.2 Luciferase mechanism overview ...... 102 5.2.1 Mechanism of chemiexcitation ...... 102 5.2.2 Identity of primary excited state and emitter ...... 105 5.2.3 Multiple forms of 4a-hydroperoxy-FMNH intermediate II ...... 106 5.2.4 Aldehyde substrate inhibition ...... 107 5.3 Flavin reductases – general remarks ...... 108 5.3.1 Mechanisms of fl avin reductases in single-enzyme reactions ...... 109 5.3.2 Mechanisms of luciferase:fl avin reductase coupled reactions ...... 109 5.3.3 Reduced fl avin transfers in two-component monooxygenases in general ...... 112

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5.4 Acknowledgments ...... 113 5.5 References ...... 113

6 Amine and amino acid oxidases and dehydrogenases ...... 119 6.1 Introduction ...... 119 6.2 D-Amino acid oxidase and related enzymes ...... 120 6.3 Monoamine oxidase and related enzymes ...... 124 6.4 Trimethylamine dehydrogenase ...... 131 6.5 Conclusions ...... 133 6.6 Acknowledgments ...... 133 6.7 References ...... 133

7 Monoamine oxidases A and B: membrane-bound ﬂ avoenzymes of medical importance ...... 139 7.1 Introduction ...... 139 7.2 Structural studies of MAO A and MAO B ...... 141 7.3 Flavin cofactor properties ...... 144 7.4 Catalytic reaction pathway ...... 144 7.5 Mechanism of C-H bond cleavage and ﬂ avin reduction ...... 147

7.6 Reaction with O2 to form H2O2 ...... 149 7.7 Biological and pharmacological signiﬁ cance of MAO A and MAO B ...... 149 7.8 Acknowledgements ...... 150 7.9 References ...... 150

8 Choline oxidase and related systems ...... 155 8.1 Introduction ...... 155 8.1.1 Glucose-methanol-choline enzyme oxidoreductase superfamily ...... 156 8.1.2 Choline, glycine betaine and choline-oxidizing enzymes in biotechnology and medicine ...... 156 8.2 Choline oxidase ...... 159 8.2.1 Three-dimensional structure ...... 159 8.2.2 Biophysical properties ...... 162 8.2.3 Substrate speciﬁ city and inhibitors ...... 163 8.2.4 Steady-state kinetic mechanism ...... 164 8.2.5 Chemical mechanism for alcohol oxidation ...... 164 8.2.6 Chemical mechanism for aldehyde oxidation ...... 167 8.2.7 Oxygen activation for reaction with reduced ﬂ avin ...... 168 8.3 Choline dehydrogenase ...... 169 8.4 Thiamine oxidase/dehydrogenase ...... 169 8.5 Conclusions ...... 170 8.6 Acknowledgements ...... 170 8.7 References ...... 170

9 Pyranose oxidases ...... 177 9.1 Introduction ...... 177

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9.2 Pyranose 2-oxidase (EC 1.13.10) ...... 178 9.2.1 Importance and applications ...... 178 9.2.2 General biochemical and biophysical properties of P2O ...... 179 9.2.3 Structural studies on P2O ...... 180 9.2.4 Substrate recognition...... 182 9.2.5 Flavin reduction (sugar oxidation) mechanism ...... 183 9.2.6 Catalytic base for sugar oxidation in the P2O reaction ...... 184 9.2.7 Detection of a C4a-hydroperoxyﬂ avin intermediate in the reaction of P2O ...... 185

9.2.8 The mechanism of H2O2 elimination from C4a-hydroperoxyﬂ avin ...... 187 9.3 Glucose 1-oxidase (EC. 1.1.3.4) ...... 188 9.3.1 Biochemical properties and application of GO ...... 188 9.3.2 Flavin reduction of GO ...... 189 9.3.3 Oxidative half-reaction of GO ...... 190 9.4 Conclusions and future prospects ...... 190 9.5 References ...... 191

10 Toward understanding the mechanism of oxygen activation by ﬂ avoprotein oxidases ...... 195 10.1 Introduction ...... 195 10.2 Results and discussion ...... 196 10.2.1 Lys265 is the oxygen activation site in MSOX ...... 196 10.2.2 Lys259 is the oxygen activation site in MTOX ...... 199 10.2.3 A pair of lysines comprise the oxygen activation site in TSOX ...... 201 10.2.4 Probing the oxygen activation site in MSOX using chloride as an oxygen surrogate ...... 203 10.2.5 Oxygen access to the proposed activation sites in TSOX and MSOX ...... 206 10.3 Common themes and mechanistic diversity ...... 208 10.4 References ...... 209

11 The acyl CoA dehydrogenases ...... 213 11.1 Introduction ...... 213 11.2 Overall structure of soluble ACADs ...... 214 11.2.1 Medium chain acyl-CoA dehydrogenase (MCAD) ...... 215 11.2.2 Short chain acyl-CoA dehydrogenase (SCAD) ...... 217 11.2.3 Glutaryl-CoA dehydrogenase (GD) ...... 217 11.2.4 Very Long Chain Acyl-CoA Dehydrogenase (VLCAD) ...... 217 11.2.5 Position of the catalytic base in primary sequence ...... 219 11.3 The basic biochemical mechanism of the α,β-dehydrogenation step ...... 220 11.3.1 Chain length specifi city and pH dependence ...... 223 11.3.2 The oxidative half-reaction/interactions of ACADs with electron transfer fl avoprotein (ETF) ...... 223 11.3.3 The inhibition/inactivation of ACADs ...... 225 11.3.4 Defi ciencies of ACADs ...... 226

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11.4 Biogenesis of mitochondrial FAO proteins ...... 228 11.5 MCAD defi ciency ...... 230 11.6 ETF-QO defi ciency ...... 232 11.7 VLCAD defi ciency ...... 234 11.8 ACAD 9 defi ciency ...... 235 11.9 SCAD defi ciency ...... 236 11.9.1 Clinical aspects of SCAD defi ciency ...... 237 11.9.2 Biochemical aspects of SCAD defi ciency ...... 237 11.9.3 Molecular genetics of SCAD defi ciency ...... 237 11.9.4 Molecular pathogenesis of SCAD defi ciency ...... 238 11.9.5 Cellular pathological aspects of SCAD defi ciency ...... 239 11.10 Acknowledgements ...... 240 11.11 Abbreviations ...... 240 11.12 References ...... 240

12 Flavoproteins in oxidative protein folding ...... 249 12.1 Oxidative protein folding ...... 249 12.2 Convergent evolution of three classes of FAD-dependent sulfhydryl oxidases ...... 251 12.3 Two fl avin-dependent pathways for protein disulfi de bond generation in eukaryotes ...... 251 12.3.1 Quiescin-sulfhydryl oxidases: structural aspects ...... 253 12.3.2 Mechanistic studies of QSOX ...... 254 12.3.3 QSOX can catalyze oxidative protein folding ...... 256 12.3.4 Cellular roles of QSOX ...... 257 12.4 Small ERV domain containing enzymes ...... 258 12.4.1 Erv2p ...... 258 12.4.2 Disulfi de bond formation in the mitochondrial intermembrane space ...... 260 12.4.3 Viral ALR proteins ...... 262 12.5 Ero1 ...... 263 12.6 Conclusions ...... 264 12.7 Acknowledgments ...... 264 12.8 References ...... 264

13 Glutamate synthase ...... 271 13.1 Introduction ...... 271 13.1.1 NADPH-GltS ...... 272 13.1.2 Fd-GltS ...... 272 13.1.3 NADH-GltS ...... 272 13.1.4 Archeal GltS ...... 272 13.2 The GltS-catalyzed reactions ...... 274 13.3 Flavins and iron-sulfur centers of GltS ...... 276 13.4 Localization of catalytic subsites and coenzymes ...... 276 13.5 Mid-point potential values of the GltS cofactors and electron transfer pathway between the GltS ﬂ avins ...... 278

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13.6 Structure of αGltS and FdGltS and the mechanism of control and coordination of the partial activities ...... 281 13.7 Structure of the NADPH-GltS αβ-protomer ...... 289 13.8 Acknowledgments ...... 291 13.9 References ...... 292

14 The dihydroorotate dehydrogenases ...... 297 14.1 Biological function ...... 297 14.2 Protein production, puriﬁ cation and kinetic characterization ...... 298 14.2.1 Puriﬁ cation ...... 298 14.2.2 Activity test ...... 299 14.3 X-ray structures ...... 299 14.3.1 Crystallization ...... 299 14.3.2 Overall description of the atomic structure...... 300 14.4 Mechanism ...... 302 14.4.1 Asymmetric behavior of Class 1A DHODH monomers ...... 304 14.4.2 Class 2 DHODHs and the interaction with membranes ...... 305 14.5 Therapeutic potential ...... 307 14.6 References ...... 308

15 Ferredoxin-NADP+ reductases...... 313 15.1 Introduction ...... 313 15.2 Classiﬁ cation of FNRs ...... 314 15.3 Structural features of FNR ...... 318 15.4 Interaction of FNR with its natural substrates ...... 318 15.5 The metabolic roles of FNR ...... 321 15.6 Activities of ferredoxin-NADP+ reductase ...... 321 15.7 Puriﬁ cation procedures ...... 323 15.7.1 Transgenic expression in E. coli ...... 323 15.7.2 Preparation of soluble protein extracts ...... 324 15.7.3 Spectroscopic properties of FNR ...... 326 15.8 Conclusions ...... 328 15.9 Acknowledgments ...... 328 15.10 Abbreviations ...... 329 15.11 References ...... 329

16 Flavoprotein dehalogenases ...... 337 16.1 Organic halides and biological dehalogenation ...... 337 16.1.1 Strategies for dehalogenation...... 338 16.2 Flavin-dependent dehalogenation ...... 340 16.2.1 Oxidative dehalogenation by fl avoproteins...... 341 16.2.2 Hydrolytic dehalogenation catalyzed by fl avoproteins ...... 341 16.2.3 Reductive dehalogenation catalyzed by fl avoproteins ...... 343 16.3 Conclusions ...... 346 16.4 References ...... 347

Index ...... 351

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