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HANDBOOK of FLAVOPROTEINS Volume 1 Oxidases, Dehydrogenases and Related Systems

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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 f Comprehensive treatment of the flavoenzymes f From basic oxidation-reduction and electron transfer chemistry and en- zyme biology to modern biotechnological applications of flavoproteins f 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 f Chemistry, General Biology f Biotechnology Biochemistry f Biochemistry, General Biochemistry f 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 Unauthenticated | 173.21.152.172 Download Date | 9/25/13 4:30 PM x Table of contents 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
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