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Structural and Functional Studies of the Light-Dependent Protochlorophyllide Oxidoreductase Enzyme

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Structural and Functional Studies of the Light-Dependent Protochlorophyllide Oxidoreductase Enzyme Structural and Functional Studies of the Light-Dependent Protochlorophyllide Oxidoreductase Enzyme David Robert Armstrong Department of Molecular Biology and Biotechnology A thesis submitted for the degree of Doctor of Philosophy September 2014 Abstract The light-dependent enzyme protochlorophyllide oxidoreductase (POR) is a key enzyme in the chlorophyll biosynthesis pathway, catalysing the reduction of the C17 - C18 bond in protochlorophyllide (Pchlide) to form chlorophyllide (Chlide). This reaction involves the light- induced transfer of a hydride from the nicotinamide adenine dinucleotide phosphate (NADPH) cofactor, followed by proton transfer from a catalytic tyrosine residue. Much work has been done to elucidate the catalytic mechanism of POR, however little is known about the protein structure. POR isoforms in plants are also notable as components of the prolamellar bodies (PLBs), large paracrystalline structures that are precursors to the thylakoid membranes in mature chloroplasts. Bioinformatics studies have identified a number of proteins, related to POR, which contain similar structural features, leading to the production of a structural model for POR. A unique loop region of POR was shown by EPR to be mobile, with point mutations within this region causing a reduction in enzymatic activity. Production of a 2H, 13C, 15N-labelled sample of POR for NMR studies has enabled significant advancement in the understanding of the protein structure. This includes the calculation of backbone torsion angles for the majority of the protein, in addition to the identification of multiple dynamic regions of the protein. The protocol for purification of Pchlide, the substrate for POR, has been significantly improved, providing high quality pigment for study of the POR ternary complex. Various biophysical techniques have been used to study the macromolecular structure of these complexes, indicating the formation of large aggregates of the cyanobacterial enzyme induced by substrate binding, similar to PLBs. This has also led to the identification of ring structures, composed of 5 and 6 monomers of POR, which are likely to be the primary components of the cyanobacterial POR structures. Page | i Acknowledgements Firstly, I would like to thank my two supervisors Mike and Neil for their endless support and expertise, which has helped me tremendously throughout my project. I have been privileged to have two supervisors with such a vast combined knowledge of all things biochemical, and I have attempted to absorb as much of that as possible! I have also been extremely lucky to have formed a number of excellent collaborations, gaining experience in many different biophysical techniques, including: NMR with Hans Wienk in Utrecht; AUC with Steve Harding and David Morou-Besong in Nottingham; EPR with Steve Rigby, and NMR with Matt Cliff, both in Manchester; and DLS at Malvern Instruments. I am also grateful to the BBSRC for funding my research (and my Friday night pub trips!). From the Hunter group, I must especially thank Mo for all her help and preventing me, literally, from burning down the lab. Notable mentions also go to Andy Proudfoot for laying the foundations for my project, Sarah for her collaboration on pigment work, and Cvet and Qian for their wizardry on AFM and EM, respectively. I am so glad to have made so many friends within this lab: Dave and Lizzy, who drew out the board game geek in me; Jimbo, for doing all my running at football; Gooch, in particular for winding up Ken; Ken, for being so enjoyable to wind up (top red!); and Craig, for his many philosophical ‘would you rather’ questions. From the NMR group, special thanks go to Andrea, who has helped me immensely and has shown a lot of patience with me over the years. All of the NMR group have given me invaluable help during lab meetings and carried me through to the weekend with Friday cake! A shout out goes to all my excellent drinking buddies, the various Kelly lab members, those from other regions of Firth Court, and the friends I’ve had since undergrad. I have had some great housemates, particularly Dean, Mike and Gav, and felt safe with Ellie’s Neighbourhood Watch alerts. I’m also indebted to Intra Mural for many hours of cheap football. My best times have always come with two pairs of brilliant friends. In Sheffield, Jack and Ash, who have always been there, from the sweaty Corp nights through to the drug checks with German police. In St Albans, Paul and Mark, who never let me forget where home is - I could never stay North for more than a few weeks without coming back to see you guys. Finally, I am so grateful for the support and love of my family. My Nana has always shown how proud she is of me and sent me back up North with many a cake! Bex, you’re the best big sister anyone could hope for. Mostly though, this is for my parents, who are two of the kindest people and have always pushed me to do my best. I love you both very much. Page | ii Table of Contents Abstract ............................................................................................................................. i Acknowledgements ........................................................................................................... ii Table of Contents ............................................................................................................. iii Table of Figures ................................................................................................................. x Table of Tables .................................................................................................................xv Table of Equations............................................................................................................xv List of Abbreviations ....................................................................................................... xvi 1. Introduction .............................................................................................................. 1 1.1 Oxygenic photosynthesis .................................................................................................. 1 1.2 Photosynthetic Bacteria .................................................................................................... 2 1.2.1 Cyanobacteria ............................................................................................................ 3 1.3 Structure of chlorophylls................................................................................................... 3 1.4 Common steps in tetrapyrrole biosynthesis ..................................................................... 4 1.4.1 Formation of δ-aminolaevulinic acid ......................................................................... 4 1.4.2 δ-aminolaevulinic acid to porphobilinogen ............................................................... 5 1.4.3 Porphobilinogen to hydroxymethylbilane ................................................................. 6 1.4.4 Hydroxymethylbilane to uroporphyrinogen III .......................................................... 6 1.4.5 Uroporphyrinogen III to coproporphyrinogen III ....................................................... 7 1.4.6 Coproporphyrinogen III to protoporphyrinogen IX ................................................... 7 1.4.7 Protoporphyrinogen IX to protoporphyrin IX ............................................................ 8 1.5 The haem and chlorophyll branch point ........................................................................... 9 1.5.1 Ferrochelatase ........................................................................................................... 9 1.6 Protoporphyrin IX to Mg protoporphyrin IX ................................................................... 10 1.7 Mg protoporphyrin IX to Mg protoporphyrin IX monomethyl ester .............................. 11 1.8 Formation of the isocyclic ring ........................................................................................ 12 1.9 Protochlorophyllide to Chlorophyllide ............................................................................ 13 1.9.1 Light-independent protochlorophyllide oxidoreductase (DPOR) ............................ 14 Page | iii 1.9.1.1 DPOR subunits and homology to nitrogenase .................................................. 14 1.9.1.2 Structure of L-protein ....................................................................................... 15 1.9.1.3 Structure of NB-protein .................................................................................... 15 1.9.1.4 Redox function of DPOR ................................................................................... 17 1.9.2 Light-dependent protochlorophyllide oxidoreductase ............................................ 17 1.9.3 POR in plants ............................................................................................................ 18 1.9.4 SDR Superfamily of enzymes ................................................................................... 19 1.9.4.1 Rossmann Fold .................................................................................................. 20 1.9.4.2 Catalysis ............................................................................................................ 20 1.9.4.3 Oligomerisation ................................................................................................. 21 1.9.5 POR homology model .............................................................................................
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