DELINEATING THE DETERMINANTS OF CARBOXYLATION IN 2-KETOPROPYL COENZYME M OXIDOREDUCTASE/CARBOXYLASE: A UNIQUE CO2-FIXING FLAVOENZYME by Gregory Andrew Prussia A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Biochemistry MONTANA STATE UNIVERSITY Bozeman, Montana November 2018 ©COPYRIGHT by Gregory Andrew Prussia 2018 All Rights Reserved ii DEDICATION To Ana, Mom, and Dad. “The story is told that when Joe was a child his cousins emptied his Christmas stocking and replaced the gifts with horse manure. Joe took one look and bolted for the door, eye glittering with excitement. ‘Wait, Joe, where are you going? What did ‘ol Santa bring you?’ According to the story Joe paused at the door for a piece of rope. ‘Brought me a bran-new pony but he got away. I’ll catch him if I hurry.’ And ever since then it seemed that Joe had been accepting more than his share of hardship as good fortune, and more than his share of shit as a sign of Shetland ponies just around the corner, Thoroughbred Stallions just up the road.” -Ken Kesey, Sometimes a Great Notion iii ACKNOWLEDGEMENTS First, I would like to acknowledge Dr. John Peters for his mentorship and scientific insight. Dr. Jennifer DuBois was instrumental in the development of my critical-thinking and writing skills. A very sincere thanks is deserved for my committee members Dr. Brian Bothner, Dr. Martin Lawrence, and Dr. Blake Wiedenheft. I would like to thank both past and present Peters lab members; Dr. Oleg Zadvornyy for sharing his knowledge of crystallography, Dr. Florence Mus for her molecular biology expertise, Dr. George Gauss for his teachings in protein chemistry, Dr. Corey Fugate, Dr. Jacob Artz, Dr. Sarah Partovi, Dr. Stephen Keable, and future Drs. Natasha Pence, and Alex Alleman. A reiterative thanks is in order for Drs. Mus, Zadvornyy, and Gauss for their invaluable mentoring. A special thanks to Doreen Brown. Finally, I would like to thank the DOE for their ongoing support of this project. iv TABLE OF CONTENTS 1. INTRODUCTION ...........................................................................................................1 Introduction to Carboxylases ...........................................................................................1 Carboxylases in Natural Pathways...................................................................................2 RubisCO in the Calvin-Benson-Bassham (CBB) Cycle ..........................................2 2-Oxoglutarate Ferredoxin: Oxidoreductase in the Reductive Tricarboxylic Acid (rTCA) Cycle .........................................................3 Acetyl-CoA Carboxylase in the Fuchs-Holo Bicycle & Biotin-Containing Carboxylases ..........................................................................4 Carboxylase Enzymes in Additional CO2-Fixing Pathways ....................................5 Paradigms Among Carboxylase Enzymes .......................................................................5 Formation of an Ene Intermediate ...........................................................................5 Solvent Exclusion ....................................................................................................6 Anion Stabilization ..................................................................................................8 Introduction to Xanthobacter autotrophicus Py2 ..........................................................10 The Epoxide Carboxylase Pathway .......................................................................12 Disulfide Oxidoreductase (DSOR) Enzymes ..................................................................14 The Conserved Catalytic Dyad ..............................................................................16 Flavin Properties in DSOR Enzymes .....................................................................17 Redox-Active Cysteine Knockouts in DSOR Enzymes ........................................18 2-Ketopropyl Coenzyme M Oxidoreductase/Carboxylase .............................................19 Substrate Binding in 2-KPCC ................................................................................19 2-KPCC Forms an Enolacetone Intermediate ........................................................21 Extended Regions in 2-KPCC Compared to Glutathione Reductase .....................................................................22 Potential Anion Stabilization in 2-KPCC ..............................................................24 2-KPCC has Substituted the Conserved Dyad .......................................................25 Proposed Catalytic Cycle of 2-KPCC ....................................................................26 Research Directions .......................................................................................................28 References ......................................................................................................................30 2. SUBSTITUTION OF A CONSERVED CATALYTIC DYAD CAUSES LOSS OF CARBOXYLATION ACTIVITY IN 2-KPCC ..........................................39 Contribution of Authors and Co-Authors ....................................................................39 Manuscript Information ...............................................................................................40 Abstract ........................................................................................................................41 Introduction ..................................................................................................................42 Methods........................................................................................................................47 Results and Discussion ................................................................................................48 v TABLE OF CONTENTS CONTINUED Conclusion ...................................................................................................................51 Acknowledgements ......................................................................................................51 References ....................................................................................................................52 3. THE REACTIVE FORM OF A C-S BOND CLEAVING, CO2-FIXING FLAVOENZYME........................................................................................................55 Contribution of Authors and Co-Authors ....................................................................55 Manuscript Information ...............................................................................................56 Abstract ........................................................................................................................57 Introduction ..................................................................................................................58 Methods........................................................................................................................65 Expression and Purification of WT and mutant 2-KPCC ......................................65 + Measurement of Kd for NADP by fluorescence titration .....................................66 Monitoring UV/vis changes in the flavin species in WT and mutant 2-KPCC as a function of pH ......................................................................66 Steady state kinetic measurements.........................................................................67 Oxidative half reactions monitored as a function of [2-KPC] and pH in the absence of CO2 ................................................................................68 Observing the single-turnover reductive half reaction by stopped flow ................68 Results ..........................................................................................................................69 The Reductive half Reaction for WT 2-KPCC proceeds similarly to the GR H439A variant in which the active site histidine has been replaced by alanine ...................................................................69 The catalytically active, reduced form of 2-KPCC is neither a CT nor a C4 α-adduct species ............................................................72 The reactive form of 2-KPCC may be a nucleophilic EH- species ........................75 The F501H mutation has little effect on the reductive half reaction .....................80 Discussion ....................................................................................................................81 Conclusion ...................................................................................................................83 Acknowledgements ......................................................................................................83 References ....................................................................................................................85 4. A ROLE FOR HISTIDINE 506 IN CARBOXYLATE STABILIZATION OF 2-KETOPROPYL COENZYME M OXIDOREDUCTASE/CARBOXYLASE ........88 Contribution of Authors and Co-Authors ....................................................................88 Manuscript Information ...............................................................................................89 Abstract ........................................................................................................................90 Introduction ..................................................................................................................91