Exploring the functional and mechanistic diversity of diiron oxidases and oxygenases
Open Access
- Author:
- Rajakovich, Lauren Julia
- Graduate Program:
- Biochemistry, Microbiology, and Molecular Biology
- Degree:
- Doctor of Philosophy
- Document Type:
- Dissertation
- Date of Defense:
- May 26, 2017
- Committee Members:
- Joseph M Bollinger Jr., Dissertation Advisor/Co-Advisor
Carsten Krebs, Committee Chair/Co-Chair
Squire J Booker, Committee Member
Amie Kathleen Boal, Committee Member
Christopher Howard House, Outside Member - Keywords:
- enzyme
iron oxygenase
gene annotation
organophosphonate
HD-domain
biofuel
alkane
ferritin-like
diiron
peroxyl radical
PetF
alkene - Abstract:
- Approximately half of all enzymes in Nature utilize a metal to perform their biological function. Many of the metalloenzymes that harbor transition metals activate dioxygen to catalyze a diverse array of oxidation reactions to functionalize unreactive sites in biomolecules. These enzymatic transformations are often inaccessible to synthetic chemists, and consequently, understanding the naturally-evolved mechanisms by which these enzymes enact such challenging reactions will enable the development of new biocatalysts for industrial and therapeutic applications. One common strategy employed in Nature is the coupling of two transition metals, typically iron, to carry out oxidation and oxygenation reactions. Decades of research on this class of non-heme diiron enzymes has focused on three founding members, which has revealed unifying mechanistic features that enable them to enact one- and two-electron oxidation reactions. Chapter 1 summarizes the principles for dioxygen activation employing this bioinorganic scaffold that emerged from this foundational work. Chapter 1 also introduces more recent discoveries of novel non-heme diiron enzymes, facilitated by advancements in genome sequencing and bioinformatics, that have expanded the scope of chemical transformations and mechanistic strategies possible within this extensive metalloenzyme class. My dissertation research focused on three of these newly discovered diiron enzymes that invoke alternative mechanistic strategies to carry out non-canonical transformations. Chapter 2 covers the hydrocarbon-producing cyanobacterial diiron enzyme, ADO, which catalyzes a C-C bond cleavage reaction to effectively remove the chemical functional group from its fatty aldehyde substrate, producing linear hydrocarbons. My work demonstrates that ADO operates by a free-radical mechanism to enact this redox-neutral transformation, and that a cyanobacterial ferredoxin (PetF)/ferredoxin reductase/NADPH reducing system can act as an efficient reducing partner, a requisite for ADO catalysis. These mechanistic studies enabled the identification of inherent vulnerabilities that limit enzymatic efficacy, thereby highlighting direct targets for bioengineering and optimization of biofuel processes deploying this catalyst. Chapter 3 describes a project designed to biochemically characterize a diiron enzyme belonging to a new functional class. This work culminated in the discovery of a novel microbial phosphonate degradation pathway, consisting of two iron-dependent oxygenases with previously misannotated functional assignments. Finally, Chapter 4 describes progress on studies of another potential biofuel catalyst, an iron-dependent enzyme, UndA. This work provides evidence that UndA employs a diiron cofactor to convert fatty acids into terminal alkenes. This finding corrects its original cofactor assignment, rationalizes its ability to perform this transformation, and suggests a feasible catalytic mechanism. Collectively, these mechanistic studies contribute unique insight into the emerging reactivities of diiron enzymes that diversify their potential biotechnological applications.