Functional, Structural and Evolutionary Analyses of the Ferritin-like Superfamily of Proteins

The ferritin-like superfamily (FLSF) of proteins is composed of a wide variety of functionally diverse proteins involved in oxygen dependent metal-mediated electron transfer reactions. Their biological importance is exemplified by the fact FLSF proteins are found in almost every organism from all three domains of life. Their functions range from protection against reactive oxygen species to iron detoxification and storage, the synthesis of DNA and lipid membrane building blocks, energy dissipation, the creation of antibiotics, the modification of tRNA nucleotides and the oxidation of hydrocarbons.;This dissertation presents studies aimed at the functional, structural and evolutionary characterization of two particular groups of FLSF proteins: bacterial multicomponent monooxygenases (BMMs) and rubrerythrins. BMMs are enzymes expressed by bacteria that allow them to grow on hydrocarbons, such as methane, butane and toluene, as their sole source of energy and carbon by inserting an oxygen atom into their rather unreactive C-H bond. Rubrerythrins, on the other hand, are peroxidases most commonly found in anaerobic bacteria; they provide protection against hydrogen peroxide damage and are believed to retain several ancestral features of the FLSF.;Five chapters of original research are presented in this dissertation, all of which are either published or accepted for publication. The first two chapters describe novel biochemical insights and physiological implications of a poorly studied BMM known as soluble butane monooxygenase. These results constitute the first in vitro biochemical characterization of an alkane oxidizing BMM from a non-methanotroph. They also provide the first description of how such bacteria can grow in natural gas even though they cannot grow on methane, the principle component of natural gas.;The third chapter uncovers a novel mechanism of protein evolution important not only in the functional diversification of BMMs like soluble butane monooxygenase, but nearly 15% of all proteins as well. In doing so, it reshapes our understanding of a poorly recognized protein secondary structure called the pi-helix and helps bring this structural motif to the forefront of structural and evolutionary biology. Based on these findings, we predict the presence of certain novel features in a previously uncharacterized rubrerythrin-like protein found only in two "living fossil" oxygenic phototrophs. The fourth and fifth chapters that follow up this prediction describe the structural characterization of this rubrerythrin-like protein that we named symerythrin due to its unprecedented level of internal symmetry. The results confirm several of our predictions regarding the novelty of symerythrin's diiron metallocenter, and also unexpectedly show that it is capable of performing unprecedented chemistry: the formation of a carbon-carbon crosslink between two unfunctionalized amino acids. We also find unanticipated evidence that the single chain FLSF fold had multiple independent evolutionary origins.