Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemistry, 2011.Vita. Cataloged from PDF version of thesis.Includes bibliographical references.Chapter 1. Geometric and Functional Versatility of Carboxylate-Bridged Nonheme- Diiron Motifs: sMMO and ToMO. Several metalloenzymes utilize a carboxylate-bridged non-heme diiron motif for dioxygen activation. Despite their conserved diiron active site structures and mechanisms of dioxygen activation, they catalyze a wide range of chemical transformations. These observations suggest that diiron-containing enzymes have distinct active sites and secondary/tertiary environments that are tuned for their dedicated biological functions. Detailed studies of two diiron-containing enzymes in the family of bacterial multicomponent monooxygenases (BMMs), soluble methane monooxygenase (sMMO) and toluene/o-xylene monooxygenase (ToMO), are described. The functions and structures of the three or four components of sMMO and ToMO are summarized. Distinctly different dioxygen activation chemistry and hydrocarbon specificity is observed for these two enzymes. A comparison of these two enzymes provides insight into the evolution of diironcontaining enzymes as well as their differing chemical mechanisms of catalysis. Chapter 2. Role of an Active Site Threonine in the Determination of Distinctive Dioxygen Reactivity in Toluene/o-Xylene Monooxygenase Hydroxylase. Dioxygen activation of toluene/o-xylene monooxygenase hydroxylase (ToMOH) exhibits the formation of a diiron(III) intermediate having unprecedented spectroscopic properties. To evaluate whether an active site threonine plays a role in the determination of the dioxygen chemistry in ToMOH, a T201S variant was prepared by site-directed mutagenesis. We reported the observation of a novel intermediate in the reaction of reduced ToMOH T201 S variant with dioxygen in the presence of its cognate regulatory protein (ToMOD). This species, T201 peroxo, is the first oxygenated intermediate of any toluene monooxygenase to display an optical band. The optical and M6ssbauer spectroscopic properties of the intermediate allowed us to assign it as a peroxodiiron(III) species, similar to Hperoxo in soluble methane monooxygenase hydroxylase (sMMOH). This result indicates that mutation of the T201 to serine altered the dioxygen chemistry of ToMOH in part to be more similar to that of sMMOH. Computational studies suggest that the T201 mutation can greatly perturb the energetics of the enzyme, which might be responsible for the distinct dioxygen reactivity of sMMOH and ToMOH. Structures of the oxygenated intermediates of ToMOH are proposed. Chapter 3. Role of an Active Site Threonine in the Kinetics of Dioxygen Activation in Toluene/o-Xylene Monooxygenase Hydroxylase. To elucidate the role of a strictly conserved T201 residue during dioxygen activation of toluene/o-xylene monooxygenase hydroxylase (ToMOH), T201S, T201G, T201C, and T201V variants of this enzyme were prepared by site-directed mutagenesis. X-ray crystal structures of all variants were obtained. Steady-state activity, regiospecificity, and single-turnover yields were also determined for the T201 mutants. Dioxygen activation by the reduced T201 variants was monitored by stopped-flow UV-vis and M6ssbauer spectroscopy. These studies demonstrated that the same dioxygen activation mechanism is preserved in the T201S, T201C, and T201G variants; however, both formation and decay kinetics of a peroxodiiron(III) intermediate, T201peroxo, were greatly altered, revealing that the T201 residue is critically involved in dioxygen activation. Rate-limiting steps in dioxygen activation of the T201S, T201C, and T201G variants were identified, revealing that T201 plays a major role in proton transfer, which is required to generate the peroxodiiron(III) intermediate. The role of the active site threonine residue in ToMOH is analogous to that of cytochrome P450 monooxygenases, suggesting it as a general threonine-dependent process in Nature to control proton transfer.(cont.) Chapter 4. Mechanistic Studies of Reactions of Peroxodiiron(III) Intermediates in the T201 Variants of Toluene/o-Xylene Monooxygenase Hydroxylase. Site-directed mutagenesis studies of a strictly conserved T201 residue in the active site of toluene/oxylene monooxygenase hydroxylase (ToMOH) revealed that a single mutation can facilitate kinetic isolation of two distinct peroxodiiron(III) species, designated T201peroxo and ToMOHperoxo, during dioxygen activation. In Chapter 2 and 3, we characterized both oxygenated intermediates by UV-vis and M6ssbauer spectroscopy, proposed structures from DFT and QM/MM computational studies, and elucidated chemical steps involved in dioxygen activation through the kinetic studies of T201peroxo formation. In Chapter 4, we investigated the kinetics of T2 0lperoxo decay to explore the reaction mechanism of the oxygenated intermediates following 02 activation. The decay rates of T201 peroxo were monitored in the absence and presence of external (phenol) or internal (tryptophan residue in I100W variant) substrates under pre-steady-state conditions. Three possible reaction models for the formation and decay of T201perX0 were evaluated, and the results demonstrate that this species is on the pathway of arene oxidation and appears to be in equilibrium with TOMOHperoxo. Chapter 5. Tracking a Defined Route of 0 2-Migration in a Dioxygen-Activating Diiron Enzyme, Toluene/o-Xylene Monooxygenase Hydroxylase. For numerous enzymes reactive toward small gaseous compounds, growing evidence indicates that these substrates diffuse into active site pockets through defined pathways in the protein matrix. Toluene/oxylene monooxygenase hydroxylase (ToMOH) is a dioxygen-activating carboxylatebridged nonheme-diiron enzyme. Structural analyses of the resting state enzyme suggest two possible pathways for dioxygen to access the c-subunit diiron center, a series of hydrophobic cavities or long solvent-exposed channel. To distinguish which pathway is utilized for dioxygen transfer, the dimensions of the cavities and channel were varied by site-directed mutagenesis and confirmed by X-ray crystallography. The rate of dioxygen access to the active site was monitored by measuring the formation rate of an oxygenated intermediate (T 2 01peroxo), a process that is dependent on 02 concentration. Altering the dimensions of the cavity but not the channel drastically changed the rate of dioxygen activation by the reduced enzyme. These results explicitly reveal that the cavities in the ToMOH a-subunit are not merely artifacts of protein packing/folding but rather programmed routes of dioxygen movement through the protein matrix. This conclusion indicates that conformational changes are required during catalysis to form a dioxygen trajectory and that the temporary opening/closing of the cavities control dioxygen transfer. Given that the cavities are present in all BMMs, the breathing motion presumably controls dioxygen consumption in all BMMs. This study represents the first approach to track kinetically a defined transient pathway by which a small gaseous molecule gains access to a diiron enzyme.(cont.) Appendix A. Insights into the Different Dioxygen Activation Pathways of Methane and Toluene Monooxygenase Hydroxylases. The methane and toluene monooxygenase hydroxylases (MMOH and TMOH, respectively) have almost identical active sites, yet the physical and chemical properties of their oxygenated intermediates, designated P*, Hperoxo, Q and Q* in MMOH, and ToMOHperoxo in toluene/o-xylene monooxygenase hydroxylase (ToMOH), are substantially different. We review and compare the structural differences in the vicinity of the active sites of these enzymes and discuss the differences that give rise to the distinct behavior of dioxygen reactivity in sMMOH and ToMOH. In particular, analysis of multiple crystal structures reveals that T213 of MMOH and analogous T201 of TMOH, located in the immediate vicinity of the active site, have different rotamer configurations. We study the rotation energy profiles of these threonine residues with the use of molecular mechanics (MM) and quantum mechanics/molecular mechanics (QM/MM) computational methods and put forward a hypothesis according to whether T201 and T213 play an important role in the formation of different types of peroxodiiron(III) species in MMOH and ToMOH. The hypothesis is indirectly supported by QM/MM calculations of the peroxodiiron(III) models of ToMOH and the theoretically computed M6ssbauer spectra. It also helps explain the formation of two distinct peroxodiiron(III) species in the T201S mutant of ToMOH. Additionally, a role for the regulatory protein (ToMOD), which is essential for oxygenated intermediate formation and the protein functioning in the ToMO system, is advanced. Appendix B. Multiple Roles of Component Proteins in Bacterial Multicomponent Monooxygenases: Phenol Hydroxylase and Toluene/o-Xylene Monooxygenase from Pseudomonas sp. OX1. Phenol hydroxylase (PH) and toluene/o-xylene monooxygenase (ToMO) from Pseudomonas sp. OXI require three or four protein components to activate dioxygen for the oxidation of aromatic substrates at a carboxylate-bridged diiron center. In this study, we investigated the influence of the hydroxylases, regulatory proteins, and electron-transfer components of these systems on substrate consumption and product generation. Single-turnover experiments revealed that only complete systems containing all three or four protein components are capable of oxidizing phenol, a major substrate for both enzymes. Under ideal conditions, the hydroxylated product yield was -50% of the diiron centers for both systems, suggesting that these enzymes operate by half-sites reactivity mechanisms. Single-turnover studies indicated that the PH and ToMO electron-transfer components exert regulatory effects on substrate oxidation processes taking place at the hydroxylase active sites, most likely through allostery. Steady state NADH consumption assays showed that the regulatory proteins facilitate the electron-transfer step in the hydrocarbon oxidation cycle in the absence of phenol. Under these conditions, electron consumption is coupled to H20 2 formation in a hydroxylase-dependent manner. Mechanistic implications of these results are discussed.by Woon Ju Song.Ph.D
