Thesis advisor: Steven D. Bruner / Complex and unique enzymology is often behind the biosynthesis of natural products. This thesis is focused on how non-proteinogenic amino acids are biosynthesized and then incorporated into natural products. Chapters two, three and four deal with a unique dioxygenase found in vancomycin biosynthesis. Chapter five elaborates on the biochemical characterization along with efforts toward structural characterization of a terminal non-ribosomal peptide synthetase module. The vancomycin biosynthetic enzyme DpgC belongs to a small class of oxygenation enzymes that are not dependent on an accessory cofactor or metal ion. The detailed mechanism of cofactor-independent oxygenases has not been established. We have solved the first structure of an enzyme of this oxygenase class complexed with a bound substrate mimic. The use of a designed, synthetic substrate analog allows unique insights into the chemistry of oxygen activation. The structure confirms the absence of cofactors, and electron density consistent with molecular oxygen is present adjacent to the site of oxidation on the substrate. Molecular oxygen is bound in a small hydrophobic pocket and the substrate provides the reducing power to activate oxygen for downstream chemical steps. Our results resolve the unique and complex chemistry of DpgC, a key enzyme in the biosynthetic pathway of an important class of antibiotics. Mechanistic parallels exist between DpgC and cofactor-dependent flavoenzymes, providing information regarding the general mechanism of enzymatic oxygen activation. / Thesis (PhD) — Boston College, 2008. / Submitted to: Boston College. Graduate School of Arts and Sciences. / Discipline: Chemistry.

Thesis advisor: Steven D. Bruner / Thesis advisor: Mary Roberts / The dioxygenase DpgC performs a key step in the biosynthesis of 3,5-dihydroxyphenylglycine (DPG), a nonproteogenic amino acid found in the vancomycin family of antibiotics. Remarkably, DpgC performs a 4-electron oxidation without the use of metals or cofactors. The tools of synthetic organic chemistry, enzymology and structural biology were used to study this enzyme. We have solved the first structure of an enzyme of this oxygenase class, in complex with a bound substrate mimic. The structure confirms the absence of cofactors, and electron density consistent with molecular oxygen is located adjacent to the site of oxidation on the substrate. The use of a designed, synthetic substrate analog allowed us to gain unique insights into the chemistry of oxygen activation. We systematically probed the importance of active site residues by engineering conservative changes using site-directed mutagenesis. The kinetic parameters of these constructs imply that the phenolic hydroxyls of the substrate are of particular importance. These conclusions were verified by kinetic evaluation of synthetic substrate analogs. We have synthesized cyclopropyl substrate derivatives to probe the electron transfer step. The single electron oxidation should produce a radical species capable of opening the cycloproyl ring, thus providing a handle of detection. Our results resolve the unique and complex chemistry of DpgC, a key enzyme in the biosynthetic pathway of an important class of antibiotics. / Thesis (PhD) — Boston College, 2009. / Submitted to: Boston College. Graduate School of Arts and Sciences. / Discipline: Chemistry.