Adenine deaminase (ADE) catalyzes the conversion of adenine to hypoxanthine. Mechanistic characterization of ADE from Escherichia coli was performed along with biophysical studies. The structure of ADE was solved from A. tumefaciens. The structure, along with the biochemical and biophysical characterization, enabled the elucidation of the mechanism of the deaminase reaction of ADE. Elucidation of the origin of the oxygenation reactions within ADE led to the discovery of a promiscuous catalase reaction. The diiron ADE from all tested bacterial species exhibited this unusual reaction, along with the generation of superoxide and hydroxyl radicals, the latter being responsible for the oxygenation of the protein. The residues that were identified to be oxygenated were primarily the metal binding residues implying the origin of this reaction was the binuclear iron center. A group of bacterial enzymes that are co-localized in the same genomic operon as ADE but of unknown function were identified. The enzyme Bh0637 from Bacillus halodurans, a representative member of this group of enzymes was characterized. This enzyme was shown to preferentially catalyze the deamination of epigenetic base, N-6-methyadenine. Lastly, gram-negative bacteria have a highly conserved phn operon composed of 14 genes to break the C-P bond of inert alkylphosphonates. The genes phnGHIJKLM are absolutely critical for this activity. We discovered that methylphosphonate reacts first with MgATP to form alpha-D-ribose-1-methylphosphonate-5-triphosphate (RPnTP) and adenine by the action of PhnI, PhnG, PhnH and PhnL. PhnI by itself was shown to perform a novel nucleosidase reaction converting MgATP to ribose-5-triphosphate and adenine. The triphosphate moiety of RPnTP is then hydrolyzed to pyrophosphate and alpha-D-ribose-1-methylphosphonate-5-phosphate (PRPn) by PhnM. The carbon-phosphorus bond of PRPn is subsequently cleaved via a radical-based reaction to alpha-D-ribose-1,2-cyclic-phosphate-5-phosphate (PRcP) and methane in the presence of S-adenosyl-L-methionine by PhnJ.