Structure-based mechanism of hydratase-aldolases in the Type I aldolase superfamily and structures of tautomerase superfamily members

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Polycyclic Aromatic Hydrocarbons (PAHs) are composed of multiple benzene-like rings and their bacterial catabolism has potential utility for bioremediation. In the breakdown of each ring, oxygenation is followed by ring cleavage and side chain removal, the latter of which is catalyzed by hydratase-aldolases. These enzymes belong to the N-acetylneuraminate lyase (NAL) subgroup of the Type I aldolase superfamily. NahE and PhdJ are hydratase-aldolases that process benzylidenepyruvate compounds in PAH degradative pathways from Pseudomonas putida G7 and Mycobacterium vanbaalenii PYR-1, respectively. Crystal structures of these enzymes in liganded and unliganded states are reported here and reveal new details about their catalytic mechanisms. Stabilization of the developing hydroxide anion during hydration could involve the amide nitrogen of Asn-157 (NahE numbering), conserved in hydratase-aldolases, but not other NAL subgroup members. For NahE, Tyr-155 might act as the general base for addition, but the identity of the base is less certain for PhdJ. The crystal structure of PhdG reveals a carbinolamine intermediate hydrogen bonding to Tyr-152, consistent with the participation of the residue in Schiff base formation. In addition, this dissertation describes structures within the tautomerase superfamily (TSF). The enzymes reported are from 4-oxalocrotonate tautomerase (4-OT), cis-3-chloroacrylic acid dehalogenase (cis-CaaD), and malonate semialdehyde decarboxylase (MSAD) subgroups. 4-OT catalyzes the ketonization of 2-hydroxymuconate (2-HM) in the meta-fission pathway. cis-CaaD and MSAD respectively catalyze dehalogenation and decarboxylation reactions in the catabolic 1,3-dichloropropene pathway, respectively. TSF members have a catalytic Pro-1 and share a common β-α-β fold. TSF members designated Ps01740, Pt0534, and Fused 4-OT have sequence similarity with the cis-CaaD and 4-OT subgroups and may provide insight into gene duplication and fusion events in the TSF. These enzymes have tautomerase activity and low or absent cis-CaaD activity. Liganded and unliganded structures suggest a structural basis for their activation. The trimeric structure of Fused 4-OT is unusual in that one monomer is inverted relative to the others. Mechanisms for 2-HM tautomerization are proposed based on a 2-HM-bound structure and kinetic parameters of mutants. Crystal structures for the MSAD homologues BP4401 and YusQ were obtained, and provide clues about their activities

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