α-Amino-β-carboxymuconate-ε-semialdehyde decarboxylase (ACMSD) and α-aminomuconate-ε-semialdehyde dehydrogenase (AMSDH) are two neighboring enzymes in the L-tryptophan and 2-nitrobenzoic acid degradation pathways. The substrates of the two enzymes, α-amino-β-carboxymuconate-ε-semialdehyde (ACMS) and α-aminomuconate-ε-semialdehyde (2-AMS), are unstable and spontaneously decay to quinolinic acid and picolinic acid, respectively. ACMSD utilizes a divalent zinc metal as cofactor and is a member of the amidohydrolase superfamily. In this dissertation work, we have identified an important histidine residue in the active site that plays dual roles in tuning metal selectivity and activating a metal bound water ligand using mutagenesis, resonance Raman, EPR, crystallography, and ICP metal analysis techniques. The crystal structures of ACMSD from Pseudomonas fluorescens (PfACMSD) have been solved as homodimers in our laboratory while human ACMSD (hACMSD) was annotated as a monomer by another group. To resolve this structural difference, we used two conserved active site arginine residues as probes to study the oligomeriztion state of ACMSD and demonstrated that these two arginine residues are involved in substrate binding and that both Pf- and h- ACMSD are catalytically active only in the dimeric state. Subsequently, we solved the crystal structure of hACMSD and found it to be a homodimer in both catalytically active and inhibitor-bound forms. AMSDH is an NAD+ dependent enzyme and belongs to the aldehyde dehydrogenase superfamily. Due to the high instability of its substrate, AMSDH has not been studied at the molecular level prior to our work. We have cloned and expressed PfAMSDH in E. coli. The purified protein has high activity towards both 2-AMS and 2-hydroxymuconate semialdehyde (2-HMS), a stable substrate analog. We have successfully crystallized AMSDH with/without NAD+ and solved the crystal structure at up to 1.95 Å resolution. Substrate bound ternary complex structures were obtained by soaking the NAD+ containing crystals with 2-AMS or 2-HMS. Notably, two covalently bound catalytic intermediates were captured and characterized using a combination of crystallography, stopped-flow, single crystal spectroscopy, and mass spectrometry. The first catalytic working model of AMSDH has been proposed based on our success in structural and spectroscopic characterization of the enzyme in five catalytically relevant states in this dissertation work.

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