Characterization of metalloenzymes involved in the bacterial catabolism of lignin-derived biaryls

Bacteria play a central role in degrading aromatic compounds, including those derived from lignin, a heterogeneous aromatic polymer and a major component of woody biomass. These catabolic pathways and enzymes play a critical role in the global carbon cycle and have biocatalytic potential in the valorization of biomass. Nevertheless, many of these pathways and enzymes remain poorly understood. This thesis describes the characterization of three such catabolic enzymes, LsdA, LigZ and LigY, each of which has a metal cofactor. LsdA from Sphingomonas paucimobilis TMY1009 is an Fe²⁺-dependent oxygenase that catalyzes the cleavage of stilbenoids into aldehydes. In kinetic anal-yses, LsdA only transformed 4-hydroxystilbenes and was inhibited by phenylazophenol. Crystallo-graphic and mutagenesis analyses established that Lys-134 is essential for catalysis, consistent with a role in deprotonating the stilbene’s 4-hydroxyl. LigZ and LigY catalyze successive reactions in 2,2’-dihydroxy-3,3’-dimethoxy-5,5’-dicarboxy-biphenyl (DDVA) catabolism by Sphingobium sp. SYK-6. In this study, highly active preparations of LigZ, an Fe²⁺-dependent extradiol dioxygenase, afforded an accurate description of the enzyme’s substrate specificity and mechanism-based inactivation. 4,11-Dicarboxy-8-hydroxy-9-methoxy-2-hydroxy-6-oxo-6-phenyl-hexa-2,4-dienoate (DCHM-HOPDA) was identified as the meta-cleavage product (MCP) of the LigZ reaction and was shown to undergo a rapid, reversible non-enzymatic transformation under physiological conditions (t½ ~5 min). The enolate form of the MCP is the substrate of LigY, which catalyzed the hydrolysis of DCHM-HOPDA to 5-carboxyvanillate (5CVA) and 4-carboxy-2-hydroxypenta-2,4-dienoate (CHPD). Phy-logenetic, biochemical and structural analyses identified LigY as a Zn²⁺-dependent amidohydrolase, in contrast to all known MCP hydrolases, which are serine-dependent enzymes. Nevertheless, transient-state kinetic analyses revealed a catalytic intermediate, ESred, with a red-shifted spectrum similar to that observed in serine-dependent MCP hydrolases. Further, 4-methyl HOPDA inhibited LigY and yielded a complex with a spectrum similar to that of ESred. Crystallographic analyses of this complex revealed the MCP binds the Zn²⁺ in a bidentate manner. Together, the data support a mechanism in which the nucleophile is activated in the same substrate-assisted manner as in the serine-dependent enzymes, but that in LigY, the nucleophile is water, such that C-C fission is preceded by a gem-diol intermediate. Overall, this thesis provides important insights into several lignin-degrading enzymes and the superfamilies to which they belong.Science, Faculty ofGraduat

Snapshots of the Catalytic Cycle of an O₂, Pyridoxal Phosphate-Dependent Hydroxylase

Enzymes that catalyze hydroxylation of unactivated carbons normally contain heme and nonheme iron cofactors. By contrast, how a pyridoxal phosphate (PLP)-dependent enzyme could catalyze such a hydroxylation was unknown. Here, we investigate RohP, a PLP-dependent enzyme that converts l-arginine to (<i>S</i>)-4-hydroxy-2-ketoarginine. We determine that the RohP reaction consumes oxygen with stoichiometric release of H₂O₂. To understand this unusual chemistry, we obtain ∼1.5 Å resolution structures that capture intermediates along the catalytic cycle. Our data suggest that RohP carries out a four-electron oxidation and a stereospecific alkene hydration to give the (<i>S</i>)-configured product. Together with our earlier studies on an O₂, PLP-dependent l-arginine oxidase, our work suggests that there is a shared pathway leading to both oxidized and hydroxylated products from l-arginine

A shared mechanistic pathway for pyridoxal phosphate–dependent arginine oxidases

The mechanism by which molecular oxygen is activated by the organic cofactor pyridoxal phosphate (PLP) for oxidation reactions remains poorly understood. Recent work has identified arginine oxidases that catalyze desaturation or hydroxylation reactions. Here, we investigate a desaturase from the Pseudoalteromonas luteoviolacea indolmycin pathway. Our work, combining X-ray crystallographic, biochemical, spectroscopic, and computational studies, supports a shared mechanism with arginine hydroxylases, involving two rounds of single-electron transfer to oxygen and superoxide rebound at the 4' carbon of the PLP cofactor. The precise positioning of a water molecule in the active site is proposed to control the final reaction outcome. This proposed mechanism provides a unified framework to understand how oxygen can be activated by PLP-dependent enzymes for oxidation of arginine and elucidates a shared mechanistic pathway and intertwined evolutionary history for arginine desaturases and hydroxylases

Biochemical and structural characterization of a sphingomonad diarylpropane lyase for cofactorless deformylation

Lignin valorization is being intensely pursued via tandem catalytic depolymerization and biological funneling to produce single products. In many lignin depolymerization processes, aromatic dimers and oligomers linked by carbon-carbon bonds remain intact, necessitating the development of enzymes capable of cleaving these compounds to monomers. Recently, the catabolism of erythro-1,2-diguaiacylpropane-1,3-diol (erythro-DGPD), a ring-opened lignin-derived β-1 dimer, was reported in Novosphingobium aromaticivorans. The first enzyme in this pathway, LdpA (formerly LsdE), is a member of the nuclear transport factor 2 (NTF-2)-like structural superfamily that converts erythro-DGPD to lignostilbene through a heretofore unknown mechanism. In this study, we performed biochemical, structural, and mechanistic characterization of the N. aromaticivorans LdpA and another homolog identified in Sphingobium sp. SYK-6, for which activity was confirmed in&nbsp;vivo. For both enzymes, we first demonstrated that formaldehyde is the C1 reaction product, and we further demonstrated that both enantiomers of erythro-DGPD were transformed simultaneously, suggesting that LdpA, while diastereomerically specific, lacks enantioselectivity. We also show that LdpA is subject to a severe competitive product inhibition by lignostilbene. Three-dimensional structures of LdpA were determined using X-ray crystallography, including substrate-bound complexes, revealing several residues that were shown to be catalytically essential. We used density functional theory to validate a proposed mechanism that proceeds via dehydroxylation and formation of a quinone methide intermediate that serves as an electron sink for the ensuing deformylation. Overall, this study expands the range of chemistry catalyzed by the NTF-2-like protein family to a prevalent lignin dimer through a cofactorless deformylation reaction

A pyridoxal phosphate–dependent enzyme that oxidizes an unactivated carbon-carbon bond

Pyridoxal 5′-phosphate (PLP)-dependent enzymes have wide catalytic versatility but are rarely known for their ability to react with oxygen to catalyze challenging reactions. Here, using in vitro reconstitution and kinetic analysis, we report that the indolmycin biosynthetic enzyme Ind4, from Streptomyces griseus ATCC 12648, is an unprecedented O2- and PLP-dependent enzyme that carries out a four-electron oxidation of L-arginine, including oxidation of an unactivated carbon-carbon (C-C) bond. We show that the conjugated product of this reaction, which is susceptible to nonenzymatic deamination, is efficiently intercepted and stereospecifically reduced by the partner enzyme Ind5 to give D-4,5-dehydroarginine. Thus, Ind4 couples the redox potential of O2 with the ability of PLP to stabilize anions to efficiently oxidize an unactivated C-C bond, with the subsequent stereochemical inversion by Ind5 preventing off-pathway reactions. Altogether, these results expand our knowledge of the catalytic versatility of PLP-dependent enzymes and enrich the toolbox for oxidative biocatalysis