Decarboxylation mechanisms in biological system

A General Iron-Catalyzed Decarboxylative Oxygenation of Aliphatic Carboxylic Acids

We report an iron-catalyzed decarboxylative C(sp3)-O bond-forming reaction under mild, base-free conditions with visible light irradiation. The transformation uses readily available and structurally diverse carboxylic acids, iron photocatalyst, and 2,2,6,6-tetramethylpiperidine 1-oxyl (TEMPO) derivatives as oxygenation reagents. The process exhibits a broad scope in acids possessing a wide range of stereoelectronic properties and functional groups. The developed reaction was applied to late-stage oxygenation of a series of bio-active molecules. The reaction leverages the ability of iron complexes to generate carbon-centered radicals directly from carboxylic acids by photoinduced carboxylate-to-iron charge transfer. Kinetic, electrochemical, EPR, UV/Vis, HRMS, and DFT studies revealed that TEMPO has a triple role in the reaction: as an oxygenation reagent, an oxidant to turn over the Fe-catalyst, and an internal base for the carboxylic acid deprotonation. The obtained TEMPO adducts represent versatile synthetic intermediates that were further engaged in C-C and C-heteroatom bond-forming reactions using commercial organo-photocatalysts and nucleophilic reagents.

Computational insights into the binding modes, keto-enol tautomerization and stereo-electronically controlled decarboxylation of oxaloacetate in the active site of macrophomate synthase

Oxaloacetic acid (OAA) is a β-ketocarboxylic acid, which plays an important role as an intermediate in some metabolic pathways, including the tricarboxylic acid cycle, gluconeogenesis and fatty acid biosynthesis. Animal studies have indicated that supplementing oxaloacetic acid shows an increase of lifespan and other substantial health benefits including mitochondrial DNA protection, and protection of retinal, neural and pancreatic tissues. Most of the chemical transformations of OAA in the metabolic pathways have been extensively studied; however, the understanding of decarboxylation of OAA at the atomic level is relatively lacking. Here, we carried out MD simulations and combined quantum mechanical/molecular mechanical (QM/MM) calculations as an example to systematically elucidate the binding modes, keto-enol tautomerization and decarboxylation of OAA in the active site of macrophomate synthase (MPS), which is a Mg(II)-dependent bifunctional enzyme that catalyzes both the decarboxylation of OAA and [4+2] cycloaddition of 2-pyrone with the decarboxylated intermediate of OAA (pyruvate enolate). On the basis of our calculations, it was found that the Mg2+-coordinated oxaloacetate may exist in enol forms and keto forms. The four keto forms can be transformed into each other by simply rotating the C2-C3 single bond, nevertheless, the keto-enol tautomerization strictly requires the assistance of pocket water molecules. In addition, the decarboxylation is stereo-electronically controlled, i.e., it is the relative orientation of the terminal carboxyl anion that determines the rate of decarboxylation. As such, the chemistry of oxaloacetate in the active site of MPS is complex. On one hand, the most stable binding mode (K-I) may undergo enol-keto tautomerization to isomerize to the enol form, which may further react with the second substrate; on the other hand, K-I may isomerize to another binding mode K-II to proceed decarboxylation to generate pyruvate enolate and CO2. Starting from K-I, the enol-keto tautomerization corresponds to a barrier of 16.2 kcal mol-1, whereas the decarboxylation is associated with an overall barrier of 19.7 kcal mol-1. These findings may provide useful information for understanding the chemistry of OAA and the catalysis of related enzymes, and they are basically in agreement with the available experimental kinetic data.

Enzymatic Photodecarboxylation on Secondary and Tertiary Carboxylic Acids

Photoenzymatic decarboxylation of bulky secondary and tertiary carboxylic acids catalyzed by engineered Chlorella variabilis fatty acid photodecarboxylase (CvFAP) is reported. Rational design and directed evolution of wild-type CvFAP are used to improve the reactivity and expand potential applications. Moreover, engineered CvFAP can catalyze light-driven kinetic resolution of α-substituted carboxylic acid. Our work sheds light on the production of chiral building blocks and bioactive molecules from bulky carboxylic acids via the photoenzymatic way.

The catalytic mechanism of direction-dependent interactions for 2,3-dihydroxybenzoate decarboxylase

Benzoic acid decarboxylases offer an elegant alternative to CO2 fixation by reverse reaction-carboxylation, which is named the bio-Kolbe-Schmitt reaction, but they are unfavorable to carboxylation. Enhancing the carboxylation efficiency of reversible benzoic acid decarboxylases is restricted by the unexplained carboxylation mechanisms. The direction of reversible enzyme catalytic reactions depends on whether catalytic residues at the active center of the enzyme are protonated, which is subjected by the pH. Therefore, the forward and reverse reactions could be separated at different pH values. Reversible 2,3-dihydroxybenzoate acid decarboxylase undergoes decarboxylation at pH 5.0 and carboxylation at pH 8.6. However, it is unknown whether the interaction of enzymes with substrates and products in the forward and reverse reactions can be exploited to improve the catalytic activity of reversible enzymes in the unfavorable direction. Here, we identify a V-shaped tunnel of 2,3-dihydroxybenzoic acid decarboxylase from Aspergillus oryzae (2,3-DHBD_Ao) through which the substrate travels in the enzyme, and demonstrate that the side chain conformation of a tyrosine residue controls the entry and exit of substrate/product during reversible reactions. Together with the kinetic studies of the mutants, it is clarified that interactions between substrate/product traveling through the enzyme tunnel in 2,3-DHBD_Ao are direction-dependent. These results enrich the understanding of the interactions of substrates/products with macromolecular reversible enzymes in different reaction directions, thereby demonstrating a possible path for engineering decarboxylases with higher carboxylation efficiency. KEY POINTS: • The residue Trp23 of 2,3-DHBD_Ao served as a switch to control the entry and exit of catechol • A V-shaped tunnel of 2,3-DHBD_Ao for decarboxylation and carboxylation reactions was identified • The results provide a promising strategy for engineering decarboxylases with direction-dependent residues inside the substrate/product traveling tunnel of the enzyme.

Modern Strategies for Carbon Isotope Exchange

In contrast to stable and natural abundant carbon-12, the synthesis of organic molecules with carbon (radio)isotopes must be conceived and optimized in order to navigate through the hurdles of radiochemical requirements, such as high costs of the starting materials, harsh conditions and radioactive waste generation. In addition, it must initiate from the small cohort of available C-labeled building blocks. For long time, multi-step approaches have represented the sole available patterns. On the other side, the development of chemical reactions based on the reversible cleavage of C-C bonds might offer new opportunities and reshape retrosynthetic analysis in radiosynthesis. This review aims to provide a short survey on the recently emerged carbon isotope exchange technologies that provide effective opportunity for late-stage labeling. At present, such strategies have relied on the use of primary and easily accessible radiolabeled C1-building blocks, such as carbon dioxide, carbon monoxide and cyanides, while the activation principles have been based on thermal, photocatalytic, metal-catalyzed and biocatalytic processes.

Structural diversity, hypothetical biosynthesis, chemical synthesis, and biological activity of Ganoderma meroterpenoids

Covering: 2018 to 2022Meroterpenoids found in fungal species of the genus Ganoderma and known as Ganoderma meroterpenoids (GMs) are substances composed of a 1,2,4-trisubstituted benzene and a polyunsaturated side chain. These substances have attracted the attention of chemists and pharmacologists due to their diverse structures and significant bioactivity. In this review, we present the structures and possible biosynthesis of representative GMs newly found from 2018 to 2022, as well as chemical synthesis and biological activity of some interesting GMs. We propose for the first time a plausible biosynthetic pathway for GMs, which will certainly motivate further research on the biosynthetic pathway in Ganoderma species, as well as on chemical synthesis of GMs as important bioactive compounds for the purpose of drug development.

Enantioselective Transformations in the Synthesis of Therapeutic Agents

The proportion of approved chiral drugs and drug candidates under medical studies has surged dramatically over the past two decades. As a consequence, the efficient synthesis of enantiopure pharmaceuticals or their synthetic intermediates poses a profound challenge to medicinal and process chemists. The significant advancement in asymmetric catalysis has provided an effective and reliable solution to this challenge. The successful application of transition metal catalysis, organocatalysis, and biocatalysis to the medicinal and pharmaceutical industries has promoted drug discovery by efficient and precise preparation of enantio-enriched therapeutic agents, and facilitated the industrial production of active pharmaceutical ingredient in an economic and environmentally friendly fashion. The present review summarizes the most recent applications (2008-2022) of asymmetric catalysis in the pharmaceutical industry ranging from process scales to pilot and industrial levels. It also showcases the latest achievements and trends in the asymmetric synthesis of therapeutic agents with state of the art technologies of asymmetric catalysis.

Enzymatic reactions towards aldehydes: An overview

Many aldehydes are volatile compounds with distinct and characteristic olfactory properties. The aldehydic functional group is reactive and, as such, an invaluable chemical multi-tool to make all sorts of products. Owing to the reactivity, the selective synthesis of aldehydic is a challenging task. Nature has evolved a number of enzymatic reactions to produce aldehydes, and this review provides an overview of aldehyde-forming reactions in biological systems and beyond. Whereas some of these biotransformations are still in their infancy in terms of synthetic applicability, others are developed to an extent that allows their implementation as industrial biocatalysts.

N-Formimidoylation/-iminoacetylation modification in aminoglycosides requires FAD-dependent and ligand-protein NOS bridge dual chemistry

Oxidized cysteine residues are highly reactive and can form functional covalent conjugates, of which the allosteric redox switch formed by the lysine-cysteine NOS bridge is an example. Here, we report a noncanonical FAD-dependent enzyme Orf1 that adds a glycine-derived N-formimidoyl group to glycinothricin to form the antibiotic BD-12. X-ray crystallography was used to investigate this complex enzymatic process, which showed Orf1 has two substrate-binding sites that sit 13.5 Å apart unlike canonical FAD-dependent oxidoreductases. One site could accommodate glycine and the other glycinothricin or glycylthricin. Moreover, an intermediate-enzyme adduct with a NOS-covalent linkage was observed in the later site, where it acts as a two-scissile-bond linkage facilitating nucleophilic addition and cofactor-free decarboxylation. The chain length of nucleophilic acceptors vies with bond cleavage sites at either N-O or O-S accounting for N-formimidoylation or N-iminoacetylation. The resultant product is no longer sensitive to aminoglycoside-modifying enzymes, a strategy that antibiotic-producing species employ to counter drug resistance in competing species.

Vitamin B6-Based Biomimetic Asymmetric Catalysis

ConspectusOne of the fundamental goals of chemists is to develop highly efficient methods for producing optically active compounds, given their wide range of applications in chemistry, pharmaceutical industry, chemical biology, and material science. Biomimetic asymmetric catalysis, which imitates the structures and functions of enzymes, has emerged as an extremely attractive strategy for producing chiral compounds. This field has drawn tremendous research interest and has led to various protocols for constructing complex molecular scaffolds. The Vitamin B₆ family, including pyridoxal, pyridoxamine, pyridoxine, and the corresponding phosphorylated derivatives, serves as the cofactors to catalyze more than 200 enzymatic functions, accounting for ∼4% of all enzyme activities. Although significant progress has been made in simulating the biological roles of vitamin B₆ during the past several decades, its extraordinary catalytic power has not yet been successfully applied into asymmetric synthesis. In recent years, our group has been devoted to developing vitamin B₆-based biomimetic asymmetric catalysis using chiral pyridoxals/pyridoxamines as catalysts. We are particularly interested in mimicking the processes of enzymatic transamination and biological aldol reaction of glycine, respectively, developing asymmetric biomimetic transamination and carbonyl catalysis enabled α-C-H transformation of primary amines. Using a chiral α,α-diarylprolinol-derived pyridoxal as the catalyst, we reported the first chiral pyridoxal catalyzed asymmetric transamination of α-keto acids in 2015. A significant breakthrough in biomimetic transamination was achieved by using an axially chiral biaryl pyridoxamine catalyst that bears a lateral amine side arm. The amine side arm acts as an intramolecular base, accelerating the transamination and proving highly effective for transamination of α-keto acids and α-keto amides. In addition, we discovered the catalytic power of chiral pyridoxals as carbonyl catalysts for asymmetric biomimetic Mannich/aldol reactions of glycinates. These chiral pyridoxals also enabled more α-C-H conversions of glycinates, such as asymmetric 1,4-addition toward α,β-unsaturated esters and asymmetric α-allylation with Morita-Baylis-Hillman acetates. Moreover, carbonyl catalysis can be further applied to highly challenging primary amines with inert α-C-H bonds, such as propargylamines and benzylamines, which represents a powerful strategy for direct asymmetric α-C-H functionalization of various primary amines without protection of the NH₂ group. These biomimetic/bioinspired transformations provide efficient new protocols for the synthesis of chiral amines. Herein, we summarize our recent efforts on the development of the vitamin B₆-based biomimetic asymmetric catalysis.

Alternating the current direction

Waveform-controlled electrolysis enables the carbon-carbon coupling of carboxylic acids.

Kynurenine Pathway Regulation at Its Critical Junctions with Fluctuation of Tryptophan

The kynurenine pathway (KP) is the primary route for the catabolism of the essential amino acid tryptophan. The central KP metabolites are neurologically active molecules or biosynthetic precursors to critical molecules, such as NAD⁺. Within this pathway are three enzymes of interest, HAO, ACMSD, and AMSDH, whose substrates and/or products can spontaneously cyclize to form side products such as quinolinic acid (QA or QUIN) and picolinic acid. Due to their unstable nature for spontaneous autocyclization, it might be expected that the levels of these side products would be dependent on tryptophan intake; however, this is not the case in healthy individuals. On top of that, the regulatory mechanisms of the KP remain unknown, even after a deeper understanding of the structure and mechanism of the enzymes that handle these unstable KP metabolic intermediates. Thus, the question arises, how do these enzymes compete with the autocyclization of their substrates, especially amidst increased tryptophan levels? Here, we propose the formation of a transient enzyme complex as a regulatory mechanism for metabolite distribution between enzymatic and non-enzymatic routes during periods of increased metabolic intake. Amid high levels of tryptophan, HAO, ACMSD, and AMSDH may bind together, forming a tunnel to shuttle the metabolites through each enzyme, consequently regulating the autocyclization of their products. Though further research is required to establish the formation of transient complexation as a solution to the regulatory mysteries of the KP, our docking model studies support this new hypothesis.

The fate and behavior of perfluorooctanoic acid (PFOA) in constructed wetlands: Insights into potential removal and transformation pathway

Although constructed wetland (CW) technology is widely used to eliminate emerging organic pollutants, the removal pathway of perfluoroalkyl and polyfluoroalkyl substances (PFASs) in CW system have not been fully understood yet. This study aims to deeply probe into the fate and behavior of perfluorooctanoic acid (PFOA) in CW system. Findings indicated that the removal efficiency of PFOA by CW system was 49.69-73.63 % with initial concentrations at 100-1000 μg/L. Substrate was the main "sink" of PFOA into the CWs (46.22-50.83 %), and the plant uptake (1.99-2.48 %) accounted for a small proportion. Transformation products in the effluent of CW systems included a series of short-chain perfluorinated carboxylic acids (PFCAs), hydrogen-containing perfluoroalkanes and other organic fluorides. Activated pathways of xenobiotics biodegradation suggested that enzyme-mediated biochemical reactions might be responsible for the PFOA transformation. The transformation pathway included enzymatic decarboxylation, hydroxylation, hydrolysis, dehydrogenation and dehalogenation, as well as non-enzymatic reactions. These discoveries provide new insights into the in-depth understanding environmental behavior of PFOA in ecosystem and lay the foundation for further ecological remediation.

Investigation of enzymatic quality and quantity using pyridoxal 5'-phosphate (PLP) regeneration system as a decoy in Escherichia coli

Pyridoxal 5'-phosphate (PLP), an essential cofactor for multiple enzymes, was used as a protein decoy to prompt enzyme expression and activity for the first time. The best chassis, denoted as WJK, was developed using a pyridoxal kinase (PdxK) and integrated at the HK022 phage attack site of Escherichia coli W3110. When compared with the original strain, the amount and activity of lysine decarboxylase (CadA) in WJK were significantly increased by 100 % and 120 %, respectively. When supplementary nineteen amino acids as second carbon source, cell growth and protein trade-off were observed. The transcriptional levels of genes from glycolysis to TCA cycle, adhE, argH and gdhA were dominating and redirected more flux into α-ketoglutarate, thus facilitated cell growth. Stepwise improvement was conducted with pyridoxal and nitrogen-rich medium; hence, CadA activity was increased to 60 g-cadaverine/g-dry cell weight/h. By reutilizing the whole-cell biocatalysts in two repeated reactions with the supplementation of fresh cells, a total cadaverine of 576 g/L was obtained even without additional PLP. Notably, PLP decoy augment the enzymatic activities of 5-aminolevulinic acid synthase and glutamate/lysine/arginine decarboxylases by over 100 %. Finally, a conserved PLP-binding pocket, Ser-His-Lys, was identified as a vital PLP sponge site that simultaneously improved protein quality and quantity.

Biomimetic Synthesis of Chejuenolides A-C by a Cryptic Lactone-Based Macrocyclization: Stereochemical Implications in Biosynthesis

A hypothetical Mannich macrocyclization in the biosynthesis of chejuenolides A-C served as the basis for the synthetic design herein. Using a lactone-based linear precursor constructed via a tactic sequence of aldol-Julia-aldol reactions on a gram scale, the biomimetic total synthesis and structural validation of chejuenolides A-C were successfully achieved for the first time. The β-oxo-δ-lactone unit in the macrocyclized adducts was fragile and readily converted to a series of C2/C18-diastereoisomers via a decarboxylation and protonation pathway. Stereochemical identification of the biosynthetic precursor (O3P2) confirmed structural adherence to the given macrocycles and previously clarified lankacidins. Moreover, the stereovariants of the linear precursor designed for the macrocyclization event highlighted the unparalleled impact of using this biomimetic approach to determine the stereoselectivity in the proposed enzymatic reaction by reviving the lost or unstable intermediate.

Bifunctional NadC Homologue PyrZ Catalyzes Nicotinic Acid Formation in Pyridomycin Biosynthesis

Pyridomycin is a potent antimycobacterial natural product by specifically inhibiting InhA, a clinically validated antituberculosis drug discovery target. Pyridyl moieties of pyridomycin play an essential role in inhibiting InhA by occupying the reduced form of the nicotinamide adenine dinucleotide (NADH) cofactor binding site. Herein, we biochemically characterize PyrZ that is a multifunctional NadC homologue and catalyzes the successive formation, dephosphorylation, and ribose hydrolysis of nicotinic acid mononucleotide (NAMN) to generate nicotinic acid (NA), a biosynthetic precursor for the pyridyl moiety of pyridomycin. Crystal structures of PyrZ in complex with substrate quinolinic acid (QA) and the final product NA revealed a specific salt bridge formed between K184 and the C3-carboxyl group of QA. This interaction positions QA for accepting the phosphoribosyl group to generate NAMN, retains NAMN within the active site, and mediates its translocation to nucleophile D296 for dephosphorylation. Combining kinetic and thermodynamic analysis with site-directed mutagenesis, the catalytic mechanism of PyrZ dephosphorylation was proposed. Our study discovered an alternative and concise NA biosynthetic pathway involving a unique multifunctional enzyme.

Carboxylic Acids as Adaptive Functional Groups in Metallaphotoredox Catalysis

The development of palladium-catalyzed cross-coupling methods for the activation of C(sp2)-Br bonds facilitated access to arene-rich molecules, enabling a concomitant increase in the prevalence of this structural motif in drug molecules in recent decades. Today, there is a growing appreciation of the value of incorporating saturated C(sp3)-rich scaffolds into pharmaceutically active molecules as a means to achieve improved solubility and physiological stability, providing the impetus to develop new coupling strategies to access these challenging motifs in the most straightforward way possible. As an alternative to classical two-electron chemistry, redox chemistry can enable access to elusive transformations, most recently, by interfacing abundant first-row transition-metal catalysis with photoredox catalysis. As such, the functionalization of ubiquitous and versatile functional handles such as (aliphatic) carboxylic acids via metallaphotoredox catalysis has emerged as a valuable field of research over the past eight years.In this Account, we will outline recent progress in the development of methodologies that employ aliphatic and (hetero)aromatic carboxylic acids as adaptive functional groups. Whereas recent decarboxylative functionalization methodologies often necessitate preactivated aliphatic carboxylic acids in the form of redox-active esters or as ligands for hypervalent iodine reagents, methods that enable the direct use of the native carboxylic acid functionality are highly desired and have been accomplished through metallaphotoredox protocols. As such, we found that bench-stable aliphatic carboxylic acids can undergo diverse transformations, such as alkylation, arylation, amination, and trifluoromethylation, by leveraging metallaphotoredox catalysis with prevalent first-row transition metals such as nickel and copper. Likewise, abundant aryl carboxylic acids are now able to undergo halogenation and borylation, enabling new entry points for traditional, primarily palladium- or copper-catalyzed cross-coupling strategies. Given the breadth of the functional group tolerance of the employed reaction conditions, the late-stage functionalization of abundant carboxylic acids toward desired targets has become a standard tool in reaction design, enabling the synthesis of various diversified drug molecules. The rapid rise of this field has positively inspired pharmaceutical discovery and will be further accelerated by novel reaction development. The achievement of generality through reaction optimization campaigns allows for future breakthroughs that can render protocols more reliable and applicable for industry. This article is intended to highlight, in particular, (i) the employment of aliphatic and (hetero)aryl carboxylic acids as powerful late-stage adaptive functional handles in drug discovery and (ii) the need for the further development of still-elusive and selective transformations.We strongly believe that access to native functionalities such as carboxylic acids as adaptive handles will further inspire researchers across the world to investigate new methodologies for complex molecular targets.

Microbial lignin valorization through depolymerization to aromatics conversion

Lignin is the most abundant source of renewable aromatic biopolymers and its valorization presents significant value for biorefinery sustainability, which promotes the utilization of renewable resources. However, it is challenging to fully convert the structurally complex, heterogeneous, and recalcitrant lignin into high-value products. The in-depth research on the lignin degradation mechanism, microbial metabolic pathways, and rational design of new systems using synthetic biology have significantly accelerated the development of lignin valorization. This review summarizes the key enzymes involved in lignin depolymerization, the mechanisms of microbial lignin conversion, and the lignin valorization application with integrated systems and synthetic biology. Current challenges and future strategies to further study lignin biodegradation and the trends of lignin valorization are also discussed.

Aldehyde-catalysed carboxylate exchange in α-amino acids with isotopically labelled CO2

The isotopic labelling of small molecules is integral to drug development and for understanding biochemical processes. The preparation of carbon-labelled α-amino acids remains difficult and time consuming, with established methods involving label incorporation at an early stage of synthesis. This explains the high cost and scarcity of C-labelled products and presents a major challenge in 11C applications (11C t1/2 = 20 min). Here we report that aldehydes catalyse the isotopic carboxylate exchange of native α-amino acids with *CO2 (* = 14, 13, 11). Proteinogenic α-amino acids and many non-natural variants containing diverse functional groups undergo labelling. The reaction probably proceeds via the trapping of *CO2 by imine-carboxylate intermediates to generate iminomalonates that are prone to monodecarboxylation. Tempering catalyst electrophilicity was key to preventing irreversible aldehyde consumption. The pre-generation of the imine carboxylate intermediate allows for the rapid and late-stage 11C-radiolabelling of α-amino acids in the presence of [11C]CO2.

Unraveling dissolved organic matter in drinking water through integrated ozonation/ceramic membrane and biological activated carbon process using FT-ICR MS

The performance of an integrated process comprising coagulation, ozonation, and catalytic ceramic membrane filtration (CMF) followed by treatment with biological active carbon (BAC) was evaluated in a pilot-scale (96 m³/d) experiment to understand the biostability and quality of the finished water. The fate of dissolved organic matter (DOM) at the molecular level was explored using Fourier-transform ion cyclotron resonance mass spectrometry (FT-ICR MS). Biostable finished water with an assimilable organic carbon (AOC) concentration of 30.2-45.4 µg/L was obtained by the integrated process, and the high hydraulic retention time (HRT) (≥ 45 min) of the BAC filter was necessary to provide biostable finished water. The coagulation/O₃/CMF unit efficiently transformed nitrogen-containing polyaromatic hydrocarbons (PAH) with aromaticity and large molecular weight (Mw) (500-1000 Da) into CHO-type highly unsaturated phenolic compounds (HuPh) with less aromaticity and medium Mw (300-500 Da), which were effectively removed by subsequent BAC filtering. The main reaction was oxygen addition, followed by deamination and dealkylation of the coagulation/O₃/CMF unit and decarboxylation of the BAC filter. Principal component analysis revealed that N-containing and large-Mw PAH are potential AOC precursors, and the chemical characteristics of CHO-type and medium-Mw HuPh make them AOC candidates (correlation coefficients > 0.96). This study provides insights into the management of drinking water biostability and its suitability for the practical application of the integrated coagulation/O₃/CMF-BAC process in drinking water treatment plants.

Microbial rhodoquinone biosynthesis proceeds via an atypical RquA-catalyzed amino transfer from S-adenosyl-L-methionine to ubiquinone

Rhodoquinone (RQ) is a close analogue of ubiquinone (UQ) that confers diverse bacterial and eukaryotic taxa the ability to utilize fumarate as an electron acceptor in hypoxic conditions. The RquA protein, identified in a Rhodospirillum rubrum RQ-deficient mutant, has been shown to be required for RQ biosynthesis in bacteria. In this report, we demonstrate that RquA, homologous to SAM-dependent methyltransferases, is necessary and sufficient to catalyze RQ biosynthesis from UQ in vitro. Remarkably, we show that RquA uses SAM as the amino group donor in a substitution reaction that converts UQ to RQ. In contrast to known aminotransferases, RquA does not use pyridoxal 5'-phosphate (PLP) as a coenzyme, but requires the presence of Mn²⁺ as a cofactor. As these findings reveal, RquA provides an example of a non-canonical SAM-dependent enzyme that does not catalyze methyl transfer, instead it uses SAM in an atypical amino transfer mechanism.

Kinetics and thermodynamics of enzymatic decarboxylation of α,β-unsaturated acid: a theoretical study

Enzymatic decarboxylation of α,β-unsaturated acid through ferulic acid decarboxylase (FDC1) has been of interest because this reaction has been anticipated to be a promising, environmentally friendly industrial process for producing styrene and its derivatives from natural resources. Because the local dielectric constant at the active site is not exactly known, enzymatic decarboxylation to generate β-methylstyrene (β-MeSt) was studied under two extreme conditions (ε = 1 and 78 in the gas phase and aqueous solution, respectively) using the B3LYP/DZP method and transition state theory (TST). The model molecular clusters consisted of an α-methylcinnamate (Cin) substrate, a prenylated flavin mononucleotide (PrFMN) cofactor and all relevant residues of FDC1. Analysis of the equilibrium structures showed that the FDC1 backbone does not play the most important role in the decarboxylation process. The potential energy profiles confirmed that the increase in the polarity of the solvent could lead to significant changes in the energy barriers, especially for the transition states that involve proton transfer. Analysis of the rate constants confirmed the low/no quantum mechanical tunneling effect in the studied temperature range and that inclusion of the fluctuation of the local dielectric environment in the mechanistic model was essential. Because the computed rate constants are not compatible with the time resolution of the stopped-flow spectrophotometric experiment, the direct route for generating β-MeSt after CO2 elimination (acid catalyst (2)) is unlikely to be utilized, thereby confirming that indirect cycloelimination in a low local dielectric environment is the rate determining step. The thermodynamic results showed that the elementary reactions that involve charge (proton) transfer are affected by solvent polarity, thereby leading to the conclusion that overall, the enzymatic decarboxylation of α,β-unsaturated acid is thermodynamically controlled at high ε. The entropy changes due to the generation of molecules in the active site appeared more pronounced than that due to only covalent bond breaking/formation or structural reorientation. This work examined in detail for the first time the scenarios in each elementary reaction and provided insight into the effect of the fluctuations in the local dielectric environment on the enzymatic decarboxylation of α,β-unsaturated acids. These results could be used as guidelines for further theoretical and experimental studies on the same and similar systems.

Fermentative production of halogenated tryptophan derivatives with Corynebacterium glutamicum overexpressing tryptophanase or decarboxylase genes

The aromatic amino acid l‐tryptophan serves as a precursor for many valuable compounds such as neuromodulators, indoleamines and indole alkaloids. In this work, tryptophan biosynthesis was extended by halogenation followed by decarboxylation to the respective tryptamines or cleavage to the respective indoles. Either the tryptophanase genes tnaAs from E. coli and Proteus vulgaris or the aromatic amino acid decarboxylase genes AADCs from Bacillus atrophaeus, Clostridium sporogenes, and Ruminococcus gnavus were expressed in Corynebacterium glutamicum strains producing (halogenated) tryptophan. Regarding indoles, final titers of 16 mg L⁻¹ 7‐Cl‐indole and 23 mg L⁻¹ 7‐Br‐indole were attained. Tryptamine production led to a much higher titer of 2.26 g L⁻¹ upon expression of AADC from B. atrophaeus. AADC enzymes were shown to be active with halogenated tryptophan in vitro and in vivo and supported production of 0.36 g L⁻¹ 7‐Br‐tryptamine with a volumetric productivity of 8.3 mg L⁻¹ h⁻¹ in a fed‐batch fermentation.

Anaerobic biotransformation mechanism of marine toxin domoic acid

Domoic acid (DA) is a major marine neurotoxin, occurs frequently in most of the world's coastlines and seriously threatens ecosystem and public health. However, information on its biotransformation process in coastal anaerobic environments remains unclear. In this study, the underlying mechanism of anaerobic biotransformation of DA by marine consortium GLY was investigated using the combination of liquid chromatography-high-resolution Orbitrap mass spectrometry and comparative metatranscriptomics analysis. The results demonstrated that DA could be cometabolically biotransformed under anaerobic conditions with pseudo-first-order reaction. Anaerobic biotransformation pathway of DA was clarified, including decarboxylation, dehydrogenation, carboxylation activation with CoA and multiple β-oxidation steps occurring at aliphatic side chain, which facilitated DA detoxification. Furthermore, anaerobic cometabolic biotransformation mechanism of glycine-DA by consortium GLY was established for the first time, a number of genes related to the metabolic pathways of glycine fermentation, fatty acid synthesis and β-oxidation were responded in the consortium GLY transcriptome and involved in the anaerobic biotransformation of DA. This study could deepen understanding of interaction mechanism between toxin DA and marine microorganisms, which provides a new insight into the DA fate and its effects on benthic microbial community in marine environments.

Integrated analysis of transcriptome and proteome for exploring the mechanism of guaiacol production by Alicyclobacillus acidoterrestris

Alicyclobacillus spp. can cause commercially pasteurized fruit juices/beverages to spoil and the spoilage is characterized by the formation of a distinct medicinal or antiseptic off-odor attributed to guaiacol. The aim of this study was to reveal the mechanism of guaiacol production in A. acidoterrestris by combining transcriptomic and proteomic approaches. RNA-sequencing and iTRAQ analyses were conducted to investigate differences in expression levels of genes and proteins in A. acidoterrestris when producing (with 500 μM vanillic acid) and not producing (without vanillic acid) guaiacol. A total of 225 differentially expressed genes and 77 differentially expressed proteins were identified. The transcription of genes vdcBCD encoding subunits of vanillic acid decarboxylase were 626.47, 185.01 and 52.81-fold up-regulated, respectively; they were the most up-regulated genes involved in guaiacol production. Expressions of the benzoate membrane transport protein, fusaric acid resistance protein, resistance-nodulation- division transporter, some ATP-binding cassette transporters and major facilitator superfamily transporters were increased at either mRNA, protein or both levels, indicating that they participated in the uptake of vanillic acid and extrusion of guaiacol. In the metabolic process of vanillic acid to guaiacol in A. acidoterrestris, genes related to the pathway of tricarboxylic acid cycle and ribosome were up-regulated, while the expression of some genes associated with valine, leucine and isoleucine biosynthesis was decreased. These findings provide novel insight to understand the mechanism of guaiacol production in A. acidoterrestris, which will serve as an important guide for developing strategies for the control of A. acidoterrestris problems in the fruit juice industry.

Mechanisms of metal-dependent non-redox decarboxylases from quantum chemical calculations

Quantum chemical calculations are today an extremely valuable tool for studying enzymatic reaction mechanisms. In this mini-review, we summarize our recent work on several metal-dependent decarboxylases, where we used the so-called cluster approach to decipher the details of the reaction mechanisms, including elucidation of the identity of the metal cofactors and the origins of substrate specificity.

Decarboxylases are of growing potential for biocatalytic applications, as they can be used in the synthesis of novel compounds of, e.g., pharmaceutical interest. They can also be employed in the reverse direction, providing a strategy to synthesize value‐added chemicals by CO₂ fixation. A number of non-redox metal-dependent decarboxylases from the amidohydrolase superfamily have been demonstrated to have promiscuous carboxylation activities and have attracted great attention in the recent years. The computational mechanistic studies provide insights that are important for the further modification and utilization of these enzymes in industrial processes. The discussed enzymes are: 5‐carboxyvanillate decarboxylase, γ‐resorcylate decarboxylase, 2,3‐dihydroxybenzoic acid decarboxylase, and iso-orotate decarboxylase.

Biochemical characterization and synthetic application of aromatic L-amino acid decarboxylase from Bacillus atrophaeus

Aromatic L-amino acid decarboxylases (AADCs) are ubiquitously found in higher organisms owing to their physiological role in the synthesis of neurotransmitters and alkaloids. However, bacterial AADC has not attracted much attention because of its rather limited availability and narrow substrate range. Here, we examined the biochemical properties of AADC from Bacillus atrophaeus (AADC-BA) and assessed the synthetic feasibility of the enzyme for the preparation of monoamine neurotransmitters. AADC-BA was expressed in Escherichia coli BL21(DE3) and the purified enzyme showed a specific activity of 2.6 ± 0.4 U/mg for 10 mM L-phenylalanine (L-Phe) at 37 °C. AADC-BA showed optimal pH and temperature ranges at 7-8 and 37-45 °C, respectively. The K_M and k_cat values for L-Phe were 7.2 mM and 7.4 s^-1, respectively, at pH 7.0 and 37 °C. Comparison of the kinetic constants at different temperatures revealed that the temperature dependency of the enzyme was mainly determined by catalytic turnover rather than substrate binding. AADC-BA showed a broad substrate scope for various aromatic amino acids, including L-Phe, L-tryptophan (610% relative to L-Phe), L-tyrosine (12%), 3,4-dihydroxyphenyl-L-alanine (24%), 5-hydroxy-L-tryptophan (L-HTP, 71%), 4-chloro-L-phenylalanine (520%), and 4-nitro-L-phenylalanine (450%). Homology modeling and docking simulations were carried out and were consistent with the observed substrate specificity. To demonstrate the synthetic potential of AADC-BA, we carried out the production of serotonin by decarboxylation of L-HTP. The reaction yield of serotonin reached 98% after 1 h at the reaction conditions of 50 mM L-HTP and 4 U/mL AADC-BA. Moreover, we carried out preparative-scale decarboxylation of L-Phe (100 mM in 40-mL reaction mixture) and isolated the resulting 2-phenylethylamine (51% recovery yield). We expect that the broad substrate specificity of AADC-BA can be exploited to produce various aromatic biogenic amines. KEY POINTS: • AADC-BA showed broad substrate specificity for various aromatic amino acids. • The substrate specificity was elucidated by in silico structural modeling. • The synthetic potential of AADC-BA was demonstrated for the production of biogenic amines.

Thermostable D-amino acid decarboxylases derived from Thermotoga maritima diaminopimelate decarboxylase

Diaminopimelate decarboxylases (DAPDCs) are highly selective enzymes that catalyze the common final step in different lysine biosynthetic pathways, i.e. the conversion of meso-diaminopimelate (DAP) to L-lysine. We examined the modification of the substrate specificity of the thermostable decarboxylase from Thermotoga maritima with the aim to introduce activity with 2-aminopimelic acid (2-APA) since its decarboxylation leads to 6-aminocaproic acid (6-ACA), a building block for the synthesis of nylon-6. Structure-based mutagenesis of the distal carboxylate binding site resulted in a set of enzyme variants with new activities toward different D-amino acids. One of the mutants (E315T) had lost most of its activity toward DAP and primarily acted as a 2-APA decarboxylase. We next used computational modeling to explain the observed shift in catalytic activities of the mutants. The results suggest that predictive computational protocols can support the redesign of the catalytic properties of this class of decarboxylating PLP-dependent enzymes.

Mechanism of 3-Methylglutaconyl CoA Decarboxylase AibA/AibB: Pericyclic Reaction versus Direct Decarboxylation

The enzyme 3-methylglutaconyl coenzyme A (CoA) decarboxylase (called AibA/AibB) catalyzes the decarboxylation of 3-methylglutaconyl CoA to generate 3,3-dimethylacrylyl-CoA, representing an important step in the biosynthesis of isovaleryl-coenzyme A in Myxococcus xanthus when the regular pathway is blocked. A novel mechanism involving a pericyclic transition state has previously been proposed for this enzyme, making AibA/AibB unique among decarboxylases. Herein, density functional calculations are used to examine the energetic feasibility of this mechanism. It is shown that the intramolecular pericyclic reaction is associated with a very high energy barrier that is similar to the barrier of the same reaction in the absence of the enzyme. Instead, the calculations show that a direct decarboxylation mechanism has feasible energy barriers that are in line with the experimental observations.

Biocatalytic in Vitro and in Vivo FMN Prenylation and (De)carboxylase Activation

Reversible UbiD-like (de)carboxylases represent a large family of mostly uncharacterized enzymes, which require the recently discovered prenylated FMN (prFMN) cofactor for activity. Functional characterization of novel UbiDs is hampered by a lack of robust protocols for prFMN generation and UbiD activation. Here, we report two systems for in vitro and in vivo FMN prenylation and UbiD activation under aerobic conditions. The in vitro one-pot prFMN cascade includes five enzymes: FMN prenyltransferase (UbiX), prenol kinase, polyphosphate kinase, formate dehydrogenase, and FMN reductase, which use prenol, polyphosphate, formate, ATP, NAD⁺, and FMN as substrates and cofactors. Under aerobic conditions, this cascade produced prFMN from FMN with over 98% conversion and activated purified ferulic acid decarboxylase Fdc1 from Aspergillus niger and protocatechuic acid decarboxylase ENC0058 from Enterobacter cloaceae. The in vivo system for FMN prenylation and UbiD activation is based on the coexpression of Fdc1 and UbiX in Escherichia coli cells under aerobic conditions in the presence of prenol. The in vitro and in vivo FMN prenylation cascades will facilitate functional characterization of novel UbiDs and their applications.

Enzymatic reaction mechanism of cis-aconitate decarboxylase based on the crystal structure of IRG1 from Bacillus subtilis

Itaconate, which is formed by decarboxylation of cis-aconitate—an intermediate metabolite in the tricarboxylic acid cycle—has been used as a building block in polymer synthesis and is an important chemical in several biomedical and industrial applications. Itaconate is an immunometabolite with antibacterial, antiviral, immunoregulatory, and tumor-promoting activities. Recent focus has been on the role of itaconate in the field of immunology, with immune-responsive gene 1 (IRG1) being identified as the cis-aconitate decarboxylase responsible for itaconate production. We solved the structure of IRG1 from Bacillus subtilis (bsIRG1) and showed that IRG1 adopts either a closed or an open conformation; bsIRG1 was in the open form. A1 and A2 loops around the active site are flexible and can control the formation of the open and closed forms of IRG1. An in silico docking simulation showed that only the open form of IRG1 can accommodate the substrate. The most energetically favorable position of cis-aconitate in the active site of bsIRG1 involved the localization of C2 and C5 of cis-aconitate into the H102 region and H151 region of bsIRG1, respectively. Based on the structural study of bsIRG1, compared with IDS epimerase, and in silico docking simulation, we proposed two tentative enzymatic reaction mechanisms of IRG1, a two-base model and a one-base model.

Direct reversible decarboxylation from stable organic acids in dimethylformamide solution

Many classical and emerging methodologies in organic chemistry rely on carbon dioxide (CO₂) extrusion to generate reactive intermediates for bond-forming events. Synthetic reactions that involve the microscopic reverse-the carboxylation of reactive intermediates-have conventionally been undertaken using very different conditions. We report that chemically stable C(sp³) carboxylates, such as arylacetic acids and malonate half-esters, undergo uncatalyzed reversible decarboxylation in dimethylformamide solution. Decarboxylation-carboxylation occurs with substrates resistant to protodecarboxylation by Brønsted acids under otherwise identical conditions. Isotopically labeled carboxylic acids can be prepared in high chemical and isotopic yield by simply supplying an atmosphere of ¹³CO₂ to carboxylate salts in polar aprotic solvents. An understanding of carboxylate reactivity in solution enables conditions for the trapping of aldehydes, ketones, and α,β-unsaturated esters.

Quantitative Profiling of Protein-Derived Electrophilic Cofactors in Bacterial Cells with a Hydrazine-Derived Probe

Post-translational modification of proteins can form electrophilic cofactors that serve as a catalytic center. The derived electrophilic cofactors greatly expand protein activities and functions. However, there are few studies concerning how to profile the electrophiles in bacteria. Herein, we utilized a clickable probe called propargyl hydrazine to profile the protein-derived electrophilic cofactors in Escherichia coli (E. coli) cells. Since the cofactors are mostly carbonyl groups, the hydrazine-based probe can specifically react with the cofactors to form a Schiff base. The labeled proteins were then pulled down for mass spectrometry (MS) analysis. Fourteen proteins were shown to undergo enrichment by the probe and competitive binding by its analogue, propyl hydrazine. The identified proteins were further analyzed with targeted proteomics based on parallel reaction monitoring (PRM). Using this strategy, we obtained a global portrait of protein electrophiles in bacterial cells, among which the proteins of speD and panD were previously reported to derive pyruvoyl group as an electrophilic center while lpp can retain N-terminal formyl methionine. This quantitative chemical proteomics strategy can be used to find out protein electrophiles in bacteria and holds great potential to further characterize the protein functions.

Metabolic and Pharmaceutical Aspects of Fluorinated Compounds

The applications of fluorine in drug design continue to expand, facilitated by an improved understanding of its effects on physicochemical properties and the development of synthetic methodologies that are providing access to new fluorinated motifs. In turn, studies of fluorinated molecules are providing deeper insights into the effects of fluorine on metabolic pathways, distribution, and disposition. Despite the high strength of the C-F bond, the departure of fluoride from metabolic intermediates can be facile. This reactivity has been leveraged in the design of mechanism-based enzyme inhibitors and has influenced the metabolic fate of fluorinated compounds. In this Perspective, we summarize the literature associated with the metabolism of fluorinated molecules, focusing on examples where the presence of fluorine influences the metabolic profile. These studies have revealed potentially problematic outcomes with some fluorinated motifs and are enhancing our understanding of how fluorine should be deployed.

Protein Engineering of a Pyridoxal-5'-Phosphate-Dependent l-Aspartate-α-Decarboxylase from Tribolium castaneum for β-Alanine Production

In the present study, a pyridoxal-5′-phosphate (PLP)-dependent L-aspartate-α-decarboxylase from Tribolium castaneum (TcPanD) was selected for protein engineering to efficiently produce β-alanine. A mutant TcPanD-R98H/K305S with a 2.45-fold higher activity than the wide type was selected through error-prone PCR, site-saturation mutagenesis, and 96-well plate screening technologies. The characterization of purified enzyme TcPanD-R98H/K305S showed that the optimal cofactor PLP concentration, temperature, and pH were 0.04% (m/v), 50 °C, and 7.0, respectively. The 1mM of Na⁺, Ni²⁺, Co²⁺, K⁺, and Ca²⁺ stimulated the activity of TcPanD-R98H/K305S, while only 5 mM of Ni²⁺ and Na⁺ could increase its activity. The kinetic analysis indicated that TcPanD-R98H/K305S had a higher substrate affinity and enzymatic reaction rate than the wild enzyme. A total of 267 g/L substrate l-aspartic acid was consumed and 170.5 g/L of β-alanine with a molar conversion of 95.5% was obtained under the optimal condition and 5-L reactor fermentation.

Crystal structure of cis-aconitate decarboxylase reveals the impact of naturally occurring human mutations on itaconate synthesis

cis-Aconitate decarboxylase (CAD, also known as ACOD1 or Irg1) converts cis-aconitate to itaconate and plays central roles in linking innate immunity with metabolism and in the biotechnological production of itaconic acid by Aspergillus terreus We have elucidated the crystal structures of human and murine CADs and compared their enzymological properties to CAD from A. terreus Recombinant CAD is fully active in vitro without a cofactor. Murine CAD has the highest catalytic activity, whereas Aspergillus CAD is best adapted to a more acidic pH. CAD is not homologous to any known decarboxylase and appears to have evolved from prokaryotic enzymes that bind negatively charged substrates. CADs are homodimers, the active center is located in the interface between 2 distinct subdomains, and structural modeling revealed conservation in zebrafish and Aspergillus We identified 8 active-site residues critical for CAD function and rare naturally occurring human mutations in the active site that abolished CAD activity, as well as a variant (Asn152Ser) that increased CAD activity and is common (allele frequency 20%) in African ethnicity. These results open the way for 1) assessing the potential impact of human CAD variants on disease risk at the population level, 2) developing therapeutic interventions to modify CAD activity, and 3) improving CAD efficiency for biotechnological production of itaconic acid.

Novel 3,6-Dihydroxypicolinic Acid Decarboxylase-Mediated Picolinic Acid Catabolism in Alcaligenes faecalis JQ135

Picolinic acid (PA), a typical C-2-carboxylated pyridine derivative, is a metabolite of l-tryptophan and many other aromatic compounds in mammalian and microbial cells. Microorganisms can degrade and utilize PA for growth. However, the precise mechanism of PA metabolism remains unknown. Alcaligenes faecalis strain JQ135 utilizes PA as its carbon and nitrogen source for growth. In this study, we screened a 6-hydroxypicolinic acid (6HPA) degradation-deficient mutant through random transposon mutagenesis. The mutant hydroxylated 6HPA into an intermediate, identified as 3,6-dihydroxypicolinic acid (3,6DHPA), with no further degradation. A novel decarboxylase, PicC, was identified to be responsible for the decarboxylation of 3,6DHPA to 2,5-dihydroxypyridine. Although, PicC belonged to the amidohydrolase 2 family, it shows low similarity (<45%) compared to other reported amidohydrolase 2 family decarboxylases. Moreover, PicC was found to form a monophyletic group in the phylogenetic tree constructed using PicC and related proteins. Further, the genetic deletion and complementation results demonstrated that picC was essential for PA degradation. The PicC was Zn²⁺-dependent nonoxidative decarboxylase that can specifically catalyze the irreversible decarboxylation of 3,6DHPA to 2,5-dihydroxypyridine. The K_m and k _cat toward 3,6DHPA were observed to be 13.44 μM and 4.77 s^-1, respectively. Site-directed mutagenesis showed that His163 and His216 were essential for PicC activity. This study provides new insights into the microbial metabolism of PA at molecular level.IMPORTANCE Picolinic acid is a natural toxic pyridine derived from l-tryptophan metabolism and other aromatic compounds in mammalian and microbial cells. Microorganisms can degrade and utilize picolinic acid for their growth, and thus a microbial degradation pathway of picolinic acid has been proposed. Picolinic acid is converted into 6-hydroxypicolinic acid, 3,6-dihydroxypicolinic acid, and 2,5-dihydroxypyridine in turn. However, there was no physiological and genetic validation for this pathway. This study demonstrated that 3,6-dihydroxypicolinic acid was an intermediate in picolinic acid catabolism and further identified and characterized a novel amidohydrolase 2 family decarboxylase PicC. PicC was also shown to catalyze the decarboxylation of 3,6-dihydroxypicolinic acid into 2,5-dihydroxypyridine. This study provides a basis for understanding picolinic acid degradation and its underlying molecular mechanism.

Biochemical and Structural Characterization of TtnD, a Prenylated FMN-Dependent Decarboxylase from the Tautomycetin Biosynthetic Pathway

Tautomycetin (TTN) is a polyketide natural product featuring a terminal alkene. Functional characterization of the genes within the ttn gene cluster from Streptomyces griseochromogenes established the biosynthesis of the TTN polyketide backbone, its dialkylmaleic anhydride moiety, the coupling of the two moieties to form the nascent intermediate TTN F-1, and the tailoring steps converting TTN F-1 to TTN. Here, we report biochemical and structural characterization of TtnD, a prenylated FMN (prFMN)-dependent decarboxylase belonging to the UbiD family that catalyzes the penultimate step of TTN biosynthesis. TtnD catalyzes decarboxylation of TTN D-1 to TTN I-1, utilizing prFMN as a cofactor generated by the TtnC flavin prenyltransferase; both TtnD and TtnC are encoded within the ttn biosynthetic gene cluster. TtnD exhibits substrate promiscuity but accepts only TTN D-1 congeners that feature an α,β-unsaturated acid, supporting the [3+2] cycloaddition mechanism during catalysis that requires the double bond of an α,β-unsaturated acid substrate. TtnD shares a similar overall structure with other members of the UbiD family but forms a homotetramer in solution. Each protomer is composed of three domains with the active site located between the middle and C-terminal domains; R169-E272-E277, constituting the catalytic triad, and E228, involved in Mn(II)-mediated binding of prFMN, were confirmed by site-directed mutagenesis. TtnD represents the first example of a prFMN-dependent decarboxylase involved in polyketide biosynthesis, expanding the substrate scope of the UbiD family of decarboxylases beyond simple aromatic and cinnamic acids. TtnD and its homologues are widespread in nature and could be exploited as biocatalysts for organic synthesis.

Two novel decarboxylase genes play a key role in the stereospecific catabolism of dehydrodiconiferyl alcohol in Sphingobium sp. strain SYK-6

Sphingobium sp. strain SYK-6 is able to use a phenylcoumaran-type biaryl, dehydrodiconiferyl alcohol (DCA), as a sole source of carbon and energy. In SYK-6 cells, the alcohol group of the B-ring side chain of DCA was first oxidized to the carboxyl group, and then the alcohol group of the A-ring side chain was oxidized to generate 5-(2-carboxyvinyl)-2-(4-hydroxy-3-methoxyphenyl)-7-methoxy-2,3-dihydrobenzofuran-3-carboxylate (DCA-CC). We identified phcF, phcG and phcH, which conferred the ability to convert DCA-CC into 3-(4-hydroxy-3-(4-hydroxy-3-methoxystyryl)-5-methoxyphenyl)acrylate (DCA-S) in a host strain. These genes exhibited no significant sequence similarity with known enzyme genes, whereas phcF and phcG, which contain a DUF3237 domain of unknown function, showed 32% amino acid sequence identity with each other. The DCA-CC conversion activities were markedly decreased by disruption of phcF and phcG, indicating that phcF and phcG play dominant roles in the conversion of DCA-CC. Purified PhcF and PhcG catalysed the decarboxylation of the A-ring side chain of DCA-CC, producing DCA-S, and showed enantiospecificity towards (+)- and (-)-DCA-CC respectively. PhcF and PhcG formed homotrimers, and their K_m for DCA-CC were determined to be 84 μM and 103 μM, and V_max were 307 μmol⋅min^-1 ⋅mg^-1 and 137 μmol⋅min^-1 ⋅mg^-1 respectively. In conclusion, PhcF and PhcG are enantiospecific decarboxylases involved in phenylcoumaran catabolism.

Unified Total Synthesis of Pyrroloazocine Indole Alkaloids Sheds Light on Their Biosynthetic Relationship

The total synthesis of seven members of the lapidilectine and grandilodine family of alkaloids has been accomplished in racemic and enantiopure form without protection/deprotection of functional groups. The two key steps, an 8- endo-dig hydroarylation and a 6- exo-trig photoredox cyclization, were catalyzed using gold. A rationale for the formation of the cyclopropane ring of the lundurines is also provided.

The role of conserved residues in Fdc decarboxylase in prenylated flavin mononucleotide oxidative maturation, cofactor isomerization, and catalysis

The UbiD family of reversible decarboxylases act on aromatic, heteroaromatic, and unsaturated aliphatic acids and utilize a prenylated flavin mononucleotide (prFMN) as cofactor, bound adjacent to a conserved Glu–Arg–Glu/Asp ionic network in the enzyme's active site. It is proposed that UbiD activation requires oxidative maturation of the cofactor, for which two distinct isomers, prFMN^ketimine and prFMN^iminium, have been observed. It also has been suggested that only the prFMN^iminium form is relevant to catalysis, which requires transient cycloaddition between substrate and cofactor. Using Aspergillus niger Fdc1 as a model system, we reveal that isomerization of prFMN^iminium to prFMN^ketimine is a light-dependent process that is largely independent of the Glu²⁷⁷–Arg¹⁷³–Glu²⁸² network and accompanied by irreversible loss of activity. On the other hand, efficient catalysis was highly dependent on an intact Glu–Arg–Glu network, as only Glu → Asp substitutions retain activity. Surprisingly, oxidative maturation to form the prFMN^iminium species is severely affected only for the R173A variant. In summary, the unusual irreversible isomerization of prFMN is light-dependent and probably proceeds via high-energy intermediates but is independent of the Glu–Arg–Glu network. Our results from mutagenesis, crystallographic, spectroscopic, and kinetic experiments indicate a clear role for the Glu–Arg–Glu network in both catalysis and oxidative maturation.

Carbon Kinetic Isotope Effects and the Mechanisms of Acid-Catalyzed Decarboxylation of 2,4-Dimethoxybenzoic Acid and CO2 Incorporation into 1,3-Dimethoxybenzene

The rate of decarboxylation of 2,4-dimethoxybenzoic acid (1) is accelerated in parallel to the extent that the carboxyl group acquires a second proton (1H⁺). However, the conjugate acid would resist C-C bond breaking as that would lead to formation of doubly protonated CO₂. An alternative via formation of a higher-energy protonated phenyl tautomer (2H⁺) prior to C-C bond breaking would produce protonated CO₂, an energetically inaccessible species that can be avoided by transfer of the carboxyl proton to water in the same step. Headspace sampling of CO₂ that evolves in the acid-catalyzed process and analysis by GC-IRMS gives a smaller than expected value of 1.022 for the carbon kinetic isotope (CKIE), k¹²/k¹³. While this value establishes that C-C cleavage is part of the rate-determining process, intrinsic CKIEs for decarboxylation reactions are typically greater than 1.03. Computational analysis of the C-C bond cleavage from 2H⁺ gives an intrinsic CKIE of 1.051 and suggests two partially rate-determining steps in the decarboxylation of 1: transfer of the second carboxyl proton to the adjacent phenyl carbon and C-C cleavage in which the carboxyl proton is also transferred to water. Applying the principle of microscopic reversibility to fixation of CO₂ in acidic solutions reveals the importance of proton transfers to both carbon and oxygen in the overall fixation process.