Enzymatic Carboxylation and Decarboxylation Mechanisms

Enzymatic carboxylation and decarboxylation represent complementary biotransformations that introduce or remove CO₂ from organic substrates under mild conditions. Carboxylases catalyse the fixation of inorganic carbon by forming new carbon–carbon bonds, whereas decarboxylases cleave those bonds, often reversing carboxylation. These processes underpin key metabolic pathways in plants, microbes and specialised industrial biocatalysts, enabling carbon recycling and the synthesis of value-added chemicals. Central to many of these reactions is the use of specialised cofactors—most notably prenylated flavin mononucleotide (prFMN)—that expand the chemical repertoire of enzymes by facilitating unusual cycloaddition and radical mechanisms.

The mechanistic diversity of these enzymes ranges from metal-dependent phenolic acid decarboxylases that operate via acid–base catalysis to prFMN-dependent UbiD family members that employ 1,3-dipolar cycloaddition pathways. Thermodynamic constraints of CO₂ fixation are often overcome through substrate coupling, bicarbonate buffering or pressurised CO₂, and engineering of substrate binding sites has broadened the substrate spectrum from simple aromatics to acrylic acid derivatives and complex polyphenols. The interplay of structural biology, mutagenesis and computational modelling has illuminated active-site architectures, cofactor maturation and proton-coupled electron transfer events, opening routes to sustainable biomanufacturing and lignin valorisation.

Research from Nature Portfolio

Recent studies have harnessed and reprogrammed decarboxylase enzymes to produce non-natural compounds and elucidate cofactor biosynthesis. One such work describes the construction of an artificial metabolic pathway in Escherichia coli for direct production of 1,3-butadiene from glucose. Rational mutagenesis of a ferulic acid decarboxylase enhanced decarboxylation of cis,cis-muconic acid, with optimisation of dissolved oxygen and pH enabling gram-per-litre titres in bioreactor conditions. This exemplifies how enzyme design and process control can yield bio-based monomers for rubber and plastics.

Structural and mechanistic analyses of the UbiX prenyltransferase have revealed that prFMN formation follows an SN1-type mechanism akin to class I terpene cyclase chemistry. High-resolution structures captured key bond-forming events between dimethylallyl substrates and FMN, clarifying how the flavin core is extended and activated. These findings inform the engineering of flavin-modifying enzymes and the broader application of prFMN in reversible (de)carboxylation reactions.

Enzymatic Carboxylation and Decarboxylation Mechanisms publication trend

The graph below shows the total number of articles in enzymatic carboxylation and decarboxylation mechanisms across all publications each year (not limited to Nature Index journals).

Technical terms

Carboxylation: Enzymatic incorporation of CO₂ into an organic substrate to form a carboxylic acid.

Decarboxylation: Enzymatic removal of a carboxyl group from an organic molecule, releasing CO₂.

Prenylated flavin mononucleotide (prFMN): A modified flavin cofactor extended by a prenyl group, essential for UbiD-family reversible (de)carboxylases.

UbiD enzyme family: A class of prFMN-dependent enzymes that catalyse reversible decarboxylation of aromatic and unsaturated carboxylic acids.

Regioselectivity: The preference of an enzyme for catalysing a reaction at a specific position on a substrate molecule.

1,3-Dipolar cycloaddition: A pericyclic reaction mechanism in which a dipolar intermediate and an alkene form a five-membered ring, utilised by prFMN-dependent decarboxylases.

References

1. Non‐Oxidative Enzymatic (De)Carboxylation of (Hetero)Aromatics and Acrylic Acid Derivatives. Advanced Synthesis & Catalysis (2019).
2. Direct 1,3-butadiene biosynthesis in Escherichia coli via a tailored ferulic acid decarboxylase mutant. Nature Communications (2021).
3. The UbiX flavin prenyltransferase reaction mechanism resembles class I terpene cyclase chemistry. Nature Communications (2019).
4. Synthetic Enzyme‐Catalyzed CO2 Fixation Reactions. ChemSusChem (2021).
5. Carboxylation of Hydroxyaromatic Compounds with HCO3− by Enzyme Catalysis: Recent Advances Open the Perspective for Valorization of Lignin-Derived Aromatics. Catalysts (2019).