New cofactor supports α,β-unsaturated acid decarboxylation via 1,3-dipolar cycloaddition

The bacterial ubiD and ubiX or the homologous fungal fdc1 and pad1 genes have been implicated in the non-oxidative reversible decarboxylation of aromatic substrates, and play a pivotal role in bacterial ubiquinone (also known as coenzyme Q) biosynthesis or microbial biodegradation of aromatic compounds, respectively. Despite biochemical studies on individual gene products, the composition and cofactor requirement of the enzyme responsible for in vivo decarboxylase activity remained unclear. Here we show that Fdc1 is solely responsible for the reversible decarboxylase activity, and that it requires a new type of cofactor: a prenylated flavin synthesized by the associated UbiX/Pad1. Atomic resolution crystal structures reveal that two distinct isomers of the oxidized cofactor can be observed, an isoalloxazine N5-iminium adduct and a N5 secondary ketimine species with markedly altered ring structure, both having azomethine ylide character. Substrate binding positions the dipolarophile enoic acid group directly above the azomethine ylide group. The structure of a covalent inhibitor–cofactor adduct suggests that 1,3-dipolar cycloaddition chemistry supports reversible decarboxylation in these enzymes. Although 1,3-dipolar cycloaddition is commonly used in organic chemistry, we propose that this presents the first example, to our knowledge, of an enzymatic 1,3-dipolar cycloaddition reaction. Our model for Fdc1/UbiD catalysis offers new routes in alkene hydrocarbon production or aryl (de)carboxylation.

• Publication year

  2015

• Venue

  Nature

• Publication date

  2015-06-17

• Fields of study

  Medicine, Chemistry

• Identifiers
  DOI 10.1038/nature14560PMID 26083754PMCID 4988494
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Isofunctional enzymes PAD1 and UbiX catalyze formation of a novel cofactor required by ferulic acid decarboxylase and 4-hydroxy-3-polyprenylbenzoic acid decarboxylase.

  2015cited by this paper
• UbiX is a flavin prenyltransferase required for bacterial ubiquinone biosynthesis

  2015cited by this paper
• Biosynthesis and physiology of coenzyme Q in bacteria.

  2014cited by this paper
• Anaerobic degradation of homocyclic aromatic compounds via arylcarboxyl-coenzyme A esters: organisms, strategies and key enzymes.

  2014cited by this paper
• Impact of scaffold rigidity on the design and evolution of an artificial Diels-Alderase

  2014cited by this paper
• Investigating the role of a backbone to substrate hydrogen bond in OMP decarboxylase using a site-specific amide to ester substitution

  2014cited by this paper
• Functional diversity of organic molecule enzyme cofactors.

  2013cited by this paper
• Flavoenzymes: versatile catalysts in biosynthetic pathways.

  2013cited by this paper
• Crystal structures of isoorotate decarboxylases reveal a novel catalytic mechanism of 5-carboxyl-uracil decarboxylation and shed light on the search for DNA decarboxylase

  2013cited by this paper
• Structural Insights into the UbiD Protein Family from the Crystal Structure of PA0254 from Pseudomonas aeruginosa

  2013cited by this paper
• Decarboxylation mechanisms in biological system.

  2012cited by this paper
• Mapping the structural requirements of inducers and substrates for decarboxylation of weak acid preservatives by the food spoilage mould Aspergillus niger.

  2012cited by this paper
• Carboxylases in Natural and Synthetic Microbial Pathways

  2011cited by this paper
• An Enzyme-Catalyzed [4+2] Cycloaddition is a Key Step in the Biosynthesis of Spinosyn A

  2011cited by this paper
• Overview of the CCP4 suite and current developments

  2011cited by this paper
• Aerobic reduction of olefins by in situ generation of diimide with synthetic flavin catalysts.

  2011cited by this paper
• Structure of PA4019, a putative aromatic acid decarboxylase from Pseudomonas aeruginosa.

  2011cited by this paper
• Atomic-resolution structure of an N5 flavin adduct in D-arginine dehydrogenase.

  2011cited by this paper
• Turning a riboflavin-binding protein into a self-sufficient monooxygenase by cofactor redesign.

  2011cited by this paper
• PAD1 and FDC1 are essential for the decarboxylation of phenylacrylic acids in Saccharomyces cerevisiae.

  2010cited by this paper
• Synthetic applications of the carbonyl generating Grob fragmentation.

  2010cited by this paper
• The decarboxylation of the weak-acid preservative, sorbic acid, is encoded by linked genes in Aspergillus spp.

  2010cited by this paper
• Structure-guided directed evolution of alkenyl and arylmalonate decarboxylases.

  2009cited by this paper
• Theory of 1,3-dipolar cycloadditions: distortion/interaction and frontier molecular orbital models.

  2008cited by this paper
• Asymmetric 1,3-Dipolar Cycloadditions

  2007cited by this paper
• The role of UbiX in Escherichia coli coenzyme Q biosynthesis.

  2007cited by this paper
• Hybrid density functional theory for π‐stacking interactions: Application to benzenes, pyridines, and DNA bases

  2006cited by this paper
• Distribution of genes encoding the microbial non-oxidative reversible hydroxyarylic acid decarboxylases/phenol carboxylases.

  2005cited by this paper
• Crystal structure of a dodecameric FMN‐dependent UbiX‐like decarboxylase (Pad1) from Escherichia coli O157: H7

  2004cited by this paper
• Regulation of the isofunctional genes ubiD and ubiX of the ubiquinone biosynthetic pathway of Escherichia coli.

  2003cited by this paper
• Comparing HPLC and UV Spectrophotometric Analysis Methods for Determining the Stability of Sorbic Acid in Nonionic Creams Containing Lactic Acid

  2000cited by this paper
• Structural proteomics of an archaeon

  2000cited by this paper
• SWISS‐MODEL and the Swiss‐Pdb Viewer: An environment for comparative protein modeling

  1997cited by this paper
• Membrane-associated reactions in ubiquinone biosynthesis in Escherichia coli. 3-Octaprenyl-4-hydroxybenzoate carboxy-lyase.

  1976cited by this paper
• Microbial L-phenylalanine ammonia-lyase. Purification, subunit structure and kinetic properties of the enzyme from Rhizoctonia solani.

  1975cited by this paper

• Deciphering the properties and reaction mechanism of anhydromevalonate phosphate decarboxylase, a prenylated flavin mononucleotide-dependent enzyme in the archaeal mevalonate pathway.

  2026cites this paper
• Metal–Organic Framework Encapsulation of Ferulic Acid Decarboxylase: Robust Biocomposites Catalyzing Synthetically Useful Decarboxylation and Synergized CO 2 Fixation Reactions

  2026cites this paper
• Mechanisms of photodecarboxylations for alkane synthesis: a theoretical study

  2026cites this paper
• Pyridoxal 5'-Phosphate-Dependent Enzymatic Decarboxylative Annulation.

  2026cites this paper
• Enzyme-Mediated Carbon Dioxide Fixation: Catalytic Mechanisms and Computational Insights

  2025cites this paper
• Structure and Mechanism of PhdC, a Prenylated-Flavin Maturase.

  2025cites this paper
• Genome-based exploration of volatile flavor diversity from food yeast species

  2025cites this paper
• Anaerobic degradation of polycyclic aromatic hydrocarbons

  2025cites this paper
• Multiscale metabolic engineering in biological lignin valorization

  2025cites this paper
• Phenolic Acid Decarboxylase for Carbon Dioxide Fixation: Mining, Biochemical Characterization, and Regioselective Enzymatic β-carboxylation of para-hydroxystyrene Derivatives

  2025cites this paper
• Thermodynamically Coupled Three-Enzyme Cascade Converts Styrene to Cinnamic Acid, l-Phenylalanine, and Phenylpyruvate via CO2 Fixation without External Energy Cofactors.

  2025cites this paper
• Quantum Chemical Study on the Reaction Mechanism of 2,5-Furandicarboxylic Acid Decarboxylase.

  2025cites this paper
• From Residues to Clove: Harnessing Novel Phenolic Acid Decarboxylase for 4-Vinyl Guaiacol Production in Industrial Yeast

  2025cites this paper
• Characterization of a consensus-designed trans-cinnamic acid decarboxylase for styrene biosynthesis

  2025cites this paper
• Integrated strategies for engineering ferulic acid decarboxylase with tunnel conformation and substrate pocket for adapting non-natural substrates

  2025cites this paper
• Antimutator and Mutational Spectrum Effects Can Combine to Reduce Evolutionary Potential in Escherichia coli ΔnudJ

  2025cites this paper
• Integration of metabolic and bioprocess engineering for the production of β-ketoadipic acid from glucose and xylose by Pseudomonas putida

  2025cites this paper
• Transcriptome analysis of Aspergillus oryzae RIB40 under chemical stress reveals mechanisms of adaptation to fungistatic compounds of lignocellulosic side streams

  2025cites this paper
• Synthetic Biology-Driven Lignin Valorization

  2025cites this paper
• Structural Flexibility and Electronic Tuning in N5-Substituted Anionic Reduced Flavins: Implications for Flavoenzyme Intermediates.

  2025cites this paper
• Characterization of the N5-dimethylallyl-FMN Intermediate in the Biosynthesis of Prenylated-FMN Catalyzed by UbiX.

  2024cites this paper
• (De)carboxylation mechanisms of heteroaromatic substrates catalyzed by prenylated FMN-dependent UbiD decarboxylases: An in-silico study.

  2024cites this paper
• Decarboxylation in Natural Products Biosynthesis

  2024cites this paper
• Mechanisms of photoisomerization of the prenylated flavin mononucleotide cofactor: a theoretical study

  2024cites this paper
• An Enzyme Catalyzing the Oxidative Maturation of Reduced Prenylated-FMN to Form the Active Coenzyme

  2024cites this paper
• Enzyme cascades for in vitro and in vivo FMN prenylation and UbiD (de)carboxylase activation under aerobic conditions.

  2024cites this paper
• Methods to study prFMN-UbiD mediated (de)carboxylation.

  2024cites this paper
• Adaptive Laboratory Evolution of Flavin Functionality Identifies Dihydrolipoyl Dehydrogenase as One of the Critical Points for the Activity of 7,8-Didemethyl-Riboflavin as a Surrogate for Riboflavin in Escherichia coli

  2024cites this paper
• Quantum chemical studies of the reaction mechanisms of enzymatic CO2 conversion.

  2024cites this paper
• Surveying the scope of aromatic decarboxylations catalyzed by prenylated-flavin dependent enzymes.

  2024cites this paper
• The prFMNH2-binding chaperone LpdD assists UbiD decarboxylase activation

  2024cites this paper
• Probing the role of protein conformational changes in the mechanism of prenylated-FMN-dependent phenazine-1-carboxylic acid decarboxylase

  2024cites this paper
• Stereoretentive Catalytic [3+2]-Cycloaddition/Rearrangement/Decarboxylation Reactions of Indoles with Non-Racemic Donor–Acceptor Cyclopropanes

  2023cites this paper
• Enzymatic Conversion of CO2: From Natural to Artificial Utilization

  2023cites this paper
• Light-driven biosynthesis of volatile, unstable and photosensitive chemicals from CO2

  2023influential citation
• Identification and Analysis of the Biosynthetic Gene Cluster for the Hydrazide-Containing Aryl Polyene Spinamycin.

  2023cites this paper
• Control of the fungus Colletotrichum lindemuthianum in common bean plants by 2-methoxy-1,4-naphthoquinone

  2023influential citation
• Stability engineering of ferulic acid decarboxylase unlocks enhanced aromatic acid decarboxylation

  2023cites this paper
• Chromatography Scrutiny, Molecular Docking, Clarifying the Selectivities and the Mechanism of [3 + 2] Cycloloaddition Reaction between Linallol and Chlorobenzene-Nitrile-oxide

  2023cites this paper
• Engineering Novosphingobium aromaticivorans to produce cis,cis-muconic acid from biomass aromatics

  2023cites this paper
• Chemical Composition, Mosquito Larvicidal and Antimicrobial Activities, and Molecular Docking Study of Essential Oils of Cinnamomum melastomaceum, Neolitsea buisanensis and Uvaria microcarpa from Vietnam

  2023cites this paper
• FhuA: From Iron-Transporting Transmembrane Protein to Versatile Scaffolds through Protein Engineering.

  2023cites this paper
• Modern Strategies for Carbon Isotope Exchange.

  2023cites this paper
• Differences in Formation Mechanisms of Phenolic Off-Flavor Compounds among Yeast Species

  2023cites this paper
• Anaerobic purinolytic enzymes enable dietary purine clearance by engineered gut bacteria.

  2023cites this paper
• Naphthalene Carboxylation in the Sulfate-Reducing Enrichment Culture N47 Is Proposed to Proceed via 1,3-Dipolar Cycloaddition to the Cofactor Prenylated Flavin Mononucleotide

  2023cites this paper
• Prenylated flavins: structures and mechanisms

  2022cites this paper
• Negative Cooperativity in the Mechanism of Prenylated-Flavin-Dependent Ferulic Acid Decarboxylase: A Proposal for a "Two-Stroke" Decarboxylation Cycle.

  2022cites this paper
• Unravelling interactions between active site residues and DMAP in the initial steps of prenylated flavin mononucleotide biosynthesis catalyzed by PaUbiX.

  2022cites this paper
• Derivatives of Natural Organocatalytic Cofactors and Artificial Organocatalytic Cofactors as Catalysts in Enzymes

  2022cites this paper
• Omics and mechanistic insights into di-(2-ethylhexyl) phthalate degradation in the O2-fluctuating estuarine sediments.

  2022cites this paper
• Kinetics and thermodynamics of enzymatic decarboxylation of α,β-unsaturated acid: a theoretical study

  2022cites this paper
• Isophthalate:coenzyme A ligase initiates anaerobic degradation of xenobiotic isophthalate

  2022cites this paper
• Structural insights into UbiD reversible decarboxylation.

  2022cites this paper
• Critical enzyme reactions in aromatic catabolism for microbial lignin conversion

  2022cites this paper
• Toolbox for the structure-guided evolution of ferulic acid decarboxylase (FDC)

  2022cites this paper
• High-Level Production of Catechol from Glucose by Engineered Escherichia coli

  2022cites this paper
• A Career in Biocatalysis: Kurt Faber

  2022cites this paper
• Biosynthesis of alkanes/alkenes from fatty acids or derivatives (triacylglycerols or fatty aldehydes).

  2022cites this paper
• Cloning, heterologous expression and characterization of o-phthalyl-CoA decarboxylase from phthalate degrading denitrifying bacterium

  2022cites this paper
• Biosynthesis of triacsin featuring an N-hydroxytriazene pharmacophore

  2021cites this paper
• One-pot synthesis of (R)- and (S)-phenylglycinol from bio-based l-phenylalanine by an artificial biocatalytic cascade

  2021cites this paper
• Copper(I)‐Catalyzed Intramolecular Cyclization of o ‐Propargyloxy Diketopiperazines to Access Diverse Diazabicyclic and Spiro‐Diketopiperazinochromanes

  2021cites this paper
• Revealing the unknown aspects of initial steps of prenylated flavin mononucleotide biosynthesis – the role of Lys129 in PaUbiX

  2021cites this paper
• Decarboxylation of Aromatic Carboxylic Acids by the Prenylated-FMN-dependent Enzyme Phenazine-1-carboxylic Acid Decarboxylase

  2021cites this paper
• Investigations into the Ability to Reduce Cinnamic Acid as Undesired Precursor of Toxicologically Relevant Styrene in Wort by Different Barley to Wheat Ratios (Grain Bill) during Mashing.

  2021cites this paper
• UbiD domain dynamics underpins aromatic decarboxylation

  2021cites this paper
• Biocatalytic Site-Selective Hydrogen Isotope Exchange of Unsaturated Fragments with D2O

  2021cites this paper
• Directed evolution of prenylated FMN-dependent Fdc supports efficient in vivo isobutene production

  2021cites this paper
• Total Biosynthesis of Triacsin Featuring an N-hydroxytriazene Pharmacophore

  2021cites this paper
• Natural Flavins: Occurrence, Role, and Noncanonical Chemistry

  2021cites this paper
• In-situ muconic acid extraction reveals sugar consumption bottleneck in a xylose-utilizing Saccharomyces cerevisiae strain

  2021cites this paper
• Degradation of Homocyclic Aromatic Compounds by Fungi

  2021cites this paper
• Modes of Flavin‐Based Catalysis

  2021cites this paper
• 2,5-Furandicarboxylic acid production from furfural by sequential biocatalytic reactions.

  2021cites this paper
• The In Vitro Production of prFMN for Reconstitution of UbiD Enzymes.

  2021cites this paper
• Expanding the synthetic scope of biocatalysis by enzyme discovery and protein engineering

  2021cites this paper
• Synthetic Enzyme‐Catalyzed CO2 Fixation Reactions

  2021cites this paper
• Biocatalytic C-C Bond Formation for One Carbon Resource Utilization

  2021cites this paper
• Crystal structures of non-oxidative decarboxylases reveal a new mechanism of action with a catalytic dyad and structural twists

  2021cites this paper
• Structure and Mechanism of Pseudomonas aeruginosa PA0254/HudA, a prFMN-Dependent Pyrrole-2-carboxylic Acid Decarboxylase Linked to Virulence

  2021cites this paper
• Designing Modular Cell-free Systems for Tunable Biotransformation of l-phenylalanine to Aromatic Compounds

  2021influential citation
• Catabolic Pathways and Enzymes Involved in the Anaerobic Degradation of Monocyclic Aromatic Compounds

  2020cites this paper
• Catabolic Pathways and Enzymes Involved in the Anaerobic Degradation of Polycyclic Aromatic Hydrocarbons

  2020cites this paper
• Reductive Dehalogenases

  2020cites this paper
• Flavin doesn’t put all oxygens in one basket

  2020cites this paper
• Kinetic Analysis of Transient Intermediates in the Mechanism of Prenyl-Flavin-Dependent Ferulic Acid Decarboxylase.

  2020cites this paper
• Bacterial pathways for the biosynthesis of ubiquinone.

  2020cites this paper
• Cell-free styrene biosynthesis at high titers

  2020cites this paper
• Development of a Rhodococcus opacus Cell Factory for Valorizing Lignin to Muconate

  2020cites this paper
• Insights into the Cultured Bacterial Fraction of Corals

  2020cites this paper
• New Catalytic Motifs in Flavoenzymology

  2020cites this paper
• Reconstruction of the “Archaeal” Mevalonate Pathway from the Methanogenic Archaeon Methanosarcina mazei in Escherichia coli Cells

  2020cites this paper
• Bacterial terpenome.

  2020cites this paper
• Weak Acid Resistance A (WarA), a Novel Transcription Factor Required for Regulation of Weak-Acid Resistance and Spore-Spore Heterogeneity in Aspergillus niger

  2020cites this paper
• Flavoenzymes for biocatalysis.

  2020cites this paper
• Biochemistry of prenylated-FMN enzymes.

  2020cites this paper
• An Aerobic Hybrid Phthalate Degradation Pathway via Phthaloyl-Coenzyme A in Denitrifying Bacteria

  2020cites this paper
• Fluorescent enzyme-coupled activity assay for phenylalanine ammonia-lyases

  2020cites this paper
• Enzymatic C–H activation of aromatic compounds through CO2 fixation

  2020cites this paper