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  • 1. Payer, Stefan E.
    et al.
    Marshall, Stephen A.
    Bärland, Natalie
    Sheng, Xiang
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Reiter, Tamara
    Dordic, Andela
    Steinkellner, Georg
    Wuensch, Christiane
    Kaltwasser, Susann
    Fisher, Karl
    Rigby, Stephen E. J.
    Macheroux, Peter
    Vonck, Janet
    Gruber, Karl
    Faber, Kurt
    Himo, Fahmi
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Leys, David
    Pavkov-Keller, Tea
    Glueck, Silvia M.
    Regioselective para-Carboxylation of Catechols with a Prenylated Flavin Dependent Decarboxylase2017In: Angewandte Chemie International Edition, ISSN 1433-7851, E-ISSN 1521-3773, Vol. 56, no 44, p. 13893-13897Article in journal (Refereed)
    Abstract [en]

    The utilization of CO2 as a carbon source for organic synthesis meets the urgent demand for more sustainability in the production of chemicals. Herein, we report on the enzyme-catalyzed para-carboxylation of catechols, employing 3,4-dihydroxybenzoic acid decarboxylases (AroY) that belong to the UbiD enzyme family. Crystal structures and accompanying solution data confirmed that AroY utilizes the recently discovered prenylated FMN (prFMN) cofactor, and requires oxidative maturation to form the catalytically competent prFMN(iminium) species. This study reports on the in vitro reconstitution and activation of a prFMN-dependent enzyme that is capable of directly carboxylating aromatic catechol substrates under ambient conditions. A reaction mechanism for the reversible decarboxylation involving an intermediate with a single covalent bond between a quinoid adduct and cofactor is proposed, which is distinct from the mechanism of prFMN-associated 1,3-dipolar cycloadditions in related enzymes.

  • 2. Payer, Stefan E.
    et al.
    Sheng, Xiang
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Pollak, Hannah
    Wuensch, Christiane
    Steinkellner, Georg
    Himo, Fahmi
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Glueck, Silvia M.
    Faber, Kurt
    Exploring the Catalytic Promiscuity of Phenolic Acid Decarboxylases: Asymmetric, 1,6-Conjugate Addition of Nucleophiles Across 4-Hydroxystyrene2017In: Advanced Synthesis and Catalysis, ISSN 1615-4150, E-ISSN 1615-4169, Vol. 359, no 12, p. 2066-2075Article in journal (Refereed)
    Abstract [en]

    The catalytic promiscuity of a ferulic acid decarboxylase from Enterobacter sp. (FDC_Es) and phenolic acid decarboxylases (PADs) for the asymmetric conjugate addition of water across the C=C bond of hydroxystyrenes was extended to the N-, C-and S-nucleophiles methoxyamine, cyanide and propanethiol to furnish the corresponding addition products in up to 91% ee. The products obtained from the biotransformation employing the most suitable enzyme/nucleophile pairs were isolated and characterized after optimizing the reaction conditions. Finally, a mechanistic rationale supported by quantum mechanical calculations for the highly (S)selective addition of cyanide is proposed.

  • 3.
    Planas, Ferran
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Sheng, Xiang
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    McLeish, Michael J.
    Himo, Fahmi
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    A Theoretical Study of the Benzoylformate Decarboxylase Reaction Mechanism2018In: Frontiers in Chemistry, E-ISSN 2296-2646, Vol. 6, article id 205Article in journal (Refereed)
    Abstract [en]

    Density functional theory calculations are used to investigate the detailed reaction mechanism of benzoylformate decarboxylase, a thiamin diphosphate (ThDP)-dependent enzyme that catalyzes the nonoxidative decarboxylation of benzoylformate yielding benzaldehyde and carbon dioxide. A large model of the active site is constructed on the basis of the X-ray structure, and it is used to characterize the involved intermediates and transition states and evaluate their energies. There is generally good agreement between the calculations and available experimental data. The roles of the various active site residues are discussed and the results are compared to mutagenesis experiments. Importantly, the calculations identify off-cycle intermediate species of the ThDP cofactor that can have implications on the kinetics of the reaction.

  • 4.
    Sheng, Xiang
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Himo, Fahmi
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Theoretical Study of Enzyme Promiscuity: Mechanisms of Hydration and Carboxylation Activities of Phenolic Acid Decarboxylase2017In: ACS Catalysis, ISSN 2155-5435, E-ISSN 2155-5435, Vol. 7, no 3, p. 1733-1741Article in journal (Refereed)
    Abstract [en]

    The cofactor-free phenolic acid decarboxylases (PADs) catalyze the nonoxidative decarboxylation of phenolic acids to their corresponding p-vinyl derivatives. Since these compounds are useful industrially, PADs have potential applications as biocatalysts. Recently, PADs have been reported to also catalyze the hydration and carboxylation of hydroxystyrenes, increasing further their biocatalytic utility. We have used quantum chemical methodology to investigate the detailed mechanisms of both promiscuous reactions. A large model of the active site is designed starting from the crystal structure of PAD from Bacillus subtilis. The calculations suggest new mechanisms, quite different from the literature proposals. For the carboxylation reaction, a carbon dioxide molecule is proposed to be generated from bicarbonate first and then act as the source for the carboxylate group of the product. For the hydration activity, the reaction is suggested to start with the formation of a quinone methide intermediate by protonation of the C=C double bond of the p-vinylphenol substrate. A water molecule then attacks the alpha-carbon to generate the alcohol product. The enantioselectivity of the hydration reaction is also investigated in this study, and the calculations are able to reproduce and rationalize the observed experimental outcome.

  • 5.
    Sheng, Xiang
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Lind, Maria E. S.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Himo, Fahmi
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Theoretical study of the reaction mechanism of phenolic acid decarboxylase2015In: The FEBS Journal, ISSN 1742-464X, E-ISSN 1742-4658, Vol. 282, no 24, p. 4703-4713Article in journal (Refereed)
    Abstract [en]

    The cofactor-free phenolic acid decarboxylases (PADs) catalyze the non-oxidative decarboxylation of phenolic acids to their corresponding p-vinyl derivatives. Phenolic acids are toxic to some organisms, and a number of them have evolved the ability to transform these compounds, including PAD-catalyzed reactions. Since the vinyl derivative products can be used as polymer precursors and are also of interest in the food-processing industry, PADs might have potential applications as biocatalysts. We have investigated the detailed reaction mechanism of PAD from Bacillus subtilis using quantum chemical methodology. A number of different mechanistic scenarios have been considered and evaluated on the basis of their energy profiles. The calculations support a mechanism in which a quinone methide intermediate is formed by protonation of the substrate double bond, followed by C-C bond cleavage. A different substrate orientation in the active site is suggested compared to the literature proposal. This suggestion is analogous to other enzymes with p-hydroxylated aromatic compounds as substrates, such as hydroxycinnamoyl-CoA hydratase-lyase and vanillyl alcohol oxidase. Furthermore, on the basis of the calculations, a different active site residue compared to previous proposals is suggested to act as the general acid in the reaction. The mechanism put forward here is consistent with the available mutagenesis experiments and the calculated energy barrier is in agreement with measured rate constants. The detailed mechanistic understanding developed here might be extended to other members of the family of PAD-type enzymes. It could also be useful to rationalize the recently developed alternative promiscuous reactivities of these enzymes.

  • 6.
    Sheng, Xiang
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Lind, Maria E. S.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Himo, Fahmi
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Theoretical Study of the Reaction Mechanism of Phenolic Acid DecarboxylaseManuscript (preprint) (Other academic)
  • 7.
    Sheng, Xiang
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Patskovsky, Yury
    Vladimirova, Anna
    Bonanno, Jeffrey B.
    Almo, Steven C.
    Himo, Fahmi
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Raushel, Frank M.
    Mechanism and Structure of gamma-Resorcylate Decarboxylase2018In: Biochemistry, ISSN 0006-2960, E-ISSN 1520-4995, Vol. 57, no 22, p. 3167-3175Article in journal (Refereed)
    Abstract [en]

    gamma-Resorcylate decarboxylase (gamma-RSD) has evolved to catalyze the reversible decarboxylation of 2,6-dihydroxybenzoate to resorcinol in a nonoxidative fashion. This enzyme is of significant interest because of its potential for the production of gamma-resorcylate and other benzoic acid derivatives under environmentally sustainable conditions. Kinetic constants for the decarboxylation of 2,6-dihydroxybenzoate catalyzed by gamma-RSD from Polaromonas sp. JS666 are reported, and the enzyme is shown to be active with 2,3-dihydroxybenzoate, 2,4,6-trihydroxybenzoate, and 2,6-dihydroxy-4-methylbenzoate. The three-dimensional structure of gamma-RSD with the inhibitor 2-nitroresorcinol (2-NR) bound in the active site is reported. 2-NR is directly ligated to a Mn2+ bound in the active site, and the nitro substituent of the inhibitor is tilted significantly from the plane of the phenyl ring. The inhibitor exhibits a binding mode different from that of the substrate bound in the previously determined structure of gamma-RSD from Rhizobtum sp. MTP-10005. On the basis of the crystal structure of the enzyme from Polaromonas sp. JS666, complementary density functional calculations were performed to investigate the reaction mechanism. In the proposed reaction mechanism, gamma-RSD binds 2,6-dihydroxybenzoate by direct coordination of the active site manganese ion to the carboxylate anion of the substrate and one of the adjacent phenolic oxygens. The enzyme subsequently catalyzes the transfer of a proton to Cl of y-resorcylate prior to the actual decarboxylation step. The reaction mechanism proposed previously, based on the structure of gamma-RSD from Rhizobtum sp. MTP-10005, is shown to be associated with high energies and thus less likely to be correct.

  • 8.
    Sheng, Xiang
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Zhu, Wen
    Huddleston, Jamison
    Xiang, Dao Fen
    Raushel, Frank M.
    Richards, Nigel G. J.
    Himo, Fahmi
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    A Combined Experimental-Theoretical Study of the LigW-Catalyzed Decarboxylation of 5-Carboxyvanillate in the Metabolic Pathway for Lignin Degradation2017In: ACS Catalysis, ISSN 2155-5435, E-ISSN 2155-5435, Vol. 7, no 8, p. 4968-4974Article in journal (Refereed)
    Abstract [en]

    Although it is a member of the amidohydrolase superfamily, LigW catalyzes the nonoxidative decarboxylation of 5-carboxyvanillate to form vanillate in the metabolic pathway for bacterial lignin degradation. We now show that membrane inlet mass spectrometry (MIMS) can be used to measure transient CO2 concentrations in real time, thereby permitting us to establish that C-C bond cleavage proceeds to give CO2 rather than HCO3- as the initial product in the LigW-catalyzed reaction. Thus, incubation of LigW at pH 7.0 with the substrate 5-carboxyvanillate results in an initial burst of CO2 formation that gradually decreases to an equilibrium value as CO2 is nonenzymatically hydrated to HCO3-. The burst of CO2 is completely eliminated with the simultaneous addition of substrate and excess carbonic anhydrase to the enzyme, demonstrating that CO2 is the initial reaction product. This finding is fully consistent with the results of density functional theory calculations, which also provide support for a mechanism in which protonation of the C5 carbon takes place prior to C-C bond cleavage. The calculated barrier of 16.8 kcal/mol for the rate-limiting step, the formation of the C5-protonated intermediate, compares well with the observed kcat value of 27 for Sphingomonas paucimobilis LigW, which corresponds to an energy barrier of 16 kcal/mol. The MIMS-based strategy is superior to alternate methods of establishing whether CO2 or HCO3- is the initial reaction product, such as the use of pH-dependent dyes to monitor very small changes in solution pH. Moreover, the MIMS-based assay is generally applicable to studies of all enzymes that produce and/or consume small-molecule, neutral gases.

1 - 8 of 8
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