1
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Zambri MA, Kluger R. Proton Transfer via π-Interactions from Pyridine Provides a Facilitated Route for Transfer of CO 2 in Its Complex with a Carbanion. J Am Chem Soc 2024; 146:1403-1409. [PMID: 38176895 DOI: 10.1021/jacs.3c10403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2024]
Abstract
Aromatic π-interactions have been recognized as enhancing enzymatic catalytic processes, providing an efficient route to overcome entropic barriers. A nonenzymic analogue, a complex of protonated pyridine and a phenyl substituent in a thiamin conjugate, facilitates the departure of CO2 by protonation of a vicinal carbanion in a reactive complex. To evaluate the efficiency of the catalytic pathway from the π-associated proton donor, a system was assessed that produced measurable competition through the rates of formation of alternative products resulting from the same thiamin-derived carbanion. The barriers to competing pathways from the decarboxylation of p-(bromomethyl)-mandelylthiamin in the presence and absence of protonated pyridine were determined, establishing the efficiency of the vicinal proton transfer between π-associated species. The formation of the complex of CO2 and the co-formed carbanion also addresses the mechanism of the uncatalyzed exchange of 13CO2 into carboxyl groups discovered by Lundgren. Finally, microscopic reversibility implicates pyridine as a vicinal Brønsted base in thiamin-aldehyde adducts, producing carbanions that could incorporate dissolved CO2 into carboxyl groups.
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Affiliation(s)
- Marc Alexander Zambri
- Davenport Chemistry Laboratories, Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
| | - Ronald Kluger
- Davenport Chemistry Laboratories, Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
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2
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Yamada S. Onium Ion-assisted Organic Reactions Through Cation–π Interactions. NONCOVALENT INTERACTIONS IN CATALYSIS 2019. [DOI: 10.1039/9781788016490-00137] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The cation–π interaction is an attractive noncovalent interaction between a cation and a π-face. Owing to the stronger interaction energy than those of the other π interactions, such as π–π and CH–π interactions, the cation–π interaction has recently been recognized as a new tool for controlling the regio- and stereoselectivities in various types of organic reactions. This chapter attempts to cover a variety of organic reactions assisted by interactions between unreactive onium ions and π-faces, which will provide comprehensive knowledge on the role of cation–π interactions in organic synthesis.
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Affiliation(s)
- Shinji Yamada
- Department of Chemistry, Ochanomizu University 2-1-1 Otsuka Bunkyo-ku Tokyo 112-8610 Japan
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3
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Affiliation(s)
- Shinji Yamada
- Department of Chemistry, Faculty of Science, Ochanomizu University, 2-1-1 Otsuka, Bunkyo-ku, Tokyo 112-8610, Japan
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4
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Planas F, Sheng X, McLeish MJ, Himo F. A Theoretical Study of the Benzoylformate Decarboxylase Reaction Mechanism. Front Chem 2018; 6:205. [PMID: 29998094 PMCID: PMC6028569 DOI: 10.3389/fchem.2018.00205] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 05/18/2018] [Indexed: 01/27/2023] Open
Abstract
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.
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Affiliation(s)
- Ferran Planas
- Arrhenius Laboratory, Department of Organic Chemistry, Stockholm University, Stockholm, Sweden
| | - Xiang Sheng
- Arrhenius Laboratory, Department of Organic Chemistry, Stockholm University, Stockholm, Sweden
| | - Michael J McLeish
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis, Indianapolis, IN, United States
| | - Fahmi Himo
- Arrhenius Laboratory, Department of Organic Chemistry, Stockholm University, Stockholm, Sweden
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5
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Qin M, Song H, Dai X, Chan C, Chan W, Guo Z. Single‐Turnover Kinetics Reveal a Distinct Mode of Thiamine Diphosphate‐Dependent Catalysis in Vitamin K Biosynthesis. Chembiochem 2018; 19:1514-1522. [DOI: 10.1002/cbic.201800143] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Indexed: 01/09/2023]
Affiliation(s)
- Mingming Qin
- Department of ChemistryThe Hong Kong University of Science and Technology Clear Water Bay Kowloon Hong Kong
| | - Haigang Song
- Department of ChemistryThe Hong Kong University of Science and Technology Clear Water Bay Kowloon Hong Kong
- Present address: Division of Structural BiologyWellcome Trust Centre of Human GenomicsUniversity of Oxford Roosevelt Drive Oxford OX3 7BN UK
| | - Xin Dai
- Department of ChemistryThe Hong Kong University of Science and Technology Clear Water Bay Kowloon Hong Kong
| | - Chi‐Kong Chan
- Department of ChemistryThe Hong Kong University of Science and Technology Clear Water Bay Kowloon Hong Kong
- Environmental Science ProgramThe Hong Kong University of Science and Technology Clear Water Bay Kowloon Hong Kong
| | - Wan Chan
- Department of ChemistryThe Hong Kong University of Science and Technology Clear Water Bay Kowloon Hong Kong
- Environmental Science ProgramThe Hong Kong University of Science and Technology Clear Water Bay Kowloon Hong Kong
| | - Zhihong Guo
- Department of ChemistryThe Hong Kong University of Science and Technology Clear Water Bay Kowloon Hong Kong
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6
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Heidari Y, Howe GW, Kluger R. The reactivity of lactyl-oxythiamin implies the role of the amino-pyrimidine in thiamin catalyzed decarboxylation. Bioorg Chem 2016; 69:153-158. [PMID: 27816798 DOI: 10.1016/j.bioorg.2016.10.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Revised: 10/24/2016] [Accepted: 10/26/2016] [Indexed: 11/29/2022]
Abstract
It has previously been established that the deprotonated amino substituent of the pyrimidine of thiamin diphosphate (ThDP) acts as an internal base to accept the C2H of the thiazolium in ThDP-dependent enzymes. The amino group has also been implicated in assisting the departure of the aldehydic product formed after loss of CO2 from ketoacid substrates. However, the potential role for the pyrimidine amino group in the key decarboxylation step has not been assessed. Oxythiamin contains a hydroxyl group in place of the pyrimidine amino group in thiamin, providing a basis for comparison of reactivity. Lactyl-oxythiamin (LOTh), the conjugate of pyruvic acid and oxythiamin was prepared by condensation of ethyl pyruvate and hydroxyl-protected oxythiamin followed by deprotection and acidic hydrolysis of the ethyl ester. The rate constants observed for the decarboxylation of LOTh in neutral and acidic solutions are about four times smaller than those for the corresponding compound that contains the amino group, lactylthiamin. The difference in reactivity is consistent with the amino group's participation in facilitating the decarboxylation step by allowing a competitive addition pathway that produces bicarbonate and has implications for the corresponding enzymic reaction.
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Affiliation(s)
- Yasaman Heidari
- Davenport Laboratories, Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
| | - Graeme W Howe
- Davenport Laboratories, Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
| | - Ronald Kluger
- Davenport Laboratories, Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada.
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7
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Kennedy CR, Lin S, Jacobsen EN. The Cation-π Interaction in Small-Molecule Catalysis. Angew Chem Int Ed Engl 2016; 55:12596-624. [PMID: 27329991 PMCID: PMC5096794 DOI: 10.1002/anie.201600547] [Citation(s) in RCA: 172] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Indexed: 11/11/2022]
Abstract
Catalysis by small molecules (≤1000 Da, 10(-9) m) that are capable of binding and activating substrates through attractive, noncovalent interactions has emerged as an important approach in organic and organometallic chemistry. While the canonical noncovalent interactions, including hydrogen bonding, ion pairing, and π stacking, have become mainstays of catalyst design, the cation-π interaction has been comparatively underutilized in this context since its discovery in the 1980s. However, like a hydrogen bond, the cation-π interaction exhibits a typical binding affinity of several kcal mol(-1) with substantial directionality. These properties render it attractive as a design element for the development of small-molecule catalysts, and in recent years, the catalysis community has begun to take advantage of these features, drawing inspiration from pioneering research in molecular recognition and structural biology. This Review surveys the burgeoning application of the cation-π interaction in catalysis.
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Affiliation(s)
- C Rose Kennedy
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford St, Cambridge, MA, 02138, USA
| | - Song Lin
- Department of Chemistry, University of California, Berkeley, 535 Latimer Hall, Berkeley, CA, 94720, USA
| | - Eric N Jacobsen
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford St, Cambridge, MA, 02138, USA.
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8
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Kennedy CR, Lin S, Jacobsen EN. Die Kation-π-Wechselwirkung in der Katalyse mit niedermolekularen Verbindungen. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201600547] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- C. Rose Kennedy
- Department of Chemistry and Chemical Biology; Harvard University; 12 Oxford St Cambridge MA 02138 USA
| | - Song Lin
- Department of Chemistry; University of California, Berkeley; 535 Latimer Hall Berkeley CA 94720 USA
| | - Eric N. Jacobsen
- Department of Chemistry and Chemical Biology; Harvard University; 12 Oxford St Cambridge MA 02138 USA
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9
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Lithium-stabilized nucleophilic addition of thiamin to a ketone provides an efficient route to mandelylthiamin, a critical pre-decarboxylation intermediate. Bioorg Chem 2015; 62:124-9. [PMID: 26333207 DOI: 10.1016/j.bioorg.2015.08.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Revised: 08/19/2015] [Accepted: 08/20/2015] [Indexed: 11/21/2022]
Abstract
Mandelylthiamin (MTh) is an accurate model of the covalent intermediate derived from the condensation of thiamin diphosphate and benzoylformate in benzoylformate decarboxylase. The properties and catalytic susceptibilities of mandelylthiamin are the subjects of considerable interest. However, the existing synthesis gives only trace amounts of the precursor to MTh as it is conducted under reversible conditions. An improved approach derives from the unique ability of lithium ions to drive to completion the otherwise unfavorable condensation of the conjugate base of thiamin and methyl benzoylformate. The unique efficiency of the condensation reaction in the presence of lithium ions is established in contrast to the effects of other Lewis acids. Interpretation of the pattern of the results indicates that the condensation of the ketone and thiamin is thermodynamically controlled. It is proposed that the addition of lithium ions displaces the equilibrium toward the product through formation of a stable lithium-alkoxide.
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10
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Abstract
AbstractDecarboxylation reactions on enzymes are consistently much faster than their nonenzymic counterparts. Examination of the potential for catalysis in the nonenzymic reactions revealed that the reaction is slowed by the failure of CO2 to be launched into solution upon C–C bond cleavage. Catalysts can facilitate the reaction by weakening the C–CO2H bond but this is not sufficient. Converting the precursor of CO2 into a precursor of bicarbonate facilitates the forward reaction as does protonation of the nascent carbanion.
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Affiliation(s)
- Ronald Kluger
- 1Department of Chemistry, University of Toronto, Toronto ON M5S 3H6, Canada
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11
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Xiang Z. Aromatic aldehyde-catalyzed gas-phase decarboxylation of amino acid anion via imine intermediate: An experimental and theoretical study. J Mol Struct 2013. [DOI: 10.1016/j.molstruc.2013.06.046] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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12
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Avoiding CO2 in Catalysis of Decarboxylation. ADVANCES IN PHYSICAL ORGANIC CHEMISTRY 2013. [DOI: 10.1016/b978-0-12-407754-6.00002-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register]
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13
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Howe GW, Bielecki M, Kluger R. Base-Catalyzed Decarboxylation of Mandelylthiamin: Direct Formation of Bicarbonate as an Alternative to Formation of CO2. J Am Chem Soc 2012; 134:20621-3. [DOI: 10.1021/ja310952a] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Graeme W. Howe
- Davenport Chemical Laboratories,
Department of Chemistry, University of Toronto, Toronto, Ontario, Canada M5S
3H6
| | - Michael Bielecki
- Davenport Chemical Laboratories,
Department of Chemistry, University of Toronto, Toronto, Ontario, Canada M5S
3H6
| | - Ronald Kluger
- Davenport Chemical Laboratories,
Department of Chemistry, University of Toronto, Toronto, Ontario, Canada M5S
3H6
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14
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Häussermann A, Rominger F, Straub BF. CO2 on a tightrope: stabilization, room-temperature decarboxylation, and sodium-induced carboxylate migration. Chemistry 2012; 18:14174-85. [PMID: 22997025 DOI: 10.1002/chem.201202298] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2012] [Indexed: 11/11/2022]
Abstract
A sterically shielded 3-substituted zwitterionic N,N-dimethylisotryptammonium carboxylate has been synthesized by consecutive chemoselective double alkylation of indole. The carboxylate undergoes a quantitative and unusually facile decarboxylation in dimethyl sulfoxide (DMSO) or dimethyl formamide (DMF) at room temperature. The breaking of a nearly equidistant hydrogen bond by solvent molecules initiates heterolytic C-C cleavage. The decarboxylation rate decreases with increasing CO(2) partial pressure, proving the competitiveness of protonation and re-carboxylation of the carbanionic intermediate. Corresponding spiro compounds containing silylene and stannylene moieties show high thermal stability. Addition of an excess of methyllithium to the sodium salt triggers a reaction sequence comprising a deprotonation, carboxylate transfer, and nucleophilic trapping of the rearranged carboxylate by another equivalent of methyllithium. Hydrolytic work-up of the geminal diolate leads to an acetyl product. The role of the sodium counterion and the mechanism of the rearrangement have been unraveled by deuteration experiments.
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Affiliation(s)
- Achim Häussermann
- Organisch-Chemisches Institut, Ruprecht-Karls-Universität Heidelberg, Germany
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15
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Roca M, Pascual-Ahuir JL, Tuñón I. Reversibility and Diffusion in Mandelythiamin Decarboxylation. Searching Dynamical Effects in Decarboxylation Reactions. J Am Chem Soc 2012; 134:10509-14. [DOI: 10.1021/ja3026455] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Maite Roca
- Departament
de Química Física, Universitat de València, 46100 Burjassot, Spain
| | | | - Iñaki Tuñón
- Departament
de Química Física, Universitat de València, 46100 Burjassot, Spain
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16
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Li T, Huo L, Pulley C, Liu A. Decarboxylation mechanisms in biological system. Bioorg Chem 2012; 43:2-14. [PMID: 22534166 DOI: 10.1016/j.bioorg.2012.03.001] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2011] [Revised: 03/04/2012] [Accepted: 03/19/2012] [Indexed: 11/30/2022]
Abstract
This review examines the mechanisms propelling cofactor-independent, organic cofactor-dependent and metal-dependent decarboxylase chemistry. Decarboxylation, the removal of carbon dioxide from organic acids, is a fundamentally important reaction in biology. Numerous decarboxylase enzymes serve as key components of aerobic and anaerobic carbohydrate metabolism and amino acid conversion. In the past decade, our knowledge of the mechanisms enabling these crucial decarboxylase reactions has continued to expand and inspire. This review focuses on the organic cofactors biotin, flavin, NAD, pyridoxal 5'-phosphate, pyruvoyl, and thiamin pyrophosphate as catalytic centers. Significant attention is also placed on the metal-dependent decarboxylase mechanisms.
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Affiliation(s)
- Tingfeng Li
- Department of Biochemistry, University of Mississippi Medical Center, 2500 North State Street, Jackson, MS 39216, USA
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17
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Tranchimand S, Starks CM, Mathews II, Hockings SC, Kappock TJ. Treponema denticola PurE Is a bacterial AIR carboxylase. Biochemistry 2011; 50:4623-37. [PMID: 21548610 DOI: 10.1021/bi102033a] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
De novo purine biosynthesis proceeds by two divergent paths. In bacteria, yeasts, and plants, 5-aminoimidazole ribonucleotide (AIR) is converted to 4-carboxy-AIR (CAIR) by two enzymes: N(5)-carboxy-AIR (N(5)-CAIR) synthetase (PurK) and N(5)-CAIR mutase (class I PurE). In animals, the conversion of AIR to CAIR requires a single enzyme, AIR carboxylase (class II PurE). The CAIR carboxylate derives from bicarbonate or CO(2), respectively. Class I PurE is a promising antimicrobial target. Class I and class II PurEs are mechanistically related but bind different substrates. The spirochete dental pathogen Treponema denticola lacks a purK gene and contains a class II purE gene, the hallmarks of CO(2)-dependent CAIR synthesis. We demonstrate that T. denticola PurE (TdPurE) is AIR carboxylase, the first example of a prokaryotic class II PurE. Steady-state and pre-steady-state experiments show that TdPurE binds AIR and CO(2) but not N(5)-CAIR. Crystal structures of TdPurE alone and in complex with AIR show a conformational change in the key active site His40 residue that is not observed for class I PurEs. A contact between the AIR phosphate and a differentially conserved residue (TdPurE Lys41) enforces different AIR conformations in each PurE class. As a consequence, the TdPurE·AIR complex contains a portal that appears to allow the CO(2) substrate to enter the active site. In the human pathogen T. denticola, purine biosynthesis should depend on available CO(2) levels. Because spirochetes lack carbonic anhydrase, the corresponding reduction in bicarbonate demand may confer a selective advantage.
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Affiliation(s)
- Sylvain Tranchimand
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907-2063, USA
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18
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Meyer D, Neumann P, Parthier C, Friedemann R, Nemeria N, Jordan F, Tittmann K. Double duty for a conserved glutamate in pyruvate decarboxylase: evidence of the participation in stereoelectronically controlled decarboxylation and in protonation of the nascent carbanion/enamine intermediate . Biochemistry 2010; 49:8197-212. [PMID: 20715795 DOI: 10.1021/bi100828r] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Pyruvate decarboxylase (PDC) catalyzes the nonoxidative decarboxylation of pyruvate into acetaldehyde and carbon dioxide and requires thiamin diphosphate (ThDP) and a divalent cation as cofactors. Recent studies have permitted the assignment of functional roles of active site residues; however, the underlying reaction mechanisms of elementary steps have remained hypothetical. Here, a kinetic and thermodynamic single-step analysis in conjunction with X-ray crystallographic studies of PDC from Zymomonas mobilis implicates active site residue Glu473 (located on the re-face of the ThDP thiazolium nucleus) in facilitating both decarboxylation of 2-lactyl-ThDP and protonation of the 2-hydroxyethyl-ThDP carbanion/enamine intermediate. Variants carrying either an isofunctional (Glu473Asp) or isosteric (Glu473Gln) substitution exhibit a residual catalytic activity of less than 0.1% but accumulate different intermediates at the steady state. Whereas the predecarboxylation intermediate 2-lactyl-ThDP is accumulated in Glu473Asp because of a 3000-fold slower decarboxylation compared to that of the wild-type enzyme, Glu473Gln is not impaired in decarboxylation but generates a long-lived 2-hydroxyethyl-ThDP carbanion/enamine postdecarboxylation intermediate. CD spectroscopic analysis of the protonic and tautomeric equilibria of the cocatalytic aminopyrimidine part of ThDP indicates that an acidic residue is required at position 473 for proper substrate binding. Wild-type PDC and the Glu473Asp variant bind the substrate analogue acetylphosphinate with the same affinity, implying a similar stabilization of the predecarboxylation intermediate analogue on the enzyme, whereas Glu473Gln fails to bind the analogue. The X-ray crystallographic structure of 2-lactyl-ThDP trapped in the decarboxylation-deficient variant Glu473Asp reveals a common stereochemistry of the intermediate C2α stereocenter; however, the scissile C2α-C(carboxylate) bond deviates by ∼25-30° from the perpendicular "maximum overlap" orientation relative to the thiazolium ring plane as commonly observed in ThDP enzymes. Because a reactant-state stabilization of the predecarboxylation intermediate can be excluded to account for the slower decarboxylation, the data suggest a strong stereoelectronic effect for the transition state of decarboxylation as supported by additional DFT studies on models. To the best of our knowledge, this is a very rare example in which the magnitude of a stereoelectronic effect could be experimentally estimated for an enzymatic system. Given that variant Glu473Gln is not decarboxylation-deficient, electrostatic stress can be excluded as a driving force for decarboxylation. The apparent dual function of Glu473 further suggests that decarboxylation and protonation of the incipient carbanion are committed and presumably proceed in the same transition state.
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Affiliation(s)
- Danilo Meyer
- Albrecht-von-Haller-Institute for Plant Sciences and Göttingen Center for Molecular Biosciences, Georg-August-University Göttingen, Ernst-Caspari-Haus, Justus-von-Liebig-Weg 11, D-37077 Göttingen, Germany
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19
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Gonzalez-James OM, Singleton DA. Isotope effect, mechanism, and origin of catalysis in the decarboxylation of mandelylthiamin. J Am Chem Soc 2010; 132:6896-7. [PMID: 20433168 DOI: 10.1021/ja101775s] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The mechanism of decarboxylations in water and the catalysis of mandelylthiamin (MTh) decarboxylation by pyridinium ions is explored. It has been recently proposed that a decarboxylation step forming an intermediate molecule/CO(2) pair is reversible and that pyridinium ions catalyze the MTh decarboxylation by trapping the intermediate, preventing reversion to MTh. A calculation of the barrier for the back reaction goes against this proposal, as the diffusional separation of CO(2) would be on the order of 10,000 times faster. A comparison of predicted and experimental isotope effects for a series of decarboxylations including the MTh reaction shows in each case the absence of significant reversibility of the decarboxylation step. An alternative origin of the pyridinium catalysis of decarboxylation is proposed, based on the formal binding of the pyridinium ions to the decarboxylation transition state.
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Affiliation(s)
- Ollie M Gonzalez-James
- Department of Chemistry, Texas A&M University, P.O. Box 30012, College Station, Texas 77842, USA
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20
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The role of pre-association in Brønsted acid-catalyzed decarboxylation and related processes. ADVANCES IN PHYSICAL ORGANIC CHEMISTRY 2010. [DOI: 10.1016/s0065-3160(08)44007-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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21
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Mundle SOC, Rathgeber S, Lacrampe-Couloume G, Sherwood Lollar B, Kluger R. Internal Return of Carbon Dioxide in Decarboxylation: Catalysis of Separation and 12C/13C Kinetic Isotope Effects. J Am Chem Soc 2009; 131:11638-9. [DOI: 10.1021/ja902686h] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Scott O. C. Mundle
- Departments of Chemistry and Geology, University of Toronto, Toronto, Ontario M5S 3H6, Canada
| | - Steven Rathgeber
- Departments of Chemistry and Geology, University of Toronto, Toronto, Ontario M5S 3H6, Canada
| | | | - Barbara Sherwood Lollar
- Departments of Chemistry and Geology, University of Toronto, Toronto, Ontario M5S 3H6, Canada
| | - Ronald Kluger
- Departments of Chemistry and Geology, University of Toronto, Toronto, Ontario M5S 3H6, Canada
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22
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Bruning M, Berheide M, Meyer D, Golbik R, Bartunik H, Liese A, Tittmann K. Structural and kinetic studies on native intermediates and an intermediate analogue in benzoylformate decarboxylase reveal a least motion mechanism with an unprecedented short-lived predecarboxylation intermediate. Biochemistry 2009; 48:3258-68. [PMID: 19182954 DOI: 10.1021/bi801957d] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The thiamin diphosphate- (ThDP-) dependent enzyme benzoylformate decarboxylase (BFDC) catalyzes the nonoxidative decarboxylation of benzoylformic acid to benzaldehyde and carbon dioxide. To date, no structural information for a cofactor-bound reaction intermediate in BFDC is available. For kinetic analysis, a chromophoric substrate analogue was employed that produces various absorbing intermediates during turnover but is a poor substrate with a 10(4)-fold compromised kcat. Here, we have analyzed the steady-state distribution of native intermediates by a combined chemical quench/1H NMR spectroscopic approach and estimated the net rate constants of elementary catalytic steps. At substrate saturation, carbonyl addition of the substrate to the cofactor (k' approximately 500 s-1 at 30 degrees C) and elimination of benzaldehyde (k' approximately 2.400 s-1) were found to be partially rate-determining for catalysis, whereas decarboxylation of the transient 2-mandelyl-ThDP intermediate is 1 order of magnitude faster with k' approximately 16.000 s-1, the largest rate constant of decarboxylation in any thiamin enzyme characterized so far. The X-ray structure of a predecarboxylation intermediate analogue was determined to 1.6 A after cocrystallization of BFDC from Pseudomonas putida with benzoylphosphonic acid methyl ester. In contrast to the free acid, for which irreversible phosphorylation of active center Ser26 was reported, the methyl ester forms a covalent adduct with ThDP with a similar configuration at C2alpha as observed for other thiamin enzymes. The C2-C2alpha bond of the intermediate analogue is out of plane by 7degrees, indicating strain. The phosphonate part of the adduct forms hydrogen bonds with Ser26 and His281, and the 1-OH group is held in place by interactions with His70 and the 4'-amino group of ThDP. The phenyl ring accommodates in a hydrophobic pocket formed by Phe464, Phe397, Leu109, and Leu403. A comparison with the previously determined structure of BFDC in noncovalent complex with the inhibitor (R)-mandelate suggests a least motion mechanism. Binding of benzoylphosphonic acid methyl ester to BFDC was further characterized by CD spectroscopy and stopped-flow kinetics, indicating a two-step binding mechanism with a 200-fold slower carbonyl addition to ThDP than determined for benzoylformic acid, in line with the observed slight structural reorganization of Phe464 due to steric clashes with the phosphonate moiety.
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Affiliation(s)
- Marc Bruning
- Institute of Technical Biocatalysis, Hamburg UniVersity of Technology, Denickestrasse 15, D-21073 Hamburg, Germany
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Kluger R, Rathgeber S. Catalyzing separation of carbon dioxide in thiamin diphosphate-promoted decarboxylation. FEBS J 2008; 275:6089-100. [DOI: 10.1111/j.1742-4658.2008.06739.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Kluger R, Tittmann K. Thiamin diphosphate catalysis: enzymic and nonenzymic covalent intermediates. Chem Rev 2008; 108:1797-833. [PMID: 18491870 DOI: 10.1021/cr068444m] [Citation(s) in RCA: 216] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ronald Kluger
- Davenport Laboratories, Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6 Canada.
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Versées W, Spaepen S, Wood MDH, Leeper FJ, Vanderleyden J, Steyaert J. Molecular Mechanism of Allosteric Substrate Activation in a Thiamine Diphosphate-dependent Decarboxylase. J Biol Chem 2007; 282:35269-78. [PMID: 17905741 DOI: 10.1074/jbc.m706048200] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Thiamine diphosphate-dependent enzymes are involved in a wide variety of metabolic pathways. The molecular mechanism behind active site communication and substrate activation, observed in some of these enzymes, has since long been an area of debate. Here, we report the crystal structures of a phenylpyruvate decarboxylase in complex with its substrates and a covalent reaction intermediate analogue. These structures reveal the regulatory site and unveil the mechanism of allosteric substrate activation. This signal transduction relies on quaternary structure reorganizations, domain rotations, and a pathway of local conformational changes that are relayed from the regulatory site to the active site. The current findings thus uncover the molecular mechanism by which the binding of a substrate in the regulatory site is linked to the mounting of the catalytic machinery in the active site in this thiamine diphosphate-dependent enzyme.
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Affiliation(s)
- Wim Versées
- Department of Ultrastructure, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium.
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