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Alvarado O, García-Meseguer R, Ruiz-Pernía JJ, Tuñon I, Delgado EJ. Mechanistic study of the biosynthesis of R-phenylacetylcarbinol by acetohydroxyacid synthase enzyme using hybrid quantum mechanics/molecular mechanics simulations. Arch Biochem Biophys 2021; 707:108849. [PMID: 33832752 DOI: 10.1016/j.abb.2021.108849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The biosynthesis of R-phenylacetylcarbinol (R-PAC) by the acetohydroxy acid synthase, (AHAS) is addressed by molecular dynamics simulations (MD), hybrid quantum mechanics/molecular mechanics (QM/MM), and QM/MM free energy calculations. The results show the reaction starts with the nucleophilic attack of the C2α atom of the HEThDP intermediate on the Cβ atom of the carbonyl group of benzaldehyde substrate via the formation of a transition state (TS1) with the HEThDP intermediate under 4'-aminopyrimidium (APH+) form. The calculated activation free energy for this step is 17.4 kcal mol-1 at 27 °C. From this point, the reaction continues with the abstraction of Hβ atom of the HEThDP intermediate by the Oβ atom of benzaldehyde to form the intermediate I. The reaction is completed with the cleavage of the bond C2α-C2 to form the product R-PAC and to regenerate the ylide intermediate under the APH+ form, allowing in this way to reinitiate to the catalytic cycle once more. The calculated activation barrier for this last step is 15.9 kcal mol-1 at 27 °C.
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Affiliation(s)
- Omar Alvarado
- Departamento de Físico-Química, Facultad de Ciencias Químicas, Universidad de Concepción, Concepción, Chile; Departamento de Química, Facultad de Ciencias, Universidad del Bío-Bío, Avenida Collao 1202, Concepción, Chile
| | - Rafael García-Meseguer
- School of Mathematics, University of Bristol, Bristol, UK; Department of Physical Chemistry, Universitat de Valencia, 46100, Burjassot, Spain
| | | | - Iñaki Tuñon
- Department of Physical Chemistry, Universitat de Valencia, 46100, Burjassot, Spain
| | - Eduardo J Delgado
- Departamento de Físico-Química, Facultad de Ciencias Químicas, Universidad de Concepción, Concepción, Chile.
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Alvarado O, García-Meseguer R, Ruiz-Pernía JJ, Tuñon I, Delgado EJ. Mechanistic study of the biosynthesis of R-phenylcarbinol by acetohydroxyacid synthase enzyme using hybrid quantum mechanics/molecular mechanics simulations. Arch Biochem Biophys 2021; 701:108807. [PMID: 33587902 DOI: 10.1016/j.abb.2021.108807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 02/06/2021] [Accepted: 02/08/2021] [Indexed: 11/26/2022]
Abstract
The biosynthesis of R-phenylacetylcarbinol (R-PAC) by the acetohydroxy acid synthase, (AHAS) is addressed by molecular dynamics simulations (MD), hybrid quantum mechanics/molecular mechanics (QM/MM), and QM/MM free energy calculations. The results show the reaction starts with the nucleophilic attack of the C2α atom of the HEThDP intermediate on the Cβ atom of the carbonyl group of benzaldehyde substrate via the formation of a transition state (TS1) with the HEThDP intermediate under 4'-aminopyrimidium (APH+) form. The calculated activation free energy for this step is 17.4kcal mol-1 at 27 °C. From this point, the reaction continues with the abstraction of Hβ atom of the HEThDP intermediate by the Oβ atom of benzaldehyde to form the intermediate I. The reaction is completed with the cleavage of the bond C2α-C2 to form the product R-PAC and to regenerate the ylide intermediate under the APH+ form, allowing in this way to reinitiate to the catalytic cycle once more. The calculated activation barrier for this last step is 15.9kcal mol-1 at 27 °C.
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Affiliation(s)
- Omar Alvarado
- Departamento de Físico-Química, Facultad de Ciencias Químicas, Universidad de Concepción, Concepción, Chile; Departamento de Química, Facultad de Ciencias, Universidad del Bío-Bío, Avenida Collao 1202, Concepción, Chile
| | - Rafael García-Meseguer
- School of Mathematics, University of Bristol, Bristol, United Kingdom; Department of Physical Chemistry, Universitat de Valencia, 46100, Burjassot, Spain
| | | | - Iñaki Tuñon
- Department of Physical Chemistry, Universitat de Valencia, 46100, Burjassot, Spain
| | - Eduardo J Delgado
- Departamento de Físico-Química, Facultad de Ciencias Químicas, Universidad de Concepción, Concepción, Chile.
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Lee YC, Chen YY, Lin JS, Chen YW, Li CC, Liang KX, Chan HH, Lin WD, Kao CH. Stereoselective synthesis of (1R, 2S)-norephedrine by recombinant whole-cell biocatalysts coupling acetohydroxyacid synthase I and ω-transaminase. Process Biochem 2018. [DOI: 10.1016/j.procbio.2018.08.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Alvarado O, Lizana I, Jaña G, Tuñon I, Delgado E. A DFT study on the chiral synthesis of R-phenylacetyl carbinol within the quantum chemical cluster approach. Chem Phys Lett 2017. [DOI: 10.1016/j.cplett.2017.03.066] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Liu Y, Li Y, Wang X. Acetohydroxyacid synthases: evolution, structure, and function. Appl Microbiol Biotechnol 2016; 100:8633-49. [DOI: 10.1007/s00253-016-7809-9] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Revised: 07/28/2016] [Accepted: 08/12/2016] [Indexed: 10/21/2022]
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Eram MS, Ma K. Pyruvate decarboxylase activity of the acetohydroxyacid synthase of Thermotoga maritima. Biochem Biophys Rep 2016; 7:394-399. [PMID: 28955930 PMCID: PMC5613635 DOI: 10.1016/j.bbrep.2016.07.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Revised: 06/20/2016] [Accepted: 07/13/2016] [Indexed: 11/30/2022] Open
Abstract
Acetohydroxyacid synthase (AHAS) catalyzes the production of acetolactate from pyruvate. The enzyme from the hyperthermophilic bacterium Thermotoga maritima has been purified and characterized (kcat ~100 s−1). It was found that the same enzyme also had the ability to catalyze the production of acetaldehyde and CO2 from pyruvate, an activity of pyruvate decarboxylase (PDC) at a rate approximately 10% of its AHAS activity. Compared to the catalytic subunit, reconstitution of the individually expressed and purified catalytic and regulatory subunits of the AHAS stimulated both activities of PDC and AHAS. Both activities had similar pH and temperature profiles with an optimal pH of 7.0 and temperature of 85 °C. The enzyme kinetic parameters were determined, however, it showed a non-Michaelis-Menten kinetics for pyruvate only. This is the first report on the PDC activity of an AHAS and the second bifunctional enzyme that might be involved in the production of ethanol from pyruvate in hyperthermophilic microorganisms. The acetohydroxyacid synthase of T. maritima has pyruvate decarboxylase activity The AHAS and PDC activities share the same temperature and pH optima Reconstitution of the catalytic and regulatory subunits increases both PDC and AHAS activities
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Affiliation(s)
- Mohammad S Eram
- Department of Biology, University of Waterloo, Waterloo, Ontario, Canada
| | - Kesen Ma
- Department of Biology, University of Waterloo, Waterloo, Ontario, Canada
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Sánchez L, Jaña GA, Delgado EJ. A QM/MM study on the reaction pathway leading to 2-Aceto-2-hydroxybutyrate in the catalytic cycle of AHAS. J Comput Chem 2014; 35:488-94. [DOI: 10.1002/jcc.23523] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2013] [Revised: 11/30/2013] [Accepted: 12/15/2013] [Indexed: 11/05/2022]
Affiliation(s)
- Leslie Sánchez
- Computational Biological Chemistry Group, Faculty of Chemical Sciences; Universidad de Concepción; Concepción
| | - Gonzalo A. Jaña
- Departamento de Ciencias Químicas, Facultad de Ciencias Exactas, Sede Concepción; Universidad Andrés Bello; Concepcion
| | - Eduardo J. Delgado
- Computational Biological Chemistry Group, Faculty of Chemical Sciences; Universidad de Concepción; Concepción
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Belenky I, Steinmetz A, Vyazmensky M, Barak Z, Tittmann K, Chipman DM. Many of the functional differences between acetohydroxyacid synthase (AHAS) isozyme I and other AHASs are a result of the rapid formation and breakdown of the covalent acetolactate-thiamin diphosphate adduct in AHAS I. FEBS J 2012; 279:1967-79. [DOI: 10.1111/j.1742-4658.2012.08577.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Rootman I, de Villiers M, Brand LA, Strauss E. Creating Cellulose-Binding Domain Fusions of the Coenzyme A Biosynthetic Enzymes to Enable Reactor-Based Biotransformations. ChemCatChem 2010. [DOI: 10.1002/cctc.201000197] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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Chipman DM, Barak Z, Shaanan B, Vyazmensky M, Binshtein E, Belenky I, Temam V, Steinmetz A, Golbik R, Tittmann K. Origin of the specificities of acetohydroxyacid synthases and glyoxylate carboligase. ACTA ACUST UNITED AC 2009. [DOI: 10.1016/j.molcatb.2009.03.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Yun H, Kim BG. Enzymatic production of (R)-phenylacetylcarbinol by pyruvate decarboxylase from Zymomonas mobilis. BIOTECHNOL BIOPROC E 2008. [DOI: 10.1007/s12257-008-0030-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Kirschning A, Solodenko W, Mennecke K. Combining Enabling Techniques in Organic Synthesis: Continuous Flow Processes with Heterogenized Catalysts. Chemistry 2006; 12:5972-90. [PMID: 16832800 DOI: 10.1002/chem.200600236] [Citation(s) in RCA: 289] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The concepts article describes enabling techniques (solid-phase assisted synthesis, new reactor design, microwave irradiation and new solvents) in organic chemistry and emphasizes the combination of several of them for creating new synthetic technology platforms. Particular focus is put on the combination of immobilized catalysts as well as biocatalysts with continuous flow processes. In this context, the PASSflow continuous flow technique fulfils both chemical as well as chemical engineering requirements. It combines reactor design with optimized, monolithic solid phases as well as reversible immobilization techniques for performing small as well as large scale synthesis with heterogenized catalysts under continuous flow conditions.
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Affiliation(s)
- Andreas Kirschning
- Institut für Organische Chemie, Universität Hannover, Schneiderberg 1B, 30167 Hannover, Germany.
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McCourt JA, Duggleby RG. Acetohydroxyacid synthase and its role in the biosynthetic pathway for branched-chain amino acids. Amino Acids 2006; 31:173-210. [PMID: 16699828 DOI: 10.1007/s00726-005-0297-3] [Citation(s) in RCA: 153] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2005] [Accepted: 12/09/2005] [Indexed: 11/25/2022]
Abstract
The branched-chain amino acids are synthesized by plants, fungi and microorganisms, but not by animals. Therefore, the enzymes of this pathway are potential target sites for the development of antifungal agents, antimicrobials and herbicides. Most research has focused upon the first enzyme in this biosynthetic pathway, acetohydroxyacid synthase (AHAS) largely because it is the target site for many commercial herbicides. In this review we provide a brief overview of the important properties of each enzyme within the pathway and a detailed summary of the most recent AHAS research, against the perspective of work that has been carried out over the past 50 years.
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Affiliation(s)
- J A McCourt
- School of Molecular and Microbial Sciences, University of Queensland, Brisbane, Australia
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Vyazmensky M, Engel S, Kryukov O, Berkovich-Berger D, Kaplun L. Construction of an active acetohydroxyacid synthase I with a flexible linker connecting the catalytic and the regulatory subunits. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2006; 1764:955-960. [PMID: 16795146 DOI: 10.1016/j.bbapap.2006.02.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Acetohydroxyacid synthase I (AHAS I), one of three isozymes in Escherichia coli catalyzing the first common step in the biosynthesis of branched amino acids, is composed of two kinds of subunits. The large catalytic (B) and small regulatory (N) subunits of the holoenzyme dissociate and associate freely and rapidly and are quite different in size, charge and hydrophobicity, so that high resolution purification methods lead to partial separation of subunits and to heterogeneity. We have prepared several linked AHAS I proteins, in which the large subunit B with a hexahistidine-tag at the N-terminus, was covalently joined by a flexible linker, containing several (X) amino acids, to the small subunit N to form His6-BuXN polypeptides. All linked BuXN polypeptides have similar specific activity, sensitivity to valine and substrate specificity as the wild type holoenzyme. The most successful BuXN linked protein (Bu30N-r) was inserted into and expressed in yeast and its catalytic properties were tested.
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Affiliation(s)
- Maria Vyazmensky
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel.
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Berget PE, Schore NE. Catalytically active, recyclable polymeric titanocene disks: a batch-flow reactor. Tetrahedron Lett 2005. [DOI: 10.1016/j.tetlet.2005.10.075] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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