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Kordesedehi R, Shahpiri A, Asadollahi MA, Biria D, Nikel PI. Enhanced chaotrope tolerance and (S)-2-hydroxypropiophenone production by recombinant Pseudomonas putida engineered with Pprl from Deinococcus radiodurans. Microb Biotechnol 2024; 17:e14448. [PMID: 38498302 PMCID: PMC10946676 DOI: 10.1111/1751-7915.14448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 03/01/2024] [Accepted: 03/04/2024] [Indexed: 03/20/2024] Open
Abstract
Pseudomonas putida is a soil bacterium with multiple uses in fermentation and biotransformation processes. P. putida ATCC 12633 can biotransform benzaldehyde and other aldehydes into valuable α-hydroxyketones, such as (S)-2-hydroxypropiophenone. However, poor tolerance of this strain toward chaotropic aldehydes hampers efficient biotransformation processes. To circumvent this problem, we expressed the gene encoding the global regulator PprI from Deinococcus radiodurans, an inducer of pleiotropic proteins promoting DNA repair, in P. putida. Fine-tuned gene expression was achieved using an expression plasmid under the control of the LacIQ /Ptrc system, and the cross-protective role of PprI was assessed against multiple stress treatments. Moreover, the stress-tolerant P. putida strain was tested for 2-hydroxypropiophenone production using whole resting cells in the presence of relevant aldehyde substrates. P. putida cells harbouring the global transcriptional regulator exhibited high tolerance toward benzaldehyde, acetaldehyde, ethanol, butanol, NaCl, H2 O2 and thermal stress, thereby reflecting the multistress protection profile conferred by PprI. Additionally, the engineered cells converted aldehydes to 2-hydroxypropiophenone more efficiently than the parental P. putida strain. 2-Hydroxypropiophenone concentration reached 1.6 g L-1 upon a 3-h incubation under optimized conditions, at a cell concentration of 0.033 g wet cell weight mL-1 in the presence of 20 mM benzaldehyde and 600 mM acetaldehyde. Product yield and productivity were 0.74 g 2-HPP g-1 benzaldehyde and 0.089 g 2-HPP g cell dry weight-1 h-1 , respectively, 35% higher than the control experiments. Taken together, these results demonstrate that introducing PprI from D. radiodurans enhances chaotrope tolerance and 2-HPP production in P. putida ATCC 12633.
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Affiliation(s)
- Reihaneh Kordesedehi
- Department of Biotechnology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
| | - Azar Shahpiri
- Department of Biotechnology, College of Agriculture, Isfahan University of Technology, Isfahan, Iran
| | - Mohammad Ali Asadollahi
- Department of Biotechnology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
| | - Davoud Biria
- Department of Biotechnology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
| | - Pablo Iván Nikel
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
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2
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Kordesedehi R, Asadollahi MA, Shahpiri A, Biria D, Nikel PI. Optimized enantioselective (S)-2-hydroxypropiophenone synthesis by free- and encapsulated-resting cells of Pseudomonas putida. Microb Cell Fact 2023; 22:89. [PMID: 37131175 PMCID: PMC10155308 DOI: 10.1186/s12934-023-02073-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Accepted: 03/25/2023] [Indexed: 05/04/2023] Open
Abstract
BACKGROUND Aromatic α-hydroxy ketones, such as S-2-hydroxypropiophenone (2-HPP), are highly valuable chiral building blocks useful for the synthesis of various pharmaceuticals and natural products. In the present study, enantioselective synthesis of 2-HPP was investigated by free and immobilized whole cells of Pseudomonas putida ATCC 12633 starting from readily-available aldehyde substrates. Whole resting cells of P. putida, previously grown in a culture medium containing ammonium mandelate, are a source of native benzoylformate decarboxylase (BFD) activity. BFD produced by induced P. putida resting cells is a highly active biocatalyst without any further treatment in comparison with partially purified enzyme preparations. These cells can convert benzaldehyde and acetaldehyde into the acyloin compound 2-HPP by BFD-catalyzed enantioselective cross-coupling reaction. RESULTS The reaction was carried out in the presence of exogenous benzaldehyde (20 mM) and acetaldehyde (600 mM) as substrates in 6 mL of 200 mM phosphate buffer (pH 7) for 3 h. The optimal biomass concentration was assessed to be 0.006 g dry cell weight (DCW) mL- 1. 2-HPP titer, yield and productivity using the free cells were 1.2 g L- 1, 0.56 g 2-HPP/g benzaldehyde (0.4 mol 2-HPP/mol benzaldehyde), 0.067 g 2-HPP g- 1 DCW h- 1, respectively, under optimized biotransformation conditions (30 °C, 200 rpm). Calcium alginate (CA)-polyvinyl alcohol (PVA)-boric acid (BA)-beads were used for cell entrapment. Encapsulated whole-cells were successfully employed in four consecutive cycles for 2-HPP production under aerobic conditions without any noticeable beads degradation. Moreover, there was no production of benzyl alcohol as an unwanted by-product. CONCLUSIONS Bioconversion by whole P. putida resting cells is an efficient strategy for the production of 2-HPP and other α-hydroxyketones.
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Affiliation(s)
- Reihaneh Kordesedehi
- Department of Biotechnology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
| | - Mohammad Ali Asadollahi
- Department of Biotechnology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran.
| | - Azar Shahpiri
- Department of Biotechnology, College of Agriculture, Isfahan University of Technology, Isfahan, Iran
| | - Davoud Biria
- Department of Biotechnology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
| | - Pablo Iván Nikel
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
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3
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Chen C, Yuan J, Yu H, Lou X, Wang B, Xu Z, Tian H. Cloning, purification, and characterization of branched-chain α-keto acid decarboxylases from Lactococcus lactis strains with different 3-methylbutanal production abilities. FOOD BIOSCI 2022. [DOI: 10.1016/j.fbio.2022.101713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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4
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Wang Q, Geng S, Wang L, Wen Z, Sun X, Huang H. Bacterial mandelic acid degradation pathway and its application in biotechnology. J Appl Microbiol 2022; 133:273-286. [PMID: 35294082 DOI: 10.1111/jam.15529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 12/22/2021] [Accepted: 03/09/2022] [Indexed: 11/28/2022]
Abstract
Mandelic acid and its derivatives are an important class of chemical synthetic blocks, which is widely used in drug synthesis and stereochemistry research. In nature, mandelic acid degradation pathway has been widely identified and analyzed as a representative pathway of aromatic compounds degradation. The most studied mandelic acid degradation pathway from Pseudomonas putida consists of mandelate racemase, S-mandelate dehydrogenase, benzoylformate decarboxylase, benzaldehyde dehydrogenase and downstream benzoic acid degradation pathways. Because of the ability to catalyze various reactions of aromatic substrates, pathway enzymes have been widely used in biocatalysis, kinetic resolution, chiral compounds synthesis or construction of new metabolic pathways. In this paper, the physiological significance and the existing range of the mandelic acid degradation pathway were introduced first. Then each of the enzymes in the pathway is reviewed one by one, including the researches on enzymatic properties and the applications in biotechnology as well as efforts that have been made to modify the substrate specificity or improving catalytic activity by enzyme engineering to adapt different applications. The composition of the important metabolic pathway of bacterial mandelic acid degradation pathway as well as the researches and applications of pathway enzymes is summarized in this review for the first time.
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Affiliation(s)
- Qingzhuo Wang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2# Xuelin Road, Qixia District, Nanjing, People's Republic of China
| | - Shanshan Geng
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2# Xuelin Road, Qixia District, Nanjing, People's Republic of China
| | - Lingru Wang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2# Xuelin Road, Qixia District, Nanjing, People's Republic of China
| | - Zhiqiang Wen
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2# Xuelin Road, Qixia District, Nanjing, People's Republic of China
| | - Xiaoman Sun
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2# Xuelin Road, Qixia District, Nanjing, People's Republic of China
| | - He Huang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2# Xuelin Road, Qixia District, Nanjing, People's Republic of China.,College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30 South Puzhu Road, Nanjing, People's Republic of China
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5
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Peng M, Siebert DL, Engqvist MKM, Niemeyer CM, Rabe KS. Modeling-Assisted Design of Thermostable Benzaldehyde Lyases from Rhodococcus erythropolis for Continuous Production of α-Hydroxy Ketones. Chembiochem 2021; 23:e202100468. [PMID: 34558792 PMCID: PMC9293332 DOI: 10.1002/cbic.202100468] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 09/23/2021] [Indexed: 12/18/2022]
Abstract
Enantiopure α-hydroxy ketones are important building blocks of active pharmaceutical ingredients (APIs), which can be produced by thiamine-diphosphate-dependent lyases, such as benzaldehyde lyase. Here we report the discovery of a novel thermostable benzaldehyde lyase from Rhodococcus erythropolis R138 (ReBAL). While the overall sequence identity to the only experimentally confirmed benzaldehyde lyase from Pseudomonas fluorescens Biovar I (PfBAL) was only 65 %, comparison of a structural model of ReBAL with the crystal structure of PfBAL revealed only four divergent amino acids in the substrate binding cavity. Based on rational design, we generated two ReBAL variants, which were characterized along with the wild-type enzyme in terms of their substrate spectrum, thermostability and biocatalytic performance in the presence of different co-solvents. We found that the new enzyme variants have a significantly higher thermostability (up to 22 °C increase in T50 ) and a different co-solvent-dependent activity. Using the most stable variant immobilized in packed-bed reactors via the SpyCatcher/SpyTag system, (R)-benzoin was synthesized from benzaldehyde over a period of seven days with a stable space-time-yield of 9.3 mmol ⋅ L-1 ⋅ d-1 . Our work expands the important class of benzaldehyde lyases and therefore contributes to the development of continuous biocatalytic processes for the production of α-hydroxy ketones and APIs.
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Affiliation(s)
- Martin Peng
- Karlsruhe Institute of Technology (KIT), Institute for Biological Interfaces (IBG 1), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Dominik L Siebert
- Karlsruhe Institute of Technology (KIT), Institute for Biological Interfaces (IBG 1), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Martin K M Engqvist
- Chalmers University of Technology, Department of Biology and Biological Engineering, Division of Systems and Synthetic Biology, Kemivägen 10, 412 96, Gothenburg, Sweden
| | - Christof M Niemeyer
- Karlsruhe Institute of Technology (KIT), Institute for Biological Interfaces (IBG 1), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Kersten S Rabe
- Karlsruhe Institute of Technology (KIT), Institute for Biological Interfaces (IBG 1), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
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6
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Muschallik L, Kipp CR, Recker I, Bongaerts J, Pohl M, Gellissen M, Schöning MJ, Selmer T, Siegert P. Synthesis of α-hydroxy ketones and vicinal diols with the Bacillus licheniformis DSM 13 T butane-2,3-diol dehydrogenase. J Biotechnol 2020; 324:61-70. [PMID: 32976868 DOI: 10.1016/j.jbiotec.2020.09.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 09/18/2020] [Indexed: 10/23/2022]
Abstract
The enantioselective synthesis of α-hydroxy ketones and vicinal diols is an intriguing field because of the broad applicability of these molecules. Although, butandiol dehydrogenases are known to play a key role in the production of 2,3-butandiol, their potential as biocatalysts is still not well studied. Here, we investigate the biocatalytic properties of the meso-butanediol dehydrogenase from Bacillus licheniformis DSM 13T (BlBDH). The encoding gene was cloned with an N-terminal StrepII-tag and recombinantly overexpressed in E. coli. BlBDH is highly active towards several non-physiological diketones and α-hydroxyketones with varying aliphatic chain lengths or even containing phenyl moieties. By adjusting the reaction parameters in biotransformations the formation of either the α-hydroxyketone intermediate or the diol can be controlled.
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Affiliation(s)
- Lukas Muschallik
- Institute of Nano- and Biotechnologies, Aachen University of Applied Sciences, 52428, Jülich, Germany
| | - Carina Ronja Kipp
- Institute of Nano- and Biotechnologies, Aachen University of Applied Sciences, 52428, Jülich, Germany
| | - Inga Recker
- Institute of Nano- and Biotechnologies, Aachen University of Applied Sciences, 52428, Jülich, Germany
| | - Johannes Bongaerts
- Institute of Nano- and Biotechnologies, Aachen University of Applied Sciences, 52428, Jülich, Germany
| | - Martina Pohl
- IBG-1: Biotechnology, Forschungszentrum Jülich, 52425, Jülich, Germany
| | - Melanie Gellissen
- Institute of Nano- and Biotechnologies, Aachen University of Applied Sciences, 52428, Jülich, Germany
| | - Michael J Schöning
- Institute of Nano- and Biotechnologies, Aachen University of Applied Sciences, 52428, Jülich, Germany
| | - Thorsten Selmer
- Institute of Nano- and Biotechnologies, Aachen University of Applied Sciences, 52428, Jülich, Germany
| | - Petra Siegert
- Institute of Nano- and Biotechnologies, Aachen University of Applied Sciences, 52428, Jülich, Germany.
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7
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Muschallik L, Molinnus D, Jablonski M, Kipp CR, Bongaerts J, Pohl M, Wagner T, Schöning MJ, Selmer T, Siegert P. Synthesis of α-hydroxy ketones and vicinal (R,R)-diols by Bacillus clausii DSM 8716T butanediol dehydrogenase. RSC Adv 2020; 10:12206-12216. [PMID: 35497574 PMCID: PMC9050739 DOI: 10.1039/d0ra02066d] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 03/05/2020] [Indexed: 12/04/2022] Open
Abstract
α-hydroxy ketones (HK) and 1,2-diols are important building blocks for fine chemical synthesis. Here, we describe the R-selective 2,3-butanediol dehydrogenase from B. clausii DSM 8716T (BcBDH) that belongs to the metal-dependent medium chain dehydrogenases/reductases family (MDR) and catalyzes the selective asymmetric reduction of prochiral 1,2-diketones to the corresponding HK and, in some cases, the reduction of the same to the corresponding 1,2-diols. Aliphatic diketones, like 2,3-pentanedione, 2,3-hexanedione, 5-methyl-2,3-hexanedione, 3,4-hexanedione and 2,3-heptanedione are well transformed. In addition, surprisingly alkyl phenyl dicarbonyls, like 2-hydroxy-1-phenylpropan-1-one and phenylglyoxal are accepted, whereas their derivatives with two phenyl groups are not substrates. Supplementation of Mn2+ (1 mM) increases BcBDH's activity in biotransformations. Furthermore, the biocatalytic reduction of 5-methyl-2,3-hexanedione to mainly 5-methyl-3-hydroxy-2-hexanone with only small amounts of 5-methyl-2-hydroxy-3-hexanone within an enzyme membrane reactor is demonstrated. Reduction of symmetric or asymmetric vicinal diketones with BcBDH leads to the synthesis of either α-hydroxyketones or vicinal diols.![]()
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Affiliation(s)
- Lukas Muschallik
- Institute of Nano- and Biotechnologies
- Aachen University of Applied Sciences
- 52428 Jülich
- Germany
| | - Denise Molinnus
- Institute of Nano- and Biotechnologies
- Aachen University of Applied Sciences
- 52428 Jülich
- Germany
| | - Melanie Jablonski
- Institute of Nano- and Biotechnologies
- Aachen University of Applied Sciences
- 52428 Jülich
- Germany
| | - Carina Ronja Kipp
- Institute of Nano- and Biotechnologies
- Aachen University of Applied Sciences
- 52428 Jülich
- Germany
| | - Johannes Bongaerts
- Institute of Nano- and Biotechnologies
- Aachen University of Applied Sciences
- 52428 Jülich
- Germany
| | - Martina Pohl
- IBG-1: Biotechnology
- Forschungszentrum Jülich
- 52425 Jülich
- Germany
| | - Torsten Wagner
- Institute of Nano- and Biotechnologies
- Aachen University of Applied Sciences
- 52428 Jülich
- Germany
| | - Michael J. Schöning
- Institute of Nano- and Biotechnologies
- Aachen University of Applied Sciences
- 52428 Jülich
- Germany
| | - Thorsten Selmer
- Institute of Nano- and Biotechnologies
- Aachen University of Applied Sciences
- 52428 Jülich
- Germany
| | - Petra Siegert
- Institute of Nano- and Biotechnologies
- Aachen University of Applied Sciences
- 52428 Jülich
- Germany
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8
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Planas F, McLeish MJ, Himo F. Computational Study of Enantioselective Carboligation Catalyzed by Benzoylformate Decarboxylase. ACS Catal 2019. [DOI: 10.1021/acscatal.9b01084] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Ferran Planas
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, SE-10691 Stockholm, Sweden
| | - Michael J. McLeish
- Department of Chemistry and Chemical Biology, Indiana University−Purdue University Indianapolis, Indianapolis, Indiana 46202, United States
| | - Fahmi Himo
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, SE-10691 Stockholm, Sweden
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9
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Buchholz PCF, Ferrario V, Pohl M, Gardossi L, Pleiss J. Navigating within thiamine diphosphate-dependent decarboxylases: Sequences, structures, functional positions, and binding sites. Proteins 2019; 87:774-785. [PMID: 31070804 DOI: 10.1002/prot.25706] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2019] [Revised: 04/23/2019] [Accepted: 05/05/2019] [Indexed: 11/10/2022]
Abstract
Thiamine diphosphate-dependent decarboxylases catalyze both cleavage and formation of CC bonds in various reactions, which have been assigned to different homologous sequence families. This work compares 53 ThDP-dependent decarboxylases with known crystal structures. Both sequence and structural information were analyzed synergistically and data were analyzed for global and local properties by means of statistical approaches (principle component analysis and principal coordinate analysis) enabling complexity reduction. The different results obtained both locally and globally, that is, individual positions compared with the overall protein sequence or structure, revealed challenges in the assignment of separated homologous families. The methods applied herein support the comparison of enzyme families and the identification of functionally relevant positions. The findings for the family of ThDP-dependent decarboxylases underline that global sequence identity alone is not sufficient to distinguish enzyme function. Instead, local sequence similarity, defined by comparisons of structurally equivalent positions, allows for a better navigation within several groups of homologous enzymes. The differentiation between homologous sequences is further enhanced by taking structural information into account, such as BioGPS analysis of the active site properties or pairwise structural superimpositions. The methods applied herein are expected to be transferrable to other enzyme families, to facilitate family assignments for homologous protein sequences.
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Affiliation(s)
- Patrick C F Buchholz
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Stuttgart, Germany
| | - Valerio Ferrario
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Stuttgart, Germany.,Laboratory of Applied and Computational Biocatalysis, Department of Chemical and Pharmaceutical Sciences, Università degli Studi di Trieste, Trieste, Italy
| | - Martina Pohl
- Forschungszentrum Jülich GmbH, IBG-1: Biotechnology, Jülich, Germany
| | - Lucia Gardossi
- Laboratory of Applied and Computational Biocatalysis, Department of Chemical and Pharmaceutical Sciences, Università degli Studi di Trieste, Trieste, Italy
| | - Jürgen Pleiss
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Stuttgart, Germany
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10
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Hampel S, Steitz JP, Baierl A, Lehwald P, Wiesli L, Richter M, Fries A, Pohl M, Schneider G, Dobritzsch D, Müller M. Structural and Mutagenesis Studies of the Thiamine-Dependent, Ketone-Accepting YerE from Pseudomonas protegens. Chembiochem 2018; 19:2283-2292. [DOI: 10.1002/cbic.201800325] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Indexed: 12/18/2022]
Affiliation(s)
- Sabrina Hampel
- Institut für Pharmazeutische Wissenschaften; Albert-Ludwigs-Universität Freiburg; Albertstrasse 25 79104 Freiburg Germany
| | - Jan-Patrick Steitz
- Institut für Pharmazeutische Wissenschaften; Albert-Ludwigs-Universität Freiburg; Albertstrasse 25 79104 Freiburg Germany
| | - Anna Baierl
- IBG-1: Biotechnology; Forschungszentrum Jülich GmbH; Wilhelm-Johnen Str. 52425 Jülich Germany
| | - Patrizia Lehwald
- Institut für Pharmazeutische Wissenschaften; Albert-Ludwigs-Universität Freiburg; Albertstrasse 25 79104 Freiburg Germany
| | - Luzia Wiesli
- Empa - Swiss Federal Laboratories for Materials Science and Technology; Laboratory for Biointerfaces; Lerchenfeldstrasse 5 9014 St. Gallen Switzerland
| | - Michael Richter
- Empa - Swiss Federal Laboratories for Materials Science and Technology; Laboratory for Biointerfaces; Lerchenfeldstrasse 5 9014 St. Gallen Switzerland
- Fraunhofer Institute for Interfacial Engineering and Biotechnology IGB; Branch BioCat; Schulgasse 11a 94315 Straubing Germany
| | - Alexander Fries
- Institut für Pharmazeutische Wissenschaften; Albert-Ludwigs-Universität Freiburg; Albertstrasse 25 79104 Freiburg Germany
| | - Martina Pohl
- IBG-1: Biotechnology; Forschungszentrum Jülich GmbH; Wilhelm-Johnen Str. 52425 Jülich Germany
| | - Gunter Schneider
- Department of Medical Biochemistry and Biophysics; Karolinska Institutet; Tomtebodavägen 6 17177 Stockholm Sweden
| | - Doreen Dobritzsch
- Vising address: Department of Chemistry-BMC; Uppsala Universitet; Husargatan 3 75237 Uppsala Sweden
| | - Michael Müller
- Institut für Pharmazeutische Wissenschaften; Albert-Ludwigs-Universität Freiburg; Albertstrasse 25 79104 Freiburg Germany
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11
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Ohs R, Leipnitz M, Schöpping M, Spiess AC. Simultaneous identification of reaction and inactivation kinetics of an enzyme‐catalyzed carboligation. Biotechnol Prog 2018; 34:1081-1092. [DOI: 10.1002/btpr.2656] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2018] [Revised: 04/19/2018] [Indexed: 01/17/2023]
Affiliation(s)
- Rüdiger Ohs
- RWTH Aachen University, Aachener Verfahrenstechnik—Enzyme Process Technology52074 Aachen Germany
- DWI—Leibniz Institute for Interactive Materials Research52074 Aachen Germany
- TU Braunschweig, Institute of Biochemical EngineeringBraunschweig38106 Germany
| | - Martin Leipnitz
- RWTH Aachen University, Aachener Verfahrenstechnik—Enzyme Process Technology52074 Aachen Germany
| | - Marie Schöpping
- RWTH Aachen University, Aachener Verfahrenstechnik—Enzyme Process Technology52074 Aachen Germany
| | - Antje C. Spiess
- RWTH Aachen University, Aachener Verfahrenstechnik—Enzyme Process Technology52074 Aachen Germany
- DWI—Leibniz Institute for Interactive Materials Research52074 Aachen Germany
- TU Braunschweig, Institute of Biochemical EngineeringBraunschweig38106 Germany
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12
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Baierl A, Theorell A, Mackfeld U, Marquardt P, Hoffmann F, Moers S, Nöh K, Buchholz PCF, Pleiss J, Pohl M. Towards a Mechanistic Understanding of Factors Controlling the Stereoselectivity of Transketolase. ChemCatChem 2018. [DOI: 10.1002/cctc.201800299] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Anna Baierl
- IBG-1: Biotechnology, Forschungszentrum Jülich GmbH; 52425 Jülich Germany
| | - Axel Theorell
- IBG-1: Biotechnology, Forschungszentrum Jülich GmbH; 52425 Jülich Germany
| | - Ursula Mackfeld
- IBG-1: Biotechnology, Forschungszentrum Jülich GmbH; 52425 Jülich Germany
| | - Philipp Marquardt
- IBG-1: Biotechnology, Forschungszentrum Jülich GmbH; 52425 Jülich Germany
| | | | - Stephanie Moers
- IBG-1: Biotechnology, Forschungszentrum Jülich GmbH; 52425 Jülich Germany
| | - Katharina Nöh
- IBG-1: Biotechnology, Forschungszentrum Jülich GmbH; 52425 Jülich Germany
| | - Patrick C. F. Buchholz
- Institute of Biochemistry and Technical Biochemistry; University of Stuttgart; 70569 Stuttgart Germany
| | - Jürgen Pleiss
- Institute of Biochemistry and Technical Biochemistry; University of Stuttgart; 70569 Stuttgart Germany
| | - Martina Pohl
- IBG-1: Biotechnology, Forschungszentrum Jülich GmbH; 52425 Jülich Germany
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13
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Hernández K, Parella T, Petrillo G, Usón I, Wandtke CM, Joglar J, Bujons J, Clapés P. Intramolecular Benzoin Reaction Catalyzed by Benzaldehyde Lyase from Pseudomonas Fluorescens Biovar I. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201702278] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Karel Hernández
- Catalonia Institute for Advanced Chemistry; Dept. Chemical Biology & Molecular Modelling; IQAC-CSIC; Jordi Girona 18-26 08034 Barcelona Spain
| | - Teodor Parella
- Servei de Ressonáncia Magnética Nuclear; Universitat Autònoma de Barcelona; Bellaterra Spain
| | - Giovanna Petrillo
- Dept. Chemical Biology & Molecular Modelling; Instituto de Química Avanzada de Cataluña; IQAC-CSIC; Instituto de Biología Molecular de Barcelona; IBMB-CSIC; Spain
| | - Isabel Usón
- Instituto de Biología Molecular de Barcelona; IBMB-CSIC; Institució Catalana de Recerca i Estudis Avançats (ICREA); Spain
| | - Claudia M. Wandtke
- Institut für Anorganische Chemie; Universität Göttingen; Göttingen Germany
| | - Jesús Joglar
- Catalonia Institute for Advanced Chemistry; Dept. Chemical Biology & Molecular Modelling; IQAC-CSIC; Jordi Girona 18-26 08034 Barcelona Spain
| | - Jordi Bujons
- Catalonia Institute for Advanced Chemistry; Dept. Chemical Biology & Molecular Modelling; IQAC-CSIC; Jordi Girona 18-26 08034 Barcelona Spain
| | - Pere Clapés
- Catalonia Institute for Advanced Chemistry; Dept. Chemical Biology & Molecular Modelling; IQAC-CSIC; Jordi Girona 18-26 08034 Barcelona Spain
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14
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Hernández K, Parella T, Petrillo G, Usón I, Wandtke CM, Joglar J, Bujons J, Clapés P. Intramolecular Benzoin Reaction Catalyzed by Benzaldehyde Lyase from Pseudomonas Fluorescens Biovar I. Angew Chem Int Ed Engl 2017; 56:5304-5307. [PMID: 28387004 DOI: 10.1002/anie.201702278] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Revised: 03/22/2017] [Indexed: 01/09/2023]
Abstract
Intramolecular benzoin reactions catalyzed by benzaldehyde lyase from Pseudomonas fluorescens biovar I (BAL) are reported. The structure of the substrates envisaged for this reaction consists of two benzaldehyde derivatives linked by an alkyl chain. The structural requirements needed to achieve the intramolecular carbon-carbon bond reaction catalyzed by BAL were established. Thus, a linker consisting of a linear alkyl chain of three carbon atoms connected through ether-type bonds to the 2 and 2' positions of two benzaldehyde moieties, which could be substituted with either Cl, Br, or OCH3 at either the 3 and 3' or 5 and 5' positions, were suitable substrates for BAL. Reactions with 61-84 % yields of the intramolecular product and ee values between 64 and 98 %, were achieved.
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Affiliation(s)
- Karel Hernández
- Catalonia Institute for Advanced Chemistry, Dept. Chemical Biology & Molecular Modelling, IQAC-CSIC, Jordi Girona 18-26, 08034, Barcelona, Spain
| | - Teodor Parella
- Servei de Ressonáncia Magnética Nuclear, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Giovanna Petrillo
- Dept. Chemical Biology & Molecular Modelling, Instituto de Química Avanzada de Cataluña, IQAC-CSIC, Instituto de Biología Molecular de Barcelona, IBMB-CSIC, Spain
| | - Isabel Usón
- Instituto de Biología Molecular de Barcelona, IBMB-CSIC, Institució Catalana de Recerca i Estudis Avançats (ICREA), Spain
| | - Claudia M Wandtke
- Institut für Anorganische Chemie, Universität Göttingen, Göttingen, Germany
| | - Jesús Joglar
- Catalonia Institute for Advanced Chemistry, Dept. Chemical Biology & Molecular Modelling, IQAC-CSIC, Jordi Girona 18-26, 08034, Barcelona, Spain
| | - Jordi Bujons
- Catalonia Institute for Advanced Chemistry, Dept. Chemical Biology & Molecular Modelling, IQAC-CSIC, Jordi Girona 18-26, 08034, Barcelona, Spain
| | - Pere Clapés
- Catalonia Institute for Advanced Chemistry, Dept. Chemical Biology & Molecular Modelling, IQAC-CSIC, Jordi Girona 18-26, 08034, Barcelona, Spain
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15
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Giovannini PP, Bortolini O, Massi A. Thiamine-Diphosphate-Dependent Enzymes as Catalytic Tools for the Asymmetric Benzoin-Type Reaction. European J Org Chem 2016. [DOI: 10.1002/ejoc.201600228] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Pier Paolo Giovannini
- Department of Chemical and Pharmaceutical Sciences; University of Ferrara; 17, Via Fossato di Mortara 44121 Ferrara Italy
| | - Olga Bortolini
- Department of Chemical and Pharmaceutical Sciences; University of Ferrara; 17, Via Fossato di Mortara 44121 Ferrara Italy
| | - Alessandro Massi
- Department of Chemical and Pharmaceutical Sciences; University of Ferrara; 17, Via Fossato di Mortara 44121 Ferrara Italy
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16
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Lehwald P, Fuchs O, Nafie LA, Müller M, Lüdeke S. Substrate-Determined Diastereoselectivity in an Enzymatic Carboligation. Chembiochem 2016; 17:1207-10. [DOI: 10.1002/cbic.201600202] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Indexed: 11/05/2022]
Affiliation(s)
- Patrizia Lehwald
- Institut für Pharmazeutische Wissenschaften; Albert-Ludwigs-Universität Freiburg; Albertstrasse 25 79104 Freiburg Germany
| | - Olga Fuchs
- Institut für Pharmazeutische Wissenschaften; Albert-Ludwigs-Universität Freiburg; Albertstrasse 25 79104 Freiburg Germany
| | | | - Michael Müller
- Institut für Pharmazeutische Wissenschaften; Albert-Ludwigs-Universität Freiburg; Albertstrasse 25 79104 Freiburg Germany
| | - Steffen Lüdeke
- Institut für Pharmazeutische Wissenschaften; Albert-Ludwigs-Universität Freiburg; Albertstrasse 25 79104 Freiburg Germany
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17
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Lizana I, Jaña GA, Delgado EJ. New Insights on the Reaction Pathway Leading to Lactyl-ThDP: A Theoretical Approach. J Chem Inf Model 2015. [DOI: 10.1021/acs.jcim.5b00197] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ignacio Lizana
- Computational
Chemistry Group, Faculty of Chemical Sciences, Universidad de Concepción, Concepción, Chile
| | - Gonzalo A. Jaña
- Departamento
de Ciencias Químicas, Facultad de Ciencias Exactas, Sede Concepción, Universidad Andrés Bello, Concepción, Chile
| | - Eduardo J. Delgado
- Computational
Chemistry Group, Faculty of Chemical Sciences, Universidad de Concepción, Concepción, Chile
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18
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Andrews FH, Horton JD, Shin D, Yoon HJ, Logsdon MG, Malik AM, Rogers MP, Kneen MM, Suh SW, McLeish MJ. The kinetic characterization and X-ray structure of a putative benzoylformate decarboxylase from M. smegmatis highlights the difficulties in the functional annotation of ThDP-dependent enzymes. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1854:1001-9. [DOI: 10.1016/j.bbapap.2015.04.027] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2014] [Revised: 04/05/2015] [Accepted: 04/23/2015] [Indexed: 10/23/2022]
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19
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Berheide M, Kara S, Liese A. Reversibility of asymmetric catalyzed C–C bond formation by benzoylformate decarboxylase. Catal Sci Technol 2015. [DOI: 10.1039/c4cy00171k] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Benzoylformate decarboxylase (BFD) fromPseudomonas putidacatalyzed the formation of 2-hydroxy-1-phenylpropanone (2-HPP), a 2-hydroxy ketone, from the kinetic resolution ofrac-benzoin in the presence of acetaldehyde.
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Affiliation(s)
- Marco Berheide
- Institute of Technical Biocatalysis
- Hamburg University of Technology
- Hamburg
- Germany
| | - Selin Kara
- Institute of Technical Biocatalysis
- Hamburg University of Technology
- Hamburg
- Germany
- Institute of Microbiology
| | - Andreas Liese
- Institute of Technical Biocatalysis
- Hamburg University of Technology
- Hamburg
- Germany
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20
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The modular structure of ThDP-dependent enzymes. Proteins 2014; 82:2523-37. [DOI: 10.1002/prot.24615] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Revised: 05/06/2014] [Accepted: 05/20/2014] [Indexed: 01/12/2023]
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21
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Controlling enantioselectivity of esterase in asymmetric hydrolysis of aryl prochiral diesters by introducing aromatic interactions. Biotechnol Bioeng 2014; 111:1729-39. [DOI: 10.1002/bit.25249] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2014] [Revised: 03/03/2014] [Accepted: 03/24/2014] [Indexed: 11/07/2022]
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22
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Tural B, Tarhan T, Tural S. Covalent immobilization of benzoylformate decarboxylase from Pseudomonas putida on magnetic epoxy support and its carboligation reactivity. ACTA ACUST UNITED AC 2014. [DOI: 10.1016/j.molcatb.2014.02.016] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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23
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Pleiss J. Systematic Analysis of Large Enzyme Families: Identification of Specificity- and Selectivity-Determining Hotspots. ChemCatChem 2014. [DOI: 10.1002/cctc.201300950] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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24
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Kourist R, Guterl JK, Miyamoto K, Sieber V. Enzymatic Decarboxylation-An Emerging Reaction for Chemicals Production from Renewable Resources. ChemCatChem 2014. [DOI: 10.1002/cctc.201300881] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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25
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26
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Westphal R, Jansen S, Vogel C, Pleiss J, Müller M, Rother D, Pohl M. MenD from Bacillus subtilis
: A Potent Catalyst for the Enantiocomplementary Asymmetric Synthesis of Functionalized α-Hydroxy Ketones. ChemCatChem 2013. [DOI: 10.1002/cctc.201300690] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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27
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Hailes HC, Rother D, Müller M, Westphal R, Ward JM, Pleiss J, Vogel C, Pohl M. Engineering stereoselectivity of ThDP-dependent enzymes. FEBS J 2013; 280:6374-94. [DOI: 10.1111/febs.12496] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2013] [Revised: 08/16/2013] [Accepted: 08/21/2013] [Indexed: 01/12/2023]
Affiliation(s)
- Helen C. Hailes
- Department of Chemistry; Christopher Ingold Laboratories; University College London; UK
| | - Dörte Rother
- IBG-1: Biotechnology; Forschungszentrum Jülich Germany
| | - Michael Müller
- Institute of Pharmaceutical Sciences; University of Freiburg; Germany
| | | | - John M. Ward
- Department of Biochemical Engineering; University College London; UK
| | - Jürgen Pleiss
- Institute of Technical Biochemistry; University of Stuttgart; Germany
| | - Constantin Vogel
- Institute of Technical Biochemistry; University of Stuttgart; Germany
| | - Martina Pohl
- IBG-1: Biotechnology; Forschungszentrum Jülich Germany
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28
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Westphal R, Hahn D, Mackfeld U, Waltzer S, Beigi M, Widmann M, Vogel C, Pleiss J, Müller M, Rother D, Pohl M. Tailoring theS-Selectivity of 2-Succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate Synthase (MenD) fromEscherichia coli. ChemCatChem 2013. [DOI: 10.1002/cctc.201300318] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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29
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Andrews FH, McLeish MJ. Using site-saturation mutagenesis to explore mechanism and substrate specificity in thiamin diphosphate-dependent enzymes. FEBS J 2013; 280:6395-411. [DOI: 10.1111/febs.12459] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2013] [Revised: 07/23/2013] [Accepted: 07/26/2013] [Indexed: 12/25/2022]
Affiliation(s)
- Forest H. Andrews
- Department of Chemistry and Chemical Biology; Indiana University-Purdue University Indianapolis; IN USA
| | - Michael J. McLeish
- Department of Chemistry and Chemical Biology; Indiana University-Purdue University Indianapolis; IN USA
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30
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Tural B, Tural S, Demir AS. Carboligation Reactions Mediated by Benzoylformate Decarboxylase Immobilized on a Magnetic Solid Support. Chirality 2013; 25:415-21. [DOI: 10.1002/chir.22181] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2013] [Accepted: 03/22/2013] [Indexed: 11/11/2022]
Affiliation(s)
- Bilsen Tural
- Department of Chemistry; Dicle University; Diyarbakir Turkey
| | - Servet Tural
- Department of Chemistry; Dicle University; Diyarbakir Turkey
| | - Ayhan S. Demir
- Department of Chemistry; Middle East Technical University; Ankara Turkey
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31
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Pérez-Sánchez M, Müller CR, Domínguez de María P. Multistep Oxidase-Lyase Reactions: Synthesis of Optically Active 2-Hydroxyketones by Using Biobased Aliphatic Alcohols. ChemCatChem 2013. [DOI: 10.1002/cctc.201300093] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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32
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Vogel C, Widmann M, Pohl M, Pleiss J. A standard numbering scheme for thiamine diphosphate-dependent decarboxylases. BMC BIOCHEMISTRY 2012; 13:24. [PMID: 23157214 PMCID: PMC3534367 DOI: 10.1186/1471-2091-13-24] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/17/2012] [Accepted: 11/08/2012] [Indexed: 01/05/2023]
Abstract
Background Standard numbering schemes for families of homologous proteins allow for the unambiguous identification of functionally and structurally relevant residues, to communicate results on mutations, and to systematically analyse sequence-function relationships in protein families. Standard numbering schemes have been successfully implemented for several protein families, including lactamases and antibodies, whereas a numbering scheme for the structural family of thiamine-diphosphate (ThDP) -dependent decarboxylases, a large subfamily of the class of ThDP-dependent enzymes encompassing pyruvate-, benzoylformate-, 2-oxo acid-, indolpyruvate- and phenylpyruvate decarboxylases, benzaldehyde lyase, acetohydroxyacid synthases and 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexadiene-1-carboxylate synthase (MenD) is still missing. Despite a high structural similarity between the members of the ThDP-dependent decarboxylases, their sequences are diverse and make a pairwise sequence comparison of protein family members difficult. Results We developed and validated a standard numbering scheme for the family of ThDP-dependent decarboxylases. A profile hidden Markov model (HMM) was created using a set of representative sequences from the family of ThDP-dependent decarboxylases. The pyruvate decarboxylase from S. cerevisiae (PDB: 2VK8) was chosen as a reference because it is a well characterized enzyme. The crystal structure with the PDB identifier 2VK8 encompasses the structure of the ScPDC mutant E477Q, the cofactors ThDP and Mg2+ as well as the substrate analogue (2S)-2-hydroxypropanoic acid. The absolute numbering of this reference sequence was transferred to all members of the ThDP-dependent decarboxylase protein family. Subsequently, the numbering scheme was integrated into the already established Thiamine-diphosphate dependent Enzyme Engineering Database (TEED) and was used to systematically analyze functionally and structurally relevant positions in the superfamily of ThDP-dependent decarboxylases. Conclusions The numbering scheme serves as a tool for the reliable sequence alignment of ThDP-dependent decarboxylases and the unambiguous identification and communication of corresponding positions. Thus, it is the basis for the systematic and automated analysis of sequence-encoded properties such as structural and functional relevance of amino acid positions, because the analysis of conserved positions, the identification of correlated mutations and the determination of subfamily specific amino acid distributions depend on reliable multisequence alignments and the unambiguous identification of the alignment columns. The method is reliable and robust and can easily be adapted to further protein families.
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Affiliation(s)
- Constantin Vogel
- Institute of Technical Biochemistry, University of Stuttgart, Allmandring 31, Stuttgart, 70569, Germany
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33
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Gerhards T, Mackfeld U, Bocola M, von Lieres E, Wiechert W, Pohl M, Rother D. Influence of Organic Solvents on Enzymatic Asymmetric Carboligations. Adv Synth Catal 2012; 354:2805-2820. [PMID: 23349644 PMCID: PMC3549479 DOI: 10.1002/adsc.201200284] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2012] [Revised: 06/25/2012] [Indexed: 11/25/2022]
Abstract
The asymmetric mixed carboligation of aldehydes with thiamine diphosphate (ThDP)-dependent enzymes is an excellent example where activity as well as changes in chemo- and stereoselectivity can be followed sensitively. To elucidate the influence of organic additives in enzymatic carboligation reactions of mixed 2-hydroxy ketones, we present a comparative study of six ThDP-dependent enzymes in 13 water-miscible organic solvents under equivalent reaction conditions. The influence of the additives on the stereoselectivity is most pronounced and follows a general trend. If the enzyme stereoselectivity in aqueous buffer is already >99.9% ee, none of the solvents reduces this high selectivity. In contrast, both stereoselectivity and chemoselectivity are strongly influenced if the enzyme is rather unselective in aqueous buffer. For the S-selective enzyme with the largest active site, we were able to prove a general correlation of the solvent-excluded volume of the additives with the effect on selectivity changes: the smaller the organic solvent molecule, the higher the impact of this additive. Further, a correlation to log P of the additives on selectivity was detected if two additives have almost the same solvent-excluded volume. The observed results are discussed in terms of structural, biochemical and energetic effects. This work demonstrates the potential of medium engineering as a powerful additional tool for varying enzyme selectivity and thus engineering the product range of biotransformations. It further demonstrates that the use of cosolvents should be carefully planned, as the solvents may compete with the substrate(s) for binding sites in the enzyme active site.
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Affiliation(s)
- Tina Gerhards
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH 52425 Jülich, Germany, ; phone: (+49)-2461-616772
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Substrate specificity in thiamin diphosphate-dependent decarboxylases. Bioorg Chem 2011; 43:26-36. [PMID: 22245019 DOI: 10.1016/j.bioorg.2011.12.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2011] [Revised: 12/19/2011] [Accepted: 12/20/2011] [Indexed: 11/20/2022]
Abstract
Thiamin diphosphate (ThDP) is the biologically active form of vitamin B(1), and ThDP-dependent enzymes are found in all forms of life. The catalytic mechanism of this family requires the formation of a common intermediate, the 2α-carbanion-enamine, regardless of whether the enzyme is involved in C-C bond formation or breakdown, or even formation of C-N, C-O and C-S bonds. This demands that the enzymes must screen substrates prior to, and/or after, formation of the common intermediate. This review is focused on the group for which the second step is the protonation of the 2α-carbanion, i.e., the ThDP-dependent decarboxylases. Based on kinetic data, sequence/structure alignments and mutagenesis studies the factors involved in substrate specificity have been identified.
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35
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Rother neé Gocke D, Kolter G, Gerhards T, Berthold CL, Gauchenova E, Knoll M, Pleiss J, Müller M, Schneider G, Pohl M. S-Selective Mixed Carboligation by Structure-Based Design of the Pyruvate Decarboxylase from Acetobacter pasteurianus. ChemCatChem 2011. [DOI: 10.1002/cctc.201100054] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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36
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Brovetto M, Gamenara D, Méndez PS, Seoane GA. C-C bond-forming lyases in organic synthesis. Chem Rev 2011; 111:4346-403. [PMID: 21417217 DOI: 10.1021/cr100299p] [Citation(s) in RCA: 160] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Margarita Brovetto
- Grupo de Fisicoquímica Orgánica y Bioprocesos, Departamento de Química Orgánica, DETEMA, Facultad de Química, Universidad de la República (UdelaR), Gral. Flores 2124, 11800 Montevideo, Uruguay
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37
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Influence of reaction conditions on the enantioselectivity of biocatalyzed C–C bond formations under high pressure conditions. J Biotechnol 2011; 152:87-92. [DOI: 10.1016/j.jbiotec.2011.01.020] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2010] [Revised: 01/17/2011] [Accepted: 01/25/2011] [Indexed: 11/22/2022]
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38
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Immobilization and characterization of benzoylformate decarboxylase from Pseudomonas putida on spherical silica carrier. Bioprocess Biosyst Eng 2011; 34:671-80. [PMID: 21286757 DOI: 10.1007/s00449-011-0516-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2010] [Accepted: 01/12/2011] [Indexed: 10/18/2022]
Abstract
If an adequate biocatalyst is identified for a specific reaction, immobilization is one possibility to further improve its properties. The immobilization allows easy recycling, improves the enzyme performance, and it often enhances the stability of the enzyme. In this work, the immobilization of the benzoylformate decarboxylase (BFD) variant, BFD A460I-F464I, from Pseudomonas putida was accomplished on spherical silica. Silicagel is characterized by its high mechanical stability, which allows its application in different reactor types without restrictions. The covalently bound enzyme was characterized in terms of its activity, stability, and kinetics for the formation of chiral 2-hydroxypropiophenone (2-HPP) from benzaldehyde and acetaldehyde. Moreover, temperature as well as pressure dependency of immobilized BFD A460I-F464I activity and enantioselectivity were analyzed. The used wide-pore silicagel shows a good accessibility of the immobilized enzyme. The activity of the immobilized BFD A460I-F464I variant was determined to be 70% related to the activity of the free enzyme. Thereby, the enantioselectivity of the enzyme was not influenced by the immobilization. In addition, a pressure-induced change in stereoselectivity was found both for the free and for the immobilized enzyme. With increasing pressure, the enantiomeric excess (ee) of (R)-2-HPP can be increased from 44% (0.1 MPa) to 76% (200 MPa) for the free enzyme and from 43% (0.1 MPa) to 66% (200 MPa) for the immobilized enzyme.
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39
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Berheide M, Peper S, Kara S, Long WS, Schenkel S, Pohl M, Niemeyer B, Liese A. Influence of the hydrostatic pressure and pH on the asymmetric 2-hydroxyketone formation catalyzed by Pseudomonas putida benzoylformate decarboxylase and variants thereof. Biotechnol Bioeng 2010; 106:18-26. [PMID: 20047192 DOI: 10.1002/bit.22650] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Benzoylformate decarboxylase (BFD) from Pseudomonas putida is a thiamine diphosphate-dependent (ThDP) enzyme that catalyzes the asymmetric C--C bond formation to (S)-2-hydroxypropiophenone [(S)-HPP] starting from benzaldehyde and acetaldehyde. The enantioselectivity of BFD was shown to be a function of temperature and substrate concentration. It can additionally be changed by site-directed mutagenesis on hot spot positions in the active site. In this article, we present the effect of hydrostatic pressure up to 250 MPa on the enantioselectivity for the recombinant wtBFD as well as for the variants BFD F464I, BFD A460I, and BFD A460I-F464I. A general tendency toward lower amounts of (S)-HPP could be observed at increasing pressures. For two of these variants an increase in pressure even caused an inversion in the enantioselectivity and thus increasing enantiomeric excesses, respectively. A pressure-induced increase in enantioselectivity could therefore be observed for the first time in biocatalysis to the best of our knowledge. Furthermore, the pH is shown to be a parameter that also significantly influences the enantioselectivity of the reaction mentioned above.
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Affiliation(s)
- Marco Berheide
- Institute of Technical Biocatalysis, Hamburg University of Technology, Denickestrasse 15, 21073 Hamburg, Germany
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40
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Hoyos P, Sinisterra JV, Molinari F, Alcántara AR, Domínguez de María P. Biocatalytic strategies for the asymmetric synthesis of alpha-hydroxy ketones. Acc Chem Res 2010; 43:288-99. [PMID: 19908854 DOI: 10.1021/ar900196n] [Citation(s) in RCA: 170] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The development of efficient syntheses for enantiomerically enriched alpha-hydroxy ketones is an important research focus in the pharmaceutical industry. For example, alpha-hydroxy ketones are found in antidepressants, in selective inhibitors of amyloid-beta protein production (used in the treatment of Alzheimer's), in farnesyl transferase inhibitors (Kurasoin A and B), and in antitumor antibiotics (Olivomycin A and Chromomycin A3). Moreover, alpha-hydroxy ketones are of particular value as fine chemicals because of their utility as building blocks for the production of larger molecules. They can also be used in preparing many other important structures, such as amino alcohols, diols, and so forth. Several purely chemical synthetic approaches have been proposed to afford these compounds, together with some organocatalytic strategies (thiazolium-based carboligations, proline alpha-hydroxylations, and so forth). However, many of these chemical approaches are not straightforward, lack selectivity, or are economically unattractive because of the large number of chemical steps required (usually combined with low enantioselectivities). In this Account, we describe three different biocatalytic approaches that have been developed to efficiently produce alpha-hydroxy ketones: (i) The use of thiamine diphosphate-dependent lyases (ThDP-lyases) to catalyze the umpolung carboligation of aldehydes. Enantiopure alpha-hydroxy ketones are formed from inexpensive aldehydes with this method. Some lyases with a broad substrate spectrum have been successfully characterized. Furthermore, the use of biphasic media with recombinant whole cells overexpressing lyases leads to productivities of approximately 80-100 g/L with high enantiomeric excesses (up to >99%). (ii) The use of hydrolases to produce alpha-hydroxy ketones by means of (in situ) dynamic kinetic resolutions (DKRs). Lipases are able to successfully resolve racemates, and many outstanding examples have been reported. However, this approach leads to a maximum theoretical yield of 50%. As a means of overcoming this problem, these traditional lipase-catalyzed kinetic resolutions are combined with racemization of remnant substrate, which can be done in situ or in separate compartments. Examples showing high conversions (>90%) and enantiomeric excesses (>99%) are described. (iii) Whole-cell redox processes, catalyzed by several microorganisms, either by means of free enzymes (applying a cofactor regeneration system) or by whole cells. Through the use of redox machineries, different strategies can lead to high yields and enantiomeric excesses. Some enantiopure alpha-hydroxy ketones can be formed by reductions of diketones and by selective oxidations of vicinal diols. Likewise, some redox processes involving sugar chemistry (involving alpha-hydroxy ketones) have been developed on the industrial scale. Finally, the redox whole-cell concept allows racemizations (and deracemizations) as well. These three strategies provide a useful and environmentally friendly synthetic toolbox. Likewise, the field represents an illustrative example of how biocatalysis can assist practical synthetic processes, and how problems derived from the integration of natural tools in synthetic pathways can be efficiently tackled to afford high yields and enantioselectivities.
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Affiliation(s)
- Pilar Hoyos
- Grupo de Biotransformaciones, Departamento de Química Orgánica y Farmacéutica, Facultad de Farmacia, Universidad Complutense de Madrid, Plaza de Ramón y Cajal, s/n. 28040 Madrid, Spain
| | - Josep-Vicent Sinisterra
- Grupo de Biotransformaciones, Departamento de Química Orgánica y Farmacéutica, Facultad de Farmacia, Universidad Complutense de Madrid, Plaza de Ramón y Cajal, s/n. 28040 Madrid, Spain
- Unidad de Biotransformaciones Industriales, Parque Científico de Madrid, PTM, C/ Santiago Grisolía, 2, 28760 Tres Cantos, Madrid, Spain
| | - Francesco Molinari
- Dipartimento di Scienze e Tecnologie Alimentari e Microbiologiche, Università degli Studi di Milano, 20133 Milano, Italy
| | - Andrés R. Alcántara
- Grupo de Biotransformaciones, Departamento de Química Orgánica y Farmacéutica, Facultad de Farmacia, Universidad Complutense de Madrid, Plaza de Ramón y Cajal, s/n. 28040 Madrid, Spain
- Unidad de Biotransformaciones Industriales, Parque Científico de Madrid, PTM, C/ Santiago Grisolía, 2, 28760 Tres Cantos, Madrid, Spain
| | - Pablo Domínguez de María
- Institute of Technical and Macromolecular Chemistry (ITMC), RWTH Aachen University, Worringerweg 1, D-52074 Aachen, Germany
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Pohl M, Gocke D, Müller M, Kolter G. Entwicklung einer Enzymplattform für die biokatalytische C-C-Verknüpfung. CHEM-ING-TECH 2010. [DOI: 10.1002/cite.200900112] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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42
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Kurlemann N, Lara M, Pohl M, Kroutil W, Liese A. Asymmetric synthesis of chiral 2-hydroxy ketones by coupled biocatalytic alkene oxidation and CC bond formation. ACTA ACUST UNITED AC 2009. [DOI: 10.1016/j.molcatb.2008.08.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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43
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Gocke D, Graf T, Brosi H, Frindi-Wosch I, Walter L, Müller M, Pohl M. Comparative characterisation of thiamin diphosphate-dependent decarboxylases. ACTA ACUST UNITED AC 2009. [DOI: 10.1016/j.molcatb.2009.03.019] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Kokova M, Zavrel M, Tittmann K, Spiess AC, Pohl M. Investigation of the carboligase activity of thiamine diphosphate-dependent enzymes using kinetic modeling and NMR spectroscopy. ACTA ACUST UNITED AC 2009. [DOI: 10.1016/j.molcatb.2009.02.021] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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45
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Topal KG, Atilgan C, Demir AS, Aviyente V. Understanding the mode of action of ThDP in benzoylformate decarboxylase. Biopolymers 2009; 93:32-46. [PMID: 19688812 DOI: 10.1002/bip.21291] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The mechanism of all elementary steps involved in the catalytic cycle of benzoylformate decarboxylase (BFD, E.C. 4.1.1.7) to generate the acyloin linkage is investigated by extensive molecular dynamics simulations. Models involving different charge states of amino acids and/or mutants of critical residues were constructed to understand the involvement of the catalytically active residues and the reactivity differences between different substrates in this reaction. Our calculations confirm that H70, S26, and H281 are catalytically active amino acids. H281 functions as a base to accept H(donor) in the first nucleophilic attack and as an acid in the second, to donate the proton back to O(acceptor). S26 assists H281 in deprotonation of the donor aldehyde and protonation of the acceptor aldehyde. In both the first and second nucleophilic attacks, H70 interacts with O(aldehyde) and aligns it toward the nucleophilic center. H70 has been found to have an electrostatic effect on the approaching aldehyde whose absence would block the initiation of the reaction. The reactivity difference between benzaldehyde (BA) and acetaldehyde (AA) is mainly explained by the steric interactions of the acceptor aldehyde with the surrounding amino acids in the active center of the enzyme.
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Gocke D, Kolter G, Gauchenova E, Knoll M, Berthold Sjöberg C, Schneider G, Pleiss J, Müller M, Pohl M. Rationales Enzymdesign für die (S)-selektive Benzoinkondensation. CHEM-ING-TECH 2009. [DOI: 10.1002/cite.200950205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Müller M, Gocke D, Pohl M. Thiamin diphosphate in biological chemistry: exploitation of diverse thiamin diphosphate-dependent enzymes for asymmetric chemoenzymatic synthesis. FEBS J 2009; 276:2894-904. [DOI: 10.1111/j.1742-4658.2009.07017.x] [Citation(s) in RCA: 122] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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48
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Brandt GS, Kneen MM, Chakraborty S, Baykal AT, Nemeria N, Yep A, Ruby DI, Petsko GA, Kenyon GL, McLeish MJ, Jordan F, Ringe D. Snapshot of a reaction intermediate: analysis of benzoylformate decarboxylase in complex with a benzoylphosphonate inhibitor. Biochemistry 2009; 48:3247-57. [PMID: 19320438 DOI: 10.1021/bi801950k] [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
Benzoylformate decarboxylase (BFDC) is a thiamin diphosphate- (ThDP-) dependent enzyme acting on aromatic substrates. In addition to its metabolic role in the mandelate pathway, BFDC shows broad substrate specificity coupled with tight stereo control in the carbon-carbon bond-forming reverse reaction, making it a useful biocatalyst for the production of chiral alpha-hydroxy ketones. The reaction of methyl benzoylphosphonate (MBP), an analogue of the natural substrate benzoylformate, with BFDC results in the formation of a stable analogue (C2alpha-phosphonomandelyl-ThDP) of the covalent ThDP-substrate adduct C2alpha-mandelyl-ThDP. Formation of the stable adduct is confirmed both by formation of a circular dichroism band characteristic of the 1',4'-iminopyrimidine tautomeric form of ThDP (commonly observed when ThDP forms tetrahedral complexes with its substrates) and by high-resolution mass spectrometry of the reaction mixture. In addition, the structure of BFDC with the MBP inhibitor was solved by X-ray crystallography to a spatial resolution of 1.37 A (PDB ID 3FSJ). The electron density clearly shows formation of a tetrahedral adduct between the C2 atom of ThDP and the carbonyl carbon atom of the MBP. This adduct resembles the intermediate from the penultimate step of the carboligation reaction between benzaldehyde and acetaldehyde. The combination of real-time kinetic information via stopped-flow circular dichroism with steady-state data from equilibrium circular dichroism measurements and X-ray crystallography reveals details of the first step of the reaction catalyzed by BFDC. The MBP-ThDP adduct on BFDC is compared to the recently solved structure of the same adduct on benzaldehyde lyase, another ThDP-dependent enzyme capable of catalyzing aldehyde condensation with high stereospecificity.
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Affiliation(s)
- Gabriel S Brandt
- Department of Chemistry, Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, Massachusetts 02454, USA
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Mikolajek RJ, Spiess AC, Pohl M, Büchs J. Propioin synthesis using thiamine diphosphate-dependent enzymes. Biotechnol Prog 2009; 25:132-8. [PMID: 19224568 DOI: 10.1002/btpr.55] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Benzaldehyde lyase (BAL, EC 4.1.2.38) from Pseudomonas fluorescens and benzoylformate decarboxylase (BFD, EC 4.1.1.7) from Pseudomonas putida are thiamine diphosphate-dependent enzymes. These enzymes share a common tetrameric structure and catalyze various C--C-bond forming and breaking reactions. Here we describe a detailed study of the asymmetric synthesis of propioin from propanal catalyzed by BAL or BFD in aqueous solution in a batch reactor. Both enzymes are deactivated in the presence of high concentration of propanal. Compared to BAL, BFD is more stable under reaction conditions as well as during storage. The kinetic studies showed a typical Michaelis-Menten kinetic for BAL with a maximal specific reaction rate of 26.2 U/mg and an unusually high K(M) of 415 mM, whereas the v/[S]-plot for BFD is almost linear in the concentration range (100-1500 mM) investigated. Both enzymes produce propioin with opposite enantiomeric excess: BAL produced the (S)-propioin (ee of 35%), whereas BFD yielded the (R)-enantiomer (ee of 67%).
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Affiliation(s)
- Renaud J Mikolajek
- Biochemical Engineering, RWTH Aachen University, Worringer Weg 1, Aachen 52056, Germany.
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50
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Zavrel M, Schmidt T, Michalik C, Ansorge-Schumacher M, Marquardt W, Büchs J, Spiess AC. Mechanistic kinetic model for symmetric carboligations using benzaldehyde lyase. Biotechnol Bioeng 2008; 101:27-38. [DOI: 10.1002/bit.21867] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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