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Liu X, Guan J, Yang Y, Wu L, Ni H, Li Q, Chen F. The aroma transformation of Japanese sea bass (Lateolabrax japonicas) through endogenous enzyme incubation during the lag phase of attached microorganisms. Food Chem 2024; 463:141215. [PMID: 39278078 DOI: 10.1016/j.foodchem.2024.141215] [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: 05/30/2024] [Revised: 08/28/2024] [Accepted: 09/08/2024] [Indexed: 09/17/2024]
Abstract
Endogenous enzymes play a crucial role in determining fish product aroma. However, the attached microorganisms can promote enzyme production, making it challenging to identify specific aromatic compounds resulting from endogenous enzymes. Thus, we investigated the aroma transformation of Japanese sea bass through enzymatic incubation by controlling attached microorganisms during the lag phase. Our results demonstrate that enzymatic incubation significantly enhances grassy and sweet notes while reducing fishy odors. These changes in aroma are associated with increased levels of 10 volatile compounds and decreased levels of 3 volatile compounds. Among them, previous studies have reported enzyme reaction pathways for octanal, 1-nonanal, vanillin, indole, linalool, geraniol, citral, and 6-methyl-5-hepten-2-one; however, the enzymatic reaction pathways for germacrene D, beta-caryophyllene, pristane, 1-tetradecene and trans-beta-ocimene remain unclear. These findings provide novel insights for further study to elucidate the impact of endogenous enzymes on fish product aromas.
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Affiliation(s)
- Xinru Liu
- College of Food and Biological Engineering, Jimei University, Xiamen 361021, China
| | - Junlan Guan
- College of Food and Biological Engineering, Jimei University, Xiamen 361021, China
| | - Yuanfan Yang
- College of Food and Biological Engineering, Jimei University, Xiamen 361021, China; Fujian Provincial Key Laboratory of Food Microbiology and Enzyme Engineering, Xiamen 361021, China; Research Center of Food Biotechnology of Xiamen City, Xiamen 361021, China
| | - Ling Wu
- College of Food and Biological Engineering, Jimei University, Xiamen 361021, China; Fujian Provincial Key Laboratory of Food Microbiology and Enzyme Engineering, Xiamen 361021, China; Research Center of Food Biotechnology of Xiamen City, Xiamen 361021, China
| | - Hui Ni
- College of Food and Biological Engineering, Jimei University, Xiamen 361021, China; Fujian Provincial Key Laboratory of Food Microbiology and Enzyme Engineering, Xiamen 361021, China; Research Center of Food Biotechnology of Xiamen City, Xiamen 361021, China; Xiamen Ocean Vocational College, Xiamen 361021, China.
| | - Qingbiao Li
- College of Food and Biological Engineering, Jimei University, Xiamen 361021, China; Fujian Provincial Key Laboratory of Food Microbiology and Enzyme Engineering, Xiamen 361021, China; Research Center of Food Biotechnology of Xiamen City, Xiamen 361021, China
| | - Feng Chen
- Department of Food Science, Nutrition and Packaging, Clemsin University, Clemsin City of South Carolina 29631, USA Department of Food, Nutrition and Packaging Sciences, Clemson University, Clemson, SC 29634, USA
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2
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Dalwani S, Wierenga RK. Enzymes of the crotonase superfamily: Diverse assembly and diverse function. Curr Opin Struct Biol 2023; 82:102671. [PMID: 37542911 DOI: 10.1016/j.sbi.2023.102671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 06/08/2023] [Accepted: 07/10/2023] [Indexed: 08/07/2023]
Abstract
The crotonase fold is generated by a framework of four repeats of a ββα-unit, extended by two helical regions. The active site of crotonase superfamily (CS) enzymes is located at the N-terminal end of the helix of the third repeat, typically being covered by a C-terminal helix. A major subset of CS-enzymes catalyzes acyl-CoA-dependent reactions, allowing for a diverse range of acyl-tail modifications. Most of these enzymes occur as trimers or hexamers (dimers of trimers), but monomeric forms are also observed. A common feature of the active sites of CS-enzymes is an oxyanion hole, formed by two peptide-NH hydrogen bond donors, which stabilises the negatively charged thioester oxygen atom of the reaction intermediate. Structural properties and possible use of these enzymes for biotechnological applications are discussed.
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Affiliation(s)
- Subhadra Dalwani
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, P.O. Box 5400, FI-90014, Finland
| | - Rik K Wierenga
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, P.O. Box 5400, FI-90014, Finland.
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3
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Production of various phenolic aldehyde compounds using the 4CL-FCHL biosynthesis platform. Int J Biol Macromol 2023; 226:608-617. [PMID: 36521700 DOI: 10.1016/j.ijbiomac.2022.12.075] [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: 09/21/2022] [Revised: 11/24/2022] [Accepted: 12/08/2022] [Indexed: 12/14/2022]
Abstract
Vanillin (3-methoxy-4-hydroxybenzaldehyde) is one of the most important flavoring substances used in the cosmetic and food industries. Feruloyl-CoA hydratase/lyase (FCHL) is an enzyme that catalyzes the production of vanillin from feruloyl-CoA. In this study, we report kinetic parameters and biochemical properties of FCHL from Sphingomonas paucimobilis SYK-6 (SpFCHL). Also, the crystal structures of an apo-form of SpFCHL and two complexed forms with acetyl-CoA and vanillin/CoA was present. Comparing the apo structure to its complexed forms of SpFCHL, a gate loop with an "open and closed" role was observed at the entrance of the substrate-binding site. With vanillin and CoA complexed to SpFCHL, we captured a conformational change in the feruloyl moiety-binding pocket that repositions the catalytic SpFCHLE146 and other key residues. This binding pocket does not tightly fit the vanillin structure, suggesting substrate promiscuity of this enzyme. This observation is in good agreement with assay results for phenylpropanoid-CoAs and indicates important physicochemical properties of the substrate for the hydratase/lyase reaction mechanism. In addition, we showed that various phenolic aldehydes could be produced using the 4CL-FCHL biosynthesis platform.
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4
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Ofori Atta L, Zhou Z, Roelfes G. In Vivo Biocatalytic Cascades Featuring an Artificial-Enzyme-Catalysed New-to-Nature Reaction. Angew Chem Int Ed Engl 2023; 62:e202214191. [PMID: 36342952 PMCID: PMC10100225 DOI: 10.1002/anie.202214191] [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: 09/26/2022] [Indexed: 11/09/2022]
Abstract
Artificial enzymes utilizing the genetically encoded non-proteinogenic amino acid p-aminophenylalanine (pAF) as a catalytic residue are able to react with carbonyl compounds through an iminium ion mechanism to promote reactions that have no equivalent in nature. Herein, we report an in vivo biocatalytic cascade that is augmented with such an artificial enzyme-catalysed new-to-nature reaction. The artificial enzyme in this study is a pAF-containing evolved variant of the lactococcal multidrug-resistance regulator, designated LmrR_V15pAF_RMH, which efficiently converts benzaldehyde derivatives produced in vivo into the corresponding hydrazone products inside E. coli cells. These in vivo biocatalytic cascades comprising an artificial-enzyme-catalysed reaction are an important step towards achieving a hybrid metabolism.
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Affiliation(s)
- Linda Ofori Atta
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747, AG Groningen, The Netherlands
| | - Zhi Zhou
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747, AG Groningen, The Netherlands.,Current address: School of Life Science and Health Engineering, Jiangnan University, Wuxi, 214122, China
| | - Gerard Roelfes
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747, AG Groningen, The Netherlands
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5
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Transcriptome profiling of Paraburkholderia aromaticivorans AR20-38 during ferulic acid bioconversion. AMB Express 2022; 12:148. [DOI: 10.1186/s13568-022-01487-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 11/01/2022] [Indexed: 11/28/2022] Open
Abstract
AbstractThe importance and need of renewable-based, sustainable feedstocks increased in recent years. Lignin-derived monomers have high potential, energetic and economic value in the microbial bioconversion to valuable biomolecules. The bacterium Paraburkholderia aromaticivorans AR20-38 produces a remarkable yield of vanillic acid from ferulic acid at moderate and low temperatures and is therefore a good candidate for biotechnological applications. To understand this bioconversion process on a molecular level, a transcriptomic study during the bioconversion process was conducted to elucidate gene expression patterns. Differentially expressed genes, cellular transporters as well as transcriptional factors involved in the bioconversion process could be described. Additional enzymes known for xenobiotic degradation were differentially expressed and a potential membrane vesicle mechanism was detected. The bioconversion mechanism on a transcriptional level of P. aromaticivorans could be elucidated and results can be used for strain optimization. Additionally, the transcriptome study showed the high potential of the strain for other degradation applications.
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Applying biochemical and structural characterization of hydroxycinnamate catabolic enzymes from soil metagenome for lignin valorization strategies. Appl Microbiol Biotechnol 2022; 106:2503-2516. [PMID: 35352150 DOI: 10.1007/s00253-022-11885-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 02/15/2022] [Accepted: 03/06/2022] [Indexed: 11/02/2022]
Abstract
The biocatalytic production of fuels and chemicals from plant biomass represents an attractive alternative to fossil fuel-based refineries. In this context, the mining and characterization of novel biocatalysts can promote disruptive innovation opportunities in the field of lignocellulose conversion and valorization. In the present work, we conducted the biochemical and structural characterization of two novel hydroxycinnamic acid catabolic enzymes, isolated from a lignin-degrading microbial consortium, a feruloyl-CoA synthetase, and a feruloyl-CoA hydratase-lyase, named LM-FCS2 and LM-FCHL2, respectively. Besides establishing the homology model structures for novel FCS and FCHL members with unique characteristics, the enzymes presented interesting biochemical features: LM-FCS2 showed stability in alkaline pHs and was able to convert a wide array of p-hydroxycinnamic acids to their respective CoA-thioesters, including sinapic acid; LM-FCHL2 efficiently converted feruloyl-CoA and p-coumaroyl-CoA into vanillin and 4-hydroxybenzaldehyde, respectively, and could produce vanillin directly from ferulic acid. The coupled reaction of LM-FCS2 and LM-FCHL2 produced vanillin, not only from commercial ferulic acid but also from a crude lignocellulosic hydrolysate. Collectively, this work illuminates the structure and function of two critical enzymes involved in converting ferulic acid into high-value molecules, thus providing valuable concepts applied to the development of plant biomass biorefineries. KEY POINTS: • Comprehensive characterization of feruloyl-CoA synthetase from metagenomic origin. • Novel low-resolution structures of hydroxycinnamate catabolic enzymes. • Production of vanillin via enzymatic reaction using lignocellulosic hydrolysates.
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7
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Jin Z, Ro DK, Kim SU, Kwon M. Piperonal synthase from black pepper ( Piper nigrum) synthesizes a phenolic aroma compound, piperonal, as a CoA-independent catalysis. APPLIED BIOLOGICAL CHEMISTRY 2022; 65:20. [PMID: 35402752 PMCID: PMC8948145 DOI: 10.1186/s13765-022-00691-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 03/12/2022] [Indexed: 06/14/2023]
Abstract
UNLABELLED Piperonal is a simple aromatic aldehyde compound with a characteristic cherry-like aroma and has been widely used in the flavor and fragrance industries. Despite piperonal being an important aroma in black pepper (Piper nigrum), its biosynthesis remains unknown. In this study, the bioinformatic analysis of the P. nigrum transcriptome identified a novel hydratase-lyase, displaying 72% amino acid identity with vanillin synthase, a member of the cysteine proteinase family. In in vivo substrate-feeding and in vitro enzyme assays, the hydratase-lyase catalyzed a side-chain cleavage of 3,4-methylenedioxycinnamic acid (3,4-MDCA) to produce 3,4-methylenedioxybenzaldehyde (piperonal) and thus was named piperonal synthase (PnPNS). The optimal pH for PnPNS activity was 7.0, and showed a K m of 317.2 μM and a k cat of 2.7 s-1. The enzyme was most highly expressed in the leaves, followed by the fruit. This characterization allows for the implementation of PnPNS in various microbial platforms for the biological production of piperonal. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1186/s13765-022-00691-0.
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Affiliation(s)
- Zhehao Jin
- Research Institute of Agriculture and Life Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826 Republic of Korea
- Present Address: Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055 Guangzhou China
| | - Dae-Kyun Ro
- Department of Biological Sciences, University of Calgary, Calgary, AB T2N 1N4 Canada
| | - Soo-Un Kim
- Research Institute of Agriculture and Life Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826 Republic of Korea
| | - Moonhyuk Kwon
- Division of Applied Life Science (BK21 Four), ABC-RLRC, PMBBRC, Gyeongsang National University, Jinju, 52828 Republic of Korea
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8
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Liberato MV, Araújo JN, Sodré V, Gonçalves TA, Vilela N, Moraes EC, Garcia W, Squina FM. The structure of a prokaryotic feruloyl-CoA hydratase-lyase from a lignin-degrading consortium with high oligomerization stability under extreme pHs. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2019; 1868:140344. [PMID: 31841665 DOI: 10.1016/j.bbapap.2019.140344] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 12/04/2019] [Accepted: 12/09/2019] [Indexed: 10/25/2022]
Abstract
In the context of increasing demand for renewable alternatives of fuels and chemicals, the valorization of lignin emerges as a value-adding strategy in biorefineries and an alternative to petroleum-derived molecules. One of the compounds derived from lignin is ferulic acid (FA), which can be converted into valuable molecules such as vanillin. In microorganisms, FA biotransformation into vanillin can occur via a two-step reaction catalyzed by the sequential activity of a feruloyl-CoA synthetase (FCS) and an feruloyl-CoA hydratase-lyase (FCHL), which could be exploited industrially. In this study, a prokaryotic FCHL derived from a lignin-degrading microbial consortium (named LM-FCHL) was cloned, successfully expressed in soluble form and purified. The crystal structure was solved and refined at 2.1 Å resolution. The LM-FCHL is a hexamer composed of a dimer of trimers, which showed to be quite stable under extreme pH conditions. Finally, small angle X-ray scattering corroborates the hexameric state in solution and indicates flexibility in the protein structure. The present study contributes to the field of lignin valorization to valuable molecules by establishing the biophysical and structural characterization for a novel FCHL member of unique characteristics.
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Affiliation(s)
- Marcelo Vizoná Liberato
- Programa de Processos Tecnológicos e Ambientais, Universidade de Sorocaba, Sorocaba, SP, Brazil
| | - Juscemácia N Araújo
- Centro de Ciências Naturais e Humanas (CCNH), Universidade Federal do ABC (UFABC), Santo André, SP, Brazil
| | - Victoria Sodré
- Programa de Processos Tecnológicos e Ambientais, Universidade de Sorocaba, Sorocaba, SP, Brazil; Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Campinas, SP, Brazil
| | - Thiago Augusto Gonçalves
- Programa de Processos Tecnológicos e Ambientais, Universidade de Sorocaba, Sorocaba, SP, Brazil; Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Campinas, SP, Brazil
| | - Nathalia Vilela
- Programa de Processos Tecnológicos e Ambientais, Universidade de Sorocaba, Sorocaba, SP, Brazil; Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Campinas, SP, Brazil
| | - Eduardo Cruz Moraes
- Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Campinas, SP, Brazil
| | - Wanius Garcia
- Centro de Ciências Naturais e Humanas (CCNH), Universidade Federal do ABC (UFABC), Santo André, SP, Brazil
| | - Fabio Marcio Squina
- Programa de Processos Tecnológicos e Ambientais, Universidade de Sorocaba, Sorocaba, SP, Brazil.
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9
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Production of methylparaben in Escherichia coli. ACTA ACUST UNITED AC 2019; 46:91-99. [DOI: 10.1007/s10295-018-2102-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Accepted: 10/27/2018] [Indexed: 10/27/2022]
Abstract
Abstract
Since the 1930s, parabens have been employed widely as preservatives in food, pharmaceutical, and personal care products. These alkyl esters of benzoic acid occur naturally in a broad range of plant species, where they are thought to enhance overall fitness through disease resistance and allelopathy. Current manufacture of parabens relies on chemical synthesis and the processing of 4-hydroxybenzoate as a precursor. A variety of bio-based production platforms have targeted 4-hydroxybenzoate for a greener alternative to chemical manufacturing, but parabens have yet to be made in microbes. Here, we deploy the plant enzyme benzoic acid carboxyl methyltransferase together with four additional recombinant enzymes to produce methylparaben in Escherichia coli. The feasibility of a tyrosine-dependent route to methylparaben is explored, establishing a framework for linking paraben production to emerging high-tyrosine E. coli strains. However, our use of a unique plant enzyme for bio-based methylparaben biosynthesis is potentially applicable to any microbial system engineered for the manufacture of 4-hydroxybenzoate.
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Meyer F, Netzer J, Meinert C, Voigt B, Riedel K, Steinbüchel A. A proteomic analysis of ferulic acid metabolism in Amycolatopsis sp. ATCC 39116. Appl Microbiol Biotechnol 2018; 102:6119-6142. [DOI: 10.1007/s00253-018-9061-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Revised: 04/26/2018] [Accepted: 04/29/2018] [Indexed: 10/16/2022]
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11
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Drienovská I, Alonso-Cotchico L, Vidossich P, Lledós A, Maréchal JD, Roelfes G. Design of an enantioselective artificial metallo-hydratase enzyme containing an unnatural metal-binding amino acid. Chem Sci 2017; 8:7228-7235. [PMID: 29081955 PMCID: PMC5633786 DOI: 10.1039/c7sc03477f] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 09/01/2017] [Indexed: 01/04/2023] Open
Abstract
The design of artificial metalloenzymes is a challenging, yet ultimately highly rewarding objective because of the potential for accessing new-to-nature reactions. One of the main challenges is identifying catalytically active substrate-metal cofactor-host geometries. The advent of expanded genetic code methods for the in vivo incorporation of non-canonical metal-binding amino acids into proteins allow to address an important aspect of this challenge: the creation of a stable, well-defined metal-binding site. Here, we report a designed artificial metallohydratase, based on the transcriptional repressor lactococcal multidrug resistance regulator (LmrR), in which the non-canonical amino acid (2,2'-bipyridin-5yl)alanine is used to bind the catalytic Cu(ii) ion. Starting from a set of empirical pre-conditions, a combination of cluster model calculations (QM), protein-ligand docking and molecular dynamics simulations was used to propose metallohydratase variants, that were experimentally verified. The agreement observed between the computationally predicted and experimentally observed catalysis results demonstrates the power of the artificial metalloenzyme design approach presented here.
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Affiliation(s)
- Ivana Drienovská
- Stratingh Institute for Chemistry , University of Groningen , Nijenborgh 4 , 9747 AG Groningen , Netherlands .
| | - Lur Alonso-Cotchico
- Departament de Química , Universitat Autònoma de Barcelona , Edifici C.n. , 08193 Cerdanyola del Vallés , Barcelona , Spain .
| | - Pietro Vidossich
- Departament de Química , Universitat Autònoma de Barcelona , Edifici C.n. , 08193 Cerdanyola del Vallés , Barcelona , Spain .
| | - Agustí Lledós
- Departament de Química , Universitat Autònoma de Barcelona , Edifici C.n. , 08193 Cerdanyola del Vallés , Barcelona , Spain .
| | - Jean-Didier Maréchal
- Departament de Química , Universitat Autònoma de Barcelona , Edifici C.n. , 08193 Cerdanyola del Vallés , Barcelona , Spain .
| | - Gerard Roelfes
- Stratingh Institute for Chemistry , University of Groningen , Nijenborgh 4 , 9747 AG Groningen , Netherlands .
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12
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Kumar P, Ghosh Sachan S, Poddar R. Mutational analysis of microbial hydroxycinnamoyl-CoA hydratase-lyase (HCHL) towards enhancement of binding affinity: A computational approach. J Mol Graph Model 2017; 77:94-105. [PMID: 28850897 DOI: 10.1016/j.jmgm.2017.08.014] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Revised: 08/12/2017] [Accepted: 08/14/2017] [Indexed: 02/07/2023]
Abstract
Improving the industrial enzyme for better yield of the product is important and a challenging task. One of such important industrial enzymes is microbial Hydroxycinnamoyl-CoA hydratase-lyase (HCHL). It converts feruloyl-CoA to vanillin. We place our efforts towards the improvement of its catalytic activity with comprehensive computational investigation. Catalytic core of the HCHL was explored with molecular modeling and docking approaches. Site-directed mutations were introduced in the catalytic site of HCHL in a sequential manner to generate different mutants of HCHL. Basis of mutation is to increase the interaction between HCHL and substrate feruloyl-CoA through interatomic forces and hydrogen bond formation. A rigorous molecular dynamics (MD) simulation was performed to check the stability of mutant's structure. Root mean square deviation (RMSD), root mean square fluctuation (RMSF), dynamic cross correlation (DCCM) and principal component analysis (PCA) were also performed to analyze flexibility and stability of structures. Docking studies were carried out between different mutants of HCHL and feruloyl-CoA. Investigation of the different binding sites and the interactions with mutant HCHLs and substrate allowed us to highlight the improved performance of mutants than wild type HCHL. This was further validated with MD simulation of complex consisting of different mutants and substrate. It further confirms all the structures are stable. However, mutant-2 showed better affinity towards substrate by forming hydrogen bond between active site and feruloyl-CoA. We propose that increase in hydrogen bond formation might facilitate in dissociation of vanillin from feruloyl-CoA. The current work may be useful for the future development of 'tailor-made' enzymes for better yield of vanillin.
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Affiliation(s)
- Pravin Kumar
- Department of Bio-Engineering, Birla Institute of Technology-Mesra, Ranchi, JH, 835 215, India
| | - Shashwati Ghosh Sachan
- Department of Bio-Engineering, Birla Institute of Technology-Mesra, Ranchi, JH, 835 215, India
| | - Raju Poddar
- Department of Bio-Engineering, Birla Institute of Technology-Mesra, Ranchi, JH, 835 215, India.
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13
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Ewing TA, Nguyen QT, Allan RC, Gygli G, Romero E, Binda C, Fraaije MW, Mattevi A, van Berkel WJH. Two tyrosine residues, Tyr-108 and Tyr-503, are responsible for the deprotonation of phenolic substrates in vanillyl-alcohol oxidase. J Biol Chem 2017; 292:14668-14679. [PMID: 28717004 DOI: 10.1074/jbc.m117.778449] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Revised: 07/05/2017] [Indexed: 11/06/2022] Open
Abstract
A number of oxidoreductases from the VAO/para-cresol methylhydroxylase flavoprotein family catalyze the oxidation of para-substituted phenols. One of the best-studied is vanillyl-alcohol oxidase (VAO) from the fungus Penicillium simplicissimum For oxidation of phenols by VAO to occur, they must first be bound in the active site of the enzyme in their phenolate anion form. The crystal structure of VAO reveals that two tyrosine residues, Tyr-108 and Tyr-503, are positioned to facilitate this deprotonation. To investigate their role in catalysis, we created three VAO variants, Y108F, Y503F, and Y108F/Y503F, and studied their biochemical properties. Steady-state kinetics indicated that the presence of at least one of the tyrosine residues is essential for efficient catalysis by VAO. Stopped-flow kinetics revealed that the reduction of VAO by chavicol or vanillyl alcohol occurs at two different rates: kobs1, which corresponds to its reaction with the deprotonated form of the substrate, and kobs2, which corresponds to its reaction with the protonated form of the substrate. In Y108F, Y503F, and Y108F/Y503F, the relative contribution of kobs2 to the reduction is larger than in wild-type VAO, suggesting deprotonation is impaired in these variants. Binding studies disclosed that the competitive inhibitor isoeugenol is predominantly in its deprotonated form when bound to wild-type VAO, but predominantly in its protonated form when bound to the variants. These results indicate that Tyr-108 and Tyr-503 are responsible for the activation of substrates in VAO, providing new insights into the catalytic mechanism of VAO and related enzymes that oxidize para-substituted phenols.
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Affiliation(s)
- Tom A Ewing
- From the Laboratory of Biochemistry, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Quoc-Thai Nguyen
- the Department of Biology and Biotechnology, University of Pavia, Via Ferrata 9, 27100 Pavia, Italy.,the Molecular Enzymology Group, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands, and.,the Faculty of Pharmacy, University of Medicine and Pharmacy, 41 Dinh Tien Hoang Street, Ben Nghe Ward, District 1, Ho Chi Minh City, Vietnam
| | - Robert C Allan
- From the Laboratory of Biochemistry, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Gudrun Gygli
- From the Laboratory of Biochemistry, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Elvira Romero
- the Molecular Enzymology Group, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands, and
| | - Claudia Binda
- the Department of Biology and Biotechnology, University of Pavia, Via Ferrata 9, 27100 Pavia, Italy
| | - Marco W Fraaije
- the Molecular Enzymology Group, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands, and
| | - Andrea Mattevi
- the Department of Biology and Biotechnology, University of Pavia, Via Ferrata 9, 27100 Pavia, Italy
| | - Willem J H van Berkel
- From the Laboratory of Biochemistry, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands,
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14
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Payer SE, Sheng X, Pollak H, Wuensch C, Steinkellner G, Himo F, Glueck SM, Faber K. Exploring the Catalytic Promiscuity of Phenolic Acid Decarboxylases: Asymmetric, 1,6-Conjugate Addition of Nucleophiles Across 4-Hydroxystyrene. Adv Synth Catal 2017; 359:2066-2075. [PMID: 28713228 PMCID: PMC5488193 DOI: 10.1002/adsc.201700247] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Revised: 04/02/2017] [Indexed: 01/29/2023]
Abstract
The catalytic promiscuity of a ferulic acid decarboxylase from Enterobacter sp. (FDC_Es) and phenolic acid decarboxylases (PADs) for the asymmetric conjugate addition of water across the C=C bond of hydroxystyrenes was extended to the N‐, C‐ and S‐nucleophiles methoxyamine, cyanide and propanethiol to furnish the corresponding addition products in up to 91% ee. The products obtained from the biotransformation employing the most suitable enzyme/nucleophile pairs were isolated and characterized after optimizing the reaction conditions. Finally, a mechanistic rationale supported by quantum mechanical calculations for the highly (S)‐selective addition of cyanide is proposed. ![]()
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Affiliation(s)
- Stefan E Payer
- Department of Chemistry University of Graz Heinrichstrasse 28, A-8010 Graz Austria
| | - Xiang Sheng
- Arrhenius Laboratory Department of Organic Chemistry Stockholm University SE-106 91 Stockholm Sweden
| | - Hannah Pollak
- Department of Chemistry University of Graz Heinrichstrasse 28, A-8010 Graz Austria
| | - Christiane Wuensch
- Austrian Centre of Industrial Biotechnology (ACIB) c/o Department of Chemistry University of Graz Heinrichstrasse 28, A-8010 Graz Austria.,Department of Chemistry University of Graz Heinrichstrasse 28, A-8010 Graz Austria
| | - Georg Steinkellner
- Austrian Centre of Industrial Biotechnology (ACIB) c/o Department of Chemistry University of Graz Heinrichstrasse 28, A-8010 Graz Austria.,Center for Molecular Biosciences University of Graz Humboldtstrasse 508010 Graz Austria
| | - Fahmi Himo
- Arrhenius Laboratory Department of Organic Chemistry Stockholm University SE-106 91 Stockholm Sweden
| | - Silvia M Glueck
- Austrian Centre of Industrial Biotechnology (ACIB) c/o Department of Chemistry University of Graz Heinrichstrasse 28, A-8010 Graz Austria.,Department of Chemistry University of Graz Heinrichstrasse 28, A-8010 Graz Austria
| | - Kurt Faber
- Department of Chemistry University of Graz Heinrichstrasse 28, A-8010 Graz Austria
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15
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Sheng X, Himo F. Theoretical Study of Enzyme Promiscuity: Mechanisms of Hydration and Carboxylation Activities of Phenolic Acid Decarboxylase. ACS Catal 2017. [DOI: 10.1021/acscatal.6b03249] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Xiang Sheng
- Department of Organic Chemistry,
Arrhenius Laboratory, Stockholm University, SE-10691 Stockholm, Sweden
| | - Fahmi Himo
- Department of Organic Chemistry,
Arrhenius Laboratory, Stockholm University, SE-10691 Stockholm, Sweden
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16
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Isotope Ratio Monitoring 13 C Nuclear Magnetic Resonance Spectrometry for the Analysis of Position-Specific Isotope Ratios. Methods Enzymol 2017; 596:369-401. [DOI: 10.1016/bs.mie.2017.07.023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/27/2023]
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17
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Jung DH, Kim EJ, Jung E, Kazlauskas RJ, Choi KY, Kim BG. Production ofp-hydroxybenzoic acid fromp-coumaric acid byBurkholderia glumaeBGR1. Biotechnol Bioeng 2015; 113:1493-503. [DOI: 10.1002/bit.25908] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Revised: 12/10/2015] [Accepted: 12/14/2015] [Indexed: 11/06/2022]
Affiliation(s)
- Da-Hye Jung
- School of Chemical and Biological Engineering; Seoul National University; Seoul 151-7442 South Korea
| | - Eun-Jung Kim
- School of Chemical and Biological Engineering; Seoul National University; Seoul 151-7442 South Korea
| | - Eunok Jung
- School of Chemical and Biological Engineering; Seoul National University; Seoul 151-7442 South Korea
| | - Romas J Kazlauskas
- Department of Biochemistry; Molecular Biology & Biophysics and The Biotechnology Institute; University of Minnesota; Saint Paul Minnesota 55108
| | - Kwon-Young Choi
- Department of Environmental Engineering; College of Engineering; Ajou University; Suwon 443-749 Kyeonggi-do South Korea
| | - Byung-Gee Kim
- School of Chemical and Biological Engineering; Seoul National University; Seoul 151-7442 South Korea
- Institute of Bioengineering; Seoul National University; Seoul 151-742 South Korea
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18
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Sheng X, Lind MES, Himo F. Theoretical study of the reaction mechanism of phenolic acid decarboxylase. FEBS J 2015; 282:4703-13. [PMID: 26408050 DOI: 10.1111/febs.13525] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Revised: 09/01/2015] [Accepted: 09/22/2015] [Indexed: 12/13/2022]
Abstract
The cofactor-free phenolic acid decarboxylases (PADs) catalyze the non-oxidative decarboxylation of phenolic acids to their corresponding p-vinyl derivatives. Phenolic acids are toxic to some organisms, and a number of them have evolved the ability to transform these compounds, including PAD-catalyzed reactions. Since the vinyl derivative products can be used as polymer precursors and are also of interest in the food-processing industry, PADs might have potential applications as biocatalysts. We have investigated the detailed reaction mechanism of PAD from Bacillus subtilis using quantum chemical methodology. A number of different mechanistic scenarios have been considered and evaluated on the basis of their energy profiles. The calculations support a mechanism in which a quinone methide intermediate is formed by protonation of the substrate double bond, followed by C-C bond cleavage. A different substrate orientation in the active site is suggested compared to the literature proposal. This suggestion is analogous to other enzymes with p-hydroxylated aromatic compounds as substrates, such as hydroxycinnamoyl-CoA hydratase-lyase and vanillyl alcohol oxidase. Furthermore, on the basis of the calculations, a different active site residue compared to previous proposals is suggested to act as the general acid in the reaction. The mechanism put forward here is consistent with the available mutagenesis experiments and the calculated energy barrier is in agreement with measured rate constants. The detailed mechanistic understanding developed here might be extended to other members of the family of PAD-type enzymes. It could also be useful to rationalize the recently developed alternative promiscuous reactivities of these enzymes.
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Affiliation(s)
- Xiang Sheng
- Arrhenius Laboratory, Department of Organic Chemistry, Stockholm University, Sweden
| | - Maria E S Lind
- Arrhenius Laboratory, Department of Organic Chemistry, Stockholm University, Sweden
| | - Fahmi Himo
- Arrhenius Laboratory, Department of Organic Chemistry, Stockholm University, Sweden
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19
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Wuensch C, Pavkov-Keller T, Steinkellner G, Gross J, Fuchs M, Hromic A, Lyskowski A, Fauland K, Gruber K, Glueck SM, Faber K. Regioselective Enzymatic β-Carboxylation of para-Hydroxy- styrene Derivatives Catalyzed by Phenolic Acid Decarboxylases. Adv Synth Catal 2015; 357:1909-1918. [PMID: 26190963 PMCID: PMC4498466 DOI: 10.1002/adsc.201401028] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Revised: 01/07/2015] [Indexed: 11/17/2022]
Abstract
We report on a 'green' method for the utilization of carbon dioxide as C1 unit for the regioselective synthesis of (E)-cinnamic acids via regioselective enzymatic carboxylation of para-hydroxystyrenes. Phenolic acid decarboxylases from bacterial sources catalyzed the β-carboxylation of para-hydroxystyrene derivatives with excellent regio- and (E/Z)-stereoselectivity by exclusively acting at the β-carbon atom of the C=C side chain to furnish the corresponding (E)-cinnamic acid derivatives in up to 40% conversion at the expense of bicarbonate as carbon dioxide source. Studies on the substrate scope of this strategy are presented and a catalytic mechanism is proposed based on molecular modelling studies supported by mutagenesis of amino acid residues in the active site.
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Affiliation(s)
- Christiane Wuensch
- Austrian Centre of Industrial Biotechnology, c/o Department of Chemistry, Organic & Bioorganic Chemistry, Heinrichstrasse 28, University of Graz 8010 Graz, Austria ; Department of Chemistry, Organic & Bioorganic Chemistry, Heinrichstrasse 28, University of Graz 8010 Graz, Austria, ; phone: (+43)-316-380-5332 ; e-mail: or
| | - Tea Pavkov-Keller
- Austrian Centre of Industrial Biotechnology, c/o Department of Chemistry, Organic & Bioorganic Chemistry, Heinrichstrasse 28, University of Graz 8010 Graz, Austria ; Institute of Molecular Biosciences, Humboldtstrasse 50, University of Graz 8010 Graz, Austria
| | - Georg Steinkellner
- Austrian Centre of Industrial Biotechnology, c/o Department of Chemistry, Organic & Bioorganic Chemistry, Heinrichstrasse 28, University of Graz 8010 Graz, Austria ; Institute of Molecular Biosciences, Humboldtstrasse 50, University of Graz 8010 Graz, Austria
| | - Johannes Gross
- Austrian Centre of Industrial Biotechnology, c/o Department of Chemistry, Organic & Bioorganic Chemistry, Heinrichstrasse 28, University of Graz 8010 Graz, Austria ; Department of Chemistry, Organic & Bioorganic Chemistry, Heinrichstrasse 28, University of Graz 8010 Graz, Austria, ; phone: (+43)-316-380-5332 ; e-mail: or
| | - Michael Fuchs
- Department of Chemistry, Organic & Bioorganic Chemistry, Heinrichstrasse 28, University of Graz 8010 Graz, Austria, ; phone: (+43)-316-380-5332 ; e-mail: or
| | - Altijana Hromic
- Austrian Centre of Industrial Biotechnology, c/o Department of Chemistry, Organic & Bioorganic Chemistry, Heinrichstrasse 28, University of Graz 8010 Graz, Austria ; Institute of Molecular Biosciences, Humboldtstrasse 50, University of Graz 8010 Graz, Austria
| | - Andrzej Lyskowski
- Austrian Centre of Industrial Biotechnology, c/o Department of Chemistry, Organic & Bioorganic Chemistry, Heinrichstrasse 28, University of Graz 8010 Graz, Austria ; Institute of Molecular Biosciences, Humboldtstrasse 50, University of Graz 8010 Graz, Austria
| | - Kerstin Fauland
- Austrian Centre of Industrial Biotechnology, c/o Department of Chemistry, Organic & Bioorganic Chemistry, Heinrichstrasse 28, University of Graz 8010 Graz, Austria ; Institute of Molecular Biosciences, Humboldtstrasse 50, University of Graz 8010 Graz, Austria
| | - Karl Gruber
- Institute of Molecular Biosciences, Humboldtstrasse 50, University of Graz 8010 Graz, Austria
| | - Silvia M Glueck
- Austrian Centre of Industrial Biotechnology, c/o Department of Chemistry, Organic & Bioorganic Chemistry, Heinrichstrasse 28, University of Graz 8010 Graz, Austria ; Department of Chemistry, Organic & Bioorganic Chemistry, Heinrichstrasse 28, University of Graz 8010 Graz, Austria, ; phone: (+43)-316-380-5332 ; e-mail: or
| | - Kurt Faber
- Department of Chemistry, Organic & Bioorganic Chemistry, Heinrichstrasse 28, University of Graz 8010 Graz, Austria, ; phone: (+43)-316-380-5332 ; e-mail: or
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20
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Gallage NJ, Møller BL. Vanillin-bioconversion and bioengineering of the most popular plant flavor and its de novo biosynthesis in the vanilla orchid. MOLECULAR PLANT 2015; 8:40-57. [PMID: 25578271 DOI: 10.1016/j.molp.2014.11.008] [Citation(s) in RCA: 151] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Accepted: 09/15/2014] [Indexed: 05/24/2023]
Abstract
In recent years, biotechnology-derived production of flavors and fragrances has expanded rapidly. The world's most popular flavor, vanillin, is no exception. This review outlines the current state of biotechnology-based vanillin synthesis with the use of ferulic acid, eugenol, and glucose as substrates and bacteria, fungi, and yeasts as microbial production hosts. The de novo biosynthetic pathway of vanillin in the vanilla orchid and the possible applied uses of this new knowledge in the biotechnology-derived and pod-based vanillin industries are also highlighted.
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Affiliation(s)
- Nethaji J Gallage
- VILLUM Research Center for Plant Plasticity, Department of Plant and Environmental Sciences, University of Copenhagen, 40 Thorvaldsensvej, DK-1871 Frederiksberg C, Copenhagen, Denmark; Center for Synthetic Biology "bioSYNergy", Department of Plant and Environmental Sciences, University of Copenhagen, 40 Thorvaldsensvej, DK-1871 Frederiksberg C, Copenhagen, Denmark; Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, 40 Thorvaldsensvej, DK-1871 Frederiksberg C, Copenhagen, Denmark
| | - Birger Lindberg Møller
- VILLUM Research Center for Plant Plasticity, Department of Plant and Environmental Sciences, University of Copenhagen, 40 Thorvaldsensvej, DK-1871 Frederiksberg C, Copenhagen, Denmark; Center for Synthetic Biology "bioSYNergy", Department of Plant and Environmental Sciences, University of Copenhagen, 40 Thorvaldsensvej, DK-1871 Frederiksberg C, Copenhagen, Denmark; Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, 40 Thorvaldsensvej, DK-1871 Frederiksberg C, Copenhagen, Denmark; Carlsberg Laboratory, 10 Gamle Carlsberg Vej, DK-1799 Copenhagen V, Denmark.
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21
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Wuensch C, Gross J, Steinkellner G, Gruber K, Glueck SM, Faber K. Asymmetric enzymatic hydration of hydroxystyrene derivatives. Angew Chem Int Ed Engl 2013; 52:2293-7. [PMID: 23335002 DOI: 10.1002/anie.201207916] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2012] [Revised: 12/10/2012] [Indexed: 11/05/2022]
Affiliation(s)
- Christiane Wuensch
- ACIB GmbH c/o Department of Chemistry, Organic & Bioorganic Chemistry, University of Graz, Heinrichstrasse 28, 8010 Graz, Austria
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22
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Wuensch C, Gross J, Steinkellner G, Gruber K, Glueck SM, Faber K. Asymmetric Enzymatic Hydration of Hydroxystyrene Derivatives. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201207916] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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23
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Sun Y, Song H, Li J, Jiang M, Li Y, Zhou J, Guo Z. Active site binding and catalytic role of bicarbonate in 1,4-dihydroxy-2-naphthoyl coenzyme A synthases from vitamin K biosynthetic pathways. Biochemistry 2012; 51:4580-9. [PMID: 22606952 DOI: 10.1021/bi300486j] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
1,4-Dihydroxy-2-naphthoyl coenzyme A (DHNA-CoA) synthase, or MenB, catalyzes a carbon-carbon bond formation reaction in the biosynthesis of both vitamin K1 and K2. Bicarbonate is crucial to the activity of a large subset of its orthologues but lacks a clearly defined structural and mechanistic role. Here we determine the crystal structure of the holoenzymes from Escherichia coli at 2.30 Å and Synechocystis sp. PCC6803 at 2.04 Å, in which the bicarbonate cofactor is bound to the enzyme active site at a position equivalent to that of the side chain carboxylate of an aspartate residue conserved among bicarbonate-insensitive DHNA-CoA synthases. Binding of the planar anion involves both nonspecific electrostatic attraction and specific hydrogen bonding and hydrophobic interactions. In the absence of bicarbonate, the anion binding site is occupied by a chloride ion or nitrate, an inhibitor directly competing with bicarbonate. These results provide a solid structural basis for the bicarbonate dependence of the enzymatic activity of type I DHNA-CoA synthases. The unique location of the bicarbonate ion in relation to the expected position of the substrate α-proton in the enzyme's active site suggests a critical catalytic role for the anionic cofactor as a catalytic base in enolate formation.
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Affiliation(s)
- Yueru Sun
- Department of Chemistry and State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China
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24
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Frank A, Eborall W, Hyde R, Hart S, Turkenburg JP, Grogan G. Mutational analysis of phenolic acid decarboxylase from Bacillus subtilis (BsPAD), which converts bio-derived phenolic acids to styrene derivatives. Catal Sci Technol 2012. [DOI: 10.1039/c2cy20015e] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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25
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Li HJ, Li X, Liu N, Zhang H, Truglio JJ, Mishra S, Kisker C, Garcia-Diaz M, Tonge PJ. Mechanism of the intramolecular Claisen condensation reaction catalyzed by MenB, a crotonase superfamily member. Biochemistry 2011; 50:9532-44. [PMID: 21830810 PMCID: PMC4119599 DOI: 10.1021/bi200877x] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
MenB, the 1,4-dihydroxy-2-naphthoyl-CoA synthase from the bacterial menaquinone biosynthesis pathway, catalyzes an intramolecular Claisen condensation (Dieckmann reaction) in which the electrophile is an unactivated carboxylic acid. Mechanistic studies on this crotonase family member have been hindered by partial active site disorder in existing MenB X-ray structures. In the current work the 2.0 Å structure of O-succinylbenzoyl-aminoCoA (OSB-NCoA) bound to the MenB from Escherichia coli provides important insight into the catalytic mechanism by revealing the position of all active site residues. This has been accomplished by the use of a stable analogue of the O-succinylbenzoyl-CoA (OSB-CoA) substrate in which the CoA thiol has been replaced by an amine. The resulting OSB-NCoA is stable, and the X-ray structure of this molecule bound to MenB reveals the structure of the enzyme-substrate complex poised for carbon-carbon bond formation. The structural data support a mechanism in which two conserved active site Tyr residues, Y97 and Y258, participate directly in the intramolecular transfer of the substrate α-proton to the benzylic carboxylate of the substrate, leading to protonation of the electrophile and formation of the required carbanion. Y97 and Y258 are also ideally positioned to function as the second oxyanion hole required for stabilization of the tetrahedral intermediate formed during carbon-carbon bond formation. In contrast, D163, which is structurally homologous to the acid-base catalyst E144 in crotonase (enoyl-CoA hydratase), is not directly involved in carbanion formation and may instead play a structural role by stabilizing the loop that carries Y97. When similar studies were performed on the MenB from Mycobacterium tuberculosis, a twisted hexamer was unexpectedly observed, demonstrating the flexibility of the interfacial loops that are involved in the generation of the novel tertiary and quaternary structures found in the crotonase superfamily. This work reinforces the utility of using a stable substrate analogue as a mechanistic probe in which only one atom has been altered leading to a decrease in α-proton acidity.
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Affiliation(s)
- Huei-Jiun Li
- Institute for Chemical Biology & Drug Discovery and Department of Chemistry, Stony Brook University, Stony Brook, New York 11794, USA
| | - Xiaokai Li
- Institute for Chemical Biology & Drug Discovery and Department of Chemistry, Stony Brook University, Stony Brook, New York 11794, USA
| | - Nina Liu
- Institute for Chemical Biology & Drug Discovery and Department of Chemistry, Stony Brook University, Stony Brook, New York 11794, USA
| | - Huaning Zhang
- Institute for Chemical Biology & Drug Discovery and Department of Chemistry, Stony Brook University, Stony Brook, New York 11794, USA
| | - James J. Truglio
- Institute for Chemical Biology & Drug Discovery and Department of Chemistry, Stony Brook University, Stony Brook, New York 11794, USA
| | - Shambhavi Mishra
- Rudolf Virchow Center for Experimental Biomedicine, Institute for Structural Biology, University of Würzburg, Würzburg, Germany
| | - Caroline Kisker
- Rudolf Virchow Center for Experimental Biomedicine, Institute for Structural Biology, University of Würzburg, Würzburg, Germany
| | - Miguel Garcia-Diaz
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, New York 11794, USA
| | - Peter J. Tonge
- Institute for Chemical Biology & Drug Discovery and Department of Chemistry, Stony Brook University, Stony Brook, New York 11794, USA
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26
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Jin J, Hanefeld U. The selective addition of water to CC bonds; enzymes are the best chemists. Chem Commun (Camb) 2011; 47:2502-10. [DOI: 10.1039/c0cc04153j] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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27
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Kichise T, Hisano T, Takeda K, Miki K. Crystal structure of phenylacetic acid degradation protein PaaG from Thermus thermophilus HB8. Proteins 2009; 76:779-86. [PMID: 19452559 DOI: 10.1002/prot.22455] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Microbial degradation of phenylacetic acid proceeds via the hybrid pathway that includes formation of a coenzyme A thioester, ring hydroxylation, non-oxygenolytic ring opening, and beta-oxidation-like reactions. A phenylacetic acid degradation protein PaaG is a member of the crotonase superfamily, and is a candidate non-oxygenolytic ring-opening enzyme. The crystal structure of PaaG from Thermus thermophilus HB8 was determined at a resolution of 1.85 A. PaaG consists of three identical subunits related by local three-fold symmetry. The monomer is comprised of a spiral and a helical domain with a fold characteristic of the crotonase superfamily. A putative active site residue, Asp136, is situated in an active site cavity and surrounded by several hydrophobic and hydrophilic residues. The active site cavity is sufficiently large to accommodate a ring substrate. Two conformations are observed for helix H2 located adjacent to the active site. Helix H2 is kinked at Asn81 in two subunits, whereas it is kinked at Leu77 in the other subunit, and the side chain of Tyr80 is closer to Asp136. This indicates that catalytic reaction of PaaG may proceed with large conformational changes at the active site. Asp136 is the only conserved polar residue in the active site. It is located at the same position as those of 4-chlorobenzoyl-CoA dehalogenase and peroxisomal Delta(3),Delta(2)-enoyl-CoA isomerase, indicating that PaaG may undergo isomerization or a ring-opening reaction via a Delta(3),Delta(2)-enoyl-CoA isomerase-like mechanism.
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Affiliation(s)
- Tomoyasu Kichise
- RIKEN SPring-8 Center at Harima Institute, Koto 1-1-1, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
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28
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Botosoa EP, Blumenstein C, MacKenzie DA, Silvestre V, Remaud GS, Kwiecień RA, Robins RJ. Quantitative isotopic 13C nuclear magnetic resonance at natural abundance to probe enzyme reaction mechanisms via site-specific isotope fractionation: The case of the chain-shortening reaction for the bioconversion of ferulic acid to vanillin. Anal Biochem 2009; 393:182-8. [DOI: 10.1016/j.ab.2009.06.031] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2009] [Revised: 05/18/2009] [Accepted: 06/24/2009] [Indexed: 10/20/2022]
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29
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Berger RG. Biotechnology of flavours--the next generation. Biotechnol Lett 2009; 31:1651-9. [PMID: 19609491 DOI: 10.1007/s10529-009-0083-5] [Citation(s) in RCA: 156] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2009] [Revised: 06/22/2009] [Accepted: 06/24/2009] [Indexed: 11/25/2022]
Abstract
Volatile organic chemicals (flavours, aromas) are the sensory principles of many consumer products and govern their acceptance and market success. Flavours from microorganisms compete with the traditional agricultural sources. Screening for overproducers, elucidation of metabolic pathways and precursors and application of conventional bioengineering has resulted in a set of more than 100 commercial aroma chemicals derived via biotechnology. Various routes may lead to volatile metabolites: De novo synthesis from elementary biochemical units, degradation of larger substrates such as lipids, and functionalization of immediate flavour precursor molecules. More recently, the field was stimulated by the increasing preference of alienated consumers for products bearing the label "natural", and by the vivid discussion on healthy and "functional" food ingredients. The unmistakable call for sustainable sources and environmentally friendly production is forcing the industry to move towards a greener chemistry. Progress is expected from the toolbox of genetic engineering which is expected to help in identifying metabolic bottlenecks and in creating novel high-yielding strains. Bioengineering, in a complementary way, provides promising technical options, such as improved substrate dosage, gas-phase or two-phase reactions and in situ product recovery.
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Affiliation(s)
- Ralf G Berger
- Institute of Food Chemistry, Gottfried Wilhelm Leibniz Universität Hannover, Callinstrasse 5, 30167, Hannover, Germany.
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