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Robescu MS, Loprete G, Gasparotto M, Vascon F, Filippini F, Cendron L, Bergantino E. The Family Keeps on Growing: Four Novel Fungal OYEs Characterized. Int J Mol Sci 2022; 23:3050. [PMID: 35328465 PMCID: PMC8954901 DOI: 10.3390/ijms23063050] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 03/07/2022] [Accepted: 03/09/2022] [Indexed: 11/16/2022] Open
Abstract
Aiming at expanding the portfolio of Old Yellow Enzymes (OYEs), which have been systematically studied to be employed in the chemical and pharmaceutical industries as useful biocatalysts, we decided to explore the immense reservoir of filamentous fungi. We drew from the genome of the two Ascomycetes Aspergillus niger and Botryotinia fuckeliana four new members of the OYE superfamily belonging to the classical and thermophilic-like subfamilies. The two BfOYEs show wider substrate spectra than the AnOYE homologues, which appear as more specialized biocatalysts. According to their mesophilic origins, the new enzymes neither show high thermostability nor extreme pH optimums. The crystal structures of BfOYE4 and AnOYE8 have been determined, revealing the conserved features of the thermophilic-like subclass as well as unique properties, such as a peculiar N-terminal loop involved in dimer surface interactions. For the classical representatives BfOYE1 and AnOYE2, model structures were built and analyzed, showing surprisingly wide open access to the active site cavities due to a shorter β6-loop and a disordered capping subdomain.
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Affiliation(s)
| | | | | | | | | | | | - Elisabetta Bergantino
- Synthetic Biology and Biotechnology Unit, Department of Biology, University of Padova, Viale G. Colombo 3, 35131 Padova, Italy; (M.S.R.); (G.L.); (M.G.); (F.V.); (F.F.); (L.C.)
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2
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A New Thermophilic Ene-Reductase from the Filamentous Anoxygenic Phototrophic Bacterium Chloroflexus aggregans. Microorganisms 2021; 9:microorganisms9050953. [PMID: 33925162 PMCID: PMC8146883 DOI: 10.3390/microorganisms9050953] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 04/23/2021] [Accepted: 04/27/2021] [Indexed: 11/25/2022] Open
Abstract
Aiming at expanding the biocatalytic toolbox of ene-reductase enzymes, we decided to explore photosynthetic extremophile microorganisms as unique reservoir of (new) biocatalytic activities. We selected a new thermophilic ene-reductase homologue in Chloroflexus aggregans, a peculiar filamentous bacterium. We report here on the functional and structural characterization of this new enzyme, which we called CaOYE. Produced in high yields in recombinant form, it proved to be a robust biocatalyst showing high thermostability, good solvent tolerance and a wide range of pH optimum. In a preliminary screening, CaOYE displayed a restricted substrate spectrum (with generally lower activities compared to other ene-reductases); however, given the amazing metabolic ductility and versatility of Chloroflexus aggregans, further investigations could pinpoint peculiar chemical activities. X-ray crystal structure has been determined, revealing conserved features of Class III (or thermophilic-like group) of the family of Old Yellow Enzymes: in the crystal packing, the enzyme was found to assemble as dimer even if it behaves as a monomer in solution. The description of CaOYE catalytic properties and crystal structure provides new details useful for enlarging knowledge, development and application of this class of enzymes.
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3
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Old yellow enzymes: structures and structure-guided engineering for stereocomplementary bioreduction. Appl Microbiol Biotechnol 2020; 104:8155-8170. [PMID: 32830294 DOI: 10.1007/s00253-020-10845-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 08/07/2020] [Accepted: 08/17/2020] [Indexed: 10/23/2022]
Abstract
Since the first discovery of old yellow enzyme 1 (OYE1) from Saccharomyces pastorianus in 1932, biocatalytic asymmetric reduction of activated alkenes by OYEs has become a valuable reaction in organic synthesis. To access stereocomplementary C=C-bond bioreduction, the mining of novel OYEs and especially the protein engineering of existing OYEs have been performed, which successfully achieved the stereocomplementary reduction in several cases and further raise the potential of applications. In this review, we analyzed the structures, active sites, and substrate recognition of OYEs, which are the bases for their substrate specificity and stereospecificity. Sequence similarity network of OYEs superfamily was also constructed to investigate the scope of characterized OYEs. The structure-guided engineering to switch the stereoselectivity of OYEs and thus access stereocomplementary bioreduction over the last decade (2009-2020) was then reviewed and discussed, which might give new insights into the mining and engineering of related biocatalysts. KEY POINTS: • The sequence similarity network of OYEs superfamily was constructed and annotated. • The structures and active sites of OYEs from different classes were compared. • "Left/right" binding mode was used to explain the stereopreferences of OYEs. • Structure-guided engineering of OYEs to switch their stereoselectivity was reviewed.
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Robescu MS, Niero M, Hall M, Cendron L, Bergantino E. Two new ene-reductases from photosynthetic extremophiles enlarge the panel of old yellow enzymes: CtOYE and GsOYE. Appl Microbiol Biotechnol 2020; 104:2051-2066. [PMID: 31930452 DOI: 10.1007/s00253-019-10287-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 11/21/2019] [Accepted: 11/28/2019] [Indexed: 01/25/2023]
Abstract
Looking for new ene-reductases with uncovered features beneficial for biotechnological applications, by mining genomes of photosynthetic extremophile organisms, we identified two new Old Yellow Enzyme homologues: CtOYE, deriving from the cyanobacterium Chroococcidiopsis thermalis, and GsOYE, from the alga Galdieria sulphuraria. Both enzymes were produced and purified with very good yields and displayed catalytic activity on a broad substrate spectrum by reducing α,β-unsaturated ketones, aldehydes, maleimides and nitroalkenes with good to excellent stereoselectivity. Both enzymes prefer NADPH but demonstrate a good acceptance of NADH as cofactor. CtOYE and GsOYE represent robust biocatalysts showing high thermostability, a wide range of pH optimum and good co-solvent tolerance. High resolution X-ray crystal structures of both enzymes have been determined, revealing conserved features of the classical OYE subfamily as well as unique properties, such as a very long loop entering the active site or an additional C-terminal alpha helix in GsOYE. Not surprisingly, the active site of CtOYE and GsOYE structures revealed high affinity toward anions caught from the mother liquor and trapped in the anion hole where electron-withdrawing groups such as carbonyl group are engaged. Ligands (para-hydroxybenzaldehyde and 2-methyl-cyclopenten-1-one) added on purpose to study complexes of GsOYE were detected in the enzyme catalytic cavity, stacking on top of the FMN cofactor, and support the key role of conserved residues and FMN cofactor in the catalysis.
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Affiliation(s)
- Marina Simona Robescu
- Department of Biology, University of Padova, Viale G. Colombo 3, 35131, Padova, Italy
| | - Mattia Niero
- Department of Biology, University of Padova, Viale G. Colombo 3, 35131, Padova, Italy
| | - Mélanie Hall
- Department of Chemistry, University of Graz, Heinrichstrasse 28, 8010, Graz, Austria
| | - Laura Cendron
- Department of Biology, University of Padova, Viale G. Colombo 3, 35131, Padova, Italy.
| | - Elisabetta Bergantino
- Department of Biology, University of Padova, Viale G. Colombo 3, 35131, Padova, Italy.
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5
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Complex molecules, clever solutions – Enzymatic approaches towards natural product and active agent syntheses. Bioorg Med Chem 2018; 26:1285-1303. [DOI: 10.1016/j.bmc.2017.06.045] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Revised: 05/29/2017] [Accepted: 06/27/2017] [Indexed: 12/31/2022]
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6
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de Paula BR, Zampieri DS, Nasário FD, Rodrigues JAR, Moran PJ. Regioselectivity Control of Enone Reduction Mediated by Aqueous Baker's Yeast with Addition of Ionic Liquid [bmim(PF 6 )]. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2017. [DOI: 10.1016/j.bcab.2017.10.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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7
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Old Yellow Enzyme-Catalysed Asymmetric Hydrogenation: Linking Family Roots with Improved Catalysis. Catalysts 2017. [DOI: 10.3390/catal7050130] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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Paula BRS, Zampieri D, Rodrigues JAR, Moran PJS. Bioreduction of α-Acetoxymethyl Enones: Proposal for an SN2′ Mechanism Catalyzed by Enereductase. Adv Synth Catal 2016. [DOI: 10.1002/adsc.201600601] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Bruno R. S. Paula
- Institute of Chemistry; University of Campinas; 13084-971 Campinas-SP Brazil
| | - Davila Zampieri
- Institute of Chemistry; University of Campinas; 13084-971 Campinas-SP Brazil
| | | | - Paulo J. S. Moran
- Institute of Chemistry; University of Campinas; 13084-971 Campinas-SP Brazil
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Pei XQ, Xu MY, Wu ZL. Two “classical” Old Yellow Enzymes from Chryseobacterium sp. CA49: Broad substrate specificity of Chr-OYE1 and limited activity of Chr-OYE2. ACTA ACUST UNITED AC 2016. [DOI: 10.1016/j.molcatb.2015.11.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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10
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Applications of protein engineering to members of the old yellow enzyme family. Biotechnol Adv 2015; 33:624-31. [PMID: 25940546 DOI: 10.1016/j.biotechadv.2015.04.011] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Revised: 04/24/2015] [Accepted: 04/25/2015] [Indexed: 01/28/2023]
Abstract
In the 20 years since Massey's initial report in 1995, interest in using alkene reductases to prepare chiral intermediates for synthesis has grown rapidly. While native alkene reductases often show very high stereoselectivities toward favorable substrates, these enzymes have somewhat size-restricted active sites that limit their substrate ranges to small alkenes. In addition, most alkene reductases have the same stereoselectivities, which makes it difficult to access the "other" product enantiomers. Protein engineering strategies have been used to address both of these issues and good progress has been made in several cases. This review summarizes published examples through late 2014 and focuses on studies of six enzymes: Saccharomyces pastorianus OYE 1, tomato OPR1, Zymomonas mobilis NCR, Enterobacter cloacae PB2 PETN reductase, Bacillus subtilis YqjM and Pichia stipitis OYE 2.6.
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11
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Rüthlein E, Classen T, Dobnikar L, Schölzel M, Pietruszka J. Finding the Selectivity Switch - A Rational Approach towards Stereocomplementary Variants of the Ene Reductase YqjM. Adv Synth Catal 2015. [DOI: 10.1002/adsc.201500149] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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12
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Park JT, Gómez Ramos LM, Bommarius AS. Engineering towards Nitroreductase Functionality in Ene-Reductase Scaffolds. Chembiochem 2015; 16:811-8. [DOI: 10.1002/cbic.201402667] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2014] [Indexed: 11/10/2022]
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13
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Xu MY, Pei XQ, Wu ZL. Identification and characterization of a novel “thermophilic-like” Old Yellow Enzyme from the genome of Chryseobacterium sp. CA49. ACTA ACUST UNITED AC 2014. [DOI: 10.1016/j.molcatb.2014.07.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Steinkellner G, Gruber CC, Pavkov-Keller T, Binter A, Steiner K, Winkler C, Łyskowski A, Schwamberger O, Oberer M, Schwab H, Faber K, Macheroux P, Gruber K. Identification of promiscuous ene-reductase activity by mining structural databases using active site constellations. Nat Commun 2014; 5:4150. [PMID: 24954722 PMCID: PMC4083419 DOI: 10.1038/ncomms5150] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Accepted: 05/15/2014] [Indexed: 12/03/2022] Open
Abstract
The exploitation of catalytic promiscuity and the application of de novo design have recently opened the access to novel, non-natural enzymatic activities. Here we describe a structural bioinformatic method for predicting catalytic activities of enzymes based on three-dimensional constellations of functional groups in active sites ('catalophores'). As a proof-of-concept we identify two enzymes with predicted promiscuous ene-reductase activity (reduction of activated C-C double bonds) and compare them with known ene-reductases, that is, members of the Old Yellow Enzyme family. Despite completely different amino acid sequences, overall structures and protein folds, high-resolution crystal structures reveal equivalent binding modes of typical Old Yellow Enzyme substrates and ligands. Biochemical and biocatalytic data show that the two enzymes indeed possess ene-reductase activity and reveal an inverted stereopreference compared with Old Yellow Enzymes for some substrates. This method could thus be a tool for the identification of viable starting points for the development and engineering of novel biocatalysts.
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Affiliation(s)
- Georg Steinkellner
- ACIB GmbH, Petersgasse 14, 8010 Graz, Austria
- These authors contributed equally to this work
| | - Christian C. Gruber
- ACIB GmbH, Petersgasse 14, 8010 Graz, Austria
- These authors contributed equally to this work
| | | | | | | | - Christoph Winkler
- Department of Chemistry, University of Graz, Heinrichstrasse 28, 8010 Graz, Austria
| | | | - Orsolya Schwamberger
- ACIB GmbH, Petersgasse 14, 8010 Graz, Austria
- Institute of Molecular Biosciences, University of Graz, Humboldtstrasse 50, 8010 Graz, Austria
| | - Monika Oberer
- Institute of Molecular Biosciences, University of Graz, Humboldtstrasse 50, 8010 Graz, Austria
| | - Helmut Schwab
- ACIB GmbH, Petersgasse 14, 8010 Graz, Austria
- Institute of Molecular Biotechnology, Graz University of Technology, Petersgasse 14, 8010 Graz, Austria
| | - Kurt Faber
- ACIB GmbH, Petersgasse 14, 8010 Graz, Austria
- Department of Chemistry, University of Graz, Heinrichstrasse 28, 8010 Graz, Austria
| | - Peter Macheroux
- ACIB GmbH, Petersgasse 14, 8010 Graz, Austria
- Institute of Biochemistry, Graz University of Technology, Petersgasse 12, 8010 Graz, Austria
| | - Karl Gruber
- ACIB GmbH, Petersgasse 14, 8010 Graz, Austria
- Institute of Molecular Biosciences, University of Graz, Humboldtstrasse 50, 8010 Graz, Austria
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Nizam S, Gazara RK, Verma S, Singh K, Verma PK. Comparative structural modeling of six old yellow enzymes (OYEs) from the necrotrophic fungus Ascochyta rabiei: insight into novel OYE classes with differences in cofactor binding, organization of active site residues and stereopreferences. PLoS One 2014; 9:e95989. [PMID: 24776850 PMCID: PMC4002455 DOI: 10.1371/journal.pone.0095989] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2014] [Accepted: 04/02/2014] [Indexed: 11/29/2022] Open
Abstract
Old Yellow Enzyme (OYE1) was the first flavin-dependent enzyme identified and characterized in detail by the entire range of physical techniques. Irrespective of this scrutiny, true physiological role of the enzyme remains a mystery. In a recent study, we systematically identified OYE proteins from various fungi and classified them into three classes viz. Class I, II and III. However, there is no information about the structural organization of Class III OYEs, eukaryotic Class II OYEs and Class I OYEs of filamentous fungi. Ascochyta rabiei, a filamentous phytopathogen which causes Ascochyta blight (AB) in chickpea possesses six OYEs (ArOYE1-6) belonging to the three OYE classes. Here we carried out comparative homology modeling of six ArOYEs representing all the three classes to get an in depth idea of structural and functional aspects of fungal OYEs. The predicted 3D structures of A. rabiei OYEs were refined and evaluated using various validation tools for their structural integrity. Analysis of FMN binding environment of Class III OYE revealed novel residues involved in interaction. The ligand para-hydroxybenzaldehyde (PHB) was docked into the active site of the enzymes and interacting residues were analyzed. We observed a unique active site organization of Class III OYE in comparison to Class I and II OYEs. Subsequently, analysis of stereopreference through structural features of ArOYEs was carried out, suggesting differences in R/S selectivity of these proteins. Therefore, our comparative modeling study provides insights into the FMN binding, active site organization and stereopreference of different classes of ArOYEs and indicates towards functional differences of these enzymes. This study provides the basis for future investigations towards the biochemical and functional characterization of these enigmatic enzymes.
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Affiliation(s)
- Shadab Nizam
- Plant Immunity Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India
| | - Rajesh Kumar Gazara
- Plant Immunity Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India
| | - Sandhya Verma
- Plant Immunity Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India
| | - Kunal Singh
- Plant Immunity Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India
| | - Praveen Kumar Verma
- Plant Immunity Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India
- * E-mail:
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16
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Classen T, Korpak M, Schölzel M, Pietruszka J. Stereoselective Enzyme Cascades: An Efficient Synthesis of Chiral γ-Butyrolactones. ACS Catal 2014. [DOI: 10.1021/cs5000262] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Thomas Classen
- Institut
für Bio- und Geowissenschaften (IBG-1: Biotechnologie), Forschungszentrum Jülich, D-52425 Jülich, Germany
| | - Margarete Korpak
- Institut
für Bioorganische Chemie, Heinrich-Heine-Universität Düsseldorf im Forschungszentrum Jülich, Stetternicher Forst, Geb. 15.8, D-52426 Jülich, Germany
| | - Melanie Schölzel
- Institut
für Bioorganische Chemie, Heinrich-Heine-Universität Düsseldorf im Forschungszentrum Jülich, Stetternicher Forst, Geb. 15.8, D-52426 Jülich, Germany
| | - Jörg Pietruszka
- Institut
für Bio- und Geowissenschaften (IBG-1: Biotechnologie), Forschungszentrum Jülich, D-52425 Jülich, Germany
- Institut
für Bioorganische Chemie, Heinrich-Heine-Universität Düsseldorf im Forschungszentrum Jülich, Stetternicher Forst, Geb. 15.8, D-52426 Jülich, Germany
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17
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Toogood HS, Scrutton NS. New developments in 'ene'-reductase catalysed biological hydrogenations. Curr Opin Chem Biol 2014; 19:107-15. [PMID: 24608082 DOI: 10.1016/j.cbpa.2014.01.019] [Citation(s) in RCA: 98] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2013] [Revised: 12/13/2013] [Accepted: 01/30/2014] [Indexed: 01/07/2023]
Abstract
Asymmetric biocatalytic hydrogenations are important reactions performed primarily by members of the Old Yellow Enzyme family. These reactions have great potential in the chemosynthesis of a variety of industrially useful synthons due to the generation of up to two stereogenic centres. In this review, additional enzyme classes capable of asymmetric hydrogenations will be discussed, as will examples of multienzyme cascading reactions. New and improved technology that enhances the commercial viability of biotransformations are included, such as the nicotinamide coenzyme-independent reactions. This review will focus on progress in this field within the last two years, with emphasis on industrial applications of this technology.
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Affiliation(s)
- Helen S Toogood
- Manchester Institute of Biotechnology, Faculty of Life Sciences, University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
| | - Nigel S Scrutton
- Manchester Institute of Biotechnology, Faculty of Life Sciences, University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
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18
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Nizam S, Verma S, Borah NN, Gazara RK, Verma PK. Comprehensive genome-wide analysis reveals different classes of enigmatic old yellow enzyme in fungi. Sci Rep 2014; 4:4013. [PMID: 24500274 PMCID: PMC3915301 DOI: 10.1038/srep04013] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2013] [Accepted: 01/17/2014] [Indexed: 11/09/2022] Open
Abstract
In this study, we systematically identify Old Yellow Enzymes (OYEs) from a diverse range of economically important fungi representing different ecology and lifestyle. Using active site residues and sequence alignments, we present a classification for these proteins into three distinct classes including a novel class (Class III) and assign names to sequences. Our in-depth phylogenetic analysis suggests a complex history of lineage-specific expansion and contraction for the OYE gene family in fungi. Comparative analyses reveal remarkable diversity in the number and classes of OYE among fungi. Quantitative real-time PCR (qRT-PCR) of Ascochyta rabiei OYEs indicates differential expression of OYE genes during oxidative stress and plant infection. This study shows relationship of OYE with fungal ecology and lifestyle, and provides a foundation for future functional analysis and characterization of OYE gene family.
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Affiliation(s)
- Shadab Nizam
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi-110067, India
| | - Sandhya Verma
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi-110067, India
| | - Nilam Nayan Borah
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi-110067, India
| | - Rajesh Kumar Gazara
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi-110067, India
| | - Praveen Kumar Verma
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi-110067, India
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19
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Litthauer S, Gargiulo S, van Heerden E, Hollmann F, Opperman D. Heterologous expression and characterization of the ene-reductases from Deinococcus radiodurans and Ralstonia metallidurans. ACTA ACUST UNITED AC 2014. [DOI: 10.1016/j.molcatb.2013.10.020] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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20
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Oberdorfer G, Binter A, Wallner S, Durchschein K, Hall M, Faber K, Macheroux P, Gruber K. The structure of glycerol trinitrate reductase NerA from Agrobacterium radiobacter reveals the molecular reason for nitro- and ene-reductase activity in OYE homologues. Chembiochem 2013; 14:836-45. [PMID: 23606302 PMCID: PMC3659409 DOI: 10.1002/cbic.201300136] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2013] [Indexed: 11/08/2022]
Abstract
In recent years, Old Yellow Enzymes (OYEs) and their homologues have found broad application in the efficient asymmetric hydrogenation of activated C=C bonds with high selectivities and yields. Members of this class of enzymes have been found in many different organisms and are rather diverse on the sequence level, with pairwise identities as low as 20 %, but they exhibit significant structural similarities with the adoption of a conserved (αβ)8-barrel fold. Some OYEs have been shown not only to reduce C=C double bonds, but also to be capable of reducing nitro groups in both saturated and unsaturated substrates. In order to understand this dual activity we determined and analyzed X-ray crystal structures of NerA from Agrobacterium radiobacter, both in its apo form and in complex with 4-hydroxybenzaldehyde and with 1-nitro-2-phenylpropene. These structures, together with spectroscopic studies of substrate binding to several OYEs, indicate that nitro-containing substrates can bind to OYEs in different binding modes, one of which leads to C=C double bond reduction and the other to nitro group reduction.
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Affiliation(s)
- Gustav Oberdorfer
- ACIB--Austrian Centre of Industrial Biotechnology, Petergasse 14, 8010 Graz, Austria
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21
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Fu Y, Castiglione K, Weuster-Botz D. Comparative characterization of novel ene-reductases from cyanobacteria. Biotechnol Bioeng 2013; 110:1293-301. [DOI: 10.1002/bit.24817] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2012] [Revised: 11/22/2012] [Accepted: 12/10/2012] [Indexed: 11/08/2022]
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22
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Paul CE, Gargiulo S, Opperman DJ, Lavandera I, Gotor-Fernández V, Gotor V, Taglieber A, Arends IWCE, Hollmann F. Mimicking nature: synthetic nicotinamide cofactors for C═C bioreduction using enoate reductases. Org Lett 2012; 15:180-3. [PMID: 23256747 DOI: 10.1021/ol303240a] [Citation(s) in RCA: 135] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A series of synthetic nicotinamide cofactors were synthesized to replace natural nicotinamide cofactors and promote enoate reductase (ER) catalyzed reactions without compromising the activity or stereoselectivity of the bioreduction process. Conversions and enantioselectivities of >99% were obtained for C═C bioreductions, and the process was successfully upscaled. Furthermore, high chemoselectivity was observed when employing these nicotinamide cofactor mimics (mNADs) with crude extracts in ER-catalyzed reactions.
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Affiliation(s)
- Caroline E Paul
- Department of Biotechnology, Delft University of Technology, Julianalaan 136, 2628BL Delft, The Netherlands
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Classen T, Pietruszka J, Schuback SM. Revisiting the Enantioselective Sequence Patterns in Enoate Reductases. ChemCatChem 2012. [DOI: 10.1002/cctc.201200668] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Reich S, Hoeffken HW, Rosche B, Nestl BM, Hauer B. Crystal structure determination and mutagenesis analysis of the ene reductase NCR. Chembiochem 2012; 13:2400-7. [PMID: 23033175 DOI: 10.1002/cbic.201200404] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2012] [Indexed: 11/09/2022]
Abstract
The crystal structure of the "ene" nicotinamide-dependent cyclohexenone reductase (NCR) from Zymomonas mobilis (PDB ID: 4A3U) has been determined in complex with acetate ion, FMN, and nicotinamide, to a resolution of 1.95 Å. To study the activity and enantioselectivity of this enzyme in the bioreduction of activated α,β-unsaturated alkenes, the rational design methods site- and loop-directed mutagenesis were applied. Based on a multiple sequence alignment of various members of the Old Yellow Enzyme family, eight single-residue variants were generated and investigated in asymmetric bioreduction. Furthermore, a structural alignment of various ene reductases predicted four surface loop regions that are located near the entrance of the active site. Four NCR loop variants, derived from loop-swapping experiments with OYE1 from Saccharomyces pastorianus, were analysed for bioreduction. The three enzyme variants, P245Q, D337Y and F314Y, displayed increased activity compared to wild-type NCR towards the set of substrates tested. The active-site mutation Y177A demonstrated a clear influence on the enantioselectivity. The loop-swapping variants retained reduction efficiency, but demonstrated decreased enzyme activity compared with the wild-type NCR ene reductase enzyme.
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Affiliation(s)
- Sabrina Reich
- Universitaet Stuttgart, Institute of Technical Biochemistry, Allmandring 31, 70569 Stuttgart, Germany
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Iqbal N, Rudroff F, Brigé A, Van Beeumen J, Mihovilovic MD. Asymmetric bioreduction of activated carbon-carbon double bonds using Shewanella yellow enzyme (SYE-4) as novel enoate reductase. Tetrahedron 2012; 68:7619-7623. [PMID: 22991485 PMCID: PMC3415682 DOI: 10.1016/j.tet.2012.05.092] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2012] [Revised: 05/03/2012] [Accepted: 05/22/2012] [Indexed: 12/01/2022]
Abstract
Shewanella yellow enzyme (SYE-4), a novel recombinant enoate reductase, was screened against a variety of different substrates bearing an activated double bond, such as unsaturated cyclic ketones, diesters, and substituted imides. Dimethyl- and ethyl esters of 2-methylmaleic acid were selectively reduced to (R)-configured succinic acid derivatives and various N-substituted maleimides furnished the desired (R)-products in up to >99% enantiomeric excess. Naturally occurring (+)-carvone was selectively reduced to (-)-cis-dihydrocarvone and (-)-carvone was converted to the diastereomeric product, respectively. Overall SYE-4 proved to be a useful biocatalyst for the selective reduction of activated C = C double bonds and complements the pool of synthetic valuable enoate reductases.
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Affiliation(s)
- Naseem Iqbal
- Institute of Applied Synthetic Chemistry, Vienna University of Technology, Getreidemarkt 9, 163-OC, A-1060 Vienna, Austria
| | - Florian Rudroff
- Institute of Applied Synthetic Chemistry, Vienna University of Technology, Getreidemarkt 9, 163-OC, A-1060 Vienna, Austria
| | - Ann Brigé
- Laboratory of Protein Biochemistry and Biomolecular Engineering, Ghent University, Ghent, Belgium
| | - Jozef Van Beeumen
- Laboratory of Protein Biochemistry and Biomolecular Engineering, Ghent University, Ghent, Belgium
| | - Marko D. Mihovilovic
- Institute of Applied Synthetic Chemistry, Vienna University of Technology, Getreidemarkt 9, 163-OC, A-1060 Vienna, Austria
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Durchschein K, Wallner S, Macheroux P, Schwab W, Winkler T, Kreis W, Faber K. Nicotinamide-Dependent Ene Reductases as Alternative Biocatalysts for the Reduction of Activated Alkenes. European J Org Chem 2012. [DOI: 10.1002/ejoc.201200776] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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