1
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Knaus T, Corrado ML, Mutti FG. One-Pot Biocatalytic Synthesis of Primary, Secondary, and Tertiary Amines with Two Stereocenters from α,β-Unsaturated Ketones Using Alkyl-Ammonium Formate. ACS Catal 2022; 12:14459-14475. [PMID: 36504913 PMCID: PMC9724091 DOI: 10.1021/acscatal.2c03052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Revised: 10/20/2022] [Indexed: 11/11/2022]
Abstract
The efficient asymmetric catalytic synthesis of amines containing more than one stereogenic center is a current challenge. Here, we present a biocatalytic cascade that combines ene-reductases (EReds) with imine reductases/reductive aminases (IReds/RedAms) to enable the conversion of α,β-unsaturated ketones into primary, secondary, and tertiary amines containing two stereogenic centers in very high chemical purity (up to >99%), a diastereomeric ratio, and an enantiomeric ratio (up to >99.8:<0.2). Compared with previously reported strategies, our strategy could synthesize two, three, or even all four of the possible stereoisomers of the amine products while precluding the formation of side-products. Furthermore, ammonium or alkylammonium formate buffer could be used as the only additional reagent since it acted both as an amine donor and as a source of reducing equivalents. This was achieved through the implementation of an NADP-dependent formate dehydrogenase (FDH) for the in situ recycling of the NADPH coenzyme, thus leading to increased atom economy for this biocatalytic transformation. Finally, this dual-enzyme ERed/IRed cascade also exhibits a complementarity with the recently reported EneIRED enzymes for the synthesis of cyclic six-membered ring amines. The ERed/IRed method yielded trans-1,2 and cis-1,3 substituted cyclohexylamines in high optical purities, whereas the EneIRED method was reported to yield one cis-1,2 and one trans-1,3 enantiomer. As a proof of concept, when 3-methylcyclohex-2-en-1-one was converted into secondary and tertiary chiral amines with different amine donors, we could obtain all the four possible stereoisomer products. This result exemplifies the versatility of this method and its potential for future wider utilization in asymmetric synthesis by expanding the toolbox of currently available dehydrogenases via enzyme engineering and discovery.
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Affiliation(s)
- Tanja Knaus
- Van’t Hoff Institute for Molecular
Sciences, HIMS-Biocat, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Maria L. Corrado
- Van’t Hoff Institute for Molecular
Sciences, HIMS-Biocat, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Francesco G. Mutti
- Van’t Hoff Institute for Molecular
Sciences, HIMS-Biocat, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
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2
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Myers AL. Metabolism of the areca alkaloids - toxic and psychoactive constituents of the areca (betel) nut. Drug Metab Rev 2022; 54:343-360. [PMID: 35543097 DOI: 10.1080/03602532.2022.2075010] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Areca nut (AN) is consumed by millions of people for its therapeutic and psychoactive effects, making it one of the most widely self-administered psychoactive substances in the world. Even so, AN use/abuse is associated with myriad oral and systemic side effects, affecting most organ systems in the body. Alkaloids abundant in the nut (e.g. arecoline, arecaidine, guvacoline, and guvacine), collectively called the areca alkaloids, are presumably responsible for the major pharmacological effects experienced by users, with arecoline being the most abundant alkaloid with notable toxicological properties. However, the mechanisms of arecoline and other areca alkaloid elimination in humans remain poorly documented. Therefore, the purpose of this review is to provide an in-depth review of areca alkaloid pharmacokinetics (PK) in biological systems, and discuss mechanisms of metabolism by presenting information found in the literature. Also, the toxicological relevance of the known and purported metabolic steps will be reviewed. In brief, several areca alkaloids contain a labile methyl ester group and are susceptible to hydrolysis, although the human esterase responsible remains presumptive. Other notable mechanisms include N-oxidation, glutathionylation, nitrosamine conversion, and carbon-carbon double-bond reduction. These metabolic conversions result in toxic and sometimes less-toxic derivatives. Arecoline and arecaidine undergo extensive metabolism while far less is known about guvacine and guvacoline. Metabolism information may help predict drug interactions with human pharmaceuticals with overlapping elimination pathways. Altogether, this review provides a first-of-its-kind comprehensive analysis of AN alkaloid metabolism, adds perspective on new mechanisms of metabolism, and highlights the need for future metabolism work in the field.
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Affiliation(s)
- Alan L Myers
- Department of Diagnostic and Biomedical Sciences, School of Dentistry, The University of Texas Health Science Center, Houston, TX, USA
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3
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Asymmetric Synthesis of Both Enantiomers of Dimethyl 2-Methylsuccinate by the Ene-Reductase-Catalyzed Reduction at High Substrate Concentration. Catalysts 2022. [DOI: 10.3390/catal12101133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Chiral dimethyl 2-methylsuccinate (1) is a very important building block for the manufacturing of many active pharmaceutical ingredients and fine chemicals. The asymmetric reduction of C=C double bond of dimethyl citraconate (2), dimethyl mesaconate (3) or dimethyl itaconate (4) by ene-reductases (ERs) represents an attractive straightforward approach, but lack of high-performance ERs, especially (S)-selective ones, has limited implementing this method to prepare the optically pure dimethyl 2-methylsuccinate. Herein, three ERs (Bac-OYE1 from Bacillus sp., SeER from Saccharomyces eubayanus and AfER from Aspergillus flavus) with high substrate tolerance and stereoselectivity towards 2, 3 and 4 have been identified. Up to 500 mM of 3 was converted to (S)-dimethyl 2-methylsuccinate ((S)-1) by SeER in high yields (80%) and enantioselectivity (98% ee), and 700 mM of 2 and 400 mM of 4 were converted to (R)-1 by Bac-OYE1 and AfER, respectively, in high yields (86% and 77%) with excellent enantioselectivity (99% ee). The reductions of diethyl citraconate (5), diethyl mesaconate (6) and diethyl itaconate (7) were also tested with the three ERs. Although up to 500 mM of 5 was completely converted to (R)-diethyl 2-methylsuccinate ((R)-8) by Bac-OYE1 with excellent enantioselectivity (99% ee), the alcohol moiety of the esters had a great effect on the activity and enantioselectivity of ERs. This work provides an efficient methodology for the enantiocomplementary production of optically pure dimethyl 2-methylsuccinate from dimethyl itaconate and its isomers at high titer.
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4
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Yamasaki K. Old yellow enzyme of a novel fungi‐specific class. FEBS J 2022; 289:5527-5530. [DOI: 10.1111/febs.16526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 05/09/2022] [Indexed: 11/28/2022]
Affiliation(s)
- Kazuhiko Yamasaki
- Biomedical Research Institute National Institute of Advanced Industrial Science and Technology (AIST) Tsukuba Japan
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5
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Jamieson CS, Misa J, Tang Y, Billingsley JM. Biosynthesis and synthetic biology of psychoactive natural products. Chem Soc Rev 2021; 50:6950-7008. [PMID: 33908526 PMCID: PMC8217322 DOI: 10.1039/d1cs00065a] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Psychoactive natural products play an integral role in the modern world. The tremendous structural complexity displayed by such molecules confers diverse biological activities of significant medicinal value and sociocultural impact. Accordingly, in the last two centuries, immense effort has been devoted towards establishing how plants, animals, and fungi synthesize complex natural products from simple metabolic precursors. The recent explosion of genomics data and molecular biology tools has enabled the identification of genes encoding proteins that catalyze individual biosynthetic steps. Once fully elucidated, the "biosynthetic pathways" are often comparable to organic syntheses in elegance and yield. Additionally, the discovery of biosynthetic enzymes provides powerful catalysts which may be repurposed for synthetic biology applications, or implemented with chemoenzymatic synthetic approaches. In this review, we discuss the progress that has been made toward biosynthetic pathway elucidation amongst four classes of psychoactive natural products: hallucinogens, stimulants, cannabinoids, and opioids. Compounds of diverse biosynthetic origin - terpene, amino acid, polyketide - are identified, and notable mechanisms of key scaffold transforming steps are highlighted. We also provide a description of subsequent applications of the biosynthetic machinery, with an emphasis placed on the synthetic biology and metabolic engineering strategies enabling heterologous production.
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Affiliation(s)
- Cooper S Jamieson
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA.
| | - Joshua Misa
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, CA, USA.
| | - Yi Tang
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA. and Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, CA, USA.
| | - John M Billingsley
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, CA, USA. and Invizyne Technologies, Inc., Monrovia, CA, USA
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6
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Back to the plant: overcoming roadblocks to the microbial production of pharmaceutically important plant natural products. J Ind Microbiol Biotechnol 2020; 47:815-828. [PMID: 32772209 DOI: 10.1007/s10295-020-02300-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 07/30/2020] [Indexed: 01/26/2023]
Abstract
Microbial fermentation platforms offer a cost-effective and sustainable alternative to plant cultivation and chemical synthesis for the production of many plant-derived pharmaceuticals. Plant alkaloids, particularly benzylisoquinoline alkaloids and monoterpene indole alkaloids, and recently cannabinoids have become attractive targets for microbial biosynthesis owing to their medicinal importance. Recent advances in the discovery of pathway components, together with the application of synthetic biology tools, have facilitated the assembly of plant alkaloid and cannabinoid pathways in the microbial hosts Escherichia coli and Saccharomyces cerevisiae. This review highlights key aspects of these pathways in the framework of overcoming bottlenecks in microbial production to further improve end-product titers. We discuss the opportunities that emerge from a better understanding of the pathway components by further study of the plant, and strategies for generation of new and advanced medicinal compounds.
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7
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Iorgu AI, Hedison TM, Hay S, Scrutton NS. Selectivity through discriminatory induced fit enables switching of NAD(P)H coenzyme specificity in Old Yellow Enzyme ene-reductases. FEBS J 2019; 286:3117-3128. [PMID: 31033202 PMCID: PMC6767020 DOI: 10.1111/febs.14862] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 03/22/2019] [Accepted: 04/24/2019] [Indexed: 11/30/2022]
Abstract
Most ene‐reductases belong to the Old Yellow Enzyme (OYE) family of flavin‐dependent oxidoreductases. OYEs use nicotinamide coenzymes as hydride donors to catalyze the reduction of alkenes that contain an electron‐withdrawing group. There have been many investigations of the structures and catalytic mechanisms of OYEs. However, the origin of coenzyme specificity in the OYE family is unknown. Structural NMR and X‐ray crystallographic data were used to rationally design variants of two OYEs, pentaerythritol tetranitrate reductase (PETNR) and morphinone reductase (MR), to discover the basis of coenzyme selectivity. PETNR has dual‐specificity and reacts with NADH and NADPH; MR accepts only NADH as hydride donor. Variants of a β‐hairpin motif in an active site loop of both these enzymes were studied using stopped‐flow spectroscopy. Specific attention was placed on the potential role of arginine residues within the β‐hairpin motif. Mutagenesis demonstrated that Arg130 governs the preference of PETNR for NADPH, and that Arg142 interacts with the coenzyme pyrophosphate group. These observations were used to switch coenzyme specificity in MR by replacing either Glu134 or Leu146 with arginine residues. These variants had increased (~15‐fold) affinity for NADH. Mutagenesis enabled MR to accept NADPH as a hydride donor, with E134R MR showing a significant (55‐fold) increase in efficiency in the reductive half‐reaction, when compared to the essentially unreactive wild‐type enzyme. Insight into the question of coenzyme selectivity in OYEs has therefore been addressed through rational redesign. This should enable coenzyme selectivity to be improved and switched in other OYEs.
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Affiliation(s)
- Andreea I Iorgu
- Manchester Institute of Biotechnology and School of Chemistry, Faculty of Science and Engineering, The University of Manchester, UK
| | - Tobias M Hedison
- Manchester Institute of Biotechnology and School of Chemistry, Faculty of Science and Engineering, The University of Manchester, UK
| | - Sam Hay
- Manchester Institute of Biotechnology and School of Chemistry, Faculty of Science and Engineering, The University of Manchester, UK
| | - Nigel S Scrutton
- Manchester Institute of Biotechnology and School of Chemistry, Faculty of Science and Engineering, The University of Manchester, UK
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8
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Peters C, Frasson D, Sievers M, Buller R. Novel Old Yellow Enzyme Subclasses. Chembiochem 2019; 20:1569-1577. [DOI: 10.1002/cbic.201800770] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Revised: 02/12/2019] [Indexed: 11/07/2022]
Affiliation(s)
- Christin Peters
- Competence Center for BiocatalysisInstitute of Chemistry and BiotechnologySchool of Life Sciences and Facility ManagementZurich University of Applied Sciences Einsiedlerstrasse 31 8820 Wädenswil Switzerland
| | - David Frasson
- Molecular BiologyInstitute of Chemistry and BiotechnologySchool of Life Sciences and Facility ManagementZurich University of Applied Sciences Einsiedlerstrasse 31 8820 Wädenswil Switzerland
| | - Martin Sievers
- Molecular BiologyInstitute of Chemistry and BiotechnologySchool of Life Sciences and Facility ManagementZurich University of Applied Sciences Einsiedlerstrasse 31 8820 Wädenswil Switzerland
| | - Rebecca Buller
- Competence Center for BiocatalysisInstitute of Chemistry and BiotechnologySchool of Life Sciences and Facility ManagementZurich University of Applied Sciences Einsiedlerstrasse 31 8820 Wädenswil Switzerland
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9
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Dastmalchi M, Chen X, Hagel JM, Chang L, Chen R, Ramasamy S, Yeaman S, Facchini PJ. Neopinone isomerase is involved in codeine and morphine biosynthesis in opium poppy. Nat Chem Biol 2019; 15:384-390. [DOI: 10.1038/s41589-019-0247-0] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 02/11/2019] [Indexed: 11/09/2022]
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10
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The crystal structure of XdpB, the bacterial old yellow enzyme, in an FMN-free form. PLoS One 2018; 13:e0195299. [PMID: 29630677 PMCID: PMC5891007 DOI: 10.1371/journal.pone.0195299] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 03/20/2018] [Indexed: 11/19/2022] Open
Abstract
Old Yellow Enzymes (OYEs) are NAD(P)H dehydrogenases of not fully resolved physiological roles that are widespread among bacteria, plants, and fungi and have a great potential for biotechnological applications. We determined the apo form crystal structure of a member of the OYE class, glycerol trinitrate reductase XdpB, from Agrobacterium bohemicum R89-1 at 2.1 Å resolution. In agreement with the structures of the related bacterial OYEs, the structure revealed the TIM barrel fold with an N-terminal β-hairpin lid, but surprisingly, the structure did not contain its cofactor FMN. Its putative binding site was occupied by a pentapeptide TTSDN from the C-terminus of a symmetry related molecule. Biochemical experiments confirmed a specific concentration-dependent oligomerization and a low FMN content. The blocking of the FMN binding site can exist in vivo and regulates enzyme activity. Our bioinformatic analysis indicated that a similar self-inhibition could be expected in more OYEs which we designated as subgroup OYE C1. This subgroup is widespread among G-bacteria and can be recognized by the conserved sequence GxxDYP in proximity of the C termini. In proteobacteria, the C1 subgroup OYEs are typically coded in one operon with short-chain dehydrogenase. This operon is controlled by the tetR-like transcriptional regulator. OYEs coded in these operons are unlikely to be involved in the oxidative stress response as the other known members of the OYE family because no upregulation of XdpB was observed after exposing A. bohemicum R89-1 to oxidative stress.
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11
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Zahradník J, Nunvar J, Pařízková H, Kolářová L, Palyzová A, Marešová H, Grulich M, Kyslíková E, Kyslík P. Agrobacterium bohemicum sp. nov. isolated from poppy seed wastes in central Bohemia. Syst Appl Microbiol 2018; 41:184-190. [PMID: 29402492 DOI: 10.1016/j.syapm.2018.01.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Revised: 01/11/2018] [Accepted: 01/17/2018] [Indexed: 10/18/2022]
Abstract
Two non-pathogenic strains R89-1 and R90T isolated from poppy seed (Papaver somniferum L.) wastes were phenotypically and genotypically characterized. Multilocus sequence analysis (MLSA) was conducted with six genes (atpD, glnA, gyrB, recA, rpoB, 16S rRNA). The strains represented a new species which clustered with Agrobacterium rubi NBRC 13261T and Agrobacterium skierniewicense Ch11T type strains. MLSA was further accompanied by whole-genome phylogeny, in silico DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) analyses for both strains. ANI and dDDH values were deep below the species delineation threshold. Phenotypic features of the novel strains unequivocally allowed their differentiation from all other Agrobacterium species. Unlike other agrobacteria, the strains were salt sensitive and were able to biotransform morphine alkaloids. The dominant cellular fatty acids are 18:1 w7c, 16:0 and 12:0 aldehyde/16:1 iso I/14:0 3OH summed in feature 2 and the major respiratory quinine is Q-10 (87%). The DNA G+C content is 56mol%. Microbial community analysis indicated probable association with P. somniferum plant material. Altogether, these characteristics showed that strains R90T and R89-1 represent a new species of the genus Agrobacterium which we propose to name Agrobacterium bohemicum. The type strain of A. bohemicum is R90T (=CCM 8736T=DSM 104667T).
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Affiliation(s)
- Jiří Zahradník
- Institute of Microbiology, v.v.i., Academy of Sciences of the Czech Republic, Vídeňská 1083, CZ-142 20 Prague 4, Czech Republic; Laboratory of Biomolecular Recognition, Institute of Biotechnology, v.v.i., BIOCEV, Průmyslová 595, CZ-252 42 Vestec, Czech Republic; Faculty of Science, Charles University Prague, Viničná 5, CZ-128 44 Prague 2, Czech Republic.
| | - Jaroslav Nunvar
- Department of Medical Microbiology, 2nd Faculty of Medicine, Charles University Prague, V Uvalu 84, CZ-150 06 Prague 5, Czech Republic
| | - Hana Pařízková
- Laboratory of Biomolecular Recognition, Institute of Biotechnology, v.v.i., BIOCEV, Průmyslová 595, CZ-252 42 Vestec, Czech Republic
| | - Lucie Kolářová
- Laboratory of Biomolecular Recognition, Institute of Biotechnology, v.v.i., BIOCEV, Průmyslová 595, CZ-252 42 Vestec, Czech Republic
| | - Andrea Palyzová
- Institute of Microbiology, v.v.i., Academy of Sciences of the Czech Republic, Vídeňská 1083, CZ-142 20 Prague 4, Czech Republic
| | - Helena Marešová
- Institute of Microbiology, v.v.i., Academy of Sciences of the Czech Republic, Vídeňská 1083, CZ-142 20 Prague 4, Czech Republic
| | - Michal Grulich
- Institute of Microbiology, v.v.i., Academy of Sciences of the Czech Republic, Vídeňská 1083, CZ-142 20 Prague 4, Czech Republic
| | - Eva Kyslíková
- Institute of Microbiology, v.v.i., Academy of Sciences of the Czech Republic, Vídeňská 1083, CZ-142 20 Prague 4, Czech Republic
| | - Pavel Kyslík
- Institute of Microbiology, v.v.i., Academy of Sciences of the Czech Republic, Vídeňská 1083, CZ-142 20 Prague 4, Czech Republic.
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12
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Yamamoto K, Oku Y, Ina A, Izumi A, Doya M, Ebata S, Asano Y. Purification and Characterization of an Enone Reductase from Sporidiobolus salmonicolor
TPU 2001 Reacting with Large Monocyclic Enones. ChemCatChem 2017. [DOI: 10.1002/cctc.201700244] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Kazunori Yamamoto
- Biotechnology Research Center and Department of Biotechnology; Toyama Prefectural University; 5180 Kurokawa Imizu Toyama Japan
- Asano Active Enzyme Molecule Project; ERATO, JST; 5180 Kurokawa Imizu Toyama Japan
| | - Yuko Oku
- Biotechnology Research Center and Department of Biotechnology; Toyama Prefectural University; 5180 Kurokawa Imizu Toyama Japan
- Asano Active Enzyme Molecule Project; ERATO, JST; 5180 Kurokawa Imizu Toyama Japan
| | - Atsutoshi Ina
- Biotechnology Research Center and Department of Biotechnology; Toyama Prefectural University; 5180 Kurokawa Imizu Toyama Japan
- Asano Active Enzyme Molecule Project; ERATO, JST; 5180 Kurokawa Imizu Toyama Japan
| | - Atsushi Izumi
- Biotechnology Research Center and Department of Biotechnology; Toyama Prefectural University; 5180 Kurokawa Imizu Toyama Japan
- Asano Active Enzyme Molecule Project; ERATO, JST; 5180 Kurokawa Imizu Toyama Japan
| | - Masaharu Doya
- Toho Earthtec, Inc.; 1450 Kurotori, Nishi-ku Niigata Niigata Japan
| | - Syuji Ebata
- Toho Earthtec, Inc.; 1450 Kurotori, Nishi-ku Niigata Niigata Japan
| | - Yasuhisa Asano
- Biotechnology Research Center and Department of Biotechnology; Toyama Prefectural University; 5180 Kurokawa Imizu Toyama Japan
- Asano Active Enzyme Molecule Project; ERATO, JST; 5180 Kurokawa Imizu Toyama Japan
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13
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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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14
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Löw SA, Löw IM, Weissenborn MJ, Hauer B. Enhanced Ene-Reductase Activity through Alteration of Artificial Nicotinamide Cofactor Substituents. ChemCatChem 2016. [DOI: 10.1002/cctc.201501230] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Sebastian A. Löw
- Institute of Technical Biochemistry; University of Stuttgart; Allmandring 31 70569 Stuttgart Germany
| | - Isabell M. Löw
- Institute of Inorganic Chemistry; University of Stuttgart; Pfaffenwaldring 55 70569 Stuttgart Germany
| | - Martin J. Weissenborn
- Institute of Technical Biochemistry; University of Stuttgart; Allmandring 31 70569 Stuttgart Germany
| | - Bernhard Hauer
- Institute of Technical Biochemistry; University of Stuttgart; Allmandring 31 70569 Stuttgart Germany
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15
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Knaus T, Paul CE, Levy CW, de Vries S, Mutti FG, Hollmann F, Scrutton NS. Better than Nature: Nicotinamide Biomimetics That Outperform Natural Coenzymes. J Am Chem Soc 2016; 138:1033-9. [PMID: 26727612 PMCID: PMC4731831 DOI: 10.1021/jacs.5b12252] [Citation(s) in RCA: 127] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
![]()
The search for affordable, green
biocatalytic processes is a challenge
for chemicals manufacture. Redox biotransformations are potentially
attractive, but they rely on unstable and expensive nicotinamide coenzymes
that have prevented their widespread exploitation. Stoichiometric
use of natural coenzymes is not viable economically, and the instability
of these molecules hinders catalytic processes that employ coenzyme
recycling. Here, we investigate the efficiency of man-made synthetic
biomimetics of the natural coenzymes NAD(P)H in redox biocatalysis.
Extensive studies with a range of oxidoreductases belonging to the
“ene” reductase family show that these biomimetics are
excellent analogues of the natural coenzymes, revealed also in crystal
structures of the ene reductase XenA with selected biomimetics. In
selected cases, these biomimetics outperform the natural coenzymes.
“Better-than-Nature” biomimetics should find widespread
application in fine and specialty chemicals production by harnessing
the power of high stereo-, regio-, and chemoselective redox biocatalysts
and enabling reactions under mild conditions at low cost.
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Affiliation(s)
- Tanja Knaus
- BBSRC/EPSRC Centre for Synthetic Biology of Fine and Speciality Chemicals, Faculty of Life Sciences, Manchester Institute of Biotechnology , 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Caroline E Paul
- Department of Biotechnology, Delft University of Technology , Julianalaan 136, 2628BL Delft, The Netherlands
| | - Colin W Levy
- BBSRC/EPSRC Centre for Synthetic Biology of Fine and Speciality Chemicals, Faculty of Life Sciences, Manchester Institute of Biotechnology , 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Simon de Vries
- Department of Biotechnology, Delft University of Technology , Julianalaan 136, 2628BL Delft, The Netherlands
| | - Francesco G Mutti
- BBSRC/EPSRC Centre for Synthetic Biology of Fine and Speciality Chemicals, Faculty of Life Sciences, Manchester Institute of Biotechnology , 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Frank Hollmann
- Department of Biotechnology, Delft University of Technology , Julianalaan 136, 2628BL Delft, The Netherlands
| | - Nigel S Scrutton
- BBSRC/EPSRC Centre for Synthetic Biology of Fine and Speciality Chemicals, Faculty of Life Sciences, Manchester Institute of Biotechnology , 131 Princess Street, Manchester M1 7DN, United Kingdom
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16
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Knaus T, Mutti FG, Humphreys LD, Turner NJ, Scrutton NS. Systematic methodology for the development of biocatalytic hydrogen-borrowing cascades: application to the synthesis of chiral α-substituted carboxylic acids from α-substituted α,β-unsaturated aldehydes. Org Biomol Chem 2015; 13:223-33. [PMID: 25372591 DOI: 10.1039/c4ob02282c] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Ene-reductases (ERs) are flavin dependent enzymes that catalyze the asymmetric reduction of activated carbon-carbon double bonds. In particular, α,β-unsaturated carbonyl compounds (e.g. enals and enones) as well as nitroalkenes are rapidly reduced. Conversely, α,β-unsaturated esters are poorly accepted substrates whereas free carboxylic acids are not converted at all. The only exceptions are α,β-unsaturated diacids, diesters as well as esters bearing an electron-withdrawing group in α- or β-position. Here, we present an alternative approach that has a general applicability for directly obtaining diverse chiral α-substituted carboxylic acids. This approach combines two enzyme classes, namely ERs and aldehyde dehydrogenases (Ald-DHs), in a concurrent reductive-oxidative biocatalytic cascade. This strategy has several advantages as the starting material is an α-substituted α,β-unsaturated aldehyde, a class of compounds extremely reactive for the reduction of the alkene moiety. Furthermore no external hydride source from a sacrificial substrate (e.g. glucose, formate) is required since the hydride for the first reductive step is liberated in the second oxidative step. Such a process is defined as a hydrogen-borrowing cascade. This methodology has wide applicability as it was successfully applied to the synthesis of chiral substituted hydrocinnamic acids, aliphatic acids, heterocycles and even acetylated amino acids with elevated yield, chemo- and stereo-selectivity. A systematic methodology for optimizing the hydrogen-borrowing two-enzyme synthesis of α-chiral substituted carboxylic acids was developed. This systematic methodology has general applicability for the development of diverse hydrogen-borrowing processes that possess the highest atom efficiency and the lowest environmental impact.
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Affiliation(s)
- Tanja Knaus
- Manchester Institute of Biotechnology, Faculty of Life Sciences, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
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17
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Kramlinger VM, Alvarado Rojas M, Kanamori T, Guengerich FP. Cytochrome P450 3A Enzymes Catalyze the O6-Demethylation of Thebaine, a Key Step in Endogenous Mammalian Morphine Biosynthesis. J Biol Chem 2015; 290:20200-10. [PMID: 26157146 DOI: 10.1074/jbc.m115.665331] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Indexed: 01/08/2023] Open
Abstract
Morphine, first characterized in opium from the poppy Papaver somniferum, is one of the strongest known analgesics. Endogenous morphine has been identified in several mammalian cells and tissues. The synthetic pathway of morphine in the opium poppy has been elucidated. The presence of common intermediates in plants and mammals suggests that biosynthesis occurs through similar pathways (beginning with the amino acid L-tyrosine), and the pathway has been completely delineated in plants. Some of the enzymes in the mammalian pathway have been identified and characterized. Two of the latter steps in the morphine biosynthesis pathway are demethylation of thebaine at the O(3)- and the O(6)-positions, the latter of which has been difficult to demonstrate. The plant enzymes responsible for both the O(3)-demethylation and the O(6)-demethylation are members of the Fe(II)/α-ketoglutarate-dependent dioxygenase family. Previous studies showed that human cytochrome P450 (P450) 2D6 can catalyze thebaine O(3)-demethylation. We report that demethylation of thebaine at the O(6)-position is selectively catalyzed by human P450s 3A4 and 3A5, with the latter being more efficient, and rat P450 3A2. Our results do not support O(6)-demethylation of thebaine by an Fe(II)/α-ketoglutarate-dependent dioxygenase. In rat brain microsomes, O(6)-demethylation was inhibited by ketoconazole, but not sulfaphenazole, suggesting that P450 3A enzymes are responsible for this activity in the brain. An alternate pathway to morphine, oripavine O(6)-demethylation, was not detected. The major enzymatic steps in mammalian morphine synthesis have now been identified.
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Affiliation(s)
- Valerie M Kramlinger
- From the Department of Biochemistry, School of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146
| | - Mónica Alvarado Rojas
- From the Department of Biochemistry, School of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146
| | - Tatsuyuki Kanamori
- From the Department of Biochemistry, School of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146
| | - F Peter Guengerich
- From the Department of Biochemistry, School of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146
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18
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Forti L, Di Mauro S, Cramarossa MR, Filippucci S, Turchetti B, Buzzini P. Non-Conventional Yeasts Whole Cells as Efficient Biocatalysts for the Production of Flavors and Fragrances. Molecules 2015; 20:10377-98. [PMID: 26053491 PMCID: PMC6272320 DOI: 10.3390/molecules200610377] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Revised: 05/31/2015] [Accepted: 06/01/2015] [Indexed: 12/25/2022] Open
Abstract
The rising consumer requests for natural flavors and fragrances have generated great interest in the aroma industry to seek new methods to obtain fragrance and flavor compounds naturally. An alternative and attractive route for these compounds is based on bio-transformations. In this review, the application of biocatalysis by Non Conventional Yeasts (NCYs) whole cells for the production of flavor and fragrances is illustrated by a discussion of the production of different class of compounds, namely Aldehydes, Ketones and related compounds, Alcohols, Lactones, Terpenes and Terpenoids, Alkenes, and Phenols.
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Affiliation(s)
- Luca Forti
- Department of Life Sciences, University of Modena & Reggio Emilia, via G. Campi 103, Modena 41125, Italy.
| | - Simone Di Mauro
- Department of Agricultural, Environmental and Food Sciences, Industrial Yeasts Collection DBVPG, University of Perugia, Borgo XX Giugno 74, Perugia 06121, Italy.
| | - Maria Rita Cramarossa
- Department of Life Sciences, University of Modena & Reggio Emilia, via G. Campi 103, Modena 41125, Italy.
| | - Sara Filippucci
- Department of Agricultural, Environmental and Food Sciences, Industrial Yeasts Collection DBVPG, University of Perugia, Borgo XX Giugno 74, Perugia 06121, Italy.
| | - Benedetta Turchetti
- Department of Agricultural, Environmental and Food Sciences, Industrial Yeasts Collection DBVPG, University of Perugia, Borgo XX Giugno 74, Perugia 06121, Italy.
| | - Pietro Buzzini
- Department of Agricultural, Environmental and Food Sciences, Industrial Yeasts Collection DBVPG, University of Perugia, Borgo XX Giugno 74, Perugia 06121, Italy.
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19
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Boyd DR, Sharma ND, Malone JF, McIntyre PBA, McRoberts C, Floyd S, Allen CCR, Gohil A, Coles SJ, Horton PN, Stevenson PJ. Toluene dioxygenase-catalyzed synthesis and reactions of cis-diol metabolites derived from 2- and 3-methoxyphenols. J Org Chem 2015; 80:3429-39. [PMID: 25756661 DOI: 10.1021/jo5028968] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Using toluene dioxygenase as biocatalyst, enantiopure cis-dihydrodiol and cis-tetrahydrodiol metabolites, isolated as their ketone tautomers, were obtained from meta and ortho methoxyphenols. Although these isomeric phenol substrates are structurally similar, the major bioproducts from each of these biotransformations were found at different oxidation levels. The relatively stable cyclohexenone cis-diol metabolite from meta methoxyphenol was isolated, while the corresponding metabolite from ortho methoxyphenol was rapidly bioreduced to a cyclohexanone cis-diol. The chemistry of the 3-methoxycyclohexenone cis-diol product was investigated and elimination, aromatization, hydrogenation, regioselective O-exchange, Stork-Danheiser transposition and O-methylation reactions were observed. An offshoot of this technology provided a two-step chemoenzymatic synthesis, from meta methoxyphenol, of a recently reported chiral fungal metabolite; this synthesis also established the previously unassigned absolute configuration.
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Affiliation(s)
- Derek R Boyd
- †School of Chemistry and Chemical Engineering, Queen's University of Belfast, Belfast BT9 5AG, U.K
| | - Narain D Sharma
- †School of Chemistry and Chemical Engineering, Queen's University of Belfast, Belfast BT9 5AG, U.K
| | - John F Malone
- †School of Chemistry and Chemical Engineering, Queen's University of Belfast, Belfast BT9 5AG, U.K
| | - Peter B A McIntyre
- †School of Chemistry and Chemical Engineering, Queen's University of Belfast, Belfast BT9 5AG, U.K
| | - Colin McRoberts
- §Agri-food and Biosciences Institute for Northern Ireland, Belfast, BT9 5PX, U.K
| | - Stewart Floyd
- §Agri-food and Biosciences Institute for Northern Ireland, Belfast, BT9 5PX, U.K
| | - Christopher C R Allen
- ‡School of Biological Sciences, Queen's University of Belfast, Belfast, BT9 5AG, U.K
| | - Amit Gohil
- ‡School of Biological Sciences, Queen's University of Belfast, Belfast, BT9 5AG, U.K
| | - Simon J Coles
- ∥National Crystallography Service, School of Chemistry, University of Southampton, Southampton, SO17 1BJ, U.K
| | - Peter N Horton
- ∥National Crystallography Service, School of Chemistry, University of Southampton, Southampton, SO17 1BJ, U.K
| | - Paul J Stevenson
- †School of Chemistry and Chemical Engineering, Queen's University of Belfast, Belfast BT9 5AG, U.K
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20
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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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21
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Practical aspects on the use of kinetic isotope effects as probes of flavoprotein enzyme mechanisms. Methods Mol Biol 2014; 1146:161-75. [PMID: 24764092 DOI: 10.1007/978-1-4939-0452-5_8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
The measurement of kinetic isotope effects (KIEs) has proved useful in many mechanistic studies of enzyme activity, most notably in enzyme-catalyzed hydrogen-transfer reactions. Primary KIEs (1° KIE) greater than unity indicate that transfer of the hydrogen species of interest is partially or fully rate limiting, and studies of the magnitude of the temperature and pressure dependence of these KIEs can inform on the mechanism of transfer. For example, KIE measurements have proved crucial in understanding the role of quantum mechanical tunneling in enzyme systems. The measurement of secondary KIEs (2° KIEs) is also informative and can be used to infer a significant tunneling contribution and details of transition state geometry. Here the deuterium label is introduced next to that of the transferred hydrogen. Measurements of 1° and 2° KIEs are being used increasingly in studies of H-transfer in flavoprotein enzymes and this requires the preparation of high purity and stereospecific labeled isotopologues. Strategies for the synthesis of labeled substrates are dependent on the enzyme system being studied. However, the nicotinamide coenzymes are often used in studies of flavoprotein enzyme mechanisms. Here, we provide practical details for the enzymatic synthesis of high purity deuterated isotopologues of the common biological coenzymes NADH and NADPH as well as the corresponding nonreactive mimics, tetrahydroNAD(P)H. Both forms of the coenzyme have proven useful in the study of mechanisms, particularly in relation to the involvement of quantum mechanical tunneling and dynamics in enzymatic H-transfer chemistry. The focus here is on practical considerations in the synthesis of these compounds. We also provide an abbreviated description of how measurements of KIEs can inform on flavoprotein mechanisms. The aim of this contribution is not to give a detailed description of the underlying theory (which has been reviewed extensively in the literature), but to provide a basic introduction and practical considerations for nonexpert readers who wish to incorporate such measurements in studies of enzyme mechanisms.
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22
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Hardman SJO, Pudney CR, Hay S, Scrutton NS. Excited state dynamics can be used to probe donor-acceptor distances for H-tunneling reactions catalyzed by flavoproteins. Biophys J 2014; 105:2549-58. [PMID: 24314085 DOI: 10.1016/j.bpj.2013.10.015] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2013] [Revised: 10/09/2013] [Accepted: 10/21/2013] [Indexed: 10/26/2022] Open
Abstract
In enzyme systems where fast motions are thought to contribute to H-transfer efficiency, the distance between hydrogen donor and acceptor is a very important factor. Sub-ångstrom changes in donor-acceptor distance can have a large effect on the rate of reaction, so a sensitive probe of these changes is a vital tool in our understanding of enzyme function. In this study we use ultrafast transient absorption spectroscopy to investigate the photoinduced electron transfer rates, which are also very sensitive to small changes in distance, between coenzyme analog, NAD(P)H4, and the isoalloxazine center in the model flavoenzymes morphinone reductase (wild-type and selected variants) and pentaerythritol tetranitrate reductase (wild-type). It is shown that upon addition of coenzyme to the protein the rate of photoinduced electron transfer is increased. By comparing the magnitude of this increase with existing values for NAD(P)H4-FMN distances, based on charge-transfer complex absorbance and experimental kinetic isotope effect reaction data, we show that this method can be used as a sensitive probe of donor-acceptor distance in a range of enzyme systems.
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Affiliation(s)
- Samantha J O Hardman
- Manchester Institute of Biotechnology and Photon Science Institute, Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
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23
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Thodey K, Galanie S, Smolke CD. A microbial biomanufacturing platform for natural and semisynthetic opioids. Nat Chem Biol 2014; 10:837-44. [PMID: 25151135 PMCID: PMC4167936 DOI: 10.1038/nchembio.1613] [Citation(s) in RCA: 190] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2014] [Accepted: 06/27/2014] [Indexed: 01/05/2023]
Abstract
Opiates and related molecules are medically essential, but their production via field cultivation of opium poppy Papaver somniferum leads to supply inefficiencies and insecurity. As an alternative production strategy, we developed baker's yeast Saccharomyces cerevisiae as a microbial host for the transformation of opiates. Yeast strains engineered to express heterologous genes from P. somniferum and bacterium Pseudomonas putida M10 convert thebaine to codeine, morphine, hydromorphone, hydrocodone and oxycodone. We discovered a new biosynthetic branch to neopine and neomorphine, which diverted pathway flux from morphine and other target products. We optimized strain titer and specificity by titrating gene copy number, enhancing cosubstrate supply, applying a spatial engineering strategy and performing high-density fermentation, which resulted in total opioid titers up to 131 mg/l. This work is an important step toward total biosynthesis of valuable benzylisoquinoline alkaloid drug molecules and demonstrates the potential for developing a sustainable and secure yeast biomanufacturing platform for opioids.
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Affiliation(s)
- Kate Thodey
- Department of Bioengineering, Stanford University, Stanford, California, USA
| | - Stephanie Galanie
- Department of Chemistry, Stanford University, Stanford, California, USA
| | - Christina D Smolke
- Department of Bioengineering, Stanford University, Stanford, California, USA
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24
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Abstract
Reduction of C = C bonds by reductases, found in a variety of microorganisms (e.g. yeasts, bacteria, and lower fungi), animals, and plants has applications in the production of metabolites that include pharmacologically active drugs and other chemicals. Therefore, the reductase enzymes that mediate this transformation have become important therapeutic targets and biotechnological tools. These reductases are broad-spectrum, in that, they can act on isolation/conjugation C = C-bond compounds, α,β-unsaturated carbonyl compounds, carboxylic acids, acid derivatives, and nitro compounds. In addition, several mutations in the reductase gene have been identified, some associated with diseases. Several of these reductases have been cloned and/or purified, and studies to further characterize them and determine their structure in order to identify potential industrial biocatalysts are still in progress. In this study, crucial reductases for bioreduction of C = C bonds have been reviewed with emphasis on their principal substrates and effective inhibitors, their distribution, genetic polymorphisms, and implications in human disease and treatment.
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Affiliation(s)
- Minmin Huang
- Department of Pharmaceutical Analysis and Drug Metabolism, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University , Hangzhou, Zhejiang , China and
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25
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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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26
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Reich S, Kress N, Nestl BM, Hauer B. Variations in the stability of NCR ene reductase by rational enzyme loop modulation. J Struct Biol 2014; 185:228-33. [DOI: 10.1016/j.jsb.2013.04.004] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2013] [Revised: 03/15/2013] [Accepted: 04/09/2013] [Indexed: 10/26/2022]
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27
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Wang HB, Pei XQ, Wu ZL. An enoate reductase Achr-OYE4 from Achromobacter sp. JA81: characterization and application in asymmetric bioreduction of C=C bonds. Appl Microbiol Biotechnol 2013; 98:705-15. [PMID: 23644746 DOI: 10.1007/s00253-013-4899-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2013] [Revised: 03/28/2013] [Accepted: 04/03/2013] [Indexed: 11/29/2022]
Abstract
A putative enoate reductase, Achr-OYE4, was mined from the genome of Achromobacter sp. JA81, expressed in Escherichia coli, and was characterized. Sequence analysis and spectral properties indicated that Achr-OYE4 is a typical flavin mononucleotide-dependent protein; it preferred NADH over NADPH as a cofactor. The heterologously expressed protein displayed good activity and excellent stereoselectivity toward some activated alkenes in the presence of NADH, NADPH, or their recycling systems. The glucose dehydrogenase-based recycling system yielded the best results in most cases, with a product yield of up to 99 % and enantiopurity of >99 % ee. Achr-OYE4 is an important addition to the asymmetric reduction reservoir as an "old yellow enzyme" from Achromobacter.
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Affiliation(s)
- Hai-Bo Wang
- Key Laboratory of Environmental and Applied Microbiology, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
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28
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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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29
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Goretti M, Branda E, Turchetti B, Cramarossa MR, Onofri A, Forti L, Buzzini P. Response surface methodology as optimization strategy for asymmetric bioreduction of (4S)-(+)-carvone by Cryptococcus gastricus. BIORESOURCE TECHNOLOGY 2012; 121:290-297. [PMID: 22858498 DOI: 10.1016/j.biortech.2012.06.070] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2012] [Revised: 06/21/2012] [Accepted: 06/24/2012] [Indexed: 06/01/2023]
Abstract
Response surface methodology was applied in optimizing the asymmetric bioreduction of (4S)-(+)-carvone to dihydrocarvone (with low incidence of unsought side reactions) by using whole-cells of Cryptococcus gastricus. A factorial design (2(5)) including five independent variables was performed: X(1)=incubation time; X(2)=pH; X(3)=amount of whole-cells; X(4)=concentration of (4S)-(+)-carvone; X(5)=concentration of cofactor-recycling system. The utilization of glucose and glycerol as cofactor-recycling systems was checked. On the basis of the results of factorial design, three independent variables (X(1), X(3) and X(4)) out of five were further selected for performing a central composite design (CCD). First and second order polynomial equations obtained by CCD were used to select the optimal values of independent variables in order to maximize the bioreduction yield of (4S)-(+)-carvone and, at the same time, to minimize the occurrence of side reactions (i.e. further reduction of dihydrocarvone to dihydrocarveol).
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Affiliation(s)
- Marta Goretti
- Department of Applied Biology & Industrial Yeasts Collection DBVPG, University of Perugia, Italy
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30
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Gao X, Ren J, Wu Q, Zhu D. Biochemical characterization and substrate profiling of a new NADH-dependent enoate reductase from Lactobacillus casei. Enzyme Microb Technol 2012; 51:26-34. [PMID: 22579387 DOI: 10.1016/j.enzmictec.2012.03.009] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2011] [Revised: 03/27/2012] [Accepted: 03/28/2012] [Indexed: 11/19/2022]
Abstract
Carbon-carbon double bond of α,β-unsaturated carbonyl compounds can be reduced by enoate reductase (ER), which is an important reaction in fine chemical synthesis. A putative enoate reductase gene from Lactobacillus casei str. Zhang was cloned into pET-21a+ and expressed in Escherichia coli BL21 (DE3) host cells. The encoded enzyme (LacER) was purified by ammonium sulfate precipitation and treatment in an acidic buffer. This enzyme was identified as a NADH-dependent enoate reductase, which had a K(m) of 0.034 ± 0.006 mM and k(cat) of (3.2 ± 0.2) × 10³ s⁻¹ toward NADH using 2-cyclohexen-1-one as the substrate. Its K(m) and k(cat) toward substrate 2-cyclohexen-1-one were 1.94 ± 0.04 mM and (8.4 ± 0.2) × 10³ s⁻¹, respectively. The enzyme showed a maximum activity at pH 8.0-9.0. The optimum temperature of the enzyme was 50-55°C, and LacER was relatively stable below 60 °C. The enzyme was active toward aliphatic alkenyl aldehyde, ketones and some cyclic anhydrides. Substituted groups of cyclic α,β-unsaturated ketones and its ring size have positive or negative effects on activity. (R)-(-)-Carvone was reduced to (2R,5R)-dihydrocarvone with 99% conversion and 98% (diasteromeric excess: de) stereoselectivity, indicating a high synthetic potential of LacER in asymmetric synthesis.
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Affiliation(s)
- Xiuzhen Gao
- National Engineering Laboratory for Industrial Enzymes, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 Xi Qi Dao, Tianjin Airport Economic Area, Tianjin 300308, China
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31
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Winkler CK, Tasnádi G, Clay D, Hall M, Faber K. Asymmetric bioreduction of activated alkenes to industrially relevant optically active compounds. J Biotechnol 2012; 162:381-9. [PMID: 22498437 PMCID: PMC3521962 DOI: 10.1016/j.jbiotec.2012.03.023] [Citation(s) in RCA: 110] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2011] [Revised: 03/23/2012] [Accepted: 03/28/2012] [Indexed: 12/01/2022]
Abstract
Ene-reductases from the ‘Old Yellow Enzyme’ family of flavoproteins catalyze the asymmetric reduction of various α,β-unsaturated compounds at the expense of a nicotinamide cofactor. They have been applied to the synthesis of valuable enantiopure products, including chiral building blocks with broad industrial applications, terpenoids, amino acid derivatives and fragrances. The combination of these highly stereoselective biocatalysts with a cofactor recycling system has allowed the development of cost-effective methods for the generation of optically active molecules, which is strengthened by the availability of stereo-complementary enzyme homologues.
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Affiliation(s)
- Christoph K Winkler
- Department of Chemistry, Organic & Bioorganic Chemistry, University of Graz, Heinrichstrasse 28, 8010 Graz, Austria
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32
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Goretti M, Ponzoni C, Caselli E, Marchegiani E, Cramarossa MR, Turchetti B, Forti L, Buzzini P. Bioreduction of α,β-unsaturated ketones and aldehydes by non-conventional yeast (NCY) whole-cells. BIORESOURCE TECHNOLOGY 2011; 102:3993-3998. [PMID: 21232941 DOI: 10.1016/j.biortech.2010.12.062] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2010] [Revised: 12/14/2010] [Accepted: 12/15/2010] [Indexed: 05/30/2023]
Abstract
The bioreduction of α,β-unsaturated ketones (ketoisophorone, 2-methyl- and 3-methyl-cyclopentenone) and aldehydes [(S)-(-)-perillaldehyde and α-methyl-cinnamaldehyde] by 23 "non-conventional" yeasts (NCYs) belonging to 21 species of the genera Candida, Cryptococcus, Debaryomyces, Hanseniaspora, Kazachstania, Kluyveromyces, Lindnera, Nakaseomyces, Vanderwaltozyma, and Wickerhamomyces was reported. The results highlight the potential of NCYs as whole-cell biocatalysts for selective biotransformation of electron-poor alkenes. A few NCYs exhibited extremely high (>90%) or even total ketoisophorone and 2-methyl-cyclopentenone bioconversion yields via asymmetric reduction of the conjugated CC bond catalyzed by enoate reductases. Catalytic efficiency declined after switching from ketones to aldehydes. High chemoselectivity due to low competing carbonyl reductases was also sometimes observed.
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Affiliation(s)
- Marta Goretti
- Department of Applied Biology and Industrial Yeasts Collection DBVPG, University of Perugia, Borgo XX Giugno 74, 06121 Perugia, Italy
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Yamaguchi K, Okamoto N, Tokuoka K, Sugiyama S, Uchiyama N, Matsumura H, Inaka K, Urade Y, Inoue T. Structure of the inhibitor complex of old yellow enzyme from Trypanosoma cruzi. JOURNAL OF SYNCHROTRON RADIATION 2011; 18:66-69. [PMID: 21169695 PMCID: PMC3004258 DOI: 10.1107/s0909049510033595] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/02/2010] [Accepted: 08/20/2010] [Indexed: 05/30/2023]
Abstract
Old yellow enzyme (OYE) is an NADPH oxidoreductase which contains flavin mononucleotide as prosthetic group. The X-ray structures of OYE from Trypanosoma cruzi (TcOYE) which produces prostaglandin (PG) F(2α) from PGH(2) have been determined in the presence or absence of menadione. The binding motif of menadione, known as one of the inhibitors for TcOYE, should accelerate the structure-based development of novel anti-chagasic drugs that inhibit PGF(2α) production specifically.
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Affiliation(s)
- Keishi Yamaguchi
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, Yamada-Oka 2-1, Suita, Osaka 565-0871, Japan
| | - Naoki Okamoto
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, Yamada-Oka 2-1, Suita, Osaka 565-0871, Japan
| | - Keiji Tokuoka
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, Yamada-Oka 2-1, Suita, Osaka 565-0871, Japan
| | - Shigeru Sugiyama
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, Yamada-Oka 2-1, Suita, Osaka 565-0871, Japan
| | - Nahoko Uchiyama
- National Institute of Health Sciences (NIHS), Tokyo 158-8501, Japan
| | - Hiroyoshi Matsumura
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, Yamada-Oka 2-1, Suita, Osaka 565-0871, Japan
| | - Koji Inaka
- MARUWA Foods and Biosciences, Tsutsui-cho 170-1, Yamatokoriyama, Nara 639-1123, Japan
| | - Yoshihiro Urade
- Department of Molecular Behavior Biology, Osaka Bioscience Institute, Osaka 565-0874, Japan
| | - Tsuyoshi Inoue
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, Yamada-Oka 2-1, Suita, Osaka 565-0871, Japan
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Toogood H, Gardiner J, Scrutton N. Biocatalytic Reductions and Chemical Versatility of the Old Yellow Enzyme Family of Flavoprotein Oxidoreductases. ChemCatChem 2010. [DOI: 10.1002/cctc.201000094] [Citation(s) in RCA: 250] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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35
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Stueckler C, Mueller NJ, Winkler CK, Glueck SM, Gruber K, Steinkellner G, Faber K. Bioreduction of alpha-methylcinnamaldehyde derivatives: chemo-enzymatic asymmetric synthesis of Lilial and Helional. Dalton Trans 2010; 39:8472-6. [PMID: 20461254 DOI: 10.1039/c002971h] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Nonracemic aryl-substituted alpha-methyldihydrocinnamaldehyde derivatives employed as olfactory principles in perfumes (Lilial, Helional) were obtained via enzymatic reduction of the corresponding cinnamaldehyde precursors using cloned and overexpressed ene-reductases. (R)-Enantiomers were obtained using the old-yellow-enzyme (OYE) homolog YqjM from Bacillus subtilis and 12-oxophytodienoic acid reductase isoenzyme OPR1 from tomato (e.e.(max) 53%), and (S)-aldehydes were furnished in up to 97% e.e. using isoenzyme OPR3, nicotinamide 2-cyclohexene-1-one reductase NCR from Zymomonas mobilis and yeast OYE isoenzymes 1-3 under optimised reaction conditions in the presence of t-butyl methyl ether as the co-solvent. The stereochemical outcome of the reduction of alpha-methylcinnamaldehyde using NCR and OYEs 1-3 [previously reported to be (R)] was unambiguously corrected to be (S).
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Affiliation(s)
- Clemens Stueckler
- Department of Chemistry, Organic & Bioorganic Chemistry, Heinrichstrasse 28, A-8010, Graz, Austria
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Stueckler C, Reiter TC, Baudendistel N, Faber K. Nicotinamide-independent asymmetric bioreduction of CC-bonds via disproportionation of enones catalyzed by enoate reductases. Tetrahedron 2010; 66:663-667. [PMID: 21270958 PMCID: PMC3007678 DOI: 10.1016/j.tet.2009.11.065] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2009] [Revised: 11/11/2009] [Accepted: 11/12/2009] [Indexed: 11/17/2022]
Abstract
The asymmetric bioreduction of activated CC-bonds catalyzed by a single flavoprotein was achieved via direct hydrogen transfer from a sacrificial 2-enone or 1,4-dione as hydrogen donor without requirement of a nicotinamide cofactor. Due to its simplicity, this system has clear advantages over conventional FAD-recycling systems.
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Affiliation(s)
- Clemens Stueckler
- Department of Chemistry, Organic & Bioorganic Chemistry, University of Graz, Heinrichstrasse 28, A-8010 Graz, Austria
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37
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Elegheert J, van den Hemel D, Dix I, Stout J, Van Beeumen J, Brigé A, Savvides SN. Towards structural studies of the old yellow enzyme homologue SYE4 from Shewanella oneidensis and its complexes at atomic resolution. Acta Crystallogr Sect F Struct Biol Cryst Commun 2009; 66:85-90. [PMID: 20057079 DOI: 10.1107/s1744309109050386] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2009] [Accepted: 11/23/2009] [Indexed: 11/10/2022]
Abstract
Shewanella oneidensis is an environmentally versatile Gram-negative gamma-proteobacterium that is endowed with an unusually large proteome of redox proteins. Of the four old yellow enzyme (OYE) homologues found in S. oneidensis, SYE4 is the homologue most implicated in resistance to oxidative stress. SYE4 was recombinantly expressed in Escherichia coli, purified and crystallized using the hanging-drop vapour-diffusion method. The crystals belonged to the orthorhombic space group P2(1)2(1)2(1) and were moderately pseudo-merohedrally twinned, emulating a P422 metric symmetry. The native crystals of SYE4 were of exceptional diffraction quality and provided complete data to 1.10 A resolution using synchrotron radiation, while crystals of the reduced enzyme and of the enzyme in complex with a wide range of ligands typically led to high-quality complete data sets to 1.30-1.60 A resolution, thus providing a rare opportunity to dissect the structure-function relationships of a good-sized enzyme (40 kDa) at true atomic resolution. Here, the attainment of a number of experimental milestones in the crystallographic studies of SYE4 and its complexes are reported, including isolation of the elusive hydride-Meisenheimer complex.
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Affiliation(s)
- Jonathan Elegheert
- Department of Biochemistry and Microbiology, Laboratory for Protein Biochemistry and Biomolecular Engineering (L-ProBE), Ghent University, K. L. Ledeganckstraat 35, 9000 Ghent, Belgium
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38
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Spiegelhauer O, Dickert F, Mende S, Niks D, Hille R, Ullmann M, Dobbek H. Kinetic characterization of xenobiotic reductase A from Pseudomonas putida 86. Biochemistry 2009; 48:11412-20. [PMID: 19839648 DOI: 10.1021/bi901370u] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Xenobiotic reductase A (XenA) from Pseudomonas putida is a member of the old-yellow-enzyme family of flavin-containing enzymes and catalyzes the NADH/NADPH-dependent reduction of various substrates, including 8-hydroxycoumarin and 2-cyclohexenone. Here we present a kinetic and thermodynamic analysis of XenA. In the reductive half-reaction, complexes of oxidized XenA with NADH or NADPH form charge-transfer (CT) intermediates with increased absorption around 520-560 nm, which occurs with a second-order rate constant of 9.4 x 10(5) M(-1) s(-1) with NADH and 6.4 x 10(5) M(-1) s(-1) with NADPH, while its disappearance is controlled by a rate constant of 210-250 s(-1) with both substrates. Transfer of hydride from NADPH proceeds 24 times more rapidly than from NADH. This modest kinetic preference of XenA for NADPH is unlike the typical discrimination between NADH and NADPH by binding affinity. Docking studies combined with electrostatic energy calculations indicate that the 2'-phosphate group attached to the adenine moiety of NADPH is responsible for this difference. The reductions of 2-cyclohexenone and coumarin in the oxidative half-reaction are both concentration-dependent under the assay conditions and reveal a more than 50-fold larger limiting rate constant for the reduction of 2-cyclohexenone compared to that of coumarin. Our work corroborates the link between XenA and other members of the old-yellow-enzyme family but demonstrates several differences in the reactivity of these enzymes.
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39
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Goretti M, Ponzoni C, Caselli E, Marchigiani E, Cramarossa MR, Turchetti B, Buzzini P, Forti L. Biotransformation of electron-poor alkenes by yeasts: Asymmetric reduction of (4S)-(+)-carvone by yeast enoate reductases. Enzyme Microb Technol 2009. [DOI: 10.1016/j.enzmictec.2009.09.004] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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40
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Schweiger P, Gross H, Wesener S, Deppenmeier U. Vinyl ketone reduction by three distinct Gluconobacter oxydans 621H enzymes. Appl Microbiol Biotechnol 2008; 80:995-1006. [PMID: 18629490 DOI: 10.1007/s00253-008-1600-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2008] [Revised: 06/27/2008] [Accepted: 06/28/2008] [Indexed: 01/20/2023]
Abstract
Three cytosolic NADPH-dependent flavin-associated proteins (Gox2107, Gox0502, and Gox2684) from Gluconobacter oxydans 621H were overproduced in Escherichia coli, and the recombinant enzymes were purified and characterized. Apparent native molecular masses of 65.2, 78.2, and 78.4 kDa were observed for Gox2107, Gox0502, and Gox2684, corresponding to a trimeric structure for Gox2107 and dimers for Gox0502 and Gox2684. Analysis of flavin content revealed Gox2107 was flavin adenine dinucleotide dependent, whereas Gox0502 and Gox2684 contained flavin mononucleotide. The enzymes were able to reduce vinyl ketones and quinones, reducing the olefinic bond of vinyl ketones as shown by (1)H nuclear magnetic resonance. Additionally, Gox0502 and Gox2684 stereospecifically reduced 5S-(+)-carvone to 2R,5S-dihydrocarvone. All enzymes displayed highest activities with 3-butene-2-one and 1,4-naphthoquinone. Gox0502 and Gox2684 displayed a broader substrate spectrum also reducing short-chain alpha-diketones, whereas Gox2107 was most catalytically efficient.
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Affiliation(s)
- Paul Schweiger
- Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI 53211, USA
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41
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Chaparro-Riggers J, Rogers T, Vazquez-Figueroa E, Polizzi K, Bommarius A. Comparison of Three Enoate Reductases and their Potential Use for Biotransformations. Adv Synth Catal 2007. [DOI: 10.1002/adsc.200700074] [Citation(s) in RCA: 101] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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42
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van den Hemel D, Brigé A, Savvides SN, Van Beeumen J. Ligand-induced conformational changes in the capping subdomain of a bacterial old yellow enzyme homologue and conserved sequence fingerprints provide new insights into substrate binding. J Biol Chem 2006; 281:28152-61. [PMID: 16857682 DOI: 10.1074/jbc.m603946200] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
We have recently reported that Shewanella oneidensis, a Gram-negative gamma-proteobacterium with a rich arsenal of redox proteins, possesses four old yellow enzyme (OYE) homologues. Here, we report a series of high resolution crystal structures for one of these OYEs, Shewanella yellow enzyme 1 (SYE1), in its oxidized form at 1.4A resolution, which binds a molecule of PEG 400 in the active site, and in its NADH-reduced and p-hydroxybenzaldehyde- and p-hydroxyacetophenone-bound forms at 1.7A resolution. Although the overall structure of SYE1 reveals a monomeric enzyme based on the alpha(8)beta(8) barrel scaffold observed for other OYEs, the active site exhibits a unique combination of features: a strongly butterfly-bent FMN cofactor both in the oxidized and NADH-reduced forms, a collapsed and narrow active site tunnel, and a novel combination of conserved residues involved in the binding of phenolic ligands. Furthermore, we identify a second p-hydroxybenzaldehyde-binding site in a hydrophobic cleft next to the entry of the active site tunnel in the capping subdomain, formed by a restructuring of Loop 3 to an "open" conformation. This constitutes the first evidence to date for the entire family of OYEs that Loop 3 may indeed play a dynamic role in ligand binding and thus provides insights into the elusive NADH complex and into substrate binding in general. Structure-based sequence alignments indicate that the novelties we observe in SYE1 are supported by conserved residues in a number of structurally uncharacterized OYEs from the beta- and gamma-proteobacteria, suggesting that SYE1 represents a new subfamily of bacterial OYEs.
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Affiliation(s)
- Debbie van den Hemel
- Department of Biochemistry, Physiology and Microbiology, Laboratory for Protein Biochemistry and Protein Engineering, K.L. Ledeganckstraat 35, Ghent University, 9000 Ghent, Belgium
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43
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Griese JJ, P Jakob R, Schwarzinger S, Dobbek H. Xenobiotic reductase A in the degradation of quinoline by Pseudomonas putida 86: physiological function, structure and mechanism of 8-hydroxycoumarin reduction. J Mol Biol 2006; 361:140-52. [PMID: 16822524 DOI: 10.1016/j.jmb.2006.06.007] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2006] [Revised: 06/01/2006] [Accepted: 06/07/2006] [Indexed: 11/28/2022]
Abstract
A continuous evolutionary pressure of the biotic and abiotic world has led to the development of a diversity of microbial pathways to degrade and biomineralize aromatic and heteroaromatic compounds. The heterogeneity of compounds metabolized by bacteria like Pseudomonas putida indicates the large variety of enzymes necessary to catalyse the required reactions. Quinoline, a N-heterocyclic aromatic compound, can be degraded by microbes along different pathways. For P. putida 86 quinoline degradation by the 8-hydroxycoumarin pathway has been described and several intermediates were identified. To select enzymes catalysing the later stages of the 8-hydroxycoumarin pathway P. putida 86 was grown with quinoline. The FMN-containing enzyme xenobiotic reductase A (XenA) was isolated and analysed for its reactivity with intermediates of the 8-hydroxycoumarin pathway. XenA catalyses the NADPH-dependent reduction of 8-hydroxycoumarin and coumarin to produce 8-hydroxy-3,4-dihydrocoumarin and 3,4-dihydrocoumarin, respectively. Crystallographic analysis of XenA alone and in complex with the two substrates revealed insights into the mechanism. XenA shows a dimeric arrangement of two (beta/alpha)(8) barrel domains each binding one FMN cofactor. High resolution crystal structures of complexes with 8-hydroxycoumarin and coumarin show different modes of binding for these molecules in the active site. While coumarin is ideally positioned for hydride transfer from N-5 of the isoalloxazine ring to C-4 of coumarin, 8-hydroxycoumarin forms a non-productive complex with oxidised XenA. Orientation of 8-hydroxycoumarin in the active site appears to be dependent on the electronic state of the flavin. We postulate that XenA catalyses the last step of the 8-hydroxycoumarin pathway before the heterocyclic ring is hydrolysed to yield 3-(2,3-dihydroxyphenyl)-propionic acid. As XenA is also found in P. putida strains unable to degrade quinoline, it appears to have more than one physiological function and is an example of how enzymes with low substrate specificity can help to explain the variety of degradation pathways possible.
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Affiliation(s)
- Julia J Griese
- Laboratorium Proteinkristallographie, Universität Bayreuth, Germany
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44
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Khan H, Barna T, Bruce NC, Munro AW, Leys D, Scrutton NS. Proton transfer in the oxidative half-reaction of pentaerythritol tetranitrate reductase. Structure of the reduced enzyme-progesterone complex and the roles of residues Tyr186, His181 and His184. FEBS J 2005; 272:4660-71. [PMID: 16156787 DOI: 10.1111/j.1742-4658.2005.04875.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The roles of His181, His184 and Tyr186 in PETN reductase have been examined by mutagenesis, spectroscopic and stopped-flow kinetics, and by determination of crystallographic structures for the Y186F PETN reductase and reduced wild-type enzyme-progesterone complex. Residues His181 and His184 are important in the binding of coenzyme, steroids, nitroaromatic ligands and the substrate 2-cyclohexen-1-one. The H181A and H184A enzymes retain activity in reductive and oxidative half-reactions, and thus do not play an essential role in catalysis. Ligand binding and catalysis is not substantially impaired in Y186F PETN reductase, which contrasts with data for the equivalent mutation (Y196F) in Old Yellow Enzyme. The structure of Y186F PETN reductase is identical to wild-type enzyme, with the obvious exception of the mutation. We show in PETN reductase that Tyr186 is not a key proton donor in the reduction of alpha/beta unsaturated carbonyl compounds. The structure of two electron-reduced PETN reductase bound to the inhibitor progesterone mimics the catalytic enzyme-steroid substrate complex and is similar to the structure of the oxidized enzyme-inhibitor complex. The reactive C1-C2 unsaturated bond of the steroid is inappropriately orientated with the flavin N5 atom for hydride transfer. With steroid substrates, the productive conformation is achieved by orientating the steroid through flipping by 180 degrees , consistent with known geometries for hydride transfer in flavoenzymes. Our data highlight mechanistic differences between Old Yellow Enzyme and PETN reductase and indicate that catalysis requires a metastable enzyme-steroid complex and not the most stable complex observed in crystallographic studies.
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Affiliation(s)
- Huma Khan
- Department of Biochemistry, University of Leicester, UK
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45
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Messiha HL, Bruce NC, Sattelle BM, Sutcliffe MJ, Munro AW, Scrutton NS. Role of active site residues and solvent in proton transfer and the modulation of flavin reduction potential in bacterial morphinone reductase. J Biol Chem 2005; 280:27103-10. [PMID: 15905167 DOI: 10.1074/jbc.m502293200] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The reactions of several active site mutant forms of bacterial morphinone reductase (MR) with NADH and 2-cyclohexen-1-one as substrates have been studied by stopped-flow and steady-state kinetic methods and redox potentiometry. The enzymes were designed to (i) probe a role for potential proton donors (Tyr-72 and Tyr-356) in the oxidative half-reaction of MR; (ii) assess the function of a highly conserved tryptophan residue (Trp-106) in catalysis; (iii) investigate the role of Thr-32 in modulating the FMN reduction potential and catalysis. The Y72F and Y356F enzymes retained activity in both steady-state and stopped-flow kinetic studies, indicating they do not serve as key proton donors in the oxidative reaction of MR. Taken together with our recently published data (Messiha, H. L., Munro, A. W., Bruce, N. C., Barsukov, I., and Scrutton, N. S. (2005) J. Biol. Chem. 280, 4627-4631) that rule out roles for Cys-191 (corresponding with the proton donor, Tyr-196, in the structurally related OYE1 enzyme) and His-186 as proton donors, we infer solvent is the source of the proton in the oxidative half-reaction of MR. We demonstrate a key role for Thr-32 in modulating the reduction potential of the FMN, which is decreased approximately 50 mV in the T32A mutant MR. This effects a change in rate-limiting step in the catalytic cycle of the T32A enzyme with the oxidizing substrate 2-cyclohexenone. Despite the conservation of Trp-106 throughout the OYE family, we show this residue does not play a major role in catalysis, although affects on substrate and coenzyme binding are observed in a W106F enzyme. Our studies show some similarities, but also major differences, in the catalytic mechanism of MR and OYE1, and emphasize the need for caution in inferring mechanism by structural comparison of highly related enzymes in the absence of solution studies.
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Affiliation(s)
- Hanan L Messiha
- Department of Biochemistry, University of Leicester, University Road, Leicester LE1 7RH
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46
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Messiha HL, Munro AW, Bruce NC, Barsukov I, Scrutton NS. Reaction of Morphinone Reductase with 2-Cyclohexen-1-one and 1-Nitrocyclohexene. J Biol Chem 2005; 280:10695-709. [PMID: 15632179 DOI: 10.1074/jbc.m410595200] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Morphinone reductase (MR) catalyzes the NADH-dependent reduction of alpha/beta unsaturated carbonyl compounds in a reaction similar to that catalyzed by Old Yellow Enzyme (OYE1). The two enzymes are related at the sequence and structural levels, but key differences in active site architecture exist which have major implications for the reaction mechanism. We report detailed kinetic and solution NMR data for wild-type MR and two mutant forms in which residues His-186 and Asn-189 have been exchanged for alanine residues. We show that both residues are involved in the binding of the reducing nicotinamide coenzyme NADH and also the binding of the oxidizing substrates 2-cyclohexen-1-one and 1-nitrocyclohexene. Reduction of 2-cyclohexen-1-one by FMNH(2) is concerted with proton transfer from an unknown proton donor in the active site. NMR spectroscopy and flavin reoxidation studies with 2-cyclohexen-1-one are consistent with His-186 being unprotonated in oxidized, reduced, and ligand-bound MR, suggesting that His-186 is not the key proton donor required for the reduction of 2-cyclohexen-1-one. Hydride transfer is decoupled from proton transfer with 1-nitrocyclohexene as oxidizing substrate, and unlike with OYE1 the intermediate nitronate species produced after hydride transfer from FMNH(2) is not converted to 1-nitrocyclohexane. The work highlights key mechanistic differences in the reactions catalyzed by MR and OYE1 and emphasizes the need for caution in inferring mechanistic similarities in structurally related proteins.
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Affiliation(s)
- Hanan Latif Messiha
- Department of Biochemistry, University of Leicester, University Road, Leicester LE1 7RH, UK
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47
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Basran J, Harris RJ, Sutcliffe MJ, Scrutton NS. H-tunneling in the multiple H-transfers of the catalytic cycle of morphinone reductase and in the reductive half-reaction of the homologous pentaerythritol tetranitrate reductase. J Biol Chem 2003; 278:43973-82. [PMID: 12941965 DOI: 10.1074/jbc.m305983200] [Citation(s) in RCA: 90] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The mechanism of flavin reduction in morphinone reductase (MR) and pentaerythritol tetranitrate (PETN) reductase, and flavin oxidation in MR, has been studied by stopped-flow and steady-state kinetic methods. The temperature dependence of the primary kinetic isotope effect for flavin reduction in MR and PETN reductase by nicotinamide coenzyme indicates that quantum mechanical tunneling plays a major role in hydride transfer. In PETN reductase, the kinetic isotope effect (KIE) is essentially independent of temperature in the experimentally accessible range, contrasting with strongly temperature-dependent reaction rates, consistent with a tunneling mechanism from the vibrational ground state of the reactive C-H/D bond. In MR, both the reaction rates and the KIE are dependent on temperature, and analysis using the Eyring equation suggests that hydride transfer has a major tunneling component, which, unlike PETN reductase, is gated by thermally induced vibrations in the protein. The oxidative half-reaction of MR is fully rate-limiting in steady-state turnover with the substrate 2-cyclohexenone and NADH at saturating concentrations. The KIE for hydride transfer from reduced flavin to the alpha/beta unsaturated bond of 2-cyclohexenone is independent of temperature, contrasting with strongly temperature-dependent reaction rates, again consistent with ground-state tunneling. A large solvent isotope effect (SIE) accompanies the oxidative half-reaction, which is also independent of temperature in the experimentally accessible range. Double isotope effects indicate that hydride transfer from the flavin N5 atom to 2-cyclohexenone, and the protonation of 2-cyclohexenone, are concerted and both the temperature-independent KIE and SIE suggest that this reaction also proceeds by ground-state quantum tunneling. Our results demonstrate the importance of quantum tunneling in the reduction of flavins by nicotinamide coenzymes. This is the first observation of (i) three H-nuclei in an enzymic reaction being transferred by tunneling and (ii) the utilization of both passive and active dynamics within the same native enzyme.
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Affiliation(s)
- Jaswir Basran
- Department of Biochemistry, University of Leicester, University Road, Leicester LE1 7RH, United Kingdom
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48
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Rathbone DA, Lister DL, Bruce NC. Biotransformation of alkaloids. THE ALKALOIDS. CHEMISTRY AND BIOLOGY 2003; 58:1-82. [PMID: 12534248 DOI: 10.1016/s0099-9598(02)58002-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Biotransformations of alkaloids over the last decade have continued to encompass a wide variety of substrates and enzymes. The elucidation of novel alkaloid biosynthetic and catabolic pathways will continue to furnish new biocatalysts for the synthetic organic chemist. Furthermore, an improved understanding of the genetic and biochemical basis of metabolic pathways will also permit the engineering of pathways in plants and other heterologous hosts for the production of therapeutically important alkaloids. The combination of increasing commercial interest and advances in molecular biology will facilitate the availability of robust biocatalysts which are a prerequsite to achieve economically feasible processes for the production of alkaloid-based therapeutics.
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Affiliation(s)
- Deborah A Rathbone
- Institute of Biotechnology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QT, United Kingdom
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49
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Barna T, Messiha HL, Petosa C, Bruce NC, Scrutton NS, Moody PCE. Crystal structure of bacterial morphinone reductase and properties of the C191A mutant enzyme. J Biol Chem 2002; 277:30976-83. [PMID: 12048188 DOI: 10.1074/jbc.m202846200] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The crystal structure of the NADH-dependent bacterial flavoenzyme morphinone reductase (MR) has been determined at 2.2-A resolution in complex with the oxidizing substrate codeinone. The structure reveals a dimeric enzyme comprising two 8-fold beta/alpha barrel domains, each bound to FMN, and a subunit folding topology and mode of flavin-binding similar to that found in Old Yellow Enzyme (OYE) and pentaerythritol tetranitrate (PETN) reductase. The subunit interface of MR is formed by interactions from an N-terminal beta strand and helices 2 and 8 of the barrel domain and is different to that seen in OYE. The active site structures of MR, OYE, and PETN reductase are highly conserved reflecting the ability of these enzymes to catalyze "generic" reactions such as the reduction of 2-cyclohexenone. A region of polypeptide presumed to define the reducing coenzyme specificity is identified by comparison of the MR structure (NADH-dependent) with that of PETN reductase (NADPH-dependent). The active site acid identified in OYE (Tyr-196) and conserved in PETN reductase (Tyr-186) is replaced by Cys-191 in MR. Mutagenesis studies have established that Cys-191 does not act as a crucial acid in the mechanism of reduction of the olefinic bond found in 2-cyclohexenone and codeinone.
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Affiliation(s)
- Terez Barna
- Department of Biochemistry, University of Leicester, University Road, Leicester LE1 7RH, UK
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Williams RE, Bruce NC. 'New uses for an Old Enzyme'--the Old Yellow Enzyme family of flavoenzymes. MICROBIOLOGY (READING, ENGLAND) 2002; 148:1607-1614. [PMID: 12055282 DOI: 10.1099/00221287-148-6-1607] [Citation(s) in RCA: 201] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Affiliation(s)
- Richard E Williams
- Institute of Biotechnology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QT, UK1
| | - Neil C Bruce
- Institute of Biotechnology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QT, UK1
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