1
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Wu S, Wang Q, Ma X, Qiu L, Yan H. Modulation of the catalytic performance of OYE3 by engineering key residues at the entrance of the catalytic pocket. Biotechnol Appl Biochem 2023; 70:1720-1730. [PMID: 37073879 DOI: 10.1002/bab.2468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Revised: 03/18/2023] [Accepted: 04/07/2023] [Indexed: 04/20/2023]
Abstract
The amino acid residues at the entrance of the catalytic pocket may impose steric hindrance on the substrate to enter the active center of the enzyme. Based on the analysis of the three-dimensional structure of the Saccharomyces cerevisiae old yellow enzyme 3 (OYE3), four bulky residues were chosen and mutated to small amino acids. The results showed that mutation of the W116 residue had interesting impacts on the catalytic performance. All four variants became inactive for the reduction of (R)-carvone and (S)-carvone, but inverted the stereoselectivity for the reduction of (E/Z)-citral. The mutation of the F250 residue had a more positive effect on the activity and stereoselectivity. Two variants, F250A and F250S, showed excellent diastereoselectivity and activity for the reduction of (R)-carvone (de > 99%, c > 99%) and increased diastereoselectivity and activity for the reduction of (S)-carvone (de > 96%, c > 80%). One variant of the P295 residue, P295G, displayed excellent diastereoselectivity and activity only for the reduction of (R)-carvone (de > 99%, c > 99%). Mutation of the Y375 residue had a negative impact on the activity of the enzyme. These findings provide some solutions for rational enzyme engineering of OYE3.
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Affiliation(s)
- Shijin Wu
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Qiang Wang
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Xiaojing Ma
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Lequan Qiu
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Hongde Yan
- College of Pharmaceutical Engineering and Biotechnology, Zhejiang Pharmaceutical University, Ningbo, China
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2
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Van Galen CJ, Pauszek RF, Koder RL, Stanley RJ. Flavin Charge Redistribution upon Optical Excitation Is Independent of Solvent Polarity. J Phys Chem B 2023; 127:661-672. [PMID: 36649202 DOI: 10.1021/acs.jpcb.2c07266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Flavin absorption spectra encode molecular details of the flavin's local environment through coupling of local electric fields with the chromophore's charge redistribution upon optical excitation. Translating experimentally measured field-tuned transition energies to local electric field magnitudes and directions across a wide range of field magnitudes requires that the charge redistribution be independent of the local field. We have measured the charge redistribution upon optical excitation of the derivatized flavin TPARF in the non-hydrogen-bonding, nonpolar solvent toluene, with and without a tridentate hydrogen-bonding ligand, DBAP, using electronic Stark spectroscopy. These measurements were interpreted using TD-DFT finite field and difference density calculations. In comparing our present results to previous Stark spectroscopic analyses of flavin in more polar solvents, we conclude that flavin charge redistribution upon optical excitation is independent of solvent polarity, indicating that dependence of flavin transition energies on local field magnitude is linear with local field magnitude.
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Affiliation(s)
- Cornelius J Van Galen
- Department of Chemistry, Temple University, 1901 N. 13th St., 250B Beury Hall, Philadelphia, Pennsylvania19122, United States
| | - Raymond F Pauszek
- Department of Chemistry, Temple University, 1901 N. 13th St., 250B Beury Hall, Philadelphia, Pennsylvania19122, United States
| | - Ronald L Koder
- Department of Physics, The City College of New York, 1.308 CDI Bldg., 85 St. Nicholas Terrace, New York, New York10031, United States
| | - Robert J Stanley
- Department of Chemistry, Temple University, 1901 N. 13th St., 250B Beury Hall, Philadelphia, Pennsylvania19122, United States
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3
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Wu S, Wang B, Yan H. Semi-rational protein engineering of a novel ene-reductase from Galdieria sulphuraria for asymmetric reduction of (R)-carvone and ketoisophorone. Biotechnol Appl Biochem 2022; 70:697-706. [PMID: 35906824 DOI: 10.1002/bab.2391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 07/17/2022] [Indexed: 11/10/2022]
Abstract
Asymmetric reduction of (R)-carvone and ketoisophorone by an engineered ene-reductase from Galdieria sulphuraria (GsOYE) combined with glucose dehydrogenase for NADPH regeneration were studied. A semi-rational protein engineering was used to enhance the activity and selectivity of GsOYE. Upon the sequence alignment and molecular docking results, two amino acid residues at positions 66 and 270 were selected as saturation mutation sites. Finally, a single substitution variant of GsOYE-N270A with complete conversion (100%) and diastereoselectivity (dep >99%) for reduction of (R)-carvone and a double substitution variant GsOYE-Y66P/N270H with improved stereoselectivity for reduction of ketoisophorone were obtained. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Shijin Wu
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Bijiao Wang
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Hongde Yan
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China.,School of Chemistry and Pharmaceutical Engineering, Chongqing Industry Polytechnic College, Chongqing, China
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4
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Gao X, Turek-Herman JR, Choi YJ, Cohen RD, Hyster TK. Photoenzymatic Synthesis of α-Tertiary Amines by Engineered Flavin-Dependent "Ene"-Reductases. J Am Chem Soc 2021; 143:19643-19647. [PMID: 34784482 PMCID: PMC10157440 DOI: 10.1021/jacs.1c09828] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
α-Tertiary amines are a common motif in pharmaceutically important molecules but are challenging to prepare using asymmetric catalysis. Here, we demonstrate engineered flavin-dependent 'ene'-reductases (EREDs) can catalyze radical additions into oximes to prepare this motif. Two different EREDs were evolved into competent catalysts for this transformation with high levels of stereoselectivity. Mechanistic studies indicate that the oxime contributes to the enzyme templated charge-transfer complex formed between the substrate and cofactor. These products can be further derivatized to prepare a variety of motifs, highlighting the versatility of ERED photoenzymatic catalysis for organic synthesis.
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Affiliation(s)
- Xin Gao
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Joshua R Turek-Herman
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States.,Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Young Joo Choi
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Ryan D Cohen
- Analytical Research & Development, Merck & Company Inc., Rahway, New Jersey 07065, United States
| | - Todd K Hyster
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States.,Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
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5
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Fu H, Lam H, Emmanuel MA, Kim JH, Sandoval BA, Hyster TK. Ground-State Electron Transfer as an Initiation Mechanism for Biocatalytic C-C Bond Forming Reactions. J Am Chem Soc 2021; 143:9622-9629. [PMID: 34114803 DOI: 10.1021/jacs.1c04334] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The development of non-natural reaction mechanisms is an attractive strategy for expanding the synthetic capabilities of substrate promiscuous enzymes. Here, we report an "ene"-reductase catalyzed asymmetric hydroalkylation of olefins using α-bromoketones as radical precursors. Radical initiation occurs via ground-state electron transfer from the flavin cofactor located within the enzyme active site, an underrepresented mechanism in flavin biocatalysis. Four rounds of site saturation mutagenesis were used to access a variant of the "ene"-reductase nicotinamide-dependent cyclohexanone reductase (NCR) from Zymomonas mobiles capable of catalyzing a cyclization to furnish β-chiral cyclopentanones with high levels of enantioselectivity. Additionally, wild-type NCR can catalyze intermolecular couplings with precise stereochemical control over the radical termination step. This report highlights the utility for ground-state electron transfers to enable non-natural biocatalytic C-C bond forming reactions.
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Affiliation(s)
- Haigen Fu
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States.,Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14850, United States
| | - Heather Lam
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States.,Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14850, United States
| | - Megan A Emmanuel
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Ji Hye Kim
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Braddock A Sandoval
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Todd K Hyster
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States.,Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14850, United States
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6
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Old yellow enzymes: structures and structure-guided engineering for stereocomplementary bioreduction. Appl Microbiol Biotechnol 2020; 104:8155-8170. [PMID: 32830294 DOI: 10.1007/s00253-020-10845-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 08/07/2020] [Accepted: 08/17/2020] [Indexed: 10/23/2022]
Abstract
Since the first discovery of old yellow enzyme 1 (OYE1) from Saccharomyces pastorianus in 1932, biocatalytic asymmetric reduction of activated alkenes by OYEs has become a valuable reaction in organic synthesis. To access stereocomplementary C=C-bond bioreduction, the mining of novel OYEs and especially the protein engineering of existing OYEs have been performed, which successfully achieved the stereocomplementary reduction in several cases and further raise the potential of applications. In this review, we analyzed the structures, active sites, and substrate recognition of OYEs, which are the bases for their substrate specificity and stereospecificity. Sequence similarity network of OYEs superfamily was also constructed to investigate the scope of characterized OYEs. The structure-guided engineering to switch the stereoselectivity of OYEs and thus access stereocomplementary bioreduction over the last decade (2009-2020) was then reviewed and discussed, which might give new insights into the mining and engineering of related biocatalysts. KEY POINTS: • The sequence similarity network of OYEs superfamily was constructed and annotated. • The structures and active sites of OYEs from different classes were compared. • "Left/right" binding mode was used to explain the stereopreferences of OYEs. • Structure-guided engineering of OYEs to switch their stereoselectivity was reviewed.
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7
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Colombo D, Brenna E, Gatti FG, Ghezzi MC, Monti D, Parmeggiani F, Tentori F. Chemoselective Biohydrogenation of Alkenes in the Presence of Alkynes for the Homologation of 2‐Alkynals/3‐Alkyn‐2‐ones into 4‐Alkynals/Alkynols. Adv Synth Catal 2019. [DOI: 10.1002/adsc.201900177] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Danilo Colombo
- Dipartimento di ChimicaMateriali ed Ingegneria Chimica “Giulio Natta” Politecnico di Milano Via Mancinelli, 7 20131 Milano Italy
| | - Elisabetta Brenna
- Dipartimento di ChimicaMateriali ed Ingegneria Chimica “Giulio Natta” Politecnico di Milano Via Mancinelli, 7 20131 Milano Italy
| | - Francesco G. Gatti
- Dipartimento di ChimicaMateriali ed Ingegneria Chimica “Giulio Natta” Politecnico di Milano Via Mancinelli, 7 20131 Milano Italy
| | - Maria Chiara Ghezzi
- Dipartimento di ChimicaMateriali ed Ingegneria Chimica “Giulio Natta” Politecnico di Milano Via Mancinelli, 7 20131 Milano Italy
| | - Daniela Monti
- Istituto di Chimica del Riconoscimento Molecolare, C.N.R. Via Mario Bianco, 9 20131 Milano Italy
| | - Fabio Parmeggiani
- Dipartimento di ChimicaMateriali ed Ingegneria Chimica “Giulio Natta” Politecnico di Milano Via Mancinelli, 7 20131 Milano Italy
| | - Francesca Tentori
- Dipartimento di ChimicaMateriali ed Ingegneria Chimica “Giulio Natta” Politecnico di Milano Via Mancinelli, 7 20131 Milano Italy
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8
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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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9
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Powell, III RW, Buteler MP, Lenka S, Crotti M, Santangelo S, Burg MJ, Bruner S, Brenna E, Roitberg AE, Stewart JD. Investigating Saccharomyces cerevisiae alkene reductase OYE 3 by substrate profiling, X-ray crystallography and computational methods. Catal Sci Technol 2018. [DOI: 10.1039/c8cy00440d] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Saccharomyces cerevisiae OYE 3 and OYE 1 share 80% sequence identity, but sometimes differ in stereoselectivities.
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Affiliation(s)
| | - M. Pilar Buteler
- Department of Chemistry
- 126 Sisler Hall
- University of Florida
- Gainesville
- USA
| | - Sunidhi Lenka
- Department of Chemistry
- 126 Sisler Hall
- University of Florida
- Gainesville
- USA
| | - Michele Crotti
- Dipartimento di Chimica
- Materiali ed Ingegneria Chimica “Giulio Natta” Politecnico di Milano
- Milano
- Italy
| | - Sara Santangelo
- Dipartimento di Chimica
- Materiali ed Ingegneria Chimica “Giulio Natta” Politecnico di Milano
- Milano
- Italy
| | - Matthew J. Burg
- Department of Chemistry
- 126 Sisler Hall
- University of Florida
- Gainesville
- USA
| | - Steven Bruner
- Department of Chemistry
- 126 Sisler Hall
- University of Florida
- Gainesville
- USA
| | - Elisabetta Brenna
- Dipartimento di Chimica
- Materiali ed Ingegneria Chimica “Giulio Natta” Politecnico di Milano
- Milano
- Italy
| | - Adrian E. Roitberg
- Department of Chemistry
- 126 Sisler Hall
- University of Florida
- Gainesville
- USA
| | - Jon D. Stewart
- Department of Chemistry
- 126 Sisler Hall
- University of Florida
- Gainesville
- USA
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10
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Opperman DJ. Structural investigation into the C-terminal extension of the ene-reductase from Ralstonia (Cupriavidus) metallidurans. Proteins 2017; 85:2252-2257. [PMID: 28833623 DOI: 10.1002/prot.25372] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Revised: 08/16/2017] [Accepted: 08/18/2017] [Indexed: 01/25/2023]
Abstract
Ene-reductases (ERs), or Old Yellow Enzymes, catalyze the asymmetric reduction of various activated alkenes. This class of biocatalysts is considered an attractive alternative to current chemical technologies for hydrogenation due to their high selectivity and specificity. Here the X-ray crystal structure of RmER, a "thermophilic"-like ER from Ralstonia (Cupriavidus) metallidurans, is reported. Unlike other members of this class of ERs, RmER is monomeric in solution which we previously related to its atypical elongated C-terminus. A typical dimer interface was however observed in our crystal structure, with the conserved Arg-"finger" forming part of the adjacent monomer's active site and the elongated C-terminus extending into the active site through contacting the "capping" domain. This dimerization also resulted in the loss of one FMN cofactor from each dimer pair. This potential transient dimerization and dissociation of FMN could conceivably explain the rapid rates previously observed when an FMN light-driven cofactor regeneration system was used during catalysis with RmER.
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Affiliation(s)
- Diederik J Opperman
- Department of Biotechnology, University of the Free State, 205 Nelson Mandela Drive, Bloemfontein, 9300, South Africa
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11
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Waller J, Toogood HS, Karuppiah V, Rattray NJW, Mansell DJ, Leys D, Gardiner JM, Fryszkowska A, Ahmed ST, Bandichhor R, Reddy GP, Scrutton NS. Structural insights into the ene-reductase synthesis of profens. Org Biomol Chem 2017; 15:4440-4448. [PMID: 28485453 DOI: 10.1039/c7ob00163k] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Reduction of double bonds of α,β-unsaturated carboxylic acids and esters by ene-reductases remains challenging and it typically requires activation by a second electron-withdrawing moiety, such as a halide or second carboxylate group. We showed that profen precursors, 2-arylpropenoic acids and their esters, were efficiently reduced by Old Yellow Enzymes (OYEs). The XenA and GYE enzymes showed activity towards acids, while a wider range of enzymes were active towards the equivalent methyl esters. Comparative co-crystal structural analysis of profen-bound OYEs highlighted key interactions important in determining substrate binding in a catalytically active conformation. The general utility of ene reductases for the synthesis of (R)-profens was established and this work will now drive future mutagenesis studies to screen for the production of pharmaceutically-active (S)-profens.
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Affiliation(s)
- J Waller
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
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12
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Kress N, Rapp J, Hauer B. Enantioselective Reduction of Citral Isomers in NCR Ene Reductase: Analysis of an Active-Site Mutant Library. Chembiochem 2017; 18:717-720. [PMID: 28176464 DOI: 10.1002/cbic.201700011] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Indexed: 11/12/2022]
Abstract
A deeper understanding of the >99 % S-selective reduction of both isomers of citral catalyzed by NCR ene reductase was achieved by active-site mutational studies and docking simulation. Though structurally similar, the E/Z isomers of citral showed a significantly varying selectivity response to introduced mutations. Although it was possible to invert (E)-citral reduction enantioselectivity to ee 46 % (R) by introducing mutation W66A, for (Z)-citral it remained ≥88 % (S) for all single-residue variants. Residue 66 seems to act as a lever for opposite binding modes. This was underlined by a W66A-based double-mutant library that enhanced the (E)-citral derived enantioselectivity to 63 % (R) and significantly lowered the S selectivity for (Z)-citral to 44 % (S). Formation of (R)-citronellal from an (E/Z)-citral mixture is a desire in industrial (-)-menthol synthesis. Our findings pave the way for a rational enzyme engineering solution.
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Affiliation(s)
- Nico Kress
- Institute of Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Johanna Rapp
- 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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13
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Nett N, Duewel S, Richter AA, Hoebenreich S. Revealing Additional Stereocomplementary Pairs of Old Yellow Enzymes by Rational Transfer of Engineered Residues. Chembiochem 2017; 18:685-691. [PMID: 28107586 DOI: 10.1002/cbic.201600688] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Indexed: 01/01/2023]
Abstract
Every year numerous protein engineering and directed evolution studies are published, increasing the knowledge that could be used by protein engineers. Here we test a protein engineering strategy that allows quick access to improved biocatalysts with very little screening effort. Conceptually it is assumed that engineered residues previously identified by rational and random methods induce similar improvements when transferred to family members. In an application to ene-reductases from the Old Yellow Enzyme (OYE) family, the newly created variants were tested with three compounds, revealing more stereocomplementary OYE pairs with potent turnover frequencies (up to 660 h-1 ) and excellent stereoselectivities (up to >99 %). Although systematic prediction of absolute enantioselectivity of OYE variants remains a challenge, "scaffold sampling" was confirmed as a promising addition to protein engineers' collection of strategies.
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Affiliation(s)
- Nathalie Nett
- Department of Chemistry, Philipps-Universität Marburg, Hans-Meerwein-Strasse 4, 35032, Marburg, Germany
| | - Sabine Duewel
- Department of Chemistry, Philipps-Universität Marburg, Hans-Meerwein-Strasse 4, 35032, Marburg, Germany
| | - Alexandra Annelis Richter
- Department of Chemistry, Philipps-Universität Marburg, Hans-Meerwein-Strasse 4, 35032, Marburg, Germany
| | - Sabrina Hoebenreich
- Department of Chemistry, Philipps-Universität Marburg, Hans-Meerwein-Strasse 4, 35032, Marburg, Germany
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14
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15
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Reich S, Nestl BM, Hauer B. Loop-Grafted Old Yellow Enzymes in the Bienzymatic Cascade Reduction of Allylic Alcohols. Chembiochem 2016; 17:561-5. [DOI: 10.1002/cbic.201500604] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Indexed: 11/05/2022]
Affiliation(s)
- Sabrina Reich
- Institute of Technical Biochemistry; Universität Stuttgart; Allmandring 31 70569 Stuttgart Germany
| | - Bettina M. Nestl
- Institute of Technical Biochemistry; Universität Stuttgart; Allmandring 31 70569 Stuttgart Germany
| | - Bernhard Hauer
- Institute of Technical Biochemistry; Universität Stuttgart; Allmandring 31 70569 Stuttgart Germany
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16
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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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17
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Reß T, Hummel W, Hanlon SP, Iding H, Gröger H. The Organic-Synthetic Potential of Recombinant Ene Reductases: Substrate-Scope Evaluation and Process Optimization. ChemCatChem 2015. [DOI: 10.1002/cctc.201402903] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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18
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Daugherty AB, Horton JR, Cheng X, Lutz S. STRUCTURAL AND FUNCTIONAL CONSEQUENCES OF CIRCULAR PERMUTATION ON THE ACTIVE SITE OF OLD YELLOW ENZYME. ACS Catal 2015; 5:892-899. [PMID: 25692074 PMCID: PMC4327928 DOI: 10.1021/cs501702k] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
Circular
permutation of the NADPH-dependent oxidoreductase
Old Yellow Enzyme from Saccharomyces pastorianus (OYE1) can significantly enhance the enzyme’s catalytic performance.
Termini relocation into four regions of the protein (sectors I–IV)
near the active site has proven effective in altering enzyme function.
To better understand the structural consequences and rationalize the
observed functional gains in these OYE1 variants, we selected representatives
from sectors I–III for further characterization by biophysical
methods and X-ray crystallography. These investigations not only show
trends in enzyme stability and quaternary structure as a function
of termini location but also provide a possible explanation for the
catalytic gains in our top-performing OYE variant (new N-terminus
at residue 303; sector III). Crystallographic analysis indicates that
termini relocation into sector III affects the loop β6 region
(amino acid positions: 290–310) of OYE1, which forms a lid
over the active site. Peptide backbone cleavage greatly enhances local
flexibility, effectively converting the loop into a tether and consequently
increasing the environmental exposure of the active site. Interestingly,
such an active site remodeling does not negatively impact the enzyme’s
activity and stereoselectivity; neither does it perturb the conformation
of other key active site residues with the exception of Y375. These
observations were confirmed in truncation experiments, deleting all
residues of the loop β6 region in our OYE variant. Intrigued
by the finding that circular permutation leaves most of the key catalytic
residues unchanged, we also tested OYE permutants for possible additive
or synergistic effects of amino acid substitutions. Distinct functional
changes in these OYE variants were detected upon mutations at W116,
known in native OYE1 to cause inversion of diastereoselectivity for
(S)-carvone reduction. Our findings demonstrate the
contribution of loop β6 toward determining the stereoselectivity
of OYE1, an important insight for future OYE engineering efforts.
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Affiliation(s)
- Ashley B. Daugherty
- Department
of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, Georgia 30322. United States
| | - John R. Horton
- Department
of Biochemistry, Emory University, 1510 Clifton Rd., Atlanta, Georgia 30322, United States
| | - Xiaodong Cheng
- Department
of Biochemistry, Emory University, 1510 Clifton Rd., Atlanta, Georgia 30322, United States
| | - Stefan Lutz
- Department
of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, Georgia 30322. United States
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19
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Zhou X, Chow HL, Wu JC. Bioreduction of activated alkenes by a novel “ene”-reductase from the thermophilic strainBacillus coagulansWCP10-4. BIOCATAL BIOTRANSFOR 2014. [DOI: 10.3109/10242422.2014.974574] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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20
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Patterson-Orazem A, Sullivan B, Stewart JD. Pichia stipitis OYE 2.6 variants with improved catalytic efficiencies from site-saturation mutagenesis libraries. Bioorg Med Chem 2014; 22:5628-32. [PMID: 25087048 DOI: 10.1016/j.bmc.2014.07.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2014] [Revised: 06/23/2014] [Accepted: 07/01/2014] [Indexed: 01/25/2023]
Abstract
An earlier directed evolution project using alkene reductase OYE 2.6 from Pichia stipitis yielded 13 active site variants with improved properties toward three homologous Baylis-Hillman adducts. Here, we probed the generality of these improvements by testing the wild-type and all 13 variants against a panel of 16 structurally-diverse electron-deficient alkenes. Several substrates were sterically demanding, and as hoped, creating additional active site volume yielded better conversions for these alkenes. The most impressive improvement was found for 2-butylidenecyclohexanone. The wild-type provided less than 20% conversion after 24h; a triple mutant afforded more than 60% conversion in the same time period. Moreover, even wild-type OYE 2.6 can reduce cyclohexenones with very bulky 4-substituents efficiently.
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Affiliation(s)
| | - Bradford Sullivan
- Department of Chemistry, University of Florida, 126 Sisler Hall, Gainesville, FL 32611, USA
| | - Jon D Stewart
- Department of Chemistry, University of Florida, 126 Sisler Hall, Gainesville, FL 32611, USA.
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21
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Walton AZ, Sullivan B, Patterson-Orazem AC, Stewart JD. Residues Controlling Facial Selectivity in an Alkene Reductase and Semirational Alterations to Create Stereocomplementary Variants. ACS Catal 2014; 4:2307-2318. [PMID: 25068071 PMCID: PMC4105185 DOI: 10.1021/cs500429k] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Revised: 05/22/2014] [Indexed: 01/07/2023]
Abstract
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A systematic
saturation mutagenesis campaign was carried out on
an alkene reductase from Pichia stipitis (OYE 2.6) to develop variants with reversed stereoselectivities.
Wild-type OYE 2.6 reduces three representative Baylis–Hillman
adducts to the corresponding S products with almost
complete stereoselectivities and good catalytic efficiencies. We created
and screened 13 first-generation, site-saturation mutagenesis libraries,
targeting residues found near the bound substrate. One variant (Tyr78Trp)
showed high R selectivity
toward one of the three substrates, but no change (cyclohexenone derivative)
and no catalytic activity (acrylate derivative) for the other two.
Subsequent rounds of mutagenesis retained the Tyr78Trp mutation and
explored other residues that impacted stereoselectivity when altered
in a wild-type background. These efforts yielded double and triple
mutants that possessed inverted stereoselectivities for two of the
three substrates (conversions >99% and at least 91% ee (R)). To understand the reasons underlying the stereochemical
changes,
we solved crystal structures of two key mutants: Tyr78Trp and Tyr78Trp/Ile113Cys,
the latter with substrate partially occupying the active site. By
combining these experimental data with modeling studies, we have proposed
a rationale that explains the impacts of the most useful mutations.
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Affiliation(s)
- Adam Z. Walton
- Department of Chemistry, 126 Sisler Hall, University of Florida, Gainesville, Florida 32611 United States
| | - Bradford Sullivan
- Department of Chemistry, 126 Sisler Hall, University of Florida, Gainesville, Florida 32611 United States
| | - Athéna C. Patterson-Orazem
- Department of Chemistry, 126 Sisler Hall, University of Florida, Gainesville, Florida 32611 United States
| | - Jon D. Stewart
- Department of Chemistry, 126 Sisler Hall, University of Florida, Gainesville, Florida 32611 United States
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22
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Toogood HS, Scrutton NS. New developments in 'ene'-reductase catalysed biological hydrogenations. Curr Opin Chem Biol 2014; 19:107-15. [PMID: 24608082 DOI: 10.1016/j.cbpa.2014.01.019] [Citation(s) in RCA: 98] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2013] [Revised: 12/13/2013] [Accepted: 01/30/2014] [Indexed: 01/07/2023]
Abstract
Asymmetric biocatalytic hydrogenations are important reactions performed primarily by members of the Old Yellow Enzyme family. These reactions have great potential in the chemosynthesis of a variety of industrially useful synthons due to the generation of up to two stereogenic centres. In this review, additional enzyme classes capable of asymmetric hydrogenations will be discussed, as will examples of multienzyme cascading reactions. New and improved technology that enhances the commercial viability of biotransformations are included, such as the nicotinamide coenzyme-independent reactions. This review will focus on progress in this field within the last two years, with emphasis on industrial applications of this technology.
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Affiliation(s)
- Helen S Toogood
- Manchester Institute of Biotechnology, Faculty of Life Sciences, University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
| | - Nigel S Scrutton
- Manchester Institute of Biotechnology, Faculty of Life Sciences, University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
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23
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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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24
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Pompeu YA, Sullivan B, Stewart JD. X-ray Crystallography Reveals How Subtle Changes Control the Orientation of Substrate Binding in an Alkene Reductase. ACS Catal 2013. [DOI: 10.1021/cs400622e] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yuri A. Pompeu
- Department
of Chemistry, University of Florida, 126 Sisler Hall, Gainesville, Florida 32611, United States
| | - Bradford Sullivan
- Department
of Chemistry, University of Florida, 126 Sisler Hall, Gainesville, Florida 32611, United States
| | - Jon D. Stewart
- Department
of Chemistry, University of Florida, 126 Sisler Hall, Gainesville, Florida 32611, United States
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25
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Daugherty AB, Govindarajan S, Lutz S. Improved biocatalysts from a synthetic circular permutation library of the flavin-dependent oxidoreductase old yellow enzyme. J Am Chem Soc 2013; 135:14425-32. [PMID: 23987134 DOI: 10.1021/ja4074886] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Members of the old yellow enzyme (OYE) family are widely used, effective biocatalysts for the stereoselective trans-hydrogenation of activated alkenes. To further expand their substrate scope and improve catalytic performance, we have applied a protein engineering strategy called circular permutation (CP) to enhance the function of OYE1 from Saccharomyces pastorianus. CP can influence a biocatalyst's function by altering protein backbone flexibility and active site accessibility, both critical performance features because the catalytic cycle for OYE1 is thought to involve rate-limiting conformational changes. To explore the impact of CP throughout the OYE1 protein sequence, we implemented a highly efficient approach for cell-free cpOYE library preparation by combining whole-gene synthesis with in vitro transcription/translation. The versatility of such an ex vivo system was further demonstrated by the rapid and reliable functional evaluation of library members under variable environmental conditions with three reference substrates ketoisophorone, cinnamaldehyde, and (S)-carvone. Library analysis identified over 70 functional OYE1 variants with several biocatalysts exhibiting over an order of magnitude improved catalytic activity. Although catalytic gains of individual cpOYE library members vary by substrate, the locations of new protein termini in functional variants for all tested substates fall within the same four distinct loop/lid regions near the active site. Our findings demonstrate the importance of these structural elements in enzyme function and support the hypothesis of conformational flexibility as a limiting factor for catalysis in wild type OYE.
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Affiliation(s)
- Ashley B Daugherty
- Department of Chemistry, Emory University , 1515 Dickey Drive, Atlanta, Georgia 30084, United States
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26
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Burda E, Reß T, Winkler T, Giese C, Kostrov X, Huber T, Hummel W, Gröger H. Highly Enantioselective Reduction of α-Methylated Nitroalkenes. Angew Chem Int Ed Engl 2013; 52:9323-6. [DOI: 10.1002/anie.201301814] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2013] [Indexed: 11/09/2022]
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27
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Burda E, Reß T, Winkler T, Giese C, Kostrov X, Huber T, Hummel W, Gröger H. Hochenantioselektive Reduktion von α‐methylierten Nitroalkenen. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201301814] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Edyta Burda
- Department Chemie und Pharmazie, Universität Erlangen‐Nürnberg, Henkestraße 42, 91054 Erlangen (Deutschland)
| | - Tina Reß
- Department Chemie und Pharmazie, Universität Erlangen‐Nürnberg, Henkestraße 42, 91054 Erlangen (Deutschland)
- Aktuelle Adresse: Fakultät für Chemie, Universität Bielefeld, Universitätsstraße 25, 33615 Bielefeld (Deutschland)
| | - Till Winkler
- Institut für Molekulare Enzymtechnologie der Heinrich‐Heine‐Universität Düsseldorf, Forschungszentrum Jülich, Stetternicher Forst, 52426 Jülich (Deutschland)
| | - Carolin Giese
- Department Chemie und Pharmazie, Universität Erlangen‐Nürnberg, Henkestraße 42, 91054 Erlangen (Deutschland)
- Aktuelle Adresse: Fakultät für Chemie, Universität Bielefeld, Universitätsstraße 25, 33615 Bielefeld (Deutschland)
| | - Xenia Kostrov
- Department Chemie und Pharmazie, Universität Erlangen‐Nürnberg, Henkestraße 42, 91054 Erlangen (Deutschland)
| | - Tobias Huber
- Department Chemie und Pharmazie, Universität Erlangen‐Nürnberg, Henkestraße 42, 91054 Erlangen (Deutschland)
| | - Werner Hummel
- Institut für Molekulare Enzymtechnologie der Heinrich‐Heine‐Universität Düsseldorf, Forschungszentrum Jülich, Stetternicher Forst, 52426 Jülich (Deutschland)
| | - Harald Gröger
- Department Chemie und Pharmazie, Universität Erlangen‐Nürnberg, Henkestraße 42, 91054 Erlangen (Deutschland)
- Aktuelle Adresse: Fakultät für Chemie, Universität Bielefeld, Universitätsstraße 25, 33615 Bielefeld (Deutschland)
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