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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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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3
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Hagiwara H. Introduction of Chiral Centers to α- and/or β-Positions of Carbonyl Groups by Biocatalytic Asymmetric Reduction of α,β-Unsaturated Carbonyl Compounds. Nat Prod Commun 2022. [DOI: 10.1177/1934578x221099054] [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
Biocatalytic asymmetric reductions of acyclic and cyclic α,β-unsaturated carbonyl compounds are favorable protocols for introduction of chiral centers to α- and/or β-positions of the carbonyl groups. Representative biocatalytic reductions of electron deficient olefins are compiled from a synthetic point of view according to compound types from the papers in 2012 to early 2022. Applications to syntheses of some enantiomericaly enriched perfumery ingredients are presented to show the feasibility of the biocatalytic reductions.
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Affiliation(s)
- Hisahiro Hagiwara
- Graduate School of Science and Technology, Niigata University, 8050, 2-Nocho, Ikarashi, Nishi-ku, Niigata, 950-2181, Japan
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4
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Ogawa Y, Katsuyama Y, Ohnishi Y. Engineering of the Ligand Specificity of Transcriptional Regulator XylS by Deep Mutational Scanning. ACS Synth Biol 2022; 11:473-485. [PMID: 34964613 DOI: 10.1021/acssynbio.1c00564] [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: 11/28/2022]
Abstract
Deep mutational scanning is a method for protein engineering. Here, we applied it to alter the ligand specificity of the transcriptional regulator XylS from Pseudomonas putida to recognize p-toluic acid instead of the native ligand m-toluic acid. For this purpose, we used an antibiotic resistance gene-based dual screening system, which was constructed for the directed evolution of XylS toward the above-mentioned ligand specificity. We constructed a xylS mutant library in which each codon for the amino acid residue of the putative ligand-binding domain (residues 1-213, except 7th residue) was randomized to generate all possible single amino acid-substituted XylS variants and introduced it into Escherichia coli harboring the selection plasmid for the screening system. The cells were cultured in the presence of appropriate antibiotics and m-toluic acid or p-toluic acid, and the frequency of each mutation present in the library was examined using a next-generation sequencer before and after cultivation. Heatmaps showing the enrichment score of each XylS variant were obtained. By searching for a p-toluic-acid-specific heatmap pattern, we focused on G71 and H77. Analysis of the ligand specificities of G71- or H77-substituted XylS variants revealed that several G71-substituted XylS variants responded specifically to p-toluic acid. Thus, the 71st residue was found to be an unprecedented residue that is important for switching ligand specificity. Our study demonstrated the usefulness of deep mutational scanning in engineering the ligand specificity of a transcriptional regulator without structural information. We also discussed the advantages and disadvantages of deep mutational scanning compared with directed evolution.
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Affiliation(s)
- Yuki Ogawa
- Department of Biotechnology, The Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Yohei Katsuyama
- Department of Biotechnology, The Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Yasuo Ohnishi
- Department of Biotechnology, The Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
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5
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Toogood HS, Scrutton NS. Discovery, Characterisation, Engineering and Applications of Ene Reductases for Industrial Biocatalysis. ACS Catal 2019; 8:3532-3549. [PMID: 31157123 PMCID: PMC6542678 DOI: 10.1021/acscatal.8b00624] [Citation(s) in RCA: 158] [Impact Index Per Article: 31.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Recent studies of multiple enzyme families collectively referred to as ene-reductases (ERs) have highlighted potential industrial application of these biocatalysts in the production of fine and speciality chemicals. Processes have been developed whereby ERs contribute to synthetic routes as isolated enzymes, components of multi-enzyme cascades, and more recently in metabolic engineering and synthetic biology programmes using microbial cell factories to support chemicals production. The discovery of ERs from previously untapped sources and the expansion of directed evolution screening programmes, coupled to deeper mechanistic understanding of ER reactions, have driven their use in natural product and chemicals synthesis. Here we review developments, challenges and opportunities for the use of ERs in fine and speciality chemicals manufacture. The ER research field is rapidly expanding and the focus of this review is on developments that have emerged predominantly over the last 4 years.
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Affiliation(s)
- Helen S. Toogood
- School of Chemistry, Faculty of Science and Engineering, University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
| | - Nigel S. Scrutton
- School of Chemistry, Faculty of Science and Engineering, University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
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6
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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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7
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Abstract
The diverse chemistry possible with flavin cofactors positions flavin-dependent enzymes as versatile synthetic tools. This focused review highlights applications of flavin-dependent enzymes in organic synthesis. Select examples of monoamine oxidases, ene-reductases, monooxygenases and halogenases in target-oriented synthesis are presented.
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Affiliation(s)
- Summer A. Baker Dockrey
- Department of Chemistry, University of Michigan, Ann Arbor Michigan, 48109
- Life Sciences Institute, University of Michigan, Ann Arbor Michigan, 48109
| | - Alison R. H. Narayan
- Department of Chemistry, University of Michigan, Ann Arbor Michigan, 48109
- Life Sciences Institute, University of Michigan, Ann Arbor Michigan, 48109
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8
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Kreß N, Halder JM, Rapp LR, Hauer B. Unlocked potential of dynamic elements in protein structures: channels and loops. Curr Opin Chem Biol 2018; 47:109-116. [DOI: 10.1016/j.cbpa.2018.09.010] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 08/22/2018] [Accepted: 09/11/2018] [Indexed: 10/28/2022]
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9
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Horita S, Kataoka M, Kitamura N, Miyakawa T, Ohtsuka J, Maejima Y, Shimomura K, Nagata K, Shimizu S, Tanokura M. Structural basis of different substrate preferences of two old yellow enzymes from yeasts in the asymmetric reduction of enone compounds. Biosci Biotechnol Biochem 2018; 83:456-462. [PMID: 30445889 DOI: 10.1080/09168451.2018.1543014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Old yellow enzymes (OYEs) are potential targets of protein engineering for useful biocatalysts because of their excellent asymmetric reductions of enone compounds. Two OYEs from different yeast strains, Candida macedoniensis AKU4588 OYE (CmOYE) and Pichia sp. AKU4542 OYE (PsOYE), have a sequence identity of 46%, but show different substrate preferences; PsOYE shows 3.4-fold and 39-fold higher catalytic activities than CmOYE toward ketoisophorone and (4S)-phorenol, respectively. To gain insights into structural basis of their different substrate preferences, we have solved a crystal structure of PsOYE, and compared its catalytic site structure with that of CmOYE, revealing the catalytic pocket of PsOYE is wider than that of CmOYE due to different positions of Phe246 (PsOYE)/Phe250 (CmOYE) in static Loop 5. This study shows a significance of 3D structural information to explain the different substrate preferences of yeast OYEs which cannot be understood from their amino acid sequences. Abbreviations: OYE: Old yellow enzymes, CmOYE: Candida macedoniensis AKU4588 OYE, PsOYE: Pichia sp. AKU4542 OYE.
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Affiliation(s)
- Shoichiro Horita
- a Department of Applied Biologic al Chemistry , Graduate School of Agricultural and Life Sciences, University of Tokyo , Tokyo , Japan.,b Department of Bioregulation and Pharmacological Medicine , Fukushima Medical University School of Medicine , Fukushima , Japan
| | - Michihiko Kataoka
- c Division of Applied Life Sciences , Graduate School of Life and Environmental Sciences, Osaka Prefecture University , Osaka , Japan
| | - Nahoko Kitamura
- d Division of Applied Life Sciences , Graduate School of Agriculture, Kyoto University , Kyoto , Japan
| | - Takuya Miyakawa
- a Department of Applied Biologic al Chemistry , Graduate School of Agricultural and Life Sciences, University of Tokyo , Tokyo , Japan
| | - Jun Ohtsuka
- a Department of Applied Biologic al Chemistry , Graduate School of Agricultural and Life Sciences, University of Tokyo , Tokyo , Japan
| | - Yuko Maejima
- b Department of Bioregulation and Pharmacological Medicine , Fukushima Medical University School of Medicine , Fukushima , Japan
| | - Kenju Shimomura
- b Department of Bioregulation and Pharmacological Medicine , Fukushima Medical University School of Medicine , Fukushima , Japan
| | - Koji Nagata
- a Department of Applied Biologic al Chemistry , Graduate School of Agricultural and Life Sciences, University of Tokyo , Tokyo , Japan
| | - Sakayu Shimizu
- d Division of Applied Life Sciences , Graduate School of Agriculture, Kyoto University , Kyoto , Japan
| | - Masaru Tanokura
- a Department of Applied Biologic al Chemistry , Graduate School of Agricultural and Life Sciences, University of Tokyo , Tokyo , Japan
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10
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Winkler CK, Faber K, Hall M. Biocatalytic reduction of activated CC-bonds and beyond: emerging trends. Curr Opin Chem Biol 2018; 43:97-105. [PMID: 29275291 DOI: 10.1016/j.cbpa.2017.12.003] [Citation(s) in RCA: 84] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Revised: 11/02/2017] [Accepted: 12/04/2017] [Indexed: 01/01/2023]
Abstract
The biocatalytic reduction of activated CC-bonds is dominated by ene-reductases from the Old Yellow Enzyme family, which gained broad practical use owing to exquisite stereoselectivity combined with wide substrate scope. Protein diversity is fostered by mining distinct protein classes and by implementing protein engineering techniques. Recent efforts are focusing on expanding the chemical complexity of the product portfolio, either through substrate functionalization or design of multi-step reactions. This review also highlights unusual chemistries catalyzed by ene-reductases and presents emerging methodologies developed to bypass the need of natural nicotinamide cofactors.
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Affiliation(s)
| | - Kurt Faber
- Department of Chemistry, University of Graz, Heinrichstrasse 28, 8010 Graz, Austria
| | - Mélanie Hall
- Department of Chemistry, University of Graz, Heinrichstrasse 28, 8010 Graz, Austria.
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11
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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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12
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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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13
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Tavanti M, Parmeggiani F, Castellanos JRG, Mattevi A, Turner NJ. One-Pot Biocatalytic Double Oxidation of α-Isophorone for the Synthesis of Ketoisophorone. ChemCatChem 2017. [DOI: 10.1002/cctc.201700620] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Michele Tavanti
- Manchester Institute of Biotechnology (MIB); School of Chemistry; The University of Manchester; 131 Princess Street M1 7DN Manchester United Kingdom
| | - Fabio Parmeggiani
- Manchester Institute of Biotechnology (MIB); School of Chemistry; The University of Manchester; 131 Princess Street M1 7DN Manchester United Kingdom
| | - J. Rubén Gómez Castellanos
- Department of Biology and Biotechnology “Lazzaro Spallanzani”; University of Pavia; Via Ferrata 9 27100 Pavia Italy
| | - Andrea Mattevi
- Department of Biology and Biotechnology “Lazzaro Spallanzani”; University of Pavia; Via Ferrata 9 27100 Pavia Italy
| | - Nicholas J. Turner
- Manchester Institute of Biotechnology (MIB); School of Chemistry; The University of Manchester; 131 Princess Street M1 7DN Manchester United Kingdom
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14
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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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15
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16
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Catucci G, Romagnolo A, Spina F, Varese GC, Gilardi G, Di Nardo G. Enzyme-substrate matching in biocatalysis: in silico studies to predict substrate preference of ten putative ene-reductases from Mucor circinelloides MUT44. ACTA ACUST UNITED AC 2016. [DOI: 10.1016/j.molcatb.2016.06.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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17
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Reetz MT. What are the Limitations of Enzymes in Synthetic Organic Chemistry? CHEM REC 2016; 16:2449-2459. [DOI: 10.1002/tcr.201600040] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Indexed: 12/31/2022]
Affiliation(s)
- Manfred T. Reetz
- Fachbereich Chemie (15) Philipps-Universität Marburg Hans-Meerwein Straße; 35032 Marburg Germany
- Max-Planck-Institut für Kohlenforschung; Kaiser-Wilhelm-Platz 1 45470 Mülheim an der Ruhr Germany
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18
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Kataoka M, Miyakawa T, Shimizu S, Tanokura M. Enzymes useful for chiral compound synthesis: structural biology, directed evolution, and protein engineering for industrial use. Appl Microbiol Biotechnol 2016; 100:5747-57. [DOI: 10.1007/s00253-016-7603-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Revised: 04/30/2016] [Accepted: 05/02/2016] [Indexed: 10/21/2022]
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19
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Lonsdale R, Reetz MT. Reduction of α,β-Unsaturated Ketones by Old Yellow Enzymes: Mechanistic Insights from Quantum Mechanics/Molecular Mechanics Calculations. J Am Chem Soc 2015; 137:14733-42. [PMID: 26521678 DOI: 10.1021/jacs.5b08687] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Enoate reductases catalyze the reduction of activated C═C bonds with high enantioselectivity. The oxidative half-reaction, which involves the addition of a hydride and a proton to opposite faces of the C═C bond, has been studied for the first time by hybrid quantum mechanics/molecular mechanics (QM/MM). The reduction of 2-cyclohexen-1-one by YqjM from Bacillus subtilis was selected as the model system. Two-dimensional QM/MM (B3LYP-D/OPLS2005) reaction pathways suggest that the hydride and proton are added as distinct steps, with the former step preceding the latter. Furthermore, we present interesting insights into the reactivity of this enzyme, including the weak binding of the substrate in the active site, the role of the two active site histidine residues for polarization of the substrate C═O bond, structural details of the transition states to hydride and proton transfer, and the role of Tyr196 as proton donor. The information presented here will be useful for the future design of enantioselective YqjM mutants for other substrates.
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Affiliation(s)
- Richard Lonsdale
- Max-Planck-Institut für Kohlenforschung , Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany.,Fachbereich Chemie der Philipps-Universität , Hans-Meerwein-Strasse, 35032 Marburg, Germany
| | - Manfred T Reetz
- Max-Planck-Institut für Kohlenforschung , Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany.,Fachbereich Chemie der Philipps-Universität , Hans-Meerwein-Strasse, 35032 Marburg, Germany
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