1
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Schwartz R, Zev S, Major DT. Mechanistic docking in terpene synthases using EnzyDock. Methods Enzymol 2024; 699:265-292. [PMID: 38942507 DOI: 10.1016/bs.mie.2024.04.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/30/2024]
Abstract
Terpene Synthases (TPS) catalyze the formation of multicyclic, complex terpenes and terpenoids from linear substrates. Molecular docking is an important research tool that can further our understanding of TPS multistep mechanisms and guide enzyme design. Standard docking programs are not well suited to tackle the unique challenges of TPS, like the many chemical steps which form multiple stereo-centers, the weak dispersion interactions between the isoprenoid chain and the hydrophobic region of the active site, description of carbocation intermediates, and finding mechanistically meaningful sets of docked poses. To address these and other unique challenges, we developed the multistate, multiscale docking program EnzyDock and used it to study many TPS and other enzymes. In this review we discuss the unique challenges of TPS, the special features of EnzyDock developed to address these challenges and demonstrate its successful use in ongoing research on the bacterial TPS CotB2.
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Affiliation(s)
- Renana Schwartz
- Department of Chemistry and Institute for Nanotechnology Advanced Materials, Bar Ilan University, Ramat Gan, Israel
| | - Shani Zev
- Department of Chemistry and Institute for Nanotechnology Advanced Materials, Bar Ilan University, Ramat Gan, Israel
| | - Dan T Major
- Department of Chemistry and Institute for Nanotechnology Advanced Materials, Bar Ilan University, Ramat Gan, Israel.
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2
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Leferink NGH, Escorcia AM, Ouwersloot BR, Johanissen LO, Hay S, van der Kamp MW, Scrutton NS. Molecular Determinants of Carbocation Cyclisation in Bacterial Monoterpene Synthases. Chembiochem 2022; 23:e202100688. [PMID: 35005823 PMCID: PMC9303655 DOI: 10.1002/cbic.202100688] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 01/07/2022] [Indexed: 11/24/2022]
Abstract
Monoterpene synthases are often promiscuous enzymes, yielding product mixtures rather than pure compounds due to the nature of the branched reaction mechanism involving reactive carbocations. Two previously identified bacterial monoterpene synthases, a linalool synthase (bLinS) and a cineole synthase (bCinS), produce nearly pure linalool and cineole from geranyl diphosphate, respectively. We used a combined experimental and computational approach to identify critical residues involved in bacterial monoterpenoid synthesis. Phe77 is essential for bCinS activity, guiding the linear carbocation intermediate towards the formation of the cyclic α-terpinyl intermediate; removal of the aromatic ring results in variants that produce acyclic products only. Computational chemistry confirmed the importance of Phe77 in carbocation stabilisation. Phe74, Phe78 and Phe179 are involved in maintaining the active site shape in bCinS without a specific role for the aromatic ring. Phe295 in bLinS, and the equivalent Ala301 in bCinS, are essential for linalool and cineole formation, respectively. Where Phe295 places steric constraints on the carbocation intermediates, Ala301 is essential for bCinS initial cyclisation and activity. Our multidisciplinary approach gives unique insights into how carefully placed amino acid residues in the active site can direct carbocations down specific paths, by placing steric constraints or offering stabilisation via cation-π interactions.
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Affiliation(s)
- Nicole G H Leferink
- Future Biomanufacturing Research Hub, Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
- Manchester Institute of Biotechnology and Department of Chemistry, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Andrés M Escorcia
- School of Biochemistry, University of Bristol, University Walk, Bristol, BS8 1TD, UK
| | - Bodi R Ouwersloot
- Future Biomanufacturing Research Hub, Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
- Manchester Institute of Biotechnology and Department of Chemistry, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Linus O Johanissen
- Manchester Institute of Biotechnology and Department of Chemistry, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Sam Hay
- Manchester Institute of Biotechnology and Department of Chemistry, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Marc W van der Kamp
- School of Biochemistry, University of Bristol, University Walk, Bristol, BS8 1TD, UK
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK
| | - Nigel S Scrutton
- Future Biomanufacturing Research Hub, Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
- Manchester Institute of Biotechnology and Department of Chemistry, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
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3
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Xu J, Peng G, Xu J, Li Y, Tong L, Yang D. Probing of the plasticity of the active site in pinene synthase elucidates its potential evolutionary mechanism. PHYTOCHEMISTRY 2021; 181:112573. [PMID: 33142148 DOI: 10.1016/j.phytochem.2020.112573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 10/19/2020] [Accepted: 10/22/2020] [Indexed: 06/11/2023]
Abstract
Terpenes form a class of highly diverse natural products. The diversity of terpenes is created by terpene synthases. During the reaction, carbocation intermediates form and their rearrangement could lead to the formation of various products. Terpene synthases determine the final product profile by controlling the conformation of the intermediate or stabilizing the carbocation. Pinene synthase is a monoterpene synthase catalyzing the cyclization of geranyl pyrophosphate (GPP) to form pinene. Our study suggests that by mutating the aromatic residue F482 to Ala, Val, Ile and Thr, the enzyme can be converted to sabinene synthase, with more than 90% of its total terpene products becoming sabinene, which indicates the aromaticity of this residue is essential for stabilizing the pinyl carbocation. We also identified a mutation S491A that could cause an about 29% increase in the overall activity of the enzyme without altering its produce selectivity. Molecular dynamic simulation indicates this mutation could decrease the flexibility of the enzyme when it forms a complex with the pinyl carbocation. Our study suggests the active pocket of pinene synthase has a certain level of plasticity, making it relatively easy to change the product selectivity or overall activity. This property could have an important implication in the evolution of terpene synthases and thereby terpene diversity, as by changing a few residues an enzyme could synthesize a completely different terpene product in a significant amount, which allows selection to take place.
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Affiliation(s)
- Jingwei Xu
- Gene Engineering and Biotechnology Beijing Key Laboratory, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Guanzu Peng
- Gene Engineering and Biotechnology Beijing Key Laboratory, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Jinkun Xu
- Gene Engineering and Biotechnology Beijing Key Laboratory, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Yi Li
- Gene Engineering and Biotechnology Beijing Key Laboratory, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Li Tong
- Gene Engineering and Biotechnology Beijing Key Laboratory, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Dong Yang
- Gene Engineering and Biotechnology Beijing Key Laboratory, College of Life Sciences, Beijing Normal University, Beijing, 100875, China.
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4
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Raz K, Driller R, Dimos N, Ringel M, Brück T, Loll B, Major DT. The Impression of a Nonexisting Catalytic Effect: The Role of CotB2 in Guiding the Complex Biosynthesis of Cyclooctat-9-en-7-ol. J Am Chem Soc 2020; 142:21562-21574. [PMID: 33289561 DOI: 10.1021/jacs.0c11348] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Terpene synthases generate terpenes employing diversified carbocation chemistry, including highly specific ring formations, proton and hydride transfers, and methyl as well as methylene migrations, followed by reaction quenching. In this enzyme family, the main catalytic challenge is not rate enhancement, but rather structural and reactive control of intrinsically unstable carbocations in order to guide the resulting product distribution. Here we employ multiscale modeling within classical and quantum dynamics frameworks to investigate the reaction mechanism in the diterpene synthase CotB2, commencing with the substrate geranyl geranyl diphosphate and terminating with the carbocation precursor to the final product cyclooctat-9-en-7-ol. The 11-step in-enzyme carbocation cascade is compared with the same reaction in the absence of the enzyme. Remarkably, the free energy profiles in gas phase and in CotB2 are surprisingly similar. This similarity contrasts the multitude of strong π-cation, dipole-cation, and ion-pair interactions between all intermediates in the reaction cascade and the enzyme, suggesting a remarkable balance of interactions in CotB2. We ascribe this balance to the similar magnitude of the interactions between the carbocations along the reaction coordinate and the enzyme environment. The effect of CotB2 mutations is studied using multiscale mechanistic docking, machine learning, and X-ray crystallography, pointing the way for future terpene synthase design.
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Affiliation(s)
- Keren Raz
- Department of Chemistry and Institute for Nanotechnology & Advanced Materials, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Ronja Driller
- Institut für Chemie und Biochemie, Strukturbiochemie, Freie Universität Berlin, Takustr. 6, 14195 Berlin, Germany
| | - Nicole Dimos
- Institut für Chemie und Biochemie, Strukturbiochemie, Freie Universität Berlin, Takustr. 6, 14195 Berlin, Germany
| | - Marion Ringel
- Werner Siemens Chair of Synthetic Biotechnology, Department of Chemistry, Technical University of Munich (TUM), Lichtenbergstr. 4, 85748 Garching, Germany
| | - Thomas Brück
- Werner Siemens Chair of Synthetic Biotechnology, Department of Chemistry, Technical University of Munich (TUM), Lichtenbergstr. 4, 85748 Garching, Germany
| | - Bernhard Loll
- Institut für Chemie und Biochemie, Strukturbiochemie, Freie Universität Berlin, Takustr. 6, 14195 Berlin, Germany
| | - Dan Thomas Major
- Department of Chemistry and Institute for Nanotechnology & Advanced Materials, Bar-Ilan University, Ramat-Gan 52900, Israel
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5
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Tasnim S, Gries R, Mattsson J. Identification of Three Monofunctional Diterpene Synthases with Specific Enzyme Activities Expressed during Heartwood Formation in Western Redcedar ( Thuja plicata) Trees. PLANTS (BASEL, SWITZERLAND) 2020; 9:E1018. [PMID: 32806789 PMCID: PMC7464036 DOI: 10.3390/plants9081018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Revised: 08/08/2020] [Accepted: 08/09/2020] [Indexed: 11/28/2022]
Abstract
Upon harvest, Western redcedar (WRC; Thuja plicata) trees have a high incidence and extent of heartwood rot. While monoterpenoids and lignans have been linked to rot resistance in this species, other specialized metabolites, such as diterpenes, are likely to contribute to rot resistance. Here we report the cloning and functional assessment of three putative diterpene synthase (TpdiTPS) genes expressed during heartwood formation in WRC. The predicted proteins of the three genes lack either of the two catalytically independent active sites typical of most diTPS, indicating monofunctional rather than bifunctional activity. To identify potential catalytic activities of these proteins, we expressed them in genetically engineered Escherichia coli strains that produce four potential substrates, geranylgeranyl diphosphate (GGDP), ent, syn, and normal stereoisomers of copalyl diphosphate (CDP). We found that TpdiTPS3 used GGDP to produce CDP. TpdiTPS2 used normal CDP to produce levopimaradiene. TpdiTPS1 showed stereoselectivity as it used normal CDP to produce sandaracopimaradiene and syn-CDP to produce syn-stemod-13(17)-ene. These genes and protein enzymatic activities have not been previously reported in WRC and provide an opportunity to assess their potential roles in heartwood rot resistance in this economically important species.
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Affiliation(s)
| | | | - Jim Mattsson
- Department of Biological Sciences, Simon Fraser University, 8888 University Drive, Burnaby, BC V5A 1S6, Canada; (S.T.); (R.G.)
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6
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Raz K, Levi S, Gupta PK, Major DT. Enzymatic control of product distribution in terpene synthases: insights from multiscale simulations. Curr Opin Biotechnol 2020; 65:248-258. [PMID: 32679412 DOI: 10.1016/j.copbio.2020.06.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 06/03/2020] [Accepted: 06/07/2020] [Indexed: 11/25/2022]
Abstract
In this opinion, we review some recent work on terpene biosynthesis using multiscale simulation approaches, with special focus on contributions from our group. Terpene synthases generate terpenes employing rich carbocation chemistry, including highly specific ring formations, proton, hydride, methyl, and methylene migrations, followed by reaction quenching. In these enzymes, the main catalytic challenge is not rate enhancement, but rather control of intrinsically reactive carbocations and the resulting product distribution. Herein, we review multiscale simulations of selected mono-, sesqui-, and diterpene synthases. We point to the many tools adopted by terpene synthases to achieve correct substrate fold, carbocation formation, carbocation reaction environment, and reaction quenching. A better understanding of the toolbox employed by terpene synthases is expected to aid in the search for new enzymatic and biomimetic synthetic routes to natural and unnatural terpenes.
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Affiliation(s)
- Keren Raz
- Department of Chemistry and Institute for Nanotechnology & Advanced Materials, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Shani Levi
- Department of Chemistry and Institute for Nanotechnology & Advanced Materials, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Prashant Kumar Gupta
- Department of Chemistry and Institute for Nanotechnology & Advanced Materials, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Dan Thomas Major
- Department of Chemistry and Institute for Nanotechnology & Advanced Materials, Bar-Ilan University, Ramat-Gan 52900, Israel.
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7
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Syntrivanis LD, Némethová I, Schmid D, Levi S, Prescimone A, Bissegger F, Major DT, Tiefenbacher K. Four-Step Access to the Sesquiterpene Natural Product Presilphiperfolan-1β-ol and Unnatural Derivatives via Supramolecular Catalysis. J Am Chem Soc 2020; 142:5894-5900. [DOI: 10.1021/jacs.0c01464] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
| | - Ivana Némethová
- Department of Chemistry, University of Basel, Mattenstrasse 24a, 4058 Basel, Switzerland
| | - Dario Schmid
- Department of Chemistry, University of Basel, Mattenstrasse 24a, 4058 Basel, Switzerland
| | - Shani Levi
- Department of Chemistry, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Alessandro Prescimone
- Department of Chemistry, University of Basel, Mattenstrasse 24a, 4058 Basel, Switzerland
| | - Fabian Bissegger
- Department of Chemistry, University of Basel, Mattenstrasse 24a, 4058 Basel, Switzerland
| | - Dan T. Major
- Department of Chemistry, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Konrad Tiefenbacher
- Department of Chemistry, University of Basel, Mattenstrasse 24a, 4058 Basel, Switzerland
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 24, 4058 Basel, Switzerland
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8
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Jia M, Zhang Y, Siegel JB, Tantillo DJ, Peters RJ. Switching on a Nontraditional Enzymatic Base - Deprotonation by Serine in the ent-Kaurene Synthase from Bradyrhizobium japonicum. ACS Catal 2019; 9:8867-8871. [PMID: 32489716 DOI: 10.1021/acscatal.9b02783] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Terpene synthases often catalyze complex carbocation cascade reactions. It has been previously shown that single residue switches involving replacement of a key aliphatic residue with serine or threonine can "short-circuit" such reactions, presumed to act indirectly via dipole stabilization of intermediate carbocations. Here a similar switch was found in the structurally characterized ent-kaurene synthase from Bradyrhizobium japonicum. Application of a recently developed computational approach to terpene synthases, TerDockin, surprisingly indicates direct action of the introduced serine hydroxyl as a catalytic base. Notably, this model suggests alternative interpretation of previous results, and potential routes towards reengineering terpene synthase activity more generally.
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Affiliation(s)
- Meirong Jia
- Roy J. Carver Department of Biochemistry, Biophysics & Molecular Biology, Iowa State University, Ames, Iowa 50011, United States
| | - Yue Zhang
- Department of Chemistry, University of California-Davis, Davis, California 95616, United States
| | - Justin B. Siegel
- Department of Chemistry, University of California-Davis, Davis, California 95616, United States
- Department of Biochemistry and Molecular Medicine, University of California-Davis, Davis, California 95616, United States
- Genome Center, University of California-Davis, Davis, California 95616, United States
| | - Dean J. Tantillo
- Department of Chemistry, University of California-Davis, Davis, California 95616, United States
| | - Reuben J. Peters
- Roy J. Carver Department of Biochemistry, Biophysics & Molecular Biology, Iowa State University, Ames, Iowa 50011, United States
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9
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A Wheat β-Patchoulene Synthase Confers Resistance Against Herbivory in Transgenic Arabidopsis. Genes (Basel) 2019; 10:genes10060441. [PMID: 31185680 PMCID: PMC6628343 DOI: 10.3390/genes10060441] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2019] [Revised: 05/27/2019] [Accepted: 06/04/2019] [Indexed: 01/11/2023] Open
Abstract
Terpenoids play important roles in plant defense. Although some terpene synthases have been characterized, terpenoids and their biosynthesis in wheat (Triticum aestivum L.) still remain largely unknown. Here, we describe the identification of a terpene synthase gene in wheat. It encodes a sesquiterpene synthase that catalyzes β-patchoulene formation with E,E-farnesyl diphosphate (FPP) as the substrate, thus named as TaPS. TaPS exhibits inducible expression in wheat in response to various elicitations. Particularly, alamethicin treatment strongly induces TaPS gene expression and β-patchoulene accumulation in wheat. Overexpression of TaPS in Arabidopsis successfully produces β-patchoulene, verifying the biochemical function of TaPS in planta. Furthermore, these transgenic Arabidopsis plants exhibit resistance against herbivory by repelling beet armyworm larvae feeding, thereby indicating anti-herbivory activity of β-patchoulene. The catalytic mechanism of TaPS is also explored by homology modeling and site-directed mutagenesis. Two key amino acids are identified to act in protonation and stability of intermediates and product formation. Taken together, one wheat sesquiterpene synthase is identified as β-patchoulene synthase. TaPS exhibits inducible gene expression and the sesquiterpene β-patchoulene is involved in repelling insect infestation.
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10
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van Rijn JPM, Escorcia AM, Thiel W. QM/MM study of the taxadiene synthase mechanism. J Comput Chem 2019; 40:1902-1910. [DOI: 10.1002/jcc.25846] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2019] [Revised: 04/05/2019] [Accepted: 04/15/2019] [Indexed: 01/10/2023]
Affiliation(s)
| | - Andrés M. Escorcia
- Max‐Planck‐Institut für Kohlenforschung Kaiser‐Wilhelm‐Platz 1, 45470 Mülheim Germany
| | - Walter Thiel
- Max‐Planck‐Institut für Kohlenforschung Kaiser‐Wilhelm‐Platz 1, 45470 Mülheim Germany
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11
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Driller R, Janke S, Fuchs M, Warner E, Mhashal AR, Major DT, Christmann M, Brück T, Loll B. Towards a comprehensive understanding of the structural dynamics of a bacterial diterpene synthase during catalysis. Nat Commun 2018; 9:3971. [PMID: 30266969 PMCID: PMC6162201 DOI: 10.1038/s41467-018-06325-8] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 08/28/2018] [Indexed: 11/24/2022] Open
Abstract
Terpenes constitute the largest and structurally most diverse natural product family. Most terpenoids exhibit a stereochemically complex macrocyclic core, which is generated by C–C bond forming of aliphatic oligo-prenyl precursors. This reaction is catalysed by terpene synthases (TPSs), which are capable of chaperoning highly reactive carbocation intermediates through an enzyme-specific reaction. Due to the instability of carbocation intermediates, the proteins’ structural dynamics and enzyme:substrate interactions during TPS catalysis remain elusive. Here, we present the structure of the diterpene synthase CotB2, in complex with an in crystallo cyclised abrupt reaction product and a substrate-derived diphosphate. We captured additional snapshots of the reaction to gain an overview of CotB2’s catalytic mechanism. To enhance insights into catalysis, structural information is augmented with multiscale molecular dynamic simulations. Our data represent fundamental TPS structure dynamics during catalysis, which ultimately enable rational engineering towards tailored terpene macrocycles that are inaccessible by conventional chemical synthesis. The bacterial diterpene synthase CotB2 catalyses the cyclisation of geranylgeranyl diphosphate to cyclooctat-9-en7-ol. Here the authors present various CotB2 structures including a trapped abrupt reaction product that were used for molecular dynamic simulations and allowed them to model all intermediates along the reaction cascade.
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Affiliation(s)
- Ronja Driller
- Institut für Chemie und Biochemie, Strukturbiochemie, Freie Universität Berlin, Takustr. 6, 14195, Berlin, Germany
| | - Sophie Janke
- Institut für Chemie und Biochemie, Organische Chemie, Freie Universität Berlin, Takustr. 3, 14195, Berlin, Germany
| | - Monika Fuchs
- Werner Siemens Chair of Synthetic Biotechnology, Department of Chemistry, Technical University of Munich (TUM), Lichtenbergstr. 4, 85748, Garching, Germany
| | - Evelyn Warner
- Institut für Chemie und Biochemie, Organische Chemie, Freie Universität Berlin, Takustr. 3, 14195, Berlin, Germany
| | - Anil R Mhashal
- Department of Chemistry, Bar-Ilan University, Ramat-Gan, 52900, Israel
| | - Dan Thomas Major
- Department of Chemistry, Bar-Ilan University, Ramat-Gan, 52900, Israel
| | - Mathias Christmann
- Institut für Chemie und Biochemie, Organische Chemie, Freie Universität Berlin, Takustr. 3, 14195, Berlin, Germany
| | - Thomas Brück
- Werner Siemens Chair of Synthetic Biotechnology, Department of Chemistry, Technical University of Munich (TUM), Lichtenbergstr. 4, 85748, Garching, Germany
| | - Bernhard Loll
- Institut für Chemie und Biochemie, Strukturbiochemie, Freie Universität Berlin, Takustr. 6, 14195, Berlin, Germany.
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12
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Jia M, O’Brien TE, Zhang Y, Siegel JB, Tantillo DJ, Peters RJ. Changing Face: A Key Residue for the Addition of Water by Sclareol Synthase. ACS Catal 2018; 8:3133-3137. [PMID: 29713562 DOI: 10.1021/acscatal.8b00121] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Sclareol synthase from Salvia sclarea (SsSS) naturally acts on 8α-hydroxy-copalyl diphosphate (1), stereoselectively adding water to produce (13R)-sclareol (2a), and similarly yields hydroxylated products with manifold other such bicyclic diterpene precursors. Here a key residue for this addition of water was identified. Strikingly, substitution with glutamine switches stereochemical outcome with 1, leading to selective production of (13S)-sclareol (2b). Moreover, changes to the stereospecificity of water addition with the structurally closely-related substrate copalyl diphosphate (4) could be accomplished with alternative substitutions. Thus, this approach is expected to provide biosynthetic access to both epimers of 13-hydroxylated derivatives of manifold labdane-related diterpenes.
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Affiliation(s)
- Meirong Jia
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa 50011, United States
| | - Terrence E. O’Brien
- Department of Chemistry, University of California−Davis, Davis, California 95616, United States
| | - Yue Zhang
- Department of Chemistry, University of California−Davis, Davis, California 95616, United States
| | - Justin B. Siegel
- Department of Chemistry, University of California−Davis, Davis, California 95616, United States
- Department of Biochemistry and Molecular Medicine, University of California−Davis, Davis, California 95616, United States
- Genome Center, University of California−Davis, Davis, California 95616, United States
| | - Dean J. Tantillo
- Department of Chemistry, University of California−Davis, Davis, California 95616, United States
| | - Reuben J. Peters
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa 50011, United States
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13
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Escorcia AM, van Rijn JPM, Cheng GJ, Schrepfer P, Brück TB, Thiel W. Molecular dynamics study of taxadiene synthase catalysis. J Comput Chem 2018; 39:1215-1225. [PMID: 29450907 DOI: 10.1002/jcc.25184] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 01/25/2018] [Accepted: 01/26/2018] [Indexed: 01/10/2023]
Abstract
Molecular dynamics (MD) simulations have been performed to study the dynamic behavior of noncovalent enzyme carbocation complexes involved in the cyclization of geranylgeranyl diphosphate to taxadiene catalyzed by taxadiene synthase (TXS). Taxadiene and the observed four side products originate from the deprotonation of carbocation intermediates. The MD simulations of the TXS carbocation complexes provide insights into potential deprotonation mechanisms of such carbocations. The MD results do not support a previous hypothesis that carbocation tumbling is a key factor in the deprotonation of the carbocations by pyrophosphate. Instead water bridges are identified which may allow the formation of side products via multiple proton transfer reactions. A novel reaction path for taxadiene formation is proposed on the basis of the simulations. © 2018 Wiley Periodicals, Inc.
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Affiliation(s)
- Andrés M Escorcia
- Max-Planck-Institut fu¨r Kohlenforschung, Kaiser-Wilhelm-Platz 1, Mu¨lheim, 45470, Germany
| | | | - Gui-Juan Cheng
- Max-Planck-Institut fu¨r Kohlenforschung, Kaiser-Wilhelm-Platz 1, Mu¨lheim, 45470, Germany
| | - Patrick Schrepfer
- Professorship of Industrial Biocatalysis, Department of Chemistry, Technical University Munich, Lichtenberg Str. 4, Garching, 85748, Germany
| | - Thomas B Brück
- Professorship of Industrial Biocatalysis, Department of Chemistry, Technical University Munich, Lichtenberg Str. 4, Garching, 85748, Germany
| | - Walter Thiel
- Max-Planck-Institut fu¨r Kohlenforschung, Kaiser-Wilhelm-Platz 1, Mu¨lheim, 45470, Germany
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14
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Freud Y, Ansbacher T, Major DT. Catalytic Control in the Facile Proton Transfer in Taxadiene Synthase. ACS Catal 2017. [DOI: 10.1021/acscatal.7b02824] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Yehoshua Freud
- Department
of Chemistry, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Tamar Ansbacher
- Department
of Chemistry, Bar-Ilan University, Ramat-Gan 52900, Israel
- Hadassah Academic College, 7 Hanevi’im
Street, Jerusalem 9101001, Israel
| | - Dan Thomas Major
- Department
of Chemistry, Bar-Ilan University, Ramat-Gan 52900, Israel
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15
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Affiliation(s)
- Dan T. Major
- Department of Chemistry and
the Lise Meitner-Minerva Center of Computational Quantum Chemistry, Bar-Ilan University, Ramat-Gan 52900, Israel
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16
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Hare SR, Pemberton RP, Tantillo DJ. Navigating Past a Fork in the Road: Carbocation-π Interactions Can Manipulate Dynamic Behavior of Reactions Facing Post-Transition-State Bifurcations. J Am Chem Soc 2017; 139:7485-7493. [PMID: 28504880 DOI: 10.1021/jacs.7b01042] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Dynamics calculations are described for carbocation rearrangements involving product-forming pathways with post-transition-state bifurcations. We show that noncovalent interactions with associated benzene rings (a simple model of aromatic amino acid side chains) can switch inherent dynamical tendencies for competing modes of disrotation, establishing that meaningful changes in dynamically controlled product selectivity can be achieved with few weak noncovalent interactions.
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Affiliation(s)
- Stephanie R Hare
- Department of Chemistry, University of California, Davis , One Shields Avenue, Davis, California 95616, United States
| | - Ryan P Pemberton
- Department of Chemistry, University of California, Davis , One Shields Avenue, Davis, California 95616, United States
| | - Dean J Tantillo
- Department of Chemistry, University of California, Davis , One Shields Avenue, Davis, California 95616, United States
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17
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Xu J, Ai Y, Wang J, Xu J, Zhang Y, Yang D. Converting S-limonene synthase to pinene or phellandrene synthases reveals the plasticity of the active site. PHYTOCHEMISTRY 2017; 137:34-41. [PMID: 28215610 DOI: 10.1016/j.phytochem.2017.02.017] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Revised: 01/25/2017] [Accepted: 02/11/2017] [Indexed: 05/27/2023]
Abstract
S-limonene synthase is a model monoterpene synthase that cyclizes geranyl pyrophosphate (GPP) to form S-limonene. It is a relatively specific enzyme as the majority of its products are composed of limonene. In this study, we converted it to pinene or phellandrene synthases after introducing N345A/L423A/S454A or N345I mutations. Further studies on N345 suggest the polarity of this residue plays a critical role in limonene production by stabilizing the terpinyl cation intermediate. If it is mutated to a non-polar residue, further cyclization or hydride shifts occurs so the carbocation migrates towards the pyrophosphate, leading to the production of pinene or phellandrene. On the other hand, mutant enzymes that still possess a polar residue at this position produce limonene as the major product. N345 is not the only polar residue that may stabilize the terpinyl cation because it is not strictly conserved among limonene synthases across species and there are also several other polar residues in this area. These residues could form a "polar pocket" that may collectively play this stabilizing role. Our study provides important insights into the catalytic mechanism of limonene synthases. Furthermore, it also has wider implications on the evolution of terpene synthases.
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Affiliation(s)
- Jinkun Xu
- Gene Engineering and Biotechnology Beijing Key Laboratory, College of Life Sciences, Beijing Normal University, Beijing, 100875 China
| | - Ying Ai
- Gene Engineering and Biotechnology Beijing Key Laboratory, College of Life Sciences, Beijing Normal University, Beijing, 100875 China
| | - Jianhui Wang
- Gene Engineering and Biotechnology Beijing Key Laboratory, College of Life Sciences, Beijing Normal University, Beijing, 100875 China
| | - Jingwei Xu
- Gene Engineering and Biotechnology Beijing Key Laboratory, College of Life Sciences, Beijing Normal University, Beijing, 100875 China
| | - Yongkang Zhang
- Gene Engineering and Biotechnology Beijing Key Laboratory, College of Life Sciences, Beijing Normal University, Beijing, 100875 China
| | - Dong Yang
- Gene Engineering and Biotechnology Beijing Key Laboratory, College of Life Sciences, Beijing Normal University, Beijing, 100875 China.
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18
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Jia M, Zhou K, Tufts S, Schulte S, Peters RJ. A Pair of Residues That Interactively Affect Diterpene Synthase Product Outcome. ACS Chem Biol 2017; 12:862-867. [PMID: 28170228 PMCID: PMC5360158 DOI: 10.1021/acschembio.6b01075] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
![]()
The
labdane-related diterpenoids (LRDs) are an important superfamily
of natural products whose structural diversity critically depends
on the hydrocarbon skeletal structures generated, in large part, by
class I diterpene synthases. In the plant kingdom, where the LRDs
are predominantly found, the relevant class I diterpene synthases
are clearly derived from the ent-kaurene synthase
(KS) required in all land plants for phytohormone biosynthesis and,
hence, are often termed KS-like (KSL). Previous work, initiated by
the distinct function of two alleles of a KSL from rice, OsKSL5, identified
a single residue switch with a profound effect on not only OsKSL5
product outcome but also that of land plant KSs more broadly, specifically,
replacement of a key isoleucine with threonine, which interrupts formation
of the tetracyclic ent-isokaurene at the tricyclic
stage, leading to production of ent-pimaradiene instead.
Here, further studies of these alleles led to discovery of another,
nearby residue that tunes product outcome. Substitution for this newly
identified residue is additionally shown to exert an epistatic effect
in KSs, altering product distribution only if combined with replacement
of the key isoleucine. On the other hand, this pair of residues was
found to exert additive effects on the product outcome mediated by
distantly related KSLs from the eudicot castor bean. Accordingly,
it was possible to use a rational combination of substitutions for
this pair of residues to engineer significantly increased (dominant)
selectivity for novel 8α-hydroxy-ent-pimar-15-ene
product outcome in the KS from the dicot Arabidopsis thaliana, demonstrating the utility of these results.
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Affiliation(s)
- Meirong Jia
- Roy J. Carver Department of Biochemistry, Biophysics & Molecular Biology, Iowa State University, Ames, Iowa 50011, United States
| | - Ke Zhou
- Roy J. Carver Department of Biochemistry, Biophysics & Molecular Biology, Iowa State University, Ames, Iowa 50011, United States
| | - Samuel Tufts
- Roy J. Carver Department of Biochemistry, Biophysics & Molecular Biology, Iowa State University, Ames, Iowa 50011, United States
| | - Samuel Schulte
- Roy J. Carver Department of Biochemistry, Biophysics & Molecular Biology, Iowa State University, Ames, Iowa 50011, United States
| | - Reuben J. Peters
- Roy J. Carver Department of Biochemistry, Biophysics & Molecular Biology, Iowa State University, Ames, Iowa 50011, United States
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19
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Dixit M, Weitman M, Gao J, Major DT. Chemical Control in the Battle against Fidelity in Promiscuous Natural Product Biosynthesis: The Case of Trichodiene Synthase. ACS Catal 2017; 7:812-818. [PMID: 29399379 PMCID: PMC5793923 DOI: 10.1021/acscatal.6b02584] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Terpene cyclases catalyze the highly stereospecific molding of polyisoprenes into terpenes, which are precursors to most known natural compounds. The isoprenoids are formed via intricate chemical cascades employing rich, yet highly erratic, carbocation chemistry. It is currently not well understood how these biocatalysts achieve chemical control. Here, we illustrate the catalytic control exerted by trichodiene synthase, and in particular, we discover two features that could be general catalytic tools adopted by other terpenoid cyclases. First, to avoid formation of byproducts, the enzyme raises the energy of bisabolyl carbocation, which is a general mechanistic branching point in many sesquiterpene cyclases, resulting in an essentially concerted cyclization cascade. Second, we identify a sulfur-carbocation dative bonding interaction that anchors the bisabolyl cation in a reactive conformation, avoiding tumbling and premature deprotonation. Specifically, Met73 acts as a chameleon, shifting from an initial sulfur-π interaction in the Michaelis complex to a sulfur-carbocation complex during catalysis.
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Affiliation(s)
- Mudit Dixit
- Department of Chemistry and the Lise Meitner-Minerva Center of Computational Quantum Chemistry, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Michal Weitman
- Department of Chemistry and the Lise Meitner-Minerva Center of Computational Quantum Chemistry, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Jiali Gao
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
- Theoretical Chemistry Institute, Jilin University, Changchun 130023, P.R. China
| | - Dan T. Major
- Department of Chemistry and the Lise Meitner-Minerva Center of Computational Quantum Chemistry, Bar-Ilan University, Ramat-Gan 52900, Israel
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20
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21
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Jia M, Peters RJ. Extending a Single Residue Switch for Abbreviating Catalysis in Plant ent-Kaurene Synthases. FRONTIERS IN PLANT SCIENCE 2016; 7:1765. [PMID: 27920791 PMCID: PMC5118566 DOI: 10.3389/fpls.2016.01765] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Accepted: 11/09/2016] [Indexed: 05/23/2023]
Abstract
Production of ent-kaurene as a precursor for important signaling molecules such as the gibberellins seems to have arisen early in plant evolution, with corresponding cyclase(s) present in all land plants (i.e., embryophyta). The relevant enzymes seem to represent fusion of the class II diterpene cyclase that produces the intermediate ent-copalyl diphosphate (ent-CPP) and the subsequently acting class I diterpene synthase that produces ent-kaurene, although the bifunctionality of the ancestral gene is only retained in certain early diverging plants, with gene duplication and sub-functionalization leading to distinct ent-CPP synthases and ent-kaurene synthases (KSs) generally observed. This evolutionary scenario implies that plant KSs should have conserved structural features uniquely required for production of ent-kaurene relative to related enzymes that have alternative function. Notably, substitution of threonine for a conserved isoleucine has been shown to "short-circuit" the complex bicyclization and rearrangement reaction catalyzed by KSs after initial cyclization, leading to predominant production of ent-pimaradiene, at least in KSs from angiosperms. Here this effect is shown to extend to KSs from earlier diverging plants (i.e., bryophytes), including a bifunctional/KS. In addition, attribution of the dramatic effect of this single residue "switch" on product outcome to electrostatic stabilization of the ent-pimarenyl carbocation intermediate formed upon initial cyclization by the hydroxyl introduced by threonine substitution has been called into question by the observation of similar effects from substitution of alanine. Here further mutational analysis and detailed product analysis is reported that supports the importance of electrostatic stabilization by a hydroxyl or water.
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22
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Li Z, Gao R, Hao Q, Zhao H, Cheng L, He F, Liu L, Liu X, Chou WKW, Zhu H, Cane DE. The T296V Mutant of Amorpha-4,11-diene Synthase Is Defective in Allylic Diphosphate Isomerization but Retains the Ability To Cyclize the Intermediate (3R)-Nerolidyl Diphosphate to Amorpha-4,11-diene. Biochemistry 2016; 55:6599-6604. [PMID: 27933789 DOI: 10.1021/acs.biochem.6b01004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The T296V mutant of amorpha-4,11-diene synthase catalyzes the abortive conversion of the natural substrate (E,E)-farnesyl diphosphate mainly into the acyclic product (E)-β-farnesene (88%) instead of the natural bicyclic sesquiterpene amorphadiene (7%). Incubation of the T296V mutant with (3R,6E)-nerolidyl diphosphate resulted in cyclization to amorphadiene. Analysis of additional mutants of amino acid residue 296 and in vitro assays with the intermediate analogue (2Z,6E)-farnesyl diphosphate as well as (3S,6E)-nerolidyl diphosphate demonstrated that the T296V mutant can no longer catalyze the allylic rearrangement of farnesyl diphosphate to the normal intermediate (3R,6E)-nerolidyl diphosphate, while retaining the ability to cyclize (3R,6E)-nerolidyl diphosphate to amorphadiene. The T296A mutant predominantly retained amorphadiene synthase activity, indicating that neither the hydroxyl nor the methyl group of the Thr296 side chain is required for cyclase activity.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Wayne K W Chou
- Department of Chemistry, Brown University , Box H, Providence, Rhode Island 02912-9108, United States
| | | | - David E Cane
- Department of Chemistry, Brown University , Box H, Providence, Rhode Island 02912-9108, United States
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23
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Identification of amino acid networks governing catalysis in the closed complex of class I terpene synthases. Proc Natl Acad Sci U S A 2016; 113:E958-67. [PMID: 26842837 DOI: 10.1073/pnas.1519680113] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Class I terpene synthases generate the structural core of bioactive terpenoids. Deciphering structure-function relationships in the reactive closed complex and targeted engineering is hampered by highly dynamic carbocation rearrangements during catalysis. Available crystal structures, however, represent the open, catalytically inactive form or harbor nonproductive substrate analogs. Here, we present a catalytically relevant, closed conformation of taxadiene synthase (TXS), the model class I terpene synthase, which simulates the initial catalytic time point. In silico modeling of subsequent catalytic steps allowed unprecedented insights into the dynamic reaction cascades and promiscuity mechanisms of class I terpene synthases. This generally applicable methodology enables the active-site localization of carbocations and demonstrates the presence of an active-site base motif and its dominating role during catalysis. It additionally allowed in silico-designed targeted protein engineering that unlocked the path to alternate monocyclic and bicyclic synthons representing the basis of a myriad of bioactive terpenoids.
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24
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Schifrin A, Khatri Y, Kirsch P, Thiel V, Schulz S, Bernhardt R. A single terpene synthase is responsible for a wide variety of sesquiterpenes in Sorangium cellulosum Soce56. Org Biomol Chem 2016; 14:3385-93. [DOI: 10.1039/c6ob00130k] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The myxobacterium Sorangium cellulosum So ce56 is a prolific producer of volatile sesquiterpenes.
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Affiliation(s)
- Alexander Schifrin
- Universität des Saarlandes
- Institut für Biochemie
- 66123 Saarbrücken
- Germany
| | - Yogan Khatri
- Universität des Saarlandes
- Institut für Biochemie
- 66123 Saarbrücken
- Germany
| | - Philine Kirsch
- Universität des Saarlandes
- Institut für Biochemie
- 66123 Saarbrücken
- Germany
| | - Verena Thiel
- Technische Universität Braunschweig
- Institut für Organische Chemie
- 38106 Braunschweig
- Germany
| | - Stefan Schulz
- Technische Universität Braunschweig
- Institut für Organische Chemie
- 38106 Braunschweig
- Germany
| | - Rita Bernhardt
- Universität des Saarlandes
- Institut für Biochemie
- 66123 Saarbrücken
- Germany
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25
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Plant diterpene synthases: exploring modularity and metabolic diversity for bioengineering. Trends Biotechnol 2015; 33:419-28. [DOI: 10.1016/j.tibtech.2015.04.006] [Citation(s) in RCA: 101] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Revised: 04/15/2015] [Accepted: 04/16/2015] [Indexed: 11/22/2022]
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26
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Frister T, Hartwig S, Alemdar S, Schnatz K, Thöns L, Scheper T, Beutel S. Characterisation of a Recombinant Patchoulol Synthase Variant for Biocatalytic Production of Terpenes. Appl Biochem Biotechnol 2015; 176:2185-201. [DOI: 10.1007/s12010-015-1707-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Accepted: 06/08/2015] [Indexed: 01/08/2023]
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27
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Zhu L, Huang SH, Yu J, Hong R. Constructive innovation of approaching bicyclo[3.2.1]octane in ent-kauranoids. Tetrahedron Lett 2015. [DOI: 10.1016/j.tetlet.2014.11.035] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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28
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Gonzalez V, Touchet S, Grundy DJ, Faraldos JA, Allemann RK. Evolutionary and Mechanistic Insights from the Reconstruction of α-Humulene Synthases from a Modern (+)-Germacrene A Synthase. J Am Chem Soc 2014; 136:14505-12. [DOI: 10.1021/ja5066366] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Veronica Gonzalez
- School of Chemistry and ‡Cardiff Catalysis Institute, School
of Chemistry, Cardiff University, Main Building, Park Place, Cardiff CF10 3AT, United Kingdom
| | - Sabrina Touchet
- School of Chemistry and ‡Cardiff Catalysis Institute, School
of Chemistry, Cardiff University, Main Building, Park Place, Cardiff CF10 3AT, United Kingdom
| | - Daniel J. Grundy
- School of Chemistry and ‡Cardiff Catalysis Institute, School
of Chemistry, Cardiff University, Main Building, Park Place, Cardiff CF10 3AT, United Kingdom
| | - Juan A. Faraldos
- School of Chemistry and ‡Cardiff Catalysis Institute, School
of Chemistry, Cardiff University, Main Building, Park Place, Cardiff CF10 3AT, United Kingdom
| | - Rudolf K. Allemann
- School of Chemistry and ‡Cardiff Catalysis Institute, School
of Chemistry, Cardiff University, Main Building, Park Place, Cardiff CF10 3AT, United Kingdom
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29
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Catalytic control in terpenoid cyclases: multiscale modeling of thermodynamic, kinetic, and dynamic effects. Curr Opin Chem Biol 2014; 21:25-33. [DOI: 10.1016/j.cbpa.2014.03.010] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Accepted: 03/09/2014] [Indexed: 02/08/2023]
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30
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Jackson AJ, Hershey DM, Chesnut T, Xu M, Peters RJ. Biochemical characterization of the castor bean ent-kaurene synthase(-like) family supports quantum chemical view of diterpene cyclization. PHYTOCHEMISTRY 2014; 103:13-21. [PMID: 24810014 PMCID: PMC4062354 DOI: 10.1016/j.phytochem.2014.04.005] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Revised: 04/04/2014] [Accepted: 04/10/2014] [Indexed: 05/20/2023]
Abstract
It has become apparent that plants have extensively diversified their arsenal of labdane-related diterpenoids (LRDs), in part via gene duplication and neo-functionalization of the ancestral ent-kaurene synthase (KS) required for gibberellin metabolism. For example, castor bean (Ricinus communis) was previously shown to produce an interesting set of biosynthetically related diterpenes, specifically ent-sandracopimaradiene, ent-beyerene, and ent-trachylobane, in addition to ent-kaurene, using four separate diterpene synthases, albeit these remain unidentified. Notably, despite mechanistic similarity of the underlying reaction to that catalyzed by KSs, ent-beyerene and ent-trachylobane synthases have not yet been identified. Given our interest in LRD biosynthesis, and the recent availability of the castor bean genome sequence, a synthetic biology approach was applied to biochemically characterize the four KS(-like) enzymes [KS(L)s] found in Ricinus communis [i.e., the RcKS(L)s]. In particular, using bacteria engineered to produce the relevant ent-copalyl diphosphate precursor and synthetic genes based on the predicted RcKS(L)s, although this ultimately required correction of a "splicing" error in one of the predicted genes, highlighting the dependence of such a synthetic biology approach on accurate gene sequences. Nevertheless, it is possible to assign each of the four RcKS(L)s to one of the previously observed diterpene synthase activities, providing access to functionally enzymes. Intriguingly, the product distribution of the RcKS(L)s seems to support the distinct diterpene synthase reaction mechanism proposed by quantum chemical calculations, rather than the classically proposed pathway.
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Affiliation(s)
- Alana J Jackson
- Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA 50011, USA
| | - David M Hershey
- Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA 50011, USA
| | - Taylor Chesnut
- Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA 50011, USA
| | - Meimei Xu
- Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA 50011, USA
| | - Reuben J Peters
- Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA 50011, USA.
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31
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Potter K, Criswell J, Zi J, Stubbs A, Peters RJ. Novel Product Chemistry from Mechanistic Analysis of
ent
‐Copalyl Diphosphate Synthases from Plant Hormone Biosynthesis. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201402911] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Kevin Potter
- Dept. Biochemistry, Biophysics & Molecular Biology, Iowa State University, Ames, IA 50011 (USA)
| | - Jared Criswell
- Dept. Biochemistry, Biophysics & Molecular Biology, Iowa State University, Ames, IA 50011 (USA)
| | - Jiachen Zi
- Dept. Biochemistry, Biophysics & Molecular Biology, Iowa State University, Ames, IA 50011 (USA)
| | - Alisha Stubbs
- Dept. Biochemistry, Biophysics & Molecular Biology, Iowa State University, Ames, IA 50011 (USA)
| | - Reuben J. Peters
- Dept. Biochemistry, Biophysics & Molecular Biology, Iowa State University, Ames, IA 50011 (USA)
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32
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Potter K, Criswell J, Zi J, Stubbs A, Peters RJ. Novel product chemistry from mechanistic analysis of ent-copalyl diphosphate synthases from plant hormone biosynthesis. Angew Chem Int Ed Engl 2014; 53:7198-202. [PMID: 24862907 DOI: 10.1002/anie.201402911] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Revised: 04/08/2014] [Indexed: 11/08/2022]
Abstract
An active-site water molecule coordinated by conserved histidine and asparagine residues seems to serve as the catalytic base in all ent-copalyl diphosphate synthases (CPSs). When these residues are substituted by alanine, the mutant CPSs produce stereochemically novel ent-8-hydroxy-CPP. Given the requisite presence of CPSs in all land plants for gibberellin phytohormone biosynthesis, such plasticity presumably underlies the observed extensive diversification of the resulting labdane-related diterpenoids.
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Affiliation(s)
- Kevin Potter
- Dept. Biochemistry, Biophysics & Molecular Biology, Iowa State University, Ames, IA 50011 (USA)
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33
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Hong YJ, Tantillo DJ. Biosynthetic consequences of multiple sequential post-transition-state bifurcations. Nat Chem 2014; 6:104-11. [PMID: 24451585 DOI: 10.1038/nchem.1843] [Citation(s) in RCA: 118] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2013] [Accepted: 12/05/2013] [Indexed: 11/09/2022]
Abstract
Selectivity in chemical reactions that form complex molecular architectures from simpler precursors is usually rationalized by comparing competing transition-state structures that lead to different possible products. Herein we describe a system for which a single transition-state structure leads to the formation of many isomeric products via pathways that feature multiple sequential bifurcations. The reaction network described connects the pimar-15-en-8-yl cation to miltiradiene, a tricyclic diterpene natural product, and isomers via cyclizations and/or rearrangements. The results suggest that the selectivity of the reaction is controlled by (post-transition-state) dynamic effects, that is, how the carbocation structure changes in response to the distribution of energy in its vibrational modes. The inherent dynamical effects revealed herein (characterized through quasiclassical direct dynamics calculations using density functional theory) have implications not only for the general principles of selectivity prediction in systems with complex potential energy surfaces, but also for the mechanisms of terpene synthase enzymes and their evolution. These findings redefine the challenges faced by nature in controlling the biosynthesis of complex natural products.
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Affiliation(s)
- Young Joo Hong
- Department of Chemistry, University of California-Davis, One Shields Avenue, Davis, California 95616, USA
| | - Dean J Tantillo
- Department of Chemistry, University of California-Davis, One Shields Avenue, Davis, California 95616, USA
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34
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Zi J, Mafu S, Peters RJ. To gibberellins and beyond! Surveying the evolution of (di)terpenoid metabolism. ANNUAL REVIEW OF PLANT BIOLOGY 2014; 65:259-86. [PMID: 24471837 PMCID: PMC4118669 DOI: 10.1146/annurev-arplant-050213-035705] [Citation(s) in RCA: 180] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The diterpenoids are classically defined by their composition--four isoprenyl units (20 carbons)--and are generally derived from [E,E,E]-geranylgeranyl diphosphate (GGPP). Such metabolism seems to be ancient and has been extensively diversified, with ∼12,000 diterpenoid natural products known. Particularly notable are the gibberellin phytohormones, whose requisite biosynthesis has provided a genetic reservoir that gave rise to not only a large superfamily of ∼7,000 diterpenoids but also, to some degree, all plant terpenoid natural products. This review focuses on the diterpenoids, particularly the defining biosynthetic characteristics of the major superfamilies defined by the cyclization and/or rearrangement of GGPP catalyzed by diterpene synthases/cyclases, although it also includes some discussion of the important subsequent elaboration in the few cases where sufficient molecular genetic information is available. It additionally addresses the array of biological activity providing the selective pressures that drive the observed gene family expansion and diversification, along with biosynthetic gene clustering.
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35
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Zerbe P, Hamberger B, Yuen MM, Chiang A, Sandhu HK, Madilao LL, Nguyen A, Hamberger B, Bach SS, Bohlmann J. Gene discovery of modular diterpene metabolism in nonmodel systems. PLANT PHYSIOLOGY 2013; 162:1073-91. [PMID: 23613273 PMCID: PMC3668041 DOI: 10.1104/pp.113.218347] [Citation(s) in RCA: 112] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2013] [Accepted: 04/21/2013] [Indexed: 05/18/2023]
Abstract
Plants produce over 10,000 different diterpenes of specialized (secondary) metabolism, and fewer diterpenes of general (primary) metabolism. Specialized diterpenes may have functions in ecological interactions of plants with other organisms and also benefit humanity as pharmaceuticals, fragrances, resins, and other industrial bioproducts. Examples of high-value diterpenes are taxol and forskolin pharmaceuticals or ambroxide fragrances. Yields and purity of diterpenes obtained from natural sources or by chemical synthesis are often insufficient for large-volume or high-end applications. Improvement of agricultural or biotechnological diterpene production requires knowledge of biosynthetic genes and enzymes. However, specialized diterpene pathways are extremely diverse across the plant kingdom, and most specialized diterpenes are taxonomically restricted to a few plant species, genera, or families. Consequently, there is no single reference system to guide gene discovery and rapid annotation of specialized diterpene pathways. Functional diversification of genes and plasticity of enzyme functions of these pathways further complicate correct annotation. To address this challenge, we used a set of 10 different plant species to develop a general strategy for diterpene gene discovery in nonmodel systems. The approach combines metabolite-guided transcriptome resources, custom diterpene synthase (diTPS) and cytochrome P450 reference gene databases, phylogenies, and, as shown for select diTPSs, single and coupled enzyme assays using microbial and plant expression systems. In the 10 species, we identified 46 new diTPS candidates and over 400 putatively terpenoid-related P450s in a resource of nearly 1 million predicted transcripts of diterpene-accumulating tissues. Phylogenetic patterns of lineage-specific blooms of genes guided functional characterization.
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Nguyen QNN, Tantillo DJ. Caryolene-forming carbocation rearrangements. Beilstein J Org Chem 2013; 9:323-31. [PMID: 23503674 PMCID: PMC3596059 DOI: 10.3762/bjoc.9.37] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2012] [Accepted: 01/21/2013] [Indexed: 11/23/2022] Open
Abstract
Density functional theory calculations on mechanisms of the formation of caryolene, a putative biosynthetic precursor to caryol-1(11)-en-10-ol, reveal two mechanisms for caryolene formation: one involves a base-catalyzed deprotonation/reprotonation sequence and tertiary carbocation minimum, whereas the other (with a higher energy barrier) involves intramolecular proton transfer and the generation of a secondary carbocation minimum and a hydrogen-bridged minimum. Both mechanisms are predicted to involve concerted suprafacial/suprafacial [2 + 2] cycloadditions, whose asynchronicity allows them to avoid the constraints of orbital symmetry.
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Affiliation(s)
- Quynh Nhu N Nguyen
- Department of Chemistry, University of California-Davis, 1 Shields Avenue, Davis, CA 95616, USA
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37
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Criswell J, Potter K, Shephard F, Beale MH, Peters RJ. A single residue change leads to a hydroxylated product from the class II diterpene cyclization catalyzed by abietadiene synthase. Org Lett 2012; 14:5828-31. [PMID: 23167845 DOI: 10.1021/ol3026022] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Class II diterpene cyclases catalyze bicyclization of geranylgeranyl diphosphate. While this reaction typically is terminated via methyl deprotonation to yield copalyl diphosphate, in rare cases hydroxylated bicycles are produced instead. Abietadiene synthase is a bifunctional diterpene cyclase that usually produces a copalyl diphosphate intermediate. Here it is shown that substitution of aspartate for a conserved histidine in the class II active site of abietadiene synthase leads to selective production of 8α-hydroxy-CPP instead, demonstrating striking plasticity.
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Affiliation(s)
- Jared Criswell
- Department of Biochemistry, Biophysics, & Molecular Biology, Iowa State University, Ames, Iowa 50011, USA
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Gao Y, Honzatko RB, Peters RJ. Terpenoid synthase structures: a so far incomplete view of complex catalysis. Nat Prod Rep 2012; 29:1153-75. [PMID: 22907771 PMCID: PMC3448952 DOI: 10.1039/c2np20059g] [Citation(s) in RCA: 244] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
The complexity of terpenoid natural products has drawn significant interest, particularly since their common (poly)isoprenyl origins were discovered. Notably, much of this complexity is derived from the highly variable cyclized and/or rearranged nature of the observed hydrocarbon skeletal structures. Indeed, at least in some cases it is difficult to immediately recognize their derivation from poly-isoprenyl precursors. Nevertheless, these diverse structures are formed by sequential elongation to acyclic precursors, most often with subsequent cyclization and/or rearrangement. Strikingly, the reactions used to assemble and diversify terpenoid backbones share a common carbocationic driven mechanism, although the means by which the initial carbocation is generated does vary. High-resolution crystal structures have been obtained for at least representative examples from each of the various types of enzymes involved in producing terpenoid hydrocarbon backbones. However, while this has certainly led to some insights into the enzymatic structure-function relationships underlying the elongation and simpler cyclization reactions, our understanding of the more complex cyclization and/or rearrangement reactions remains limited. Accordingly, selected examples are discussed here to demonstrate our current understanding, its limits, and potential ways forward.
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Affiliation(s)
- Yang Gao
- Department of Biochemistry, Biophysics, & Molecular Biology, Iowa State University, Ames, IA 50011, USA
| | - Richard B. Honzatko
- Department of Biochemistry, Biophysics, & Molecular Biology, Iowa State University, Ames, IA 50011, USA
| | - Reuben J. Peters
- Department of Biochemistry, Biophysics, & Molecular Biology, Iowa State University, Ames, IA 50011, USA
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39
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Zu L, Xu M, Lodewyk MW, Cane DE, Peters RJ, Tantillo DJ. Effect of isotopically sensitive branching on product distribution for pentalenene synthase: support for a mechanism predicted by quantum chemistry. J Am Chem Soc 2012; 134:11369-71. [PMID: 22738258 DOI: 10.1021/ja3043245] [Citation(s) in RCA: 77] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Mechanistic proposals for the carbocation cascade reaction leading to the tricyclic sesquiterpene pentalenene are assessed in light of the results of isotopically sensitive branching experiments with the H309A mutant of pentalenene synthase. These experimental results support a mechanism for pentalenene formation involving a 7-protoilludyl cation whose intermediacy was first predicted using quantum-chemical calculations.
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Affiliation(s)
- Liansuo Zu
- Department of Chemistry, University of California, Davis, California 95616, USA
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40
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Zhou K, Gao Y, Hoy JA, Mann FM, Honzatko RB, Peters RJ. Insights into diterpene cyclization from structure of bifunctional abietadiene synthase from Abies grandis. J Biol Chem 2012; 287:6840-50. [PMID: 22219188 DOI: 10.1074/jbc.m111.337592] [Citation(s) in RCA: 77] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Abietadiene synthase from Abies grandis (AgAS) is a model system for diterpene synthase activity, catalyzing class I (ionization-initiated) and class II (protonation-initiated) cyclization reactions. Reported here is the crystal structure of AgAS at 2.3 Å resolution and molecular dynamics simulations of that structure with and without active site ligands. AgAS has three domains (α, β, and γ). The class I active site is within the C-terminal α domain, and the class II active site is between the N-terminal γ and β domains. The domain organization resembles that of monofunctional diterpene synthases and is consistent with proposed evolutionary origins of terpene synthases. Molecular dynamics simulations were carried out to determine the effect of substrate binding on enzymatic structure. Although such studies of the class I active site do lead to an enclosed substrate-Mg(2+) complex similar to that observed in crystal structures of related plant enzymes, it does not enforce a single substrate conformation consistent with the known product stereochemistry. Simulations of the class II active site were more informative, with observation of a well ordered external loop migration. This "loop-in" conformation not only limits solvent access but also greatly increases the number of conformational states accessible to the substrate while destabilizing the nonproductive substrate conformation present in the "loop-out" conformation. Moreover, these conformational changes at the class II active site drive the substrate toward the proposed transition state. Docked substrate complexes were further assessed with regard to the effects of site-directed mutations on class I and II activities.
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Affiliation(s)
- Ke Zhou
- Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, Iowa 50011, USA
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Ueberbacher BT, Hall M, Faber K. Electrophilic and nucleophilic enzymatic cascade reactions in biosynthesis. Nat Prod Rep 2012; 29:337-50. [DOI: 10.1039/c2np00078d] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Faraldos JA, Antonczak AK, González V, Fullerton R, Tippmann EM, Allemann RK. Probing eudesmane cation-π interactions in catalysis by aristolochene synthase with non-canonical amino acids. J Am Chem Soc 2011; 133:13906-9. [PMID: 21815676 DOI: 10.1021/ja205927u] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Stabilization of the reaction intermediate eudesmane cation (3) through interaction with Trp 334 during catalysis by aristolochene synthase from Penicillium roqueforti was investigated by site-directed incorporation of proteinogenic and non-canonical aromatic amino acids. The amount of germacrene A (2) generated by the mutant enzymes served as a measure of the stabilization of 3. 2 is a neutral intermediate, from which 3 is formed during PR-AS catalysis by protonation of the C6,C7 double bond. The replacement of Trp 334 with para-substituted phenylalanines of increasing electron-withdrawing properties led to a progressive accumulation of 2 that showed a good correlation with the interaction energies of simple cations such as Na(+) with substituted benzenes. These results provide compelling evidence for the stabilizing role played by Trp 334 in aristolochene synthase catalysis for the energetically demanding transformation of 2 to 3.
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Affiliation(s)
- Juan A Faraldos
- School of Chemistry, Cardiff University, Park Place, Cardiff, United Kingdom
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