1
|
Roth S, Niese R, Müller M, Hall M. Redox Out of the Box: Catalytic Versatility Across NAD(P)H-Dependent Oxidoreductases. Angew Chem Int Ed Engl 2024; 63:e202314740. [PMID: 37924279 DOI: 10.1002/anie.202314740] [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: 10/01/2023] [Revised: 11/02/2023] [Accepted: 11/03/2023] [Indexed: 11/06/2023]
Abstract
The asymmetric reduction of double bonds using NAD(P)H-dependent oxidoreductases has proven to be an efficient tool for the synthesis of important chiral molecules in research and on industrial scale. These enzymes are commercially available in screening kits for the reduction of C=O (ketones), C=C (activated alkenes), or C=N bonds (imines). Recent reports, however, indicate that the ability to accommodate multiple reductase activities on distinct C=X bonds occurs in different enzyme classes, either natively or after mutagenesis. This challenges the common perception of highly selective oxidoreductases for one type of electrophilic substrate. Consideration of this underexplored potential in enzyme screenings and protein engineering campaigns may contribute to the identification of complementary biocatalytic processes for the synthesis of chiral compounds. This review will contribute to a global understanding of the promiscuous behavior of NAD(P)H-dependent oxidoreductases on C=X bond reduction and inspire future discoveries with respect to unconventional biocatalytic routes in asymmetric synthesis.
Collapse
Affiliation(s)
- Sebastian Roth
- Institute of Chemistry, University of Graz, Heinrichstrasse 28, 8010, Graz, Austria
| | - Richard Niese
- Institute of Pharmaceutical Sciences, University of Freiburg, Albertstrasse 25, 79104, Freiburg, Germany
| | - Michael Müller
- Institute of Pharmaceutical Sciences, University of Freiburg, Albertstrasse 25, 79104, Freiburg, Germany
| | - Mélanie Hall
- Institute of Chemistry, University of Graz, Heinrichstrasse 28, 8010, Graz, Austria
- BioHealth, Field of Excellence, University of Graz, 8010, Graz, Austria
| |
Collapse
|
2
|
Bierbaumer S, Nattermann M, Schulz L, Zschoche R, Erb TJ, Winkler CK, Tinzl M, Glueck SM. Enzymatic Conversion of CO 2: From Natural to Artificial Utilization. Chem Rev 2023; 123:5702-5754. [PMID: 36692850 PMCID: PMC10176493 DOI: 10.1021/acs.chemrev.2c00581] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Enzymatic carbon dioxide fixation is one of the most important metabolic reactions as it allows the capture of inorganic carbon from the atmosphere and its conversion into organic biomass. However, due to the often unfavorable thermodynamics and the difficulties associated with the utilization of CO2, a gaseous substrate that is found in comparatively low concentrations in the atmosphere, such reactions remain challenging for biotechnological applications. Nature has tackled these problems by evolution of dedicated CO2-fixing enzymes, i.e., carboxylases, and embedding them in complex metabolic pathways. Biotechnology employs such carboxylating and decarboxylating enzymes for the carboxylation of aromatic and aliphatic substrates either by embedding them into more complex reaction cascades or by shifting the reaction equilibrium via reaction engineering. This review aims to provide an overview of natural CO2-fixing enzymes and their mechanistic similarities. We also discuss biocatalytic applications of carboxylases and decarboxylases for the synthesis of valuable products and provide a separate summary of strategies to improve the efficiency of such processes. We briefly summarize natural CO2 fixation pathways, provide a roadmap for the design and implementation of artificial carbon fixation pathways, and highlight examples of biocatalytic cascades involving carboxylases. Additionally, we suggest that biochemical utilization of reduced CO2 derivates, such as formate or methanol, represents a suitable alternative to direct use of CO2 and provide several examples. Our discussion closes with a techno-economic perspective on enzymatic CO2 fixation and its potential to reduce CO2 emissions.
Collapse
Affiliation(s)
- Sarah Bierbaumer
- Institute of Chemistry, University of Graz, NAWI Graz, Heinrichstraße 28, 8010 Graz, Austria
| | - Maren Nattermann
- Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Straße 10, 35043 Marburg, Germany
| | - Luca Schulz
- Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Straße 10, 35043 Marburg, Germany
| | | | - Tobias J Erb
- Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Straße 10, 35043 Marburg, Germany
| | - Christoph K Winkler
- Institute of Chemistry, University of Graz, NAWI Graz, Heinrichstraße 28, 8010 Graz, Austria
| | - Matthias Tinzl
- Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Straße 10, 35043 Marburg, Germany
| | - Silvia M Glueck
- Institute of Chemistry, University of Graz, NAWI Graz, Heinrichstraße 28, 8010 Graz, Austria
| |
Collapse
|
3
|
Armstrong FA, Cheng B, Herold RA, Megarity CF, Siritanaratkul B. From Protein Film Electrochemistry to Nanoconfined Enzyme Cascades and the Electrochemical Leaf. Chem Rev 2022; 123:5421-5458. [PMID: 36573907 PMCID: PMC10176485 DOI: 10.1021/acs.chemrev.2c00397] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Protein film electrochemistry (PFE) has given unrivalled insight into the properties of redox proteins and many electron-transferring enzymes, allowing investigations of otherwise ill-defined or intractable topics such as unstable Fe-S centers and the catalytic bias of enzymes. Many enzymes have been established to be reversible electrocatalysts when attached to an electrode, and further investigations have revealed how unusual dependences of catalytic rates on electrode potential have stark similarities with electronics. A special case, the reversible electrochemistry of a photosynthetic enzyme, ferredoxin-NADP+ reductase (FNR), loaded at very high concentrations in the 3D nanopores of a conducting metal oxide layer, is leading to a new technology that brings PFE to myriad enzymes of other classes, the activities of which become controlled by the primary electron exchange. This extension is possible because FNR-based recycling of NADP(H) can be coupled to a dehydrogenase, and thence to other enzymes linked in tandem by the tight channelling of cofactors and intermediates within the nanopores of the material. The earlier interpretations of catalytic wave-shapes and various analogies with electronics are thus extended to initiate a field perhaps aptly named "cascade-tronics", in which the flow of reactions along an enzyme cascade is monitored and controlled through an electrochemical analyzer. Unlike in photosynthesis where FNR transduces electron transfer and hydride transfer through the unidirectional recycling of NADPH, the "electrochemical leaf" (e-Leaf) can be used to drive reactions in both oxidizing and reducing directions. The e-Leaf offers a natural way to study how enzymes are affected by nanoconfinement and crowding, mimicking the physical conditions under which enzyme cascades operate in living cells. The reactions of the trapped enzymes, often at very high local concentration, are thus studied electrochemically, exploiting the potential domain to control rates and direction and the current-rate analogy to derive kinetic data. Localized NADP(H) recycling is very efficient, resulting in very high cofactor turnover numbers and new opportunities for controlling and exploiting biocatalysis.
Collapse
Affiliation(s)
- Fraser A. Armstrong
- Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QR, United Kingdom
| | - Beichen Cheng
- Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QR, United Kingdom
| | - Ryan A. Herold
- Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QR, United Kingdom
| | - Clare F. Megarity
- Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QR, United Kingdom
| | - Bhavin Siritanaratkul
- Stephenson Institute for Renewable Energy and the Department of Chemistry, University of Liverpool, Liverpool L69 7ZF, United Kingdom
| |
Collapse
|
4
|
DeMirci H, Rao Y, Stoffel GM, Vögeli B, Schell K, Gomez A, Batyuk A, Gati C, Sierra RG, Hunter MS, Dao EH, Ciftci HI, Hayes B, Poitevin F, Li PN, Kaur M, Tono K, Saez DA, Deutsch S, Yoshikuni Y, Grubmüller H, Erb TJ, Vöhringer-Martinez E, Wakatsuki S. Intersubunit Coupling Enables Fast CO 2-Fixation by Reductive Carboxylases. ACS CENTRAL SCIENCE 2022; 8:1091-1101. [PMID: 36032767 PMCID: PMC9413435 DOI: 10.1021/acscentsci.2c00057] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Enoyl-CoA carboxylases/reductases (ECRs) are some of the most efficient CO2-fixing enzymes described to date. However, the molecular mechanisms underlying the extraordinary catalytic activity of ECRs on the level of the protein assembly remain elusive. Here we used a combination of ambient-temperature X-ray free electron laser (XFEL) and cryogenic synchrotron experiments to study the structural organization of the ECR from Kitasatospora setae. The K. setae ECR is a homotetramer that differentiates into a pair of dimers of open- and closed-form subunits in the catalytically active state. Using molecular dynamics simulations and structure-based mutagenesis, we show that catalysis is synchronized in the K. setae ECR across the pair of dimers. This conformational coupling of catalytic domains is conferred by individual amino acids to achieve high CO2-fixation rates. Our results provide unprecedented insights into the dynamic organization and synchronized inter- and intrasubunit communications of this remarkably efficient CO2-fixing enzyme during catalysis.
Collapse
Affiliation(s)
- Hasan DeMirci
- Biosciences
Division, SLAC National Accelerator Laboratory Menlo Park, California 94025, United States
- PULSE
Institute, SLAC National Accelerator Laboratory Menlo Park, California 94025, United States
- Department
of Molecular Biology and Genetics, Koc University, 34450 Sariyer/Istanbul, Turkey
- Email for H.D.:
| | - Yashas Rao
- Biosciences
Division, SLAC National Accelerator Laboratory Menlo Park, California 94025, United States
- Departamento
de Físico Química, Facultad de Ciencias Químicas, Universidad de Concepción, Concepción 4030000, Chile
| | - Gabriele M. Stoffel
- Department
of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Straße 10, D-35043 Marburg, Germany
| | - Bastian Vögeli
- Department
of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Straße 10, D-35043 Marburg, Germany
| | - Kristina Schell
- Department
of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Straße 10, D-35043 Marburg, Germany
| | - Aharon Gomez
- Departamento
de Físico Química, Facultad de Ciencias Químicas, Universidad de Concepción, Concepción 4030000, Chile
| | - Alexander Batyuk
- Linac Coherent
Light Source, SLAC National Accelerator
Laboratory Menlo Park, California 94025, United States
| | - Cornelius Gati
- Biosciences
Division, SLAC National Accelerator Laboratory Menlo Park, California 94025, United States
- Structural
Biology Department, Stanford University Stanford, California 94305, United States
| | - Raymond G. Sierra
- Linac Coherent
Light Source, SLAC National Accelerator
Laboratory Menlo Park, California 94025, United States
| | - Mark S. Hunter
- Linac Coherent
Light Source, SLAC National Accelerator
Laboratory Menlo Park, California 94025, United States
| | - E. Han Dao
- Biosciences
Division, SLAC National Accelerator Laboratory Menlo Park, California 94025, United States
- PULSE
Institute, SLAC National Accelerator Laboratory Menlo Park, California 94025, United States
| | - Halil I. Ciftci
- PULSE
Institute, SLAC National Accelerator Laboratory Menlo Park, California 94025, United States
| | - Brandon Hayes
- Linac Coherent
Light Source, SLAC National Accelerator
Laboratory Menlo Park, California 94025, United States
| | - Fredric Poitevin
- Linac Coherent
Light Source, SLAC National Accelerator
Laboratory Menlo Park, California 94025, United States
| | - Po-Nan Li
- Biosciences
Division, SLAC National Accelerator Laboratory Menlo Park, California 94025, United States
- Electrical
Engineering Department, Stanford University Stanford, California 94305, United States
| | - Manat Kaur
- Structural
Biology Department, Stanford University Stanford, California 94305, United States
| | - Kensuke Tono
- RIKEN
SPring-8 Center, Sayo, Hyogo 679-5148, Japan
- Japan Synchrotron Radiation Research Institute, Sayo, Hyogo 679-5198, Japan
| | - David Adrian Saez
- Departamento
de Físico Química, Facultad de Ciencias Químicas, Universidad de Concepción, Concepción 4030000, Chile
- Departamento
de Farmacia, Facultad de Farmacia, Universidad
de Concepción, Concepción 00000, Chile
| | - Samuel Deutsch
- U.S.
Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Walnut Creek, California 94720, United States
| | - Yasuo Yoshikuni
- U.S.
Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Walnut Creek, California 94720, United States
| | - Helmut Grubmüller
- Department
of Theoretical and Computational Biophysics, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077 Göttingen, Germany
| | - Tobias J. Erb
- Department
of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Straße 10, D-35043 Marburg, Germany
- LOEWE Center for Synthetic Microbiology (SYNMIKRO), 35032 Marburg, Germany
- Email for T.J.E.:
| | - Esteban Vöhringer-Martinez
- Departamento
de Físico Química, Facultad de Ciencias Químicas, Universidad de Concepción, Concepción 4030000, Chile
- Email for E.V.-M.:
| | - Soichi Wakatsuki
- Biosciences
Division, SLAC National Accelerator Laboratory Menlo Park, California 94025, United States
- Structural
Biology Department, Stanford University Stanford, California 94305, United States
- Email for S.W.:
| |
Collapse
|
5
|
Hopf FSM, Roth CD, de Souza EV, Galina L, Czeczot AM, Machado P, Basso LA, Bizarro CV. Bacterial Enoyl-Reductases: The Ever-Growing List of Fabs, Their Mechanisms and Inhibition. Front Microbiol 2022; 13:891610. [PMID: 35814645 PMCID: PMC9260719 DOI: 10.3389/fmicb.2022.891610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 05/27/2022] [Indexed: 11/13/2022] Open
Abstract
Enoyl-ACP reductases (ENRs) are enzymes that catalyze the last step of the elongation cycle during fatty acid synthesis. In recent years, new bacterial ENR types were discovered, some of them with structures and mechanisms that differ from the canonical bacterial FabI enzymes. Here, we briefly review the diversity of structural and catalytic properties of the canonical FabI and the new FabK, FabV, FabL, and novel ENRs identified in a soil metagenome study. We also highlight recent efforts to use the newly discovered Fabs as targets for drug development and consider the complex evolutionary history of this diverse set of bacterial ENRs.
Collapse
Affiliation(s)
- Fernanda S. M. Hopf
- Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF) and Instituto Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, Brazil
- Programa de Pós-Graduação em Biologia Celular e Molecular, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Brazil
| | - Candida D. Roth
- Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF) and Instituto Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, Brazil
| | - Eduardo V. de Souza
- Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF) and Instituto Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, Brazil
- Programa de Pós-Graduação em Biologia Celular e Molecular, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Brazil
| | - Luiza Galina
- Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF) and Instituto Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, Brazil
- Programa de Pós-Graduação em Medicina e Ciências da Saúde, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Brazil
| | - Alexia M. Czeczot
- Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF) and Instituto Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, Brazil
- Programa de Pós-Graduação em Medicina e Ciências da Saúde, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Brazil
| | - Pablo Machado
- Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF) and Instituto Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, Brazil
- Programa de Pós-Graduação em Biologia Celular e Molecular, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Brazil
| | - Luiz A. Basso
- Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF) and Instituto Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, Brazil
- Programa de Pós-Graduação em Biologia Celular e Molecular, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Brazil
- Programa de Pós-Graduação em Medicina e Ciências da Saúde, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Brazil
| | - Cristiano V. Bizarro
- Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF) and Instituto Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, Brazil
- Programa de Pós-Graduação em Biologia Celular e Molecular, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Brazil
- *Correspondence: Cristiano V. Bizarro,
| |
Collapse
|
6
|
Saez DA, Vogt-Geisse S, Vöhringer-Martinez E. Ene-adducts from 1,4-dihydropyridines and α,β-unsaturated nitriles: asynchronous transition states displaying aromatic features. Org Biomol Chem 2022; 20:8662-8671. [DOI: 10.1039/d2ob00989g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Covalent adducts between 1,4-ditrimethylsilyl-1,4-dihydropyridine and α,β-unsaturated nitriles are formed through ionic or Ene mechanisms modulated by environmental or structural features, sharing common transition states with aromatic properties.
Collapse
Affiliation(s)
- David Adrian Saez
- Departamento de Farmacia, Facultad de Farmacia, Universidad de Concepción, Concepción, Chile
| | - Stefan Vogt-Geisse
- Departamento de Físico-Química, Facultad de Ciencias Químicas, Universidad de Concepción, Concepción, Chile
| | - Esteban Vöhringer-Martinez
- Departamento de Físico-Química, Facultad de Ciencias Químicas, Universidad de Concepción, Concepción, Chile
| |
Collapse
|
7
|
Helfrich F, Scheidig AJ. Structural and catalytic characterization of Blastochloris viridis and Pseudomonas aeruginosa homospermidine synthases supports the essential role of cation-π interaction. Acta Crystallogr D Struct Biol 2021; 77:1317-1335. [PMID: 34605434 PMCID: PMC8489232 DOI: 10.1107/s2059798321008937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Accepted: 08/27/2021] [Indexed: 11/16/2022] Open
Abstract
Polyamines influence medically relevant processes in the opportunistic pathogen Pseudomonas aeruginosa, including virulence, biofilm formation and susceptibility to antibiotics. Although homospermidine synthase (HSS) is part of the polyamine metabolism in various strains of P. aeruginosa, neither its role nor its structure has been examined so far. The reaction mechanism of the nicotinamide adenine dinucleotide (NAD+)-dependent bacterial HSS has previously been characterized based on crystal structures of Blastochloris viridis HSS (BvHSS). This study presents the crystal structure of P. aeruginosa HSS (PaHSS) in complex with its substrate putrescine. A high structural similarity between PaHSS and BvHSS with conservation of the catalytically relevant residues is demonstrated, qualifying BvHSS as a model for mechanistic studies of PaHSS. Following this strategy, crystal structures of single-residue variants of BvHSS are presented together with activity assays of PaHSS, BvHSS and BvHSS variants. For efficient homospermidine production, acidic residues are required at the entrance to the binding pocket (`ionic slide') and near the active site (`inner amino site') to attract and bind the substrate putrescine via salt bridges. The tryptophan residue at the active site stabilizes cationic reaction components by cation-π interaction, as inferred from the interaction geometry between putrescine and the indole ring plane. Exchange of this tryptophan for other amino acids suggests a distinct catalytic requirement for an aromatic interaction partner with a highly negative electrostatic potential. These findings substantiate the structural and mechanistic knowledge on bacterial HSS, a potential target for antibiotic design.
Collapse
Affiliation(s)
- F. Helfrich
- Zoological Institute, University of Kiel, Am Botanischen Garten 1–9, 24118 Kiel, Germany
| | - Axel J. Scheidig
- Zoological Institute, University of Kiel, Am Botanischen Garten 1–9, 24118 Kiel, Germany
| |
Collapse
|
8
|
Herold RA, Reinbold R, Megarity CF, Abboud MI, Schofield CJ, Armstrong FA. Exploiting Electrode Nanoconfinement to Investigate the Catalytic Properties of Isocitrate Dehydrogenase (IDH1) and a Cancer-Associated Variant. J Phys Chem Lett 2021; 12:6095-6101. [PMID: 34170697 PMCID: PMC8273889 DOI: 10.1021/acs.jpclett.1c01517] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 06/22/2021] [Indexed: 06/13/2023]
Abstract
Human isocitrate dehydrogenase (IDH1) and its cancer-associated variant (IDH1 R132H) are rendered electroactive through coconfinement with a rapid NADP(H) recycling enzyme (ferredoxin-NADP+ reductase) in nanopores formed within an indium tin oxide electrode. Efficient coupling to localized NADP(H) enables IDH activity to be energized, controlled, and monitored in real time, leading directly to a thermodynamic redox landscape for accumulation of the oncometabolite, 2-hydroxyglutarate, that would occur in biological environments when the R132H variant is present. The technique enables time-resolved, in situ measurements of the kinetics of binding and dissociation of inhibitory drugs.
Collapse
|
9
|
Paiva P, Medina FE, Viegas M, Ferreira P, Neves RPP, Sousa JPM, Ramos MJ, Fernandes PA. Animal Fatty Acid Synthase: A Chemical Nanofactory. Chem Rev 2021; 121:9502-9553. [PMID: 34156235 DOI: 10.1021/acs.chemrev.1c00147] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Fatty acids are crucial molecules for most living beings, very well spread and conserved across species. These molecules play a role in energy storage, cell membrane architecture, and cell signaling, the latter through their derivative metabolites. De novo synthesis of fatty acids is a complex chemical process that can be achieved either by a metabolic pathway built by a sequence of individual enzymes, such as in most bacteria, or by a single, large multi-enzyme, which incorporates all the chemical capabilities of the metabolic pathway, such as in animals and fungi, and in some bacteria. Here we focus on the multi-enzymes, specifically in the animal fatty acid synthase (FAS). We start by providing a historical overview of this vast field of research. We follow by describing the extraordinary architecture of animal FAS, a homodimeric multi-enzyme with seven different active sites per dimer, including a carrier protein that carries the intermediates from one active site to the next. We then delve into this multi-enzyme's detailed chemistry and critically discuss the current knowledge on the chemical mechanism of each of the steps necessary to synthesize a single fatty acid molecule with atomic detail. In line with this, we discuss the potential and achieved FAS applications in biotechnology, as biosynthetic machines, and compare them with their homologous polyketide synthases, which are also finding wide applications in the same field. Finally, we discuss some open questions on the architecture of FAS, such as their peculiar substrate-shuttling arm, and describe possible reasons for the emergence of large megasynthases during evolution, questions that have fascinated biochemists from long ago but are still far from answered and understood.
Collapse
Affiliation(s)
- Pedro Paiva
- LAQV, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Fabiola E Medina
- Departamento de Ciencias Químicas, Facultad de Ciencias Exactas, Universidad Andres Bello, Autopista Concepción-Talcahuano, 7100 Talcahuano, Chile
| | - Matilde Viegas
- LAQV, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Pedro Ferreira
- LAQV, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Rui P P Neves
- LAQV, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - João P M Sousa
- LAQV, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Maria J Ramos
- LAQV, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Pedro A Fernandes
- LAQV, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| |
Collapse
|
10
|
Megarity CF, Siritanaratkul B, Herold RA, Morello G, Armstrong FA. Electron flow between the worlds of Marcus and Warburg. J Chem Phys 2021; 153:225101. [PMID: 33317312 DOI: 10.1063/5.0024701] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Living organisms are characterized by the ability to process energy (all release heat). Redox reactions play a central role in biology, from energy transduction (photosynthesis, respiratory chains) to highly selective catalyzed transformations of complex molecules. Distance and scale are important: electrons transfer on a 1 nm scale, hydrogen nuclei transfer between molecules on a 0.1 nm scale, and extended catalytic processes (cascades) operate most efficiently when the different enzymes are under nanoconfinement (10 nm-100 nm scale). Dynamic electrochemistry experiments (defined broadly within the term "protein film electrochemistry," PFE) reveal details that are usually hidden in conventional kinetic experiments. In PFE, the enzyme is attached to an electrode, often in an innovative way, and electron-transfer reactions, individual or within steady-state catalytic flow, can be analyzed in terms of precise potentials, proton coupling, cooperativity, driving-force dependence of rates, and reversibility (a mark of efficiency). The electrochemical experiments reveal subtle factors that would have played an essential role in molecular evolution. This article describes how PFE is used to visualize and analyze different aspects of biological redox chemistry, from long-range directional electron transfer to electron/hydride (NADPH) interconversion by a flavoenzyme and finally to NADPH recycling in a nanoconfined enzyme cascade.
Collapse
Affiliation(s)
- Clare F Megarity
- Department of Chemistry, University of Oxford, Oxford OX1 3QR, United Kingdom
| | | | - Ryan A Herold
- Department of Chemistry, University of Oxford, Oxford OX1 3QR, United Kingdom
| | - Giorgio Morello
- Department of Chemistry, University of Oxford, Oxford OX1 3QR, United Kingdom
| | - Fraser A Armstrong
- Department of Chemistry, University of Oxford, Oxford OX1 3QR, United Kingdom
| |
Collapse
|
11
|
Lindenburg L, Hollfelder F. “NAD‐display”: Ultrahigh‐Throughput in Vitro Screening of NAD(H) Dehydrogenases Using Bead Display and Flow Cytometry. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202013486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Laurens Lindenburg
- Department of Biochemistry University of Cambridge Tennis Court Road Cambridge CB2 1GA UK
- Current address: Genmab Uppsalalaan 15 3584 CT Utrecht The Netherlands
| | - Florian Hollfelder
- Department of Biochemistry University of Cambridge Tennis Court Road Cambridge CB2 1GA UK
| |
Collapse
|
12
|
Lindenburg L, Hollfelder F. "NAD-display": Ultrahigh-Throughput in Vitro Screening of NAD(H) Dehydrogenases Using Bead Display and Flow Cytometry. Angew Chem Int Ed Engl 2021; 60:9015-9021. [PMID: 33470025 PMCID: PMC8048591 DOI: 10.1002/anie.202013486] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 12/21/2020] [Indexed: 12/25/2022]
Abstract
NAD(H)‐utiliing enzymes have been the subject of directed evolution campaigns to improve their function. To enable access to a larger swath of sequence space, we demonstrate the utility of a cell‐free, ultrahigh‐throughput directed evolution platform for dehydrogenases. Microbeads (1.5 million per sample) carrying both variant DNA and an immobilised analogue of NAD+ were compartmentalised in water‐in‐oil emulsion droplets, together with cell‐free expression mixture and enzyme substrate, resulting in the recording of the phenotype on each bead. The beads’ phenotype could be read out and sorted for on a flow cytometer by using a highly sensitive fluorescent protein‐based sensor of the NAD+:NADH ratio. Integration of this “NAD‐display” approach with our previously described Split & Mix (SpliMLiB) method for generating large site‐saturation libraries allowed straightforward screening of fully balanced site saturation libraries of formate dehydrogenase, with diversities of 2×104. Based on modular design principles of synthetic biology NAD‐display offers access to sophisticated in vitro selections, avoiding complex technology platforms.
Collapse
Affiliation(s)
- Laurens Lindenburg
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA, UK.,Current address: Genmab, Uppsalalaan 15, 3584 CT, Utrecht, The Netherlands
| | - Florian Hollfelder
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA, UK
| |
Collapse
|
13
|
Miller TE, Beneyton T, Schwander T, Diehl C, Girault M, McLean R, Chotel T, Claus P, Cortina NS, Baret JC, Erb TJ. Light-powered CO 2 fixation in a chloroplast mimic with natural and synthetic parts. Science 2020; 368:649-654. [PMID: 32381722 DOI: 10.1126/science.aaz6802] [Citation(s) in RCA: 164] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 03/24/2020] [Indexed: 12/21/2022]
Abstract
Nature integrates complex biosynthetic and energy-converting tasks within compartments such as chloroplasts and mitochondria. Chloroplasts convert light into chemical energy, driving carbon dioxide fixation. We used microfluidics to develop a chloroplast mimic by encapsulating and operating photosynthetic membranes in cell-sized droplets. These droplets can be energized by light to power enzymes or enzyme cascades and analyzed for their catalytic properties in multiplex and real time. We demonstrate how these microdroplets can be programmed and controlled by adjusting internal compositions and by using light as an external trigger. We showcase the capability of our platform by integrating the crotonyl-coenzyme A (CoA)/ethylmalonyl-CoA/hydroxybutyryl-CoA (CETCH) cycle, a synthetic network for carbon dioxide conversion, to create an artificial photosynthetic system that interfaces the natural and the synthetic biological worlds.
Collapse
Affiliation(s)
- Tarryn E Miller
- Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, D-35043 Marburg, Germany
| | - Thomas Beneyton
- University of Bordeaux, CNRS, Centre de Recherche Paul Pascal, UMR 5031, Pessac 33600, France
| | - Thomas Schwander
- Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, D-35043 Marburg, Germany
| | - Christoph Diehl
- Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, D-35043 Marburg, Germany
| | | | - Richard McLean
- Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, D-35043 Marburg, Germany
| | - Tanguy Chotel
- University of Bordeaux, CNRS, Centre de Recherche Paul Pascal, UMR 5031, Pessac 33600, France
| | - Peter Claus
- Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, D-35043 Marburg, Germany
| | - Niña Socorro Cortina
- Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, D-35043 Marburg, Germany
| | - Jean-Christophe Baret
- University of Bordeaux, CNRS, Centre de Recherche Paul Pascal, UMR 5031, Pessac 33600, France. .,Institut Universitaire de France, Paris 75005, France
| | - Tobias J Erb
- Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, D-35043 Marburg, Germany. .,Center for Synthetic Microbiology, Max Planck Institute for Terrestrial Microbiology, D-35043 Marburg, Germany
| |
Collapse
|
14
|
Prejanò M, Medina FE, Ramos MJ, Russo N, Fernandes PA, Marino T. How the Destabilization of a Reaction Intermediate Affects Enzymatic Efficiency: The Case of Human Transketolase. ACS Catal 2020; 10:2872-2881. [PMID: 33828899 PMCID: PMC8016368 DOI: 10.1021/acscatal.9b04690] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 02/04/2020] [Indexed: 12/16/2022]
Abstract
![]()
Atomic
resolution X-ray crystallography has shown that an intermediate
(the X5P-ThDP adduct) of the catalytic cycle of transketolase (TK)
displays a significant, putatively highly energetic, out-of-plane
distortion in a sp2 carbon
adjacent to a lytic bond, suggested to lower the barrier of the subsequent
step, and thus was postulated to embody a clear-cut demonstration
of the intermediate destabilization effect. The lytic
bond of the subsequent rate-limiting step was very elongated in the
X-ray structure (1.61 Å), which was proposed to be a consequence
of the out-of-plane distortion. Here we use high-level QM and QM/MM
calculations to study the intermediate destabilization effect. We show that the intrinsic energy penalty for the observed
distortion is small (0.2 kcal·mol–1) and that
the establishment of a favorable hydrogen bond within X5P-ThDP, instead
of enzyme steric strain, was found to be the main cause for the distortion.
As the net energetic effect of the distortion is small, the establishment
of the internal hydrogen bond (−0.6 kcal·mol–1) offsets the associated penalty. This makes the distorted structure
more stable than the nondistorted one. Even though the energy contributions
determined here are close to the accuracy of the computational methods
in estimating penalties for geometric distortions, our data show that
the intermediate destabilization effect provides
a small contribution to the observed reaction rate and does not represent
a catalytic effect that justifies the many orders of magnitude which
enzymes accelerate reaction rates. The results help to understand
the intrinsic enzymatic machinery behind enzyme’s amazing proficiency.
Collapse
Affiliation(s)
- Mario Prejanò
- Dipartimento di Chimica e Tecnologie Chimiche, Università della Calabria, 87036 Arcavacata di Rende (CS), Italy
| | - Fabiola E. Medina
- UCIBIO, REQUIMTE, Departamento de Quı́mica e Bioquı́mica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Maria J. Ramos
- UCIBIO, REQUIMTE, Departamento de Quı́mica e Bioquı́mica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Nino Russo
- Dipartimento di Chimica e Tecnologie Chimiche, Università della Calabria, 87036 Arcavacata di Rende (CS), Italy
| | - Pedro A. Fernandes
- UCIBIO, REQUIMTE, Departamento de Quı́mica e Bioquı́mica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Tiziana Marino
- Dipartimento di Chimica e Tecnologie Chimiche, Università della Calabria, 87036 Arcavacata di Rende (CS), Italy
| |
Collapse
|
15
|
Jamieson CS, Ohashi M, Liu F, Tang Y, Houk KN. The expanding world of biosynthetic pericyclases: cooperation of experiment and theory for discovery. Nat Prod Rep 2019; 36:698-713. [PMID: 30311924 DOI: 10.1039/c8np00075a] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Covering: 2000 to 2018 Pericyclic reactions are a distinct class of reactions that have wide synthetic utility. Before the recent discoveries described in this review, enzyme-catalyzed pericyclic reactions were not widely known to be involved in biosynthesis. This situation is changing rapidly. We define the scope of pericyclic reactions, give a historical account of their discoveries as biosynthetic reactions, and provide evidence that there are many enzymes in nature that catalyze pericyclic reactions. These enzymes, the "pericyclases," are the subject of this review.
Collapse
Affiliation(s)
- Cooper S Jamieson
- Department of Chemical and Biomolecular Engineering, Department of Chemistry and Biochemistry, University of California, Los Angeles 90095, USA.
| | | | | | | | | |
Collapse
|
16
|
Medina FE, Ramos MJ, Fernandes PA. Complexities of the Reaction Mechanisms of CC Double Bond Reduction in Mammalian Fatty Acid Synthase Studied with Quantum Mechanics/Molecular Mechanics Calculations. ACS Catal 2019. [DOI: 10.1021/acscatal.9b03531] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Fabiola E. Medina
- UCIBIO, REQUIMTE, Departamento de Quı́mica e Bioquı́mica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Maria J. Ramos
- UCIBIO, REQUIMTE, Departamento de Quı́mica e Bioquı́mica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Pedro A. Fernandes
- UCIBIO, REQUIMTE, Departamento de Quı́mica e Bioquı́mica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| |
Collapse
|
17
|
Prejanò M, Medina FE, Fernandes PA, Russo N, Ramos MJ, Marino T. The Catalytic Mechanism of Human Transketolase. Chemphyschem 2019; 20:2881-2886. [PMID: 31489766 DOI: 10.1002/cphc.201900650] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 08/29/2019] [Indexed: 01/10/2023]
Abstract
We have computationally determined the catalytic mechanism of human transketolase (hTK) using a cluster model approach and density functional theory calculations. We were able to determine all the relevant structures, bringing solid evidences to the proposed experimental mechanism, and to add important detail to the structure of the transition states and the energy profile associated with catalysis. Furthermore, we have established the existence of a crucial intermediate of the catalytic cycle, in agreement with experiments. The calculated data brought new insights to hTK's catalytic mechanism, providing free-energy values for the chemical reaction, as well as adding atomistic detail to the experimental mechanism.
Collapse
Affiliation(s)
- Mario Prejanò
- Dipartimento di Chimica e Tecnologie Chimiche, Università della Calabria, Via Ponte Pietro Bucci, 87036, Arcavacata di Rende (CS), Italy
| | - Fabiola Estefany Medina
- UCIBIO, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007, Porto, Portugal
| | - Pedro Alexandrino Fernandes
- UCIBIO, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007, Porto, Portugal
| | - Nino Russo
- Dipartimento di Chimica e Tecnologie Chimiche, Università della Calabria, Via Ponte Pietro Bucci, 87036, Arcavacata di Rende (CS), Italy
| | - Maria Joao Ramos
- UCIBIO, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007, Porto, Portugal
| | - Tiziana Marino
- Dipartimento di Chimica e Tecnologie Chimiche, Università della Calabria, Via Ponte Pietro Bucci, 87036, Arcavacata di Rende (CS), Italy
| |
Collapse
|
18
|
Four amino acids define the CO 2 binding pocket of enoyl-CoA carboxylases/reductases. Proc Natl Acad Sci U S A 2019; 116:13964-13969. [PMID: 31243147 PMCID: PMC6628652 DOI: 10.1073/pnas.1901471116] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Carboxylases capture and convert CO2, which makes them key enzymes in photosynthesis and the global carbon cycle. However, the question how enzymes bind atmospheric CO2 is still unsolved. We studied enoyl-CoA carboxylases/reductases (Ecrs), the fastest CO2-fixing enzymes in nature, using structural biology, biochemistry, and advanced computational methods. Ecrs create a highly specific CO2-binding pocket with 4 amino acids at the active site. The pocket controls the fate of the gaseous molecule during catalysis and shields the catalytic center from oxygen and water. This exquisite control makes Ecrs highly efficient carboxylases outcompeting RuBisCO, the key enzyme of photosynthesis, by an order of magnitude. Our findings define the atomic framework for the future development of CO2-converting catalysts in biology and chemistry. Carboxylases are biocatalysts that capture and convert carbon dioxide (CO2) under mild conditions and atmospheric concentrations at a scale of more than 400 Gt annually. However, how these enzymes bind and control the gaseous CO2 molecule during catalysis is only poorly understood. One of the most efficient classes of carboxylating enzymes are enoyl-CoA carboxylases/reductases (Ecrs), which outcompete the plant enzyme RuBisCO in catalytic efficiency and fidelity by more than an order of magnitude. Here we investigated the interactions of CO2 within the active site of Ecr from Kitasatospora setae. Combining experimental biochemistry, protein crystallography, and advanced computer simulations we show that 4 amino acids, N81, F170, E171, and H365, are required to create a highly efficient CO2-fixing enzyme. Together, these 4 residues anchor and position the CO2 molecule for the attack by a reactive enolate created during the catalytic cycle. Notably, a highly ordered water molecule plays an important role in an active site that is otherwise carefully shielded from water, which is detrimental to CO2 fixation. Altogether, our study reveals unprecedented molecular details of selective CO2 binding and C–C-bond formation during the catalytic cycle of nature’s most efficient CO2-fixing enzyme. This knowledge provides the basis for the future development of catalytic frameworks for the capture and conversion of CO2 in biology and chemistry.
Collapse
|
19
|
Bernhardsgrütter I, Schell K, Peter DM, Borjian F, Saez DA, Vöhringer-Martinez E, Erb TJ. Awakening the Sleeping Carboxylase Function of Enzymes: Engineering the Natural CO 2-Binding Potential of Reductases. J Am Chem Soc 2019; 141:9778-9782. [PMID: 31188584 PMCID: PMC6650136 DOI: 10.1021/jacs.9b03431] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
![]()
Developing new carbon
dioxide (CO2) fixing enzymes is
a prerequisite to create new biocatalysts for diverse applications
in chemistry, biotechnology and synthetic biology. Here we used bioinformatics
to identify a “sleeping carboxylase function” in the
superfamily of medium-chain dehydrogenases/reductases (MDR), i.e.
enzymes that possess a low carboxylation side activity next to their
original enzyme reaction. We show that propionyl-CoA synthase from Erythrobacter sp. NAP1, as well as an acrylyl-CoA
reductase from Nitrosopumilus maritimus possess carboxylation yields of 3 ± 1 and 4.5 ± 0.9%.
We use rational design to engineer these enzymes further into carboxylases
by increasing interactions of the proteins with CO2 and
suppressing diffusion of water to the active site. The engineered
carboxylases show improved CO2-binding and kinetic parameters
comparable to naturally existing CO2-fixing enzymes. Our
results provide a strategy to develop novel CO2-fixing
enzymes and shed light on the emergence of natural carboxylases during
evolution.
Collapse
Affiliation(s)
- Iria Bernhardsgrütter
- Department of Biochemistry and Synthetic Metabolism , Max Planck Institute for Terrestrial Microbiology , Karl-von-Frisch-Straße 10 , D-35043 Marburg , Germany
| | - Kristina Schell
- Department of Biochemistry and Synthetic Metabolism , Max Planck Institute for Terrestrial Microbiology , Karl-von-Frisch-Straße 10 , D-35043 Marburg , Germany
| | - Dominik M Peter
- Department of Biochemistry and Synthetic Metabolism , Max Planck Institute for Terrestrial Microbiology , Karl-von-Frisch-Straße 10 , D-35043 Marburg , Germany
| | - Farshad Borjian
- Institute for Molecular Microbiology and Biotechnology, University of Münster , Corrensstr. 3 , D-48149 Münster , Germany
| | - David Adrian Saez
- Departamento de Físico Química, Facultad de Ciencias Químicas , Universidad de Concepción , 1290 Concepción , Chile
| | - Esteban Vöhringer-Martinez
- Departamento de Físico Química, Facultad de Ciencias Químicas , Universidad de Concepción , 1290 Concepción , Chile
| | - Tobias J Erb
- Department of Biochemistry and Synthetic Metabolism , Max Planck Institute for Terrestrial Microbiology , Karl-von-Frisch-Straße 10 , D-35043 Marburg , Germany.,LOEWE Center for Synthetic Microbiology (Synmikro) , Karl-von-Frisch-Straße 16 , D-35043 Marburg , Germany
| |
Collapse
|
20
|
Jensen AW, Mohanty DK, Dilling WL. The growing relevance of biological ene reactions. Bioorg Med Chem 2019; 27:686-691. [PMID: 30709643 DOI: 10.1016/j.bmc.2019.01.020] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 01/15/2019] [Accepted: 01/21/2019] [Indexed: 11/26/2022]
Abstract
The ene reaction involves the addition of an 'ene' to an 'enophile.' The retro-ene reaction is the reverse of the ene reaction. In recent years various biological molecules have been found to form covalent intermediates (ene-adducts) that might be the result of an ene reactions. Such adducts have been characterized or implicated for dihydropyridines and pyridininum cofactors derived from vitamin B3, such as the reduced and oxidized forms of nicotinamide adenine dinucleotide (NADH/NAD); flavin cofactors derived from vitamin B2, such as flavin adenine dinucleotide, FAD, and flavin mononucleotide, FMN; vitamin C; the oxime intermediate of nitric oxide synthase; tyrosine; and other biomolecules. Given the ubiquitous nature of these cofactors, it might be speculated that the formation of ene-adducts is a more common principle in biochemistry.
Collapse
Affiliation(s)
- Anton W Jensen
- Department of Chemistry and Biochemistry, Central Michigan University, Mount Pleasant, MI 48858, USA.
| | - Dillip K Mohanty
- Department of Chemistry and Biochemistry, Central Michigan University, Mount Pleasant, MI 48858, USA.
| | - Wendell L Dilling
- Department of Chemistry and Biochemistry, Central Michigan University, Mount Pleasant, MI 48858, USA.
| |
Collapse
|
21
|
Ling B, Li H, Yan L, Liu R, Liu Y. Conversion mechanism of enoyl thioesters into acyl thioesters catalyzed by 2-enoyl-thioester reductases from Candida Tropicalis. Phys Chem Chem Phys 2019; 21:10105-10113. [DOI: 10.1039/c9cp00987f] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Enoyl thioester reductase from Candida tropicalis (Etr1p) catalyzes the NADPH-dependent conversion of enoyl thioesters into acyl thioesters, which are essential in fatty acid and second metabolite biosynthesis.
Collapse
Affiliation(s)
- Baoping Ling
- School of Chemistry and Chemical Engineering & School of Environmental Science and Engineering, Shandong University
- Jinan
- China
- School of Chemistry and Chemical Engineering, Qufu Normal University
- Qufu
| | - Hong Li
- School of Chemistry and Chemical Engineering & School of Environmental Science and Engineering, Shandong University
- Jinan
- China
| | - Lijuan Yan
- School of Chemistry and Chemical Engineering & School of Environmental Science and Engineering, Shandong University
- Jinan
- China
| | - Rutao Liu
- School of Chemistry and Chemical Engineering & School of Environmental Science and Engineering, Shandong University
- Jinan
- China
| | - Yongjun Liu
- School of Chemistry and Chemical Engineering & School of Environmental Science and Engineering, Shandong University
- Jinan
- China
| |
Collapse
|
22
|
Kaysser L. Built to bind: biosynthetic strategies for the formation of small-molecule protease inhibitors. Nat Prod Rep 2019; 36:1654-1686. [DOI: 10.1039/c8np00095f] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The discovery and characterization of natural product protease inhibitors has inspired the development of numerous pharmaceutical agents.
Collapse
Affiliation(s)
- Leonard Kaysser
- Department of Pharmaceutical Biology
- University of Tübingen
- 72076 Tübingen
- Germany
- German Centre for Infection Research (DZIF)
| |
Collapse
|
23
|
Vögeli B, Rosenthal RG, Stoffel GMM, Wagner T, Kiefer P, Cortina NS, Shima S, Erb TJ. InhA, the enoyl-thioester reductase from Mycobacterium tuberculosis forms a covalent adduct during catalysis. J Biol Chem 2018; 293:17200-17207. [PMID: 30217823 PMCID: PMC6222099 DOI: 10.1074/jbc.ra118.005405] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 09/09/2018] [Indexed: 11/06/2022] Open
Abstract
The enoyl-thioester reductase InhA catalyzes an essential step in fatty acid biosynthesis of Mycobacterium tuberculosis and is a key target of antituberculosis drugs to combat multidrug-resistant M. tuberculosis strains. This has prompted intense interest in the mechanism and intermediates of the InhA reaction. Here, using enzyme mutagenesis, NMR, stopped-flow spectroscopy, and LC-MS, we found that the NADH cofactor and the CoA thioester substrate form a covalent adduct during the InhA catalytic cycle. We used the isolated adduct as a molecular probe to directly access the second half-reaction of the catalytic cycle of InhA (i.e. the proton transfer), independently of the first half-reaction (i.e. the initial hydride transfer) and to assign functions to two conserved active-site residues, Tyr-158 and Thr-196. We found that Tyr-158 is required for the stereospecificity of protonation and that Thr-196 is partially involved in hydride transfer and protonation. The natural tendency of InhA to form a covalent C2-ene adduct calls for a careful reconsideration of the enzyme's reaction mechanism. It also provides the basis for the development of effective tools to study, manipulate, and inhibit the catalytic cycle of InhA and related enzymes of the short-chain dehydrogenase/reductase (SDR) superfamily. In summary, our work has uncovered the formation of a covalent adduct during the InhA catalytic cycle and identified critical residues required for catalysis, providing further insights into the InhA reaction mechanism important for the development of antituberculosis drugs.
Collapse
Affiliation(s)
- Bastian Vögeli
- From the Departments of Biochemistry and Synthetic Metabolism and
| | | | | | - Tristan Wagner
- Microbial Protein Structure, Max-Planck-Institute for Terrestrial Microbiology, 35043 Marburg, Germany and
| | - Patrick Kiefer
- the Institute of Microbiology, ETH Zürich, 8093 Zürich, Switzerland
| | | | - Seigo Shima
- Microbial Protein Structure, Max-Planck-Institute for Terrestrial Microbiology, 35043 Marburg, Germany and
| | - Tobias J Erb
- From the Departments of Biochemistry and Synthetic Metabolism and
| |
Collapse
|
24
|
Roth S, Kilgore MB, Kutchan TM, Müller M. Exploiting the Catalytic Diversity of Short-Chain Dehydrogenases/Reductases: Versatile Enzymes from Plants with Extended Imine Substrate Scope. Chembiochem 2018; 19:1849-1852. [PMID: 29931726 DOI: 10.1002/cbic.201800291] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Indexed: 01/20/2023]
Abstract
Numerous short-chain dehydrogenases/reductases (SDRs) have found biocatalytic applications in C=O and C=C (enone) reduction. For NADPH-dependent C=N reduction, imine reductases (IREDs) have primarily been investigated for extension of the substrate range. Here, we show that SDRs are also suitable for a broad range of imine reductions. The SDR noroxomaritidine reductase (NR) is involved in Amaryllidaceae alkaloid biosynthesis, serving as an enone reductase. We have characterized NR by using a set of typical imine substrates and established that the enzyme is active with all four tested imine compounds (up to 99 % conversion, up to 92 % ee). Remarkably, NR reduced two keto compounds as well, thus highlighting this enzyme family's versatility. Using NR as a template, we have identified an as yet unexplored SDR from the Amaryllidacea Zephyranthes treatiae with imine-reducing activity (≤95 % ee). Our results encourage the future characterization of SDR family members as a means of discovering new imine-reducing enzymes.
Collapse
Affiliation(s)
- Sebastian Roth
- Institut für Pharmazeutische Wissenschaften, Albert-Ludwigs-Universität Freiburg, Albertstrasse 25, 79104, Freiburg, Germany
| | - Matthew B Kilgore
- Donald Danforth Plant Science Center, 975 N. Warson Road, St. Louis, MO, 63132, USA
| | - Toni M Kutchan
- Donald Danforth Plant Science Center, 975 N. Warson Road, St. Louis, MO, 63132, USA
| | - Michael Müller
- Institut für Pharmazeutische Wissenschaften, Albert-Ludwigs-Universität Freiburg, Albertstrasse 25, 79104, Freiburg, Germany
| |
Collapse
|
25
|
Krink-Koutsoubelis N, Loechner AC, Lechner A, Link H, Denby CM, Vögeli B, Erb TJ, Yuzawa S, Jakociunas T, Katz L, Jensen MK, Sourjik V, Keasling JD. Engineered Production of Short-Chain Acyl-Coenzyme A Esters in Saccharomyces cerevisiae. ACS Synth Biol 2018; 7:1105-1115. [PMID: 29498824 DOI: 10.1021/acssynbio.7b00466] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Short-chain acyl-coenzyme A esters serve as intermediate compounds in fatty acid biosynthesis, and the production of polyketides, biopolymers and other value-added chemicals. S. cerevisiae is a model organism that has been utilized for the biosynthesis of such biologically and economically valuable compounds. However, its limited repertoire of short-chain acyl-CoAs effectively prevents its application as a production host for a plethora of natural products. Therefore, we introduced biosynthetic metabolic pathways to five different acyl-CoA esters into S. cerevisiae. Our engineered strains provide the following acyl-CoAs: propionyl-CoA, methylmalonyl-CoA, n-butyryl-CoA, isovaleryl-CoA and n-hexanoyl-CoA. We established a yeast-specific metabolite extraction protocol to determine the intracellular acyl-CoA concentrations in the engineered strains. Propionyl-CoA was produced at 4-9 μM; methylmalonyl-CoA at 0.5 μM; and isovaleryl-CoA, n-butyryl-CoA, and n-hexanoyl-CoA at 6 μM each. The acyl-CoAs produced in this study are common building blocks of secondary metabolites and will enable the engineered production of a variety of natural products in S. cerevisiae. By providing this toolbox of acyl-CoA producing strains, we have laid the foundation to explore S. cerevisiae as a heterologous production host for novel secondary metabolites.
Collapse
Affiliation(s)
- Nicolas Krink-Koutsoubelis
- Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
- LOEWE Center for Synthetic Microbiology (SYNMIKRO), 35043 Marburg, Germany
| | - Anne C. Loechner
- Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
- LOEWE Center for Synthetic Microbiology (SYNMIKRO), 35043 Marburg, Germany
| | - Anna Lechner
- Joint BioEnergy Institute, Emeryville, California 94608, United States
| | - Hannes Link
- Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
- LOEWE Center for Synthetic Microbiology (SYNMIKRO), 35043 Marburg, Germany
| | - Charles M. Denby
- Joint BioEnergy Institute, Emeryville, California 94608, United States
- Biological System & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Bastian Vögeli
- Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
- LOEWE Center for Synthetic Microbiology (SYNMIKRO), 35043 Marburg, Germany
| | - Tobias J. Erb
- Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
- LOEWE Center for Synthetic Microbiology (SYNMIKRO), 35043 Marburg, Germany
| | - Satoshi Yuzawa
- Joint BioEnergy Institute, Emeryville, California 94608, United States
- Biological System & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Tadas Jakociunas
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Leonard Katz
- Synthetic Biology Engineering Research Center, Emeryville, California 94608, United States
| | - Michael K. Jensen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Victor Sourjik
- Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
- LOEWE Center for Synthetic Microbiology (SYNMIKRO), 35043 Marburg, Germany
| | - Jay D. Keasling
- Joint BioEnergy Institute, Emeryville, California 94608, United States
- Biological System & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Synthetic Biology Engineering Research Center, Emeryville, California 94608, United States
- Department of Chemical and Biomolecular Engineering & Department of Bioengineering, University of California, Berkeley, California 94720, United States
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| |
Collapse
|
26
|
Ogata K, Yajima Y, Nakamura S, Kaneko R, Goto M, Ohshima T, Yoshimune K. Inhibition of homoserine dehydrogenase by formation of a cysteine-NAD covalent complex. Sci Rep 2018; 8:5749. [PMID: 29636528 PMCID: PMC5893615 DOI: 10.1038/s41598-018-24063-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 03/27/2018] [Indexed: 02/02/2023] Open
Abstract
Homoserine dehydrogenase (EC 1.1.1.3, HSD) is an important regulatory enzyme in the aspartate pathway, which mediates synthesis of methionine, threonine and isoleucine from aspartate. Here, HSD from the hyperthermophilic archaeon Sulfolobus tokodaii (StHSD) was found to be inhibited by cysteine, which acted as a competitive inhibitor of homoserine with a Ki of 11 μM and uncompetitive an inhibitor of NAD and NADP with Ki's of 0.55 and 1.2 mM, respectively. Initial velocity and product (NADH) inhibition analyses of homoserine oxidation indicated that StHSD first binds NAD and then homoserine through a sequentially ordered mechanism. This suggests that feedback inhibition of StHSD by cysteine occurs through the formation of an enzyme-NAD-cysteine complex. Structural analysis of StHSD complexed with cysteine and NAD revealed that cysteine situates within the homoserine binding site. The distance between the sulfur atom of cysteine and the C4 atom of the nicotinamide ring was approximately 1.9 Å, close enough to form a covalent bond. The UV absorption-difference spectrum of StHSD with and without cysteine in the presence of NAD, exhibited a peak at 325 nm, which also suggests formation of a covalent bond between cysteine and the nicotinamide ring.
Collapse
Affiliation(s)
- Kohei Ogata
- Department of Biomolecular Science, Graduate School of Science, Toho University, 2-2-1, Miyama, Funabashi, Chiba, 274-8510, Japan
| | - Yui Yajima
- Department of Applied Molecular Chemistry, College of Industrial Technology, Nihon University, 1-2-1, Izumichou, Narashino, Chiba, 275-8575, Japan
| | - Sanenori Nakamura
- Department of Applied Molecular Chemistry, Graduate School of Industrial Technology, Nihon University, 1-2-1, Izumichou, Narashino, Chiba, 275-8575, Japan
| | - Ryosuke Kaneko
- Department of Biomolecular Science, Graduate School of Science, Toho University, 2-2-1, Miyama, Funabashi, Chiba, 274-8510, Japan
| | - Masaru Goto
- Department of Biomolecular Science, Graduate School of Science, Toho University, 2-2-1, Miyama, Funabashi, Chiba, 274-8510, Japan
| | - Toshihisa Ohshima
- Department of Biomedical Engineering, Osaka Institute of Technology, 5-16-1, Ohmiya, Asahi-ku, Osaka, 535-8585, Japan
| | - Kazuaki Yoshimune
- Department of Applied Molecular Chemistry, College of Industrial Technology, Nihon University, 1-2-1, Izumichou, Narashino, Chiba, 275-8575, Japan. .,Department of Applied Molecular Chemistry, Graduate School of Industrial Technology, Nihon University, 1-2-1, Izumichou, Narashino, Chiba, 275-8575, Japan.
| |
Collapse
|
27
|
Sandor R, Slanina J, Midlik A, Sebrlova K, Novotna L, Carnecka M, Slaninova I, Taborsky P, Taborska E, Pes O. Sanguinarine is reduced by NADH through a covalent adduct. PHYTOCHEMISTRY 2018; 145:77-84. [PMID: 29107809 DOI: 10.1016/j.phytochem.2017.10.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Revised: 10/26/2017] [Accepted: 10/27/2017] [Indexed: 06/07/2023]
Abstract
Sanguinarine is a benzo[c]phenanthridine alkaloid with interesting cytotoxic properties, such as induction of oxidative DNA damage and very rapid apoptosis, which is not mediated by p53-dependent signaling. It has been previously documented that sanguinarine is reduced with NADH even in absence of any enzymes while being converted to its dihydro form. We found that the dark blue fluorescent species, observed during sanguinarine reduction with NADH and misinterpreted by Matkar et al. (Arch. Biochem. Biophys. 2008, 477, 43-52) as an anionic form of the alkaloid, is a covalent adduct formed by the interaction of NADH and sanguinarine. The covalent adduct is then converted slowly to the products, dihydrosanguinarine and NAD+, in the second step of reduction. The product of the reduction, dihydrosanguinarine, was continually re-oxidized by the atmospheric oxygen back to sanguinarine, resulting in further reacting with NADH and eventually depleting all NADH molecules. The ability of sanguinarine to diminish the pool of NADH and NADPH is further considered when explaining the sanguinarine-induced apoptosis in living cells.
Collapse
Affiliation(s)
- Roman Sandor
- Department of Biochemistry, Faculty of Medicine, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic
| | - Jiri Slanina
- Department of Biochemistry, Faculty of Medicine, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic
| | - Adam Midlik
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University Brno, Kamenice 5, 62500 Brno, Czech Republic; Central European Institute of Technology CEITEC MU, Kamenice 5, 62500 Brno, Czech Republic
| | - Kristyna Sebrlova
- Department of Biochemistry, Faculty of Medicine, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic
| | - Lucie Novotna
- Department of Biochemistry, Faculty of Medicine, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic
| | - Martina Carnecka
- Department of Biochemistry, Faculty of Medicine, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic
| | - Iva Slaninova
- Department of Biology, Faculty of Medicine, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic
| | - Petr Taborsky
- Department of Chemistry, Faculty of Science, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic
| | - Eva Taborska
- Department of Biochemistry, Faculty of Medicine, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic
| | - Ondrej Pes
- Department of Biochemistry, Faculty of Medicine, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic.
| |
Collapse
|
28
|
Schwander T, McLean R, Zarzycki J, Erb TJ. Structural basis for substrate specificity of methylsuccinyl-CoA dehydrogenase, an unusual member of the acyl-CoA dehydrogenase family. J Biol Chem 2017; 293:1702-1712. [PMID: 29275330 PMCID: PMC5798300 DOI: 10.1074/jbc.ra117.000764] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 12/20/2017] [Indexed: 11/13/2022] Open
Abstract
(2S)-methylsuccinyl-CoA dehydrogenase (MCD) belongs to the family of FAD-dependent acyl-CoA dehydrogenase (ACD) and is a key enzyme of the ethylmalonyl-CoA pathway for acetate assimilation. It catalyzes the oxidation of (2S)-methylsuccinyl-CoA to α,β-unsaturated mesaconyl-CoA and shows only about 0.5% activity with succinyl-CoA. Here we report the crystal structure of MCD at a resolution of 1.37 Å. The enzyme forms a homodimer of two 60-kDa subunits. Compared with other ACDs, MCD contains an ∼170-residue-long N-terminal extension that structurally mimics a dimer–dimer interface of these enzymes that are canonically organized as tetramers. MCD catalyzes the unprecedented oxidation of an α-methyl branched dicarboxylic acid CoA thioester. Substrate specificity is achieved by a cluster of three arginines that accommodates the terminal carboxyl group and a dedicated cavity that facilitates binding of the C2 methyl branch. MCD apparently evolved toward preventing the nonspecific oxidation of succinyl-CoA, which is a close structural homolog of (2S)-methylsuccinyl-CoA and an essential intermediate in central carbon metabolism. For different metabolic engineering and biotechnological applications, however, an enzyme that can oxidize succinyl-CoA to fumaryl-CoA is sought after. Based on the MCD structure, we were able to shift substrate specificity of MCD toward succinyl-CoA through active-site mutagenesis.
Collapse
Affiliation(s)
- Thomas Schwander
- From the Department of Biochemistry and Synthetic Metabolism, Max-Planck-Institute for Terrestrial Microbiology Marburg, Karl-von-Frisch-Strasse 10, D-35043 Marburg, Germany and
| | - Richard McLean
- From the Department of Biochemistry and Synthetic Metabolism, Max-Planck-Institute for Terrestrial Microbiology Marburg, Karl-von-Frisch-Strasse 10, D-35043 Marburg, Germany and
| | - Jan Zarzycki
- From the Department of Biochemistry and Synthetic Metabolism, Max-Planck-Institute for Terrestrial Microbiology Marburg, Karl-von-Frisch-Strasse 10, D-35043 Marburg, Germany and
| | - Tobias J Erb
- From the Department of Biochemistry and Synthetic Metabolism, Max-Planck-Institute for Terrestrial Microbiology Marburg, Karl-von-Frisch-Strasse 10, D-35043 Marburg, Germany and .,the LOEWE Center for Synthetic Microbiology (SYNMIKRO), D-35043 Marburg, Germany
| |
Collapse
|
29
|
Erb TJ, Zarzycki J. A short history of RubisCO: the rise and fall (?) of Nature's predominant CO 2 fixing enzyme. Curr Opin Biotechnol 2017; 49:100-107. [PMID: 28843191 DOI: 10.1016/j.copbio.2017.07.017] [Citation(s) in RCA: 146] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Revised: 07/26/2017] [Accepted: 07/26/2017] [Indexed: 11/18/2022]
Abstract
Ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO) is arguably one of the most abundant proteins in the biosphere and a key enzyme in the global carbon cycle. Although RubisCO has been intensively studied, its evolutionary origins and rise as Nature's most dominant carbon dioxide (CO2)-fixing enzyme still remain in the dark. In this review we will bring together biochemical, structural, physiological, microbiological, as well as phylogenetic data to speculate on the evolutionary roots of the CO2-fixation reaction of RubisCO, the emergence of RubisCO-based autotrophic CO2-fixation in the context of the Calvin-Benson-Bassham cycle, and the further evolution of RubisCO into the 'RubisCOsome', a complex of various proteins assembling and interacting with the enzyme to improve its operational capacity (functionality) under different biological and environmental conditions.
Collapse
Affiliation(s)
- Tobias J Erb
- Max Planck Institute for Terrestrial Microbiology, Department of Biochemistry and Synthetic Metabolism, Karl-von-Frisch-Str. 10, 35043 Marburg, Germany.
| | - Jan Zarzycki
- Max Planck Institute for Terrestrial Microbiology, Department of Biochemistry and Synthetic Metabolism, Karl-von-Frisch-Str. 10, 35043 Marburg, Germany
| |
Collapse
|
30
|
Trinchera P, Sun W, Smith JE, Palomas D, Crespo-Otero R, Jones CR. Intermolecular Aryne Ene Reaction of Hantzsch Esters: Stable Covalent Ene Adducts from a 1,4-Dihydropyridine Reaction. Org Lett 2017; 19:4644-4647. [PMID: 28817286 DOI: 10.1021/acs.orglett.7b02272] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Piera Trinchera
- School of Biological and
Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, U.K
| | - Weitao Sun
- School of Biological and
Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, U.K
| | - Jane E. Smith
- School of Biological and
Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, U.K
| | - David Palomas
- School of Biological and
Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, U.K
| | - Rachel Crespo-Otero
- School of Biological and
Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, U.K
| | - Christopher R. Jones
- School of Biological and
Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, U.K
| |
Collapse
|
31
|
Moore JM, Hall JM, Dilling WL, Jensen AW, Squattrito PJ, Giolando P, Kirschbaum K. N-Benzylnicotinamide and N-benzyl-1,4-dihydronicotinamide: useful models for NAD + and NADH. ACTA CRYSTALLOGRAPHICA SECTION C-STRUCTURAL CHEMISTRY 2017; 73:531-535. [PMID: 28677604 DOI: 10.1107/s2053229617008877] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Accepted: 06/14/2017] [Indexed: 11/10/2022]
Abstract
3-Aminocarbonyl-1-benzylpyridinium bromide (N-benzylnicotinamide, BNA), C13H13N2O+·Br-, (I), and 1-benzyl-1,4-dihydropyridine-3-carboxamide (N-benzyl-1,4-dihydronicotinamide, rBNA), C13H14N2O, (II), are valuable model compounds used to study the enzymatic cofactors NAD(P)+ and NAD(P)H. BNA was crystallized successfully and its structure determined for the first time, while a low-temperature high-resolution structure of rBNA was obtained. Together, these structures provide the most detailed view of the reactive portions of NAD(P)+ and NAD(P)H. The amide group in BNA is rotated 8.4 (4)° out of the plane of the pyridine ring, while the two rings display a dihedral angle of 70.48 (17)°. In the rBNA structure, the dihydropyridine ring is essentially planar, indicating significant delocalization of the formal double bonds, and the amide group is coplanar with the ring [dihedral angle = 4.35 (9)°]. This rBNA conformation may lower the transition-state energy of an ene reaction between a substrate double bond and the dihydropyridine ring. The transition state would involve one atom of the double bond binding to the carbon ortho to both the ring N atom and the amide substituent of the dihydropyridine ring, while the other end of the double bond accepts an H atom from the methylene group para to the N atom.
Collapse
Affiliation(s)
- John M Moore
- Department of Chemistry and Biochemistry, Central Michigan University, Mount Pleasant, Michigan 48859, USA
| | - Jasmine M Hall
- Department of Chemistry and Biochemistry, Central Michigan University, Mount Pleasant, Michigan 48859, USA
| | - Wendell L Dilling
- Department of Chemistry and Biochemistry, Central Michigan University, Mount Pleasant, Michigan 48859, USA
| | - Anton W Jensen
- Department of Chemistry and Biochemistry, Central Michigan University, Mount Pleasant, Michigan 48859, USA
| | - Philip J Squattrito
- Department of Chemistry and Biochemistry, Central Michigan University, Mount Pleasant, Michigan 48859, USA
| | - Patrick Giolando
- College of Natural Sciences and Mathematics, University of Toledo, Toledo, OH 43606, USA
| | - Kristin Kirschbaum
- College of Natural Sciences and Mathematics, University of Toledo, Toledo, OH 43606, USA
| |
Collapse
|
32
|
A conserved threonine prevents self-intoxication of enoyl-thioester reductases. Nat Chem Biol 2017; 13:745-749. [PMID: 28504678 DOI: 10.1038/nchembio.2375] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2016] [Accepted: 02/13/2017] [Indexed: 01/17/2023]
Abstract
Enzymes are highly specific biocatalysts, yet they can promote unwanted side reactions. Here we investigated the factors that direct catalysis in the enoyl-thioester reductase Etr1p. We show that a single conserved threonine is essential to suppress the formation of a side product that would otherwise act as a high-affinity inhibitor of the enzyme. Substitution of this threonine with isosteric valine increases side-product formation by more than six orders of magnitude, while decreasing turnover frequency by only one order of magnitude. Our results show that the promotion of wanted reactions and the suppression of unwanted side reactions operate independently at the active site of Etr1p, and that the active suppression of side reactions is highly conserved in the family of medium-chain dehydrogenases/reductases (MDRs). Our discovery emphasizes the fact that the active destabilization of competing transition states is an important factor during catalysis that has implications for the understanding and the de novo design of enzymes.
Collapse
|
33
|
Abstract
Oxidative cyclizations are important transformations that occur widely during natural product biosynthesis. The transformations from acyclic precursors to cyclized products can afford morphed scaffolds, structural rigidity, and biological activities. Some of the most dramatic structural alterations in natural product biosynthesis occur through oxidative cyclization. In this Review, we examine the different strategies used by nature to create new intra(inter)molecular bonds via redox chemistry. This Review will cover both oxidation- and reduction-enabled cyclization mechanisms, with an emphasis on the former. Radical cyclizations catalyzed by P450, nonheme iron, α-KG-dependent oxygenases, and radical SAM enzymes are discussed to illustrate the use of molecular oxygen and S-adenosylmethionine to forge new bonds at unactivated sites via one-electron manifolds. Nonradical cyclizations catalyzed by flavin-dependent monooxygenases and NAD(P)H-dependent reductases are covered to show the use of two-electron manifolds in initiating cyclization reactions. The oxidative installations of epoxides and halogens into acyclic scaffolds to drive subsequent cyclizations are separately discussed as examples of "disappearing" reactive handles. Last, oxidative rearrangement of rings systems, including contractions and expansions, will be covered.
Collapse
Affiliation(s)
- Man-Cheng Tang
- Department of Chemical and Biomolecular Engineering, Department of Chemistry and Biochemistry, University of California, Los Angeles, 420 Westwood Plaza, Los Angeles, CA 90095, USA
| | - Yi Zou
- Department of Chemical and Biomolecular Engineering, Department of Chemistry and Biochemistry, University of California, Los Angeles, 420 Westwood Plaza, Los Angeles, CA 90095, USA
| | - Kenji Watanabe
- Department of Pharmaceutical Sciences, University of Shizuoka, Shizuoka 422-8526, Japan
| | - Christopher T. Walsh
- Stanford University Chemistry, Engineering, and Medicine for Human Health (ChEM-H), Stanford University, 443 Via Ortega, Stanford, CA 94305
| | - Yi Tang
- Department of Chemical and Biomolecular Engineering, Department of Chemistry and Biochemistry, University of California, Los Angeles, 420 Westwood Plaza, Los Angeles, CA 90095, USA
| |
Collapse
|
34
|
Ray L, Valentic TR, Miyazawa T, Withall DM, Song L, Milligan JC, Osada H, Takahashi S, Tsai SC, Challis GL. A crotonyl-CoA reductase-carboxylase independent pathway for assembly of unusual alkylmalonyl-CoA polyketide synthase extender units. Nat Commun 2016; 7:13609. [PMID: 28000660 PMCID: PMC5187497 DOI: 10.1038/ncomms13609] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Accepted: 10/19/2016] [Indexed: 11/12/2022] Open
Abstract
Type I modular polyketide synthases assemble diverse bioactive natural products. Such multienzymes typically use malonyl and methylmalonyl-CoA building blocks for polyketide chain assembly. However, in several cases more exotic alkylmalonyl-CoA extender units are also known to be incorporated. In all examples studied to date, such unusual extender units are biosynthesized via reductive carboxylation of α, β-unsaturated thioesters catalysed by crotonyl-CoA reductase/carboxylase (CCRC) homologues. Here we show using a chemically-synthesized deuterium-labelled mechanistic probe, and heterologous gene expression experiments that the unusual alkylmalonyl-CoA extender units incorporated into the stambomycin family of polyketide antibiotics are assembled by direct carboxylation of medium chain acyl-CoA thioesters. X-ray crystal structures of the unusual β-subunit of the acyl-CoA carboxylase (YCC) responsible for this reaction, alone and in complex with hexanoyl-CoA, reveal the molecular basis for substrate recognition, inspiring the development of methodology for polyketide bio-orthogonal tagging via incorporation of 6-azidohexanoic acid and 8-nonynoic acid into novel stambomycin analogues.
Polyketides are typically assembled from a starter unit and malonyl- and/or methylmalonyl-CoA-derived extender units, but the macrolide antibiotics stambomycins incorporate non-standard alkylmalonyl-CoA extender units. Here, the authors describe the biosynthetic pathway responsible for this unusual synthesis.
Collapse
Affiliation(s)
- Lauren Ray
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, UK
| | - Timothy R Valentic
- Departments of Molecular Biology and Biochemistry, Chemistry, and Pharmaceutical Sciences, University of California, Irvine, California 92697, USA
| | - Takeshi Miyazawa
- Chemical Biology Research Group, RIKEN Center for Sustainable Resource Science, Saitama 351-0198, Japan.,Graduate School of Science and Engineering, Saitama University, Saitama 338-8570, Japan
| | - David M Withall
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, UK
| | - Lijiang Song
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, UK
| | - Jacob C Milligan
- Departments of Molecular Biology and Biochemistry, Chemistry, and Pharmaceutical Sciences, University of California, Irvine, California 92697, USA
| | - Hiroyuki Osada
- Chemical Biology Research Group, RIKEN Center for Sustainable Resource Science, Saitama 351-0198, Japan.,Graduate School of Science and Engineering, Saitama University, Saitama 338-8570, Japan
| | - Shunji Takahashi
- Chemical Biology Research Group, RIKEN Center for Sustainable Resource Science, Saitama 351-0198, Japan
| | - Shiou-Chuan Tsai
- Departments of Molecular Biology and Biochemistry, Chemistry, and Pharmaceutical Sciences, University of California, Irvine, California 92697, USA
| | - Gregory L Challis
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, UK
| |
Collapse
|
35
|
|
36
|
Schwander T, Schada von Borzyskowski L, Burgener S, Cortina NS, Erb TJ. A synthetic pathway for the fixation of carbon dioxide in vitro. Science 2016; 354:900-904. [PMID: 27856910 PMCID: PMC5892708 DOI: 10.1126/science.aah5237] [Citation(s) in RCA: 339] [Impact Index Per Article: 42.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 10/05/2016] [Indexed: 01/20/2023]
Abstract
Carbon dioxide (CO2) is an important carbon feedstock for a future green economy. This requires the development of efficient strategies for its conversion into multicarbon compounds. We describe a synthetic cycle for the continuous fixation of CO2 in vitro. The crotonyl-coenzyme A (CoA)/ethylmalonyl-CoA/hydroxybutyryl-CoA (CETCH) cycle is a reaction network of 17 enzymes that converts CO2 into organic molecules at a rate of 5 nanomoles of CO2 per minute per milligram of protein. The CETCH cycle was drafted by metabolic retrosynthesis, established with enzymes originating from nine different organisms of all three domains of life, and optimized in several rounds by enzyme engineering and metabolic proofreading. The CETCH cycle adds a seventh, synthetic alternative to the six naturally evolved CO2 fixation pathways, thereby opening the way for in vitro and in vivo applications.
Collapse
Affiliation(s)
- Thomas Schwander
- Biochemistry and Synthetic Biology of Microbial Metabolism Group, Max Planck Institute for Terrestrial Microbiology Marburg, D-35043 Marburg, Germany
| | - Lennart Schada von Borzyskowski
- Biochemistry and Synthetic Biology of Microbial Metabolism Group, Max Planck Institute for Terrestrial Microbiology Marburg, D-35043 Marburg, Germany
- Institute for Microbiology, ETH Zürich, CH-8093 Zürich, Switzerland
| | - Simon Burgener
- Biochemistry and Synthetic Biology of Microbial Metabolism Group, Max Planck Institute for Terrestrial Microbiology Marburg, D-35043 Marburg, Germany
- Institute for Microbiology, ETH Zürich, CH-8093 Zürich, Switzerland
| | - Niña Socorro Cortina
- Biochemistry and Synthetic Biology of Microbial Metabolism Group, Max Planck Institute for Terrestrial Microbiology Marburg, D-35043 Marburg, Germany
| | - Tobias J Erb
- Biochemistry and Synthetic Biology of Microbial Metabolism Group, Max Planck Institute for Terrestrial Microbiology Marburg, D-35043 Marburg, Germany.
- Institute for Microbiology, ETH Zürich, CH-8093 Zürich, Switzerland
- LOEWE Center for Synthetic Microbiology, Universität Marburg, D-35037 Marburg, Germany
| |
Collapse
|
37
|
|
38
|
Abstract
Most of the stereocenters of polyketide natural products are established during assembly line biosynthesis. The body of knowledge for how stereocenters are set is now large enough to begin constructing physical models of key reactions. Interactions between stereocenter-forming enzymes and polyketide intermediates are examined here at atomic resolution, drawing from the most current structural and functional information of ketosynthases (KSs), ketoreductases (KRs), dehydratases (DHs), enoylreductases (ERs), and related enzymes. While many details remain to be experimentally determined, our understanding of the chemical and physical mechanisms utilized by the chirality-molding enzymes of modular PKSs is rapidly advancing.
Collapse
Affiliation(s)
- Adrian T Keatinge-Clay
- Department of Molecular Biosciences, The University of Texas at Austin, 2506 Speedway Stop A5000, Austin, TX 78712, USA. and Department of Chemistry, The University of Texas at Austin, 105 E 24th St. Stop A5300, Austin, TX 78712, USA
| |
Collapse
|
39
|
Abstract
This highlight provides an overview of recent advances in understanding the diversity of polyketide synthase (PKS) substrate building blocks. Substrates functioning as starter units and extender units contribute significantly to the chemical complexity and structural diversity exhibited by this class of natural products. This article complements and extends upon the current comprehensive reviews that have been published on these two topics (Moore and Hertweck, Nat. Prod. Rep., 2002, 19, 70; Chan et al., Nat. Prod. Rep., 2009, 1, 90; Wilson and Moore, Nat. Prod. Rep., 2012, 29, 72).
Collapse
Affiliation(s)
- Lauren Ray
- Scripps Institution of Oceanography, University of California at San Diego, La Jolla, California 92093-0204, USA.
| | - Bradley S Moore
- Scripps Institution of Oceanography, University of California at San Diego, La Jolla, California 92093-0204, USA. and Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, La Jolla, California 92093-0204, USA
| |
Collapse
|
40
|
Zhang L, Mori T, Zheng Q, Awakawa T, Yan Y, Liu W, Abe I. Rational Control of Polyketide Extender Units by Structure‐Based Engineering of a Crotonyl‐CoA Carboxylase/Reductase in Antimycin Biosynthesis. Angew Chem Int Ed Engl 2015; 54:13462-5. [DOI: 10.1002/anie.201506899] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2015] [Indexed: 11/06/2022]
Affiliation(s)
- Lihan Zhang
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7‐3‐1 Hongo, Bunkyo‐ku, Tokyo 113‐0033 (Japan)
| | - Takahiro Mori
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7‐3‐1 Hongo, Bunkyo‐ku, Tokyo 113‐0033 (Japan)
| | - Qingfei Zheng
- State Key Laboratory of Bio‐Organic & Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Lingling road 345, Shanghai 200032 (China)
| | - Takayoshi Awakawa
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7‐3‐1 Hongo, Bunkyo‐ku, Tokyo 113‐0033 (Japan)
| | - Yan Yan
- State Key Laboratory of Bio‐Organic & Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Lingling road 345, Shanghai 200032 (China)
| | - Wen Liu
- State Key Laboratory of Bio‐Organic & Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Lingling road 345, Shanghai 200032 (China)
| | - Ikuro Abe
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7‐3‐1 Hongo, Bunkyo‐ku, Tokyo 113‐0033 (Japan)
| |
Collapse
|
41
|
Zhang L, Mori T, Zheng Q, Awakawa T, Yan Y, Liu W, Abe I. Rational Control of Polyketide Extender Units by Structure‐Based Engineering of a Crotonyl‐CoA Carboxylase/Reductase in Antimycin Biosynthesis. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201506899] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Lihan Zhang
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7‐3‐1 Hongo, Bunkyo‐ku, Tokyo 113‐0033 (Japan)
| | - Takahiro Mori
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7‐3‐1 Hongo, Bunkyo‐ku, Tokyo 113‐0033 (Japan)
| | - Qingfei Zheng
- State Key Laboratory of Bio‐Organic & Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Lingling road 345, Shanghai 200032 (China)
| | - Takayoshi Awakawa
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7‐3‐1 Hongo, Bunkyo‐ku, Tokyo 113‐0033 (Japan)
| | - Yan Yan
- State Key Laboratory of Bio‐Organic & Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Lingling road 345, Shanghai 200032 (China)
| | - Wen Liu
- State Key Laboratory of Bio‐Organic & Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Lingling road 345, Shanghai 200032 (China)
| | - Ikuro Abe
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7‐3‐1 Hongo, Bunkyo‐ku, Tokyo 113‐0033 (Japan)
| |
Collapse
|
42
|
Structural Basis for Cyclopropanation by a Unique Enoyl-Acyl Carrier Protein Reductase. Structure 2015; 23:2213-2223. [PMID: 26526850 DOI: 10.1016/j.str.2015.09.013] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Revised: 09/12/2015] [Accepted: 09/15/2015] [Indexed: 11/20/2022]
Abstract
The natural product curacin A, a potent anticancer agent, contains a rare cyclopropane group. The five enzymes for cyclopropane biosynthesis are highly similar to enzymes that generate a vinyl chloride moiety in the jamaicamide natural product. The structural biology of this remarkable catalytic adaptability is probed with high-resolution crystal structures of the curacin cyclopropanase (CurF ER), an in vitro enoyl reductase (JamJ ER), and a canonical curacin enoyl reductase (CurK ER). The JamJ and CurK ERs catalyze NADPH-dependent double bond reductions typical of enoyl reductases (ERs) of the medium-chain dehydrogenase reductase (MDR) superfamily. Cyclopropane formation by CurF ER is specified by a short loop which, when transplanted to JamJ ER, confers cyclopropanase activity on the chimeric enzyme. Detection of an adduct of NADPH with the model substrate crotonyl-CoA provides indirect support for a recent proposal of a C2-ene intermediate on the reaction pathway of MDR enoyl-thioester reductases.
Collapse
|
43
|
Peter DM, Schada von Borzyskowski L, Kiefer P, Christen P, Vorholt JA, Erb TJ. Screening and Engineering the Synthetic Potential of Carboxylating Reductases from Central Metabolism and Polyketide Biosynthesis. Angew Chem Int Ed Engl 2015; 54:13457-61. [PMID: 26383129 DOI: 10.1002/anie.201505282] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Indexed: 11/06/2022]
Abstract
Carboxylating enoyl-thioester reductases (ECRs) are a recently discovered class of enzymes. They catalyze the highly efficient addition of CO2 to the double bond of α,β-unsaturated CoA-thioesters and serve two biological functions. In primary metabolism of many bacteria they produce ethylmalonyl-CoA during assimilation of the central metabolite acetyl-CoA. In secondary metabolism they provide distinct α-carboxyl-acyl-thioesters to vary the backbone of numerous polyketide natural products. Different ECRs were systematically assessed with a diverse library of potential substrates. We identified three active site residues that distinguish ECRs restricted to C4 and C5-enoyl-CoAs from highly promiscuous ECRs and successfully engineered a selected ECR as proof-of-principle. This study defines the molecular basis of ECR reactivity, allowing for predicting and manipulating a key reaction in natural product diversification.
Collapse
Affiliation(s)
- Dominik M Peter
- Biochemistry and Synthetic Biology of Microbial Metabolism Group, Max-Planck-Institute for terrestrial Microbiology, Karl-von-Frisch-Strasse 10, 35043 Marburg (Germany).,Institute of Microbiology, Eidgenössisch Technische Hochschule (ETH) Zürich, Vladimir-Prelog-Weg 4, 8050 Zürich (Switzerland)
| | - Lennart Schada von Borzyskowski
- Biochemistry and Synthetic Biology of Microbial Metabolism Group, Max-Planck-Institute for terrestrial Microbiology, Karl-von-Frisch-Strasse 10, 35043 Marburg (Germany).,Institute of Microbiology, Eidgenössisch Technische Hochschule (ETH) Zürich, Vladimir-Prelog-Weg 4, 8050 Zürich (Switzerland)
| | - Patrick Kiefer
- Institute of Microbiology, Eidgenössisch Technische Hochschule (ETH) Zürich, Vladimir-Prelog-Weg 4, 8050 Zürich (Switzerland)
| | - Philipp Christen
- Institute of Microbiology, Eidgenössisch Technische Hochschule (ETH) Zürich, Vladimir-Prelog-Weg 4, 8050 Zürich (Switzerland)
| | - Julia A Vorholt
- Institute of Microbiology, Eidgenössisch Technische Hochschule (ETH) Zürich, Vladimir-Prelog-Weg 4, 8050 Zürich (Switzerland)
| | - Tobias J Erb
- Biochemistry and Synthetic Biology of Microbial Metabolism Group, Max-Planck-Institute for terrestrial Microbiology, Karl-von-Frisch-Strasse 10, 35043 Marburg (Germany). .,Institute of Microbiology, Eidgenössisch Technische Hochschule (ETH) Zürich, Vladimir-Prelog-Weg 4, 8050 Zürich (Switzerland).
| |
Collapse
|
44
|
Peter DM, Schada von Borzyskowski L, Kiefer P, Christen P, Vorholt JA, Erb TJ. Klassifizierung und Manipulation des synthetischen Potenzials carboxylierender Reduktasen aus dem Zentralmetabolismus und der Polyketid‐Biosynthese. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201505282] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Dominik M. Peter
- Biochemie & Synthetische Biologie des Mikrobiellen Metabolismus, Max‐Planck‐Institut für Terrestrische Mikrobiologie, Karl‐von‐Frisch‐Straße 10, 35043 Marburg (Deutschland)
- Institut für Mikrobiologie, Eidgenössische Technische Hochschule (ETH) Zürich, Vladimir‐Prelog‐Weg 4, 8050 Zürich (Schweiz)
| | - Lennart Schada von Borzyskowski
- Biochemie & Synthetische Biologie des Mikrobiellen Metabolismus, Max‐Planck‐Institut für Terrestrische Mikrobiologie, Karl‐von‐Frisch‐Straße 10, 35043 Marburg (Deutschland)
- Institut für Mikrobiologie, Eidgenössische Technische Hochschule (ETH) Zürich, Vladimir‐Prelog‐Weg 4, 8050 Zürich (Schweiz)
| | - Patrick Kiefer
- Institut für Mikrobiologie, Eidgenössische Technische Hochschule (ETH) Zürich, Vladimir‐Prelog‐Weg 4, 8050 Zürich (Schweiz)
| | - Philipp Christen
- Institut für Mikrobiologie, Eidgenössische Technische Hochschule (ETH) Zürich, Vladimir‐Prelog‐Weg 4, 8050 Zürich (Schweiz)
| | - Julia A. Vorholt
- Institut für Mikrobiologie, Eidgenössische Technische Hochschule (ETH) Zürich, Vladimir‐Prelog‐Weg 4, 8050 Zürich (Schweiz)
| | - Tobias J. Erb
- Biochemie & Synthetische Biologie des Mikrobiellen Metabolismus, Max‐Planck‐Institut für Terrestrische Mikrobiologie, Karl‐von‐Frisch‐Straße 10, 35043 Marburg (Deutschland)
- Institut für Mikrobiologie, Eidgenössische Technische Hochschule (ETH) Zürich, Vladimir‐Prelog‐Weg 4, 8050 Zürich (Schweiz)
| |
Collapse
|
45
|
The use of ene adducts to study and engineer enoyl-thioester reductases. Nat Chem Biol 2015; 11:398-400. [DOI: 10.1038/nchembio.1794] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Accepted: 03/09/2015] [Indexed: 11/08/2022]
|
46
|
Mesa J, Alsina C, Oppermann U, Parés X, Farrés J, Porté S. Human prostaglandin reductase 1 (PGR1): Substrate specificity, inhibitor analysis and site-directed mutagenesis. Chem Biol Interact 2015; 234:105-13. [PMID: 25619643 DOI: 10.1016/j.cbi.2015.01.021] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Revised: 12/19/2014] [Accepted: 01/15/2015] [Indexed: 11/24/2022]
Abstract
Prostaglandins (PGs) are lipid compounds derived from arachidonic acid by the action of cyclooxygenases, acting locally as messenger molecules in a wide variety of physiological processes, such as inflammation, cell survival, apoptosis, smooth muscle contraction, adipocyte differentiation, vasodilation and platelet aggregation inhibition. In the inactivating pathway of PGs, the first metabolic intermediates are 15-keto-PGs, which are further converted into 13,14-dihydro-15-keto-PGs by different enzymes having 15-keto-PG reductase activity. Three human PG reductases (PGR), zinc-independent members of the medium-chain dehydrogenase/reductase (MDR) superfamily, perform the first irreversible step of the degradation pathway. We have focused on the characterization of the recombinant human enzyme prostaglandin reductase 1 (PGR1), also known as leukotriene B4 dehydrogenase. Only a partial characterization of this enzyme, isolated from human placenta, had been previously reported. In the present work, we have developed a new HPLC-based method for the determination of the 15-keto-PG reductase activity. We have performed an extensive kinetic characterization of PGR1, which catalyzes the NADPH-dependent reduction of the α,β-double bond of aliphatic and aromatic aldehydes and ketones, and 15-keto-PGs. PGR1 also shows low activity in the oxidation of leukotriene B4. The best substrates in terms of kcat/Km were 15-keto-PGE2, trans-3-nonen-2-one and trans-2-decenal. Molecular docking simulations, based on the three-dimensional structure of the human enzyme (PDB ID 2Y05), and site-directed mutagenesis studies were performed to pinpoint important structural determinants, highlighting the role of Arg56 and Tyr245 in 15-keto-PG binding. Finally, inhibition analysis was done using non-steroidal anti-inflammatory drugs (NSAIDs) as potential inhibitors.
Collapse
Affiliation(s)
- Julio Mesa
- Department of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, Faculty of Biosciences, E-08193 Bellaterra (Barcelona), Spain
| | - Cristina Alsina
- Department of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, Faculty of Biosciences, E-08193 Bellaterra (Barcelona), Spain
| | - Udo Oppermann
- University of Oxford, Nuffield Department of Orthopaedics, Oxford, UK
| | - Xavier Parés
- Department of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, Faculty of Biosciences, E-08193 Bellaterra (Barcelona), Spain
| | - Jaume Farrés
- Department of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, Faculty of Biosciences, E-08193 Bellaterra (Barcelona), Spain
| | - Sergio Porté
- Department of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, Faculty of Biosciences, E-08193 Bellaterra (Barcelona), Spain.
| |
Collapse
|
47
|
Estelmann S, Boll M. Glutaryl-coenzyme A dehydrogenase from Geobacter metallireducens - interaction with electron transferring flavoprotein and kinetic basis of unidirectional catalysis. FEBS J 2014; 281:5120-31. [PMID: 25223645 DOI: 10.1111/febs.13051] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Revised: 09/04/2014] [Accepted: 09/12/2014] [Indexed: 11/28/2022]
Abstract
Glutaryl-CoA dehydrogenases (GDHs) are FAD containing acyl-CoA dehydrogenases that usually catalyze the dehydrogenation and decarboxylation of glutaryl-CoA to crotonyl-CoA with an electron transferring flavoprotein (ETF) acting as natural electron acceptor. In anaerobic bacteria, GDHs play an important role in the benzoyl-CoA degradation pathway of monocyclic aromatic compounds. In the present study, we identified, purified and characterized the benzoate-induced BamOP as the electron accepting ETF of GDH (BamM) from the Fe(III)-respiring Geobacter metallireducens. The BamOP heterodimer contained FAD and AMP as cofactors. In the absence of an artificial electron acceptor, at pH values above 8, the BamMOP-components catalyzed the expected glutaryl-CoA oxidation to crotonyl-CoA and CO2 ; however, at pH values below 7, the redox-neutral glutaryl-CoA conversion to butyryl-CoA and CO2 became the dominant reaction. This previously unknown, strictly ETF-dependent coupled glutaryl-CoA oxidation/crotonyl-CoA reduction activity was facilitated by an unexpected two-electron transfer between FAD(BamM) and FAD(BamOP) , as well as by the similar redox potentials of the two FAD cofactors in the substrate-bound state. The strict order of electron/proton transfer and C-C-cleavage events including transient charge-transfer complexes did not allow an energetic coupling of electron transfer and decarboxylation. This explains why it was difficult to release the glutaconyl-CoA intermediate from reduced GDH. Moreover, it provides a kinetic rational for the apparent inability of BamM to catalyze the reverse reductive crotonyl-CoA carboxylation, even under thermodynamically favourable conditions. For this reason reductive crotonyl-CoA carboxylation, a key reaction in C2-assimilation via the ethylmalonyl-CoA pathway, is accomplished by a different crotonyl-CoA carboxylase/reductase via a covalent NADPH/ene-adduct.
Collapse
|
48
|
Curson ARJ, Burns OJ, Voget S, Daniel R, Todd JD, McInnis K, Wexler M, Johnston AWB. Screening of metagenomic and genomic libraries reveals three classes of bacterial enzymes that overcome the toxicity of acrylate. PLoS One 2014; 9:e97660. [PMID: 24848004 PMCID: PMC4029986 DOI: 10.1371/journal.pone.0097660] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Accepted: 04/22/2014] [Indexed: 11/22/2022] Open
Abstract
Acrylate is produced in significant quantities through the microbial cleavage of the highly abundant marine osmoprotectant dimethylsulfoniopropionate, an important process in the marine sulfur cycle. Acrylate can inhibit bacterial growth, likely through its conversion to the highly toxic molecule acrylyl-CoA. Previous work identified an acrylyl-CoA reductase, encoded by the gene acuI, as being important for conferring on bacteria the ability to grow in the presence of acrylate. However, some bacteria lack acuI, and, conversely, many bacteria that may not encounter acrylate in their regular environments do contain this gene. We therefore sought to identify new genes that might confer tolerance to acrylate. To do this, we used functional screening of metagenomic and genomic libraries to identify novel genes that corrected an E. coli mutant that was defective in acuI, and was therefore hyper-sensitive to acrylate. The metagenomic libraries yielded two types of genes that overcame this toxicity. The majority encoded enzymes resembling AcuI, but with significant sequence divergence among each other and previously ratified AcuI enzymes. One other metagenomic gene, arkA, had very close relatives in Bacillus and related bacteria, and is predicted to encode an enoyl-acyl carrier protein reductase, in the same family as FabK, which catalyses the final step in fatty-acid biosynthesis in some pathogenic Firmicute bacteria. A genomic library of Novosphingobium, a metabolically versatile alphaproteobacterium that lacks both acuI and arkA, yielded vutD and vutE, two genes that, together, conferred acrylate resistance. These encode sequential steps in the oxidative catabolism of valine in a pathway in which, significantly, methacrylyl-CoA is a toxic intermediate. These findings expand the range of bacteria for which the acuI gene encodes a functional acrylyl-CoA reductase, and also identify novel enzymes that can similarly function in conferring acrylate resistance, likely, again, through the removal of the toxic product acrylyl-CoA.
Collapse
Affiliation(s)
- Andrew R. J. Curson
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
- * E-mail:
| | - Oliver J. Burns
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Sonja Voget
- Department of Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University Göttingen, Göttingen, Germany
| | - Rolf Daniel
- Department of Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University Göttingen, Göttingen, Germany
| | - Jonathan D. Todd
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Kathryn McInnis
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Margaret Wexler
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Andrew W. B. Johnston
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| |
Collapse
|
49
|
Substrate interaction dynamics and oxygen control in the active site of thymidylate synthase ThyX. Biochem J 2014; 459:37-45. [PMID: 24422556 DOI: 10.1042/bj20131567] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Thymidylate synthase ThyX, required for DNA synthesis in many pathogenic bacteria, is considered a promising antimicrobial target. It binds FAD and three substrates, producing dTMP (2'-deoxythymidine-5'-monophosphate) from dUMP (2'-deoxyuridine-5'-monophosphate). However, ThyX proteins also act as NADPH oxidase by reacting directly with O2. In the present study we investigated the dynamic interplay between the substrates and their role in competing with this wasteful and potentially harmful oxidase reaction in catalytically efficient ThyX from Paramecium bursaria Chlorella virus-1. dUMP binding accelerates the O2-insensitive half-reaction between NADPH and FAD by over four orders of magnitude to ~30 s-1. Thus, although dUMP does not have a direct role in FAD reduction, any turnover with molecular O2 requires its presence. Inversely, NADPH accommodation accelerates dUMP binding ~3-fold and apparently precedes dUMP binding under physiological conditions. In the oxidative half-reaction, excess CH2H4folate (N5,N10-methylene-5,6,7,8-tetrahydrofolate) was found to re-oxidize FADH2 within 1 ms, thus very efficiently competing with FADH2 oxidation by O2 (1.5 s-1 under aerobic conditions). The resulting reaction scheme points out how the interplay between the fast reactions with the native substrates, although not rate-limiting for overall catalysis, avoids NADPH oxidase activity in aerobic micro-organisms, including many pathogens. These observations also explain why ThyX proteins are also present in aerobic micro-organisms.
Collapse
|
50
|
Fuchs G, Berg IA. Unfamiliar metabolic links in the central carbon metabolism. J Biotechnol 2014; 192 Pt B:314-22. [PMID: 24576434 DOI: 10.1016/j.jbiotec.2014.02.015] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2013] [Revised: 02/13/2014] [Accepted: 02/17/2014] [Indexed: 11/18/2022]
Abstract
The central carbon metabolism of all organisms is considered to follow a well established fixed scheme. However, recent studies of autotrophic carbon fixation in prokaryotes revealed unfamiliar metabolic links. A new route interconnects acetyl-coenzyme A (CoA) via 3-hydroxypropionate with succinyl-CoA. Succinyl-CoA in turn may be metabolized via 4-hydroxybutyrate to two molecules of acetyl-CoA; a reversal of this route would result in the assimilation of two molecules of acetyl-CoA into C4 compounds. C5-dicarboxylic acids are a rather neglected class of metabolites; yet, they play a key role not only in one of the CO2 fixation cycles, but also in two acetate assimilation pathways that replace the glyoxylate cycle. C5 compounds such as ethylmalonate, methylsuccinate, methylmalate, mesaconate, itaconate and citramalate or their CoA esters are thereby linked to the acetyl-CoA, propionyl-CoA, glyoxylate and pyruvate pools. A novel carboxylase/reductase converts crotonyl-CoA into ethylmalonyl-CoA; similar reductive carboxylations apply to other alpha-beta-unsaturated carboxy-CoA thioesters. These unfamiliar metabolic links may provide useful tools for metabolic engineering.
Collapse
Affiliation(s)
- Georg Fuchs
- Mikrobiologie, Fakultät für Biologie, Universität Freiburg, Schänzlestr. 1, D 79104 Freiburg, Germany.
| | - Ivan A Berg
- Mikrobiologie, Fakultät für Biologie, Universität Freiburg, Schänzlestr. 1, D 79104 Freiburg, Germany.
| |
Collapse
|