1
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Libardi SH, Ahmad A, Ferreira FB, Oliveira RJ, Caruso ÍP, Melo FA, de Albuquerque S, Cardoso DR, Burtoloso ACB, Borges JC. Interaction between diterpene icetexanes and old yellow enzymes of Leishmania braziliensis and Trypanosoma cruzi. Int J Biol Macromol 2024; 259:129192. [PMID: 38216013 DOI: 10.1016/j.ijbiomac.2023.129192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Revised: 12/21/2023] [Accepted: 12/31/2023] [Indexed: 01/14/2024]
Abstract
Old Yellow Enzymes (OYEs) are flavin-dependent redox enzymes that promote the asymmetric reduction of activated alkenes. Due to the high importance of flavoenzymes in the metabolism of organisms, the interaction between OYEs from the parasites Trypanosoma cruzi and Leishmania braziliensis and three diterpene icetexanes (brussonol and two analogs), were evaluated in the present study, and differences in the binding mechanism and inhibition capacity of these molecules were examined. Although the aforementioned compounds showed poor and negligible activities against T. cruzi and L. braziliensis cells, respectively, the experiments with the purified enzymes indicated that the interaction occurs by divergent mechanisms. Overall, the ligands' inhibitory effect depends on their accessibility to the N5 position of the flavin's isoalloxazine ring. The results also indicated that the OYEs found in both parasites share structural similarities and showed affinities for the diterpene icetexanes in the same range. Nevertheless, the interaction between OYEs and ligands is directed by enthalpy and/or entropy in distinct ways. In conclusion, the binding site of both OYEs exhibits remarkable plasticity, and a large range of different molecules, including that can be substrates and inhibitors, can bind this site. This plasticity should be considered in drug design using OYE as a target.
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Affiliation(s)
- Silvia H Libardi
- Instituto de Química de São Carlos, Universidade de São Paulo - USP, 13560-970 São Carlos, SP, Brazil
| | - Anees Ahmad
- Instituto de Química de São Carlos, Universidade de São Paulo - USP, 13560-970 São Carlos, SP, Brazil
| | | | - Ronaldo J Oliveira
- Instituto de Ciências Exatas, Naturais e Educação, Universidade Federal do Triângulo Mineiro, 38064-200 Uberaba, MG, Brazil
| | - Ícaro P Caruso
- Instituto de Biociências, Letras e Ciências Exatas (IBILCE) - UNESP, 15054-000 São José do Rio Preto, SP, Brazil; Instituto de Bioquímica Médica Leopoldo de Meis and Centro Nacional para Biologia Estrutural e Bioimagem, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil
| | - Fernando A Melo
- Instituto de Biociências, Letras e Ciências Exatas (IBILCE) - UNESP, 15054-000 São José do Rio Preto, SP, Brazil
| | - Sergio de Albuquerque
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo - USP, Ribeirão Preto, SP CEP 14040-903, Brazil
| | - Daniel R Cardoso
- Instituto de Química de São Carlos, Universidade de São Paulo - USP, 13560-970 São Carlos, SP, Brazil
| | - Antonio C B Burtoloso
- Instituto de Química de São Carlos, Universidade de São Paulo - USP, 13560-970 São Carlos, SP, Brazil
| | - Júlio C Borges
- Instituto de Química de São Carlos, Universidade de São Paulo - USP, 13560-970 São Carlos, SP, Brazil.
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2
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Jiang G, Huang C, Harrison W, Li H, Zhou M, Zhao H. Ene Reductase Enabled Intramolecular β-C-H Functionalization of Substituted Cyclohexanones for Efficient Synthesis of Bridged Bicyclic Nitrogen Scaffolds. Angew Chem Int Ed Engl 2023; 62:e202302125. [PMID: 37002909 PMCID: PMC10222568 DOI: 10.1002/anie.202302125] [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: 02/18/2023] [Revised: 03/24/2023] [Accepted: 03/31/2023] [Indexed: 04/03/2023]
Abstract
Herein we report that ene reductases (EREDs) can facilitate an unprecedented intramolecular β-C-H functionalization reaction for the synthesis of bridged bicyclic nitrogen heterocycles containing the 6-azabicyclo[3.2.1]octane scaffold. To streamline the synthesis of these privileged motifs, we developed a gram-scale one-pot chemoenzymatic cascade by combining iridium photocatalysis with EREDs, using readily available N-phenylglycines and cyclohexenones that can be obtained from biomass. Further derivatization using enzymatic or chemical methods can convert 6-azabicyclo[3.2.1]octan-3-one into 6-azabicyclo[3.2.1]octan-3α-ols, which can be potentially utilized for the synthesis of azaprophen and its analogues for drug discovery. Mechanistic studies revealed the reaction requires oxygen, presumably to produce oxidized flavin, which can selectively dehydrogenate the 3-substituted cyclohexanone derivatives to form the α,β-unsaturated ketone, which subsequently undergoes spontaneous intramolecular aza-Michael addition under basic conditions.
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Affiliation(s)
- Guangde Jiang
- Department of Chemical and Biomolecular Engineering, Center for Advanced Bioenergy and Bioproducts Innovation, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Chunshuai Huang
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Wesley Harrison
- Department of Chemical and Biomolecular Engineering, Center for Advanced Bioenergy and Bioproducts Innovation, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Hongxiang Li
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Megan Zhou
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Huimin Zhao
- Department of Chemical and Biomolecular Engineering, Center for Advanced Bioenergy and Bioproducts Innovation, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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3
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Smith MM, Forouzesh DC, Kaley NE, Liu D, Moran GR. Mammalian dihydropyrimidine dehydrogenase: Added mechanistic details from transient-state analysis of charge transfer complexes. Arch Biochem Biophys 2023; 736:109517. [PMID: 36681231 DOI: 10.1016/j.abb.2023.109517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 01/03/2023] [Accepted: 01/06/2023] [Indexed: 01/19/2023]
Abstract
Dihydropyrimidine dehydrogenase (DPD) is a flavin dependent enzyme that catalyzes the reduction of the 5,6-vinylic bond of pyrimidines uracil and thymine with electrons from NADPH. DPD has two active sites that are separated by ∼60 Å. At one site NADPH binds adjacent to an FAD cofactor and at the other pyrimidine binds proximal to an FMN. Four Fe4S4 centers span the distance between these active sites. It has recently been established that the enzyme undergoes reductive activation prior to reducing the pyrimidine. In this initial process NADPH is oxidized at the FAD site and electrons are transmitted to the FMN via the Fe4S4 centers to yield the active state with a cofactor set of FAD•4(Fe4S4)•FMNH2. The catalytic chemistry of DPD can be studied in transient-state by observation of either NADPH consumption or charge transfer absorption associated with complexation of NADPH adjacent to the FAD. Here we have utilized both sets of absorption transitions to find evidence for specific additional aspects of the DPD mechanism. Competition for binding with NADP+ indicates that the two charge transfer species observed in activation/single turnover reactions arise from NADPH populating the FAD site before and after reductive activation. An additional charge transfer species is observed to accumulate at longer times when high NADPH concentrations are mixed with the enzyme•pyrimidine complex and this data can be modelled based on asymmetry in the homodimer. It was also shown that, like pyrimidines, dihydropyrimidines induce rapid reductive activation indicating that the reduced pyrimidine formed in turnover can stimulate the reinstatement of the active state of the enzyme. Investigation of the reverse reaction revealed that dihydropyrimidines alone can reductively activate the enzyme, albeit inefficiently. In the presence of dihydropyrimidine and NADP+ DPD will form NADPH but apparently without measurable reductive activation. Pyrimidines that have 5-substituent halogens were utilized to probe both reductive activation and turnover. The linearity of the Hammett plot based on the rate of hydride transfer to the pyrimidine establishes that, at least to the radius of an iodo-group, the 5-substituent volume does not have influence on the observed kinetics of pyrimidine reduction.
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Affiliation(s)
- Madison M Smith
- Department of Chemistry and Biochemistry, 1068 W Sheridan Rd, Loyola University Chicago, Chicago, IL, 60660, USA
| | - Dariush C Forouzesh
- Department of Chemistry and Biochemistry, 1068 W Sheridan Rd, Loyola University Chicago, Chicago, IL, 60660, USA
| | - Nicholas E Kaley
- Department of Chemistry and Biochemistry, 1068 W Sheridan Rd, Loyola University Chicago, Chicago, IL, 60660, USA
| | - Dali Liu
- Department of Chemistry and Biochemistry, 1068 W Sheridan Rd, Loyola University Chicago, Chicago, IL, 60660, USA
| | - Graham R Moran
- Department of Chemistry and Biochemistry, 1068 W Sheridan Rd, Loyola University Chicago, Chicago, IL, 60660, USA.
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4
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Breukelaar W, Polidori N, Singh A, Daniel B, Glueck SM, Gruber K, Kroutil W. Mechanistic Insights into the Ene-Reductase-Catalyzed Promiscuous Reduction of Oximes to Amines. ACS Catal 2023; 13:2610-2618. [PMID: 36846821 PMCID: PMC9942197 DOI: 10.1021/acscatal.2c06137] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 01/18/2023] [Indexed: 02/08/2023]
Abstract
The biocatalytic reduction of the oxime moiety to the corresponding amine group has only recently been found to be a promiscuous activity of ene-reductases transforming α-oximo β-keto esters. However, the reaction pathway of this two-step reduction remained elusive. By studying the crystal structures of enzyme oxime complexes, analyzing molecular dynamics simulations, and investigating biocatalytic cascades and possible intermediates, we obtained evidence that the reaction proceeds via an imine intermediate and not via the hydroxylamine intermediate. The imine is reduced further by the ene-reductase to the amine product. Remarkably, a non-canonical tyrosine residue was found to contribute to the catalytic activity of the ene-reductase OPR3, protonating the hydroxyl group of the oxime in the first reduction step.
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Affiliation(s)
- Willem
B. Breukelaar
- Department
of Chemistry, NAWI Graz, University of Graz, Heinrichstraße 28, 8010 Graz, Austria
| | - Nakia Polidori
- Institute
of Molecular Biosciences, University of
Graz, Humboldtstraße 50, 8010 Graz, Austria
| | - Amit Singh
- Institute
of Molecular Biosciences, University of
Graz, Humboldtstraße 50, 8010 Graz, Austria
| | - Bastian Daniel
- Institute
of Molecular Biosciences, University of
Graz, Humboldtstraße 50, 8010 Graz, Austria
| | - Silvia M. Glueck
- Department
of Chemistry, NAWI Graz, University of Graz, Heinrichstraße 28, 8010 Graz, Austria
| | - Karl Gruber
- Institute
of Molecular Biosciences, University of
Graz, Humboldtstraße 50, 8010 Graz, Austria,Field
of Excellence BioHealth, University of Graz, 8010 Graz, Austria,BioTechMed
Graz, 8010 Graz, Austria,
| | - Wolfgang Kroutil
- Department
of Chemistry, NAWI Graz, University of Graz, Heinrichstraße 28, 8010 Graz, Austria,Field
of Excellence BioHealth, University of Graz, 8010 Graz, Austria,BioTechMed
Graz, 8010 Graz, Austria,
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5
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Using enzymes to tame nitrogen-centred radicals for enantioselective hydroamination. Nat Chem 2023; 15:206-212. [PMID: 36376390 DOI: 10.1038/s41557-022-01083-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Accepted: 10/02/2022] [Indexed: 11/16/2022]
Abstract
The formation of C-N bonds-of great importance to the pharmaceutical industry-can be facilitated enzymatically using nucleophilic and nitrene transfer mechanisms. However, neither natural nor engineered enzymes are known to generate and control nitrogen-centred radicals, which serve as valuable species for C-N bond formation. Here we use flavin-dependent 'ene'-reductases with an exogenous photoredox catalyst to selectively generate amidyl radicals within the protein active site. These enzymes are engineered through directed evolution to catalyse 5-exo, 6-endo, 7-endo, 8-endo, and intermolecular hydroamination reactions with high levels of enantioselectivity. Mechanistic studies suggest that radical initiation occurs via an enzyme-gated mechanism, where the protein thermodynamically activates the substrate for reduction by the photocatalyst. Molecular dynamics studies indicate that the enzymes bind substrates using non-canonical binding interactions, which may serve as a handle to further manipulate reactivity. This approach demonstrates the versatility of these enzymes for controlling the reactivity of high-energy radical intermediates and highlights the opportunity for synergistic catalyst strategies to unlock previously inaccessible enzymatic functions.
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6
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Unusual reactivity of a flavin in a bifurcating electron-transferring flavoprotein leads to flavin modification and a charge-transfer complex. J Biol Chem 2022; 298:102606. [PMID: 36257407 PMCID: PMC9713284 DOI: 10.1016/j.jbc.2022.102606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Revised: 10/08/2022] [Accepted: 10/10/2022] [Indexed: 11/06/2022] Open
Abstract
From the outset, canonical electron transferring flavoproteins (ETFs) earned a reputation for containing modified flavin. We now show that modification occurs in the recently recognized bifurcating (Bf) ETFs as well. In Bf ETFs, the 'electron transfer' (ET) flavin mediates single electron transfer via a stable anionic semiquinone state, akin to the FAD of canonical ETFs, whereas a second flavin mediates bifurcation (the Bf FAD). We demonstrate that the ET FAD undergoes transformation to two different modified flavins by a sequence of protein-catalyzed reactions that occurs specifically in the ET site, when the enzyme is maintained at pH 9 in an amine-based buffer. Our optical and mass spectrometric characterizations identify 8-formyl flavin early in the process and 8-amino flavins (8AFs) at later times. The latter have not previously been documented in an ETF to our knowledge. Mass spectrometry of flavin products formed in Tris or bis-tris-aminopropane solutions demonstrates that the source of the amine adduct is the buffer. Stepwise reduction of the 8AF demonstrates that it can explain a charge transfer band observed near 726 nm in Bf ETF, as a complex involving the hydroquinone state of the 8AF in the ET site with the oxidized state of unmodified flavin in the Bf site. This supports the possibility that Bf ETF can populate a conformation enabling direct electron transfer between its two flavins, as has been proposed for cofactors brought together in complexes between ETF and its partner proteins.
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7
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Singh Y, Sharma R, Mishra M, Verma PK, Saxena AK. Crystal structure of ArOYE6 reveals a novel C‐terminal helical extension and mechanistic insights into the distinct class III OYEs from pathogenic fungi. FEBS J 2022; 289:5531-5550. [DOI: 10.1111/febs.16445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 03/02/2022] [Accepted: 03/18/2022] [Indexed: 11/28/2022]
Affiliation(s)
- Yeshveer Singh
- Plant Immunity Laboratory National Institute of Plant Genome Research New Delhi India
| | - Ruby Sharma
- Rm‐403/440 Structural Biology Laboratory School of Life Science Jawaharlal Nehru University New Delhi India
| | - Manasi Mishra
- Plant Immunity Laboratory National Institute of Plant Genome Research New Delhi India
| | - Praveen Kumar Verma
- Plant Immunity Laboratory National Institute of Plant Genome Research New Delhi India
- Plant Immunity Laboratory School of Life Science Jawaharlal Nehru University New Delhi India
| | - Ajay Kumar Saxena
- Rm‐403/440 Structural Biology Laboratory School of Life Science Jawaharlal Nehru University New Delhi India
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8
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Li RJ, Tian K, Li X, Gaikaiwari AR, Li Z. Engineering P450 Monooxygenases for Highly Regioselective and Active p-Hydroxylation of m-Alkylphenols. ACS Catal 2022. [DOI: 10.1021/acscatal.1c06011] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Ren-Jie Li
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore 117585, Singapore
- Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, 28 Medical Drive, Singapore 117456, Singapore
| | - Kaiyuan Tian
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore 117585, Singapore
| | - Xirui Li
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore 117585, Singapore
| | - Anand Raghavendra Gaikaiwari
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore 117585, Singapore
| | - Zhi Li
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore 117585, Singapore
- Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, 28 Medical Drive, Singapore 117456, Singapore
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9
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Mohamed-Raseek N, Miller AF. Contrasting roles for two conserved arginines: stabilizing flavin semiquinone or quaternary structure, in bifurcating electron transfer flavoproteins. J Biol Chem 2022; 298:101733. [PMID: 35176283 PMCID: PMC8958531 DOI: 10.1016/j.jbc.2022.101733] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 02/11/2022] [Accepted: 02/12/2022] [Indexed: 01/02/2023] Open
Abstract
Bifurcating electron transfer flavoproteins (Bf ETFs) are important redox enzymes that contain two flavin adenine dinucleotide (FAD) cofactors, with contrasting reactivities and complementary roles in electron bifurcation. However, for both the “electron transfer” (ET) and the “bifurcating” (Bf) FADs, the only charged amino acid within 5 Å of the flavin is a conserved arginine (Arg) residue. To understand how the two sites produce different reactivities utilizing the same residue, we investigated the consequences of replacing each of the Arg residues with lysine, glutamine, histidine, or alanine. We show that absence of a positive charge in the ET site diminishes accumulation of the anionic semiquinone (ASQ) that enables the ET flavin to act as a single electron carrier, due to depression of the oxidized versus. ASQ reduction midpoint potential, E°OX/ASQ. Perturbation of the ET site also affected the remote Bf site, whereas abrogation of Bf FAD binding accelerated chemical modification of the ET flavin. In the Bf site, removal of the positive charge impaired binding of FAD or AMP, resulting in unstable protein. Based on pH dependence, we propose that the Bf site Arg interacts with the phosphate(s) of Bf FAD or AMP, bridging the domain interface via a conserved peptide loop (“zipper”) and favoring nucleotide binding. We further propose a model that rationalizes conservation of the Bf site Arg even in non-Bf ETFs, as well as AMP's stabilizing role in the latter, and provides a mechanism for coupling Bf flavin redox changes to domain-scale motion.
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10
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Lettau E, Zill D, Späth M, Lorent C, Singh P, Lauterbach L. Catalytic and spectroscopic properties of the halotolerant soluble methane monooxygenase reductase from Methylomonas methanica MC09. Chembiochem 2021; 23:e202100592. [PMID: 34905639 PMCID: PMC9305295 DOI: 10.1002/cbic.202100592] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 12/13/2021] [Indexed: 11/10/2022]
Abstract
The soluble methane monooxygenase receives electrons from NADH via its reductase MmoC for oxidation of methane, which is itself an attractive C1 building block for a future bioeconomy. Herein, we present biochemical and spectroscopic insights into the reductase from the marine methanotroph Methylomonas methanica MC09. The presence of a flavin adenine dinucleotide (FAD) and [2Fe2S] cluster as its prosthetic group were revealed by reconstitution experiments, iron determination and electron paramagnetic resonance spectroscopy. As a true halotolerant enzyme, MmoC still showed 50 % of its specific activity at 2 M NaCl. We show that MmoC produces only trace amounts of superoxide, but mainly hydrogen peroxide during uncoupled turnover reactions. The characterization of a highly active reductase is an important step for future biotechnological applications of a halotolerant sMMO.
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Affiliation(s)
- Elisabeth Lettau
- Rheinisch-Westfälische Technische Hochschule Aachen: Rheinisch-Westfalische Technische Hochschule Aachen, Institute of Applied Microbiology, GERMANY
| | - Domenic Zill
- Rheinisch Westfalische Technische Hochschule Aachen Fakultat fur Mathematik Informatik und Naturwissenschaften, Institute of Applied Microbiology, GERMANY
| | - Marta Späth
- Technische Universität Berlin: Technische Universitat Berlin, Institute of Chemistry, GERMANY
| | - Christian Lorent
- Technische Universität Berlin: Technische Universitat Berlin, Institute of Chemistry, GERMANY
| | - Praveen Singh
- Rheinisch-Westfälische Technische Hochschule Aachen: Rheinisch-Westfalische Technische Hochschule Aachen, Institute of Applied Microbiology, GERMANY
| | - Lars Lauterbach
- Technische Universitat Berlin, Chemistry, Strasse des 17. Juni 135, Max-Volmer-Laboratorium, Sekr. PC 14, 10623, Berlin, Germany, GERMANY
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11
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Dratch BD, Orozco-Gonzalez Y, Gadda G, Gozem S. Ionic Atmosphere Effect on the Absorption Spectrum of a Flavoprotein: A Reminder to Consider Solution Ions. J Phys Chem Lett 2021; 12:8384-8396. [PMID: 34435784 DOI: 10.1021/acs.jpclett.1c02173] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
This study utilizes the FMN-dependent NADH:quinone oxidoreductase from Pseudomonas aeruginosa PAO1 to investigate the effect of introducing an active site negative charge on the flavin absorption spectrum both in the absence and presence of a long-range electrostatic potential coming from solution ions. There were no observed changes in the flavin UV-visible spectrum when an active site tyrosine (Y277) becomes deprotonated in vitro. These results could only be reproduced computationally using average solvent electrostatic configuration (ASEC) QM/MM simulations that include both positive and negative solution ions. The same calculations performed with minimal ions to neutralize the total protein charge predicted that deprotonating Y277 would significantly alter the flavin absorption spectrum. Analyzing the distribution of solution ions indicated that the ions reorganize around the protein surface upon Y277 deprotonation to cancel the effect of the tyrosinate on the flavin absorption spectrum. Additional biochemical experiments were performed to test this hypothesis.
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Affiliation(s)
- Benjamin D Dratch
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30302, United States
| | | | - Giovanni Gadda
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30302, United States
- Department of Biology, Georgia State University, Atlanta, Georgia 30302, United States
- Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia 30302, United States
| | - Samer Gozem
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30302, United States
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12
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Beaupre BA, Forouzesh DC, Butrin A, Liu D, Moran GR. Perturbing the Movement of Hydrogens to Delineate and Assign Events in the Reductive Activation and Turnover of Porcine Dihydropyrimidine Dehydrogenase. Biochemistry 2021; 60:1764-1775. [PMID: 34032117 DOI: 10.1021/acs.biochem.1c00243] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The native function of dihydropyrimidine dehydrogenase (DPD) is to reduce the 5,6-vinylic bond of pyrimidines uracil and thymine with electrons obtained from NADPH. NADPH and pyrimidines bind at separate active sites separated by ∼60 Å that are bridged by four Fe4S4 centers. We have shown that DPD undergoes reductive activation, taking up two electrons from NADPH [Beaupre, B. A., et al. (2020) Biochemistry 59, 2419-2431]. pH studies indicate that the rate of turnover is not controlled by the protonation state of the general acid, cysteine 671. The activation of the C671 variants is delineated into two phases particularly at low pH values. Spectral deconvolution of the delineated reductive activation reaction reveals that the initial phase results in the accumulation of charge transfer absorption added to the binding difference spectrum for NADPH. The second phase results in reduction of one of the two flavins. X-ray crystal structure analysis of the C671S variant soaked with NADPH and the slow substrate, thymine, in a low-oxygen atmosphere resolved the presumed activated form of the enzyme that has the FMN cofactor reduced. These data reveal that charge transfer arises from the proximity of the NADPH and FAD bases and that the ensuing flavin is a result of rapid transfer of electrons to the FMN without accumulation of reduced forms of the FAD or Fe4S4 centers. These data suggest that the slow rate of turnover of DPD is governed by the movement of a mobile structural feature that carries the C671 residue.
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Affiliation(s)
- Brett A Beaupre
- Department of Chemistry and Biochemistry, Loyola University Chicago, 1068 West Sheridan Road, Chicago, Illinois 60660, United States
| | - Dariush C Forouzesh
- Department of Chemistry and Biochemistry, Loyola University Chicago, 1068 West Sheridan Road, Chicago, Illinois 60660, United States
| | - Arseniy Butrin
- Department of Chemistry and Biochemistry, Loyola University Chicago, 1068 West Sheridan Road, Chicago, Illinois 60660, United States
| | - Dali Liu
- Department of Chemistry and Biochemistry, Loyola University Chicago, 1068 West Sheridan Road, Chicago, Illinois 60660, United States
| | - Graham R Moran
- Department of Chemistry and Biochemistry, Loyola University Chicago, 1068 West Sheridan Road, Chicago, Illinois 60660, United States
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13
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Landry AP, Ballou DP, Banerjee R. Hydrogen Sulfide Oxidation by Sulfide Quinone Oxidoreductase. Chembiochem 2021; 22:949-960. [PMID: 33080111 PMCID: PMC7969369 DOI: 10.1002/cbic.202000661] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 10/19/2020] [Indexed: 02/05/2023]
Abstract
Hydrogen sulfide (H2 S) is an environmental toxin and a heritage of ancient microbial metabolism that has stimulated new interest following its discovery as a neuromodulator. While many physiological responses have been attributed to low H2 S levels, higher levels inhibit complex IV in the electron transport chain. To prevent respiratory poisoning, a dedicated set of enzymes that make up the mitochondrial sulfide oxidation pathway exists to clear H2 S. The committed step in this pathway is catalyzed by sulfide quinone oxidoreductase (SQOR), which couples sulfide oxidation to coenzyme Q10 reduction in the electron transport chain. The SQOR reaction prevents H2 S accumulation and generates highly reactive persulfide species as products; these can be further oxidized or can modify cysteine residues in proteins by persulfidation. Here, we review the kinetic and structural characteristics of human SQOR, and how its unconventional redox cofactor configuration and substrate promiscuity lead to sulfide clearance and potentially expand the signaling potential of H2 S. This dual role of SQOR makes it a promising target for H2 S-based therapeutics.
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Affiliation(s)
- Aaron P. Landry
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan 48109, United States
| | - David P. Ballou
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan 48109, United States
| | - Ruma Banerjee
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan 48109, United States
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14
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Varner TA, Mohamed-Raseek N, Miller AF. Assignments of 19F NMR resonances and exploration of dynamics in a long-chain flavodoxin. Arch Biochem Biophys 2021; 703:108839. [PMID: 33727041 DOI: 10.1016/j.abb.2021.108839] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 03/04/2021] [Accepted: 03/09/2021] [Indexed: 12/23/2022]
Abstract
Flavodoxin is a small protein that employs a non-covalently bound flavin to mediate single-electron transfer at low potentials. The long-chain flavodoxins possess a long surface loop that is proposed to interact with partner proteins. We have incorporated 19F-labeled tyrosine in long-chain flavodoxin from Rhodopseudomonas palustris to gain a probe of possible loop dynamics, exploiting the presence of a Tyr in the long loop in addition to Tyr residues near the flavin. We report 19F resonance assignments for all four Tyrs, and demonstration of a pair of resonances in slow exchange, both corresponding to a Tyr adjacent to the flavin. We also provide evidence for dynamics affecting the Tyr in the long loop. Thus, we show that 19F NMR of 19F-Tyr labeled flavodoxin holds promise for monitoring possible changes in conformation upon binding to partner proteins.
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Affiliation(s)
- Taylor A Varner
- Department of Chemistry, University of Kentucky, Lexington, KY, 40506, USA
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15
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Kudisch B, Oblinsky DG, Black MJ, Zieleniewska A, Emmanuel MA, Rumbles G, Hyster TK, Scholes GD. Active-Site Environmental Factors Customize the Photophysics of Photoenzymatic Old Yellow Enzymes. J Phys Chem B 2020; 124:11236-11249. [PMID: 33231450 DOI: 10.1021/acs.jpcb.0c09523] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The development of non-natural photoenzymatic systems has reinvigorated the study of photoinduced electron transfer (ET) within protein active sites, providing new and unique platforms for understanding how biological environments affect photochemical processes. In this work, we use ultrafast spectroscopy to compare the photoinduced electron transfer in known photoenzymes. 12-Oxophytodienoate reductase 1 (OPR1) is compared to Old Yellow Enzyme 1 (OYE1) and morphinone reductase (MR). The latter enzymes are structurally homologous to OPR1. We find that slight differences in the amino acid composition of the active sites of these proteins determine their distinct electron-transfer dynamics. Our work suggests that the inside of a protein active site is a complex/heterogeneous dielectric network where genetically programmed heterogeneity near the site of biological ET can significantly affect the presence and lifetime of various intermediate states. Our work motivates additional tunability of Old Yellow Enzyme active-site reorganization energy and electron-transfer energetics that could be leveraged for photoenzymatic redox approaches.
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Affiliation(s)
- Bryan Kudisch
- Department of Chemistry, Princeton University, Princeton, New Jersey 08540, United States
| | - Daniel G Oblinsky
- Department of Chemistry, Princeton University, Princeton, New Jersey 08540, United States
| | - Michael J Black
- Department of Chemistry, Princeton University, Princeton, New Jersey 08540, United States
| | - Anna Zieleniewska
- National Renewable Energy Laboratory, Golden, Colorado 80401, United States
| | - Megan A Emmanuel
- Department of Chemistry, Princeton University, Princeton, New Jersey 08540, United States
| | - Garry Rumbles
- National Renewable Energy Laboratory, Golden, Colorado 80401, United States.,Department of Chemistry and RASEI, University of Colorado Boulder, Colorado 80309, United States
| | - Todd K Hyster
- Department of Chemistry, Princeton University, Princeton, New Jersey 08540, United States
| | - Gregory D Scholes
- Department of Chemistry, Princeton University, Princeton, New Jersey 08540, United States
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16
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Duan HD, Mohamed-Raseek N, Miller AF. Spectroscopic evidence for direct flavin-flavin contact in a bifurcating electron transfer flavoprotein. J Biol Chem 2020; 295:12618-12634. [PMID: 32661195 DOI: 10.1074/jbc.ra120.013174] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 07/10/2020] [Indexed: 12/15/2022] Open
Abstract
A remarkable charge transfer (CT) band is described in the bifurcating electron transfer flavoprotein (Bf-ETF) from Rhodopseudomonas palustris (RpaETF). RpaETF contains two FADs that play contrasting roles in electron bifurcation. The Bf-FAD accepts electrons pairwise from NADH, directs one to a lower-reduction midpoint potential (E°) carrier, and the other to the higher-E° electron transfer FAD (ET-FAD). Previous work noted that a CT band at 726 nm formed when ET-FAD was reduced and Bf-FAD was oxidized, suggesting that both flavins participate. However, existing crystal structures place them too far apart to interact directly. We present biochemical experiments addressing this conundrum and elucidating the nature of this CT species. We observed that RpaETF missing either FAD lacked the 726 nm band. Site-directed mutagenesis near either FAD produced altered yields of the CT species, supporting involvement of both flavins. The residue substitutions did not alter the absorption maximum of the signal, ruling out contributions from residue orbitals. Instead, we propose that the residue identities modulate the population of a protein conformation that brings the ET-flavin and Bf-flavin into direct contact, explaining the 726 nm band based on a CT complex of reduced ET-FAD and oxidized Bf-FAD. This is corroborated by persistence of the 726 nm species during gentle protein denaturation and simple density functional theory calculations of flavin dimers. Although such a CT complex has been demonstrated for free flavins, this is the first observation of such, to our knowledge, in an enzyme. Thus, Bf-ETFs may optimize electron transfer efficiency by enabling direct flavin-flavin contact.
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Affiliation(s)
- H Diessel Duan
- Department of Chemistry, University of Kentucky, Lexington, Kentucky, USA
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17
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Nakano Y, Black MJ, Meichan AJ, Sandoval BA, Chung MM, Biegasiewicz KF, Zhu T, Hyster TK. Photoenzymatic Hydrogenation of Heteroaromatic Olefins Using 'Ene'-Reductases with Photoredox Catalysts. Angew Chem Int Ed Engl 2020; 59:10484-10488. [PMID: 32181943 DOI: 10.1002/anie.202003125] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Indexed: 12/20/2022]
Abstract
Flavin-dependent 'ene'-reductases (EREDs) are highly selective catalysts for the asymmetric reduction of activated alkenes. This function is, however, limited to enones, enoates, and nitroalkenes using the native hydride transfer mechanism. Here we demonstrate that EREDs can reduce vinyl pyridines when irradiated with visible light in the presence of a photoredox catalyst. Experimental evidence suggests the reaction proceeds via a radical mechanism where the vinyl pyridine is reduced to the corresponding neutral benzylic radical in solution. DFT calculations reveal this radical to be "dynamically stable", suggesting it is sufficiently long-lived to diffuse into the enzyme active site for stereoselective hydrogen atom transfer. This reduction mechanism is distinct from the native one, highlighting the opportunity to expand the synthetic capabilities of existing enzyme platforms by exploiting new mechanistic models.
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Affiliation(s)
- Yuji Nakano
- Department of Chemistry, Princeton University, Princeton, NJ, 08544, USA.,Present address: Monash Institute of Pharmaceutical Science, Monash University, Parkville, Victoria, 3052, Australia
| | - Michael J Black
- Department of Chemistry, Princeton University, Princeton, NJ, 08544, USA
| | - Andrew J Meichan
- Department of Chemistry, Princeton University, Princeton, NJ, 08544, USA
| | | | - Megan M Chung
- Department of Chemistry, Princeton University, Princeton, NJ, 08544, USA
| | - Kyle F Biegasiewicz
- Department of Chemistry, Princeton University, Princeton, NJ, 08544, USA.,Present address: School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287, USA
| | - Tianyu Zhu
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Todd K Hyster
- Department of Chemistry, Princeton University, Princeton, NJ, 08544, USA
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18
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Nakano Y, Black MJ, Meichan AJ, Sandoval BA, Chung MM, Biegasiewicz KF, Zhu T, Hyster TK. Photoenzymatic Hydrogenation of Heteroaromatic Olefins Using ‘Ene’‐Reductases with Photoredox Catalysts. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202003125] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Yuji Nakano
- Department of Chemistry Princeton University Princeton NJ 08544 USA
- Present address: Monash Institute of Pharmaceutical Science Monash University Parkville Victoria 3052 Australia
| | - Michael J. Black
- Department of Chemistry Princeton University Princeton NJ 08544 USA
| | | | | | - Megan M. Chung
- Department of Chemistry Princeton University Princeton NJ 08544 USA
| | - Kyle F. Biegasiewicz
- Department of Chemistry Princeton University Princeton NJ 08544 USA
- Present address: School of Molecular Sciences Arizona State University Tempe AZ 85287 USA
| | - Tianyu Zhu
- Division of Chemistry and Chemical Engineering California Institute of Technology Pasadena CA 91125 USA
| | - Todd K. Hyster
- Department of Chemistry Princeton University Princeton NJ 08544 USA
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19
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Thibodeaux CJ, Chang WC, Liu HW. Unraveling flavoenzyme reaction mechanisms using flavin analogues and linear free energy relationships. Methods Enzymol 2019; 620:167-188. [DOI: 10.1016/bs.mie.2019.03.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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20
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Heckenbichler K, Schweiger A, Brandner LA, Binter A, Toplak M, Macheroux P, Gruber K, Breinbauer R. Asymmetric Reductive Carbocyclization Using Engineered Ene Reductases. Angew Chem Int Ed Engl 2018; 57:7240-7244. [PMID: 29689601 PMCID: PMC6033016 DOI: 10.1002/anie.201802962] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Indexed: 01/14/2023]
Abstract
Ene reductases from the Old Yellow Enzyme (OYE) family reduce the C=C double bond in α,β-unsaturated compounds bearing an electron-withdrawing group, for example, a carbonyl group. This asymmetric reduction has been exploited for biocatalysis. Going beyond its canonical function, we show that members of this enzyme family can also catalyze the formation of C-C bonds. α,β-Unsaturated aldehydes and ketones containing an additional electrophilic group undergo reductive cyclization. Mechanistically, the two-electron-reduced enzyme cofactor FMN delivers a hydride to generate an enolate intermediate, which reacts with the internal electrophile. Single-site replacement of a crucial Tyr residue with a non-protic Phe or Trp favored the cyclization over the natural reduction reaction. The new transformation enabled the enantioselective synthesis of chiral cyclopropanes in up to >99 % ee.
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Affiliation(s)
- Kathrin Heckenbichler
- Institute of Organic ChemistryGraz University of TechnologyStremayrgasse 98010GrazAustria
| | - Anna Schweiger
- Institute of Organic ChemistryGraz University of TechnologyStremayrgasse 98010GrazAustria
| | - Lea Alexandra Brandner
- Institute of Organic ChemistryGraz University of TechnologyStremayrgasse 98010GrazAustria
| | - Alexandra Binter
- Institute of BiochemistryGraz University of TechnologyPetersgasse 10–128010GrazAustria
- Austrian Centre of Industrial Biotechnology (ACIB)Petersgasse 148010GrazAustria
| | - Marina Toplak
- Institute of BiochemistryGraz University of TechnologyPetersgasse 10–128010GrazAustria
| | - Peter Macheroux
- Institute of BiochemistryGraz University of TechnologyPetersgasse 10–128010GrazAustria
| | - Karl Gruber
- Austrian Centre of Industrial Biotechnology (ACIB)Petersgasse 148010GrazAustria
- Institute of Molecular BiosciencesUniversity of GrazHumboldtstraße 508010GrazAustria
| | - Rolf Breinbauer
- Institute of Organic ChemistryGraz University of TechnologyStremayrgasse 98010GrazAustria
- Austrian Centre of Industrial Biotechnology (ACIB)Petersgasse 148010GrazAustria
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21
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Heckenbichler K, Schweiger A, Brandner LA, Binter A, Toplak M, Macheroux P, Gruber K, Breinbauer R. Asymmetrische reduktive Carbocyclisierung durch modifizierte En-Reduktasen. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201802962] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Kathrin Heckenbichler
- Institut für Organische Chemie; Technische Universität Graz; Stremayrgasse 9 8010 Graz Österreich
| | - Anna Schweiger
- Institut für Organische Chemie; Technische Universität Graz; Stremayrgasse 9 8010 Graz Österreich
| | - Lea Alexandra Brandner
- Institut für Organische Chemie; Technische Universität Graz; Stremayrgasse 9 8010 Graz Österreich
| | - Alexandra Binter
- Institut für Biochemie; Technische Universität Graz; Petersgasse 10-12 8010 Graz Österreich
- Austrian Centre of Industrial Biotechnology (ACIB); Petersgasse 14 8010 Graz Österreich
| | - Marina Toplak
- Institut für Biochemie; Technische Universität Graz; Petersgasse 10-12 8010 Graz Österreich
| | - Peter Macheroux
- Institut für Biochemie; Technische Universität Graz; Petersgasse 10-12 8010 Graz Österreich
| | - Karl Gruber
- Austrian Centre of Industrial Biotechnology (ACIB); Petersgasse 14 8010 Graz Österreich
- Institut für Molekulare Biowissenschaften; Karl-Franzens-Universität Graz; Humboldtstraße 50 8010 Graz Österreich
| | - Rolf Breinbauer
- Institut für Organische Chemie; Technische Universität Graz; Stremayrgasse 9 8010 Graz Österreich
- Austrian Centre of Industrial Biotechnology (ACIB); Petersgasse 14 8010 Graz Österreich
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22
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Sena FV, Sousa FM, Oliveira ASF, Soares CM, Catarino T, Pereira MM. Regulation of the mechanism of Type-II NADH: Quinone oxidoreductase from S. aureus. Redox Biol 2018. [PMID: 29524843 PMCID: PMC5857484 DOI: 10.1016/j.redox.2018.02.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Type-II NADH:quinone oxidoreductases (NDH-2s) are membrane proteins involved in respiratory chains and the only enzymes with NADH:quinone oxidoreductase activity expressed in Staphylococcus aureus (S. aureus), one of the most common causes of clinical infections. NDH-2s are members of the two-Dinucleotide Binding Domains Flavoprotein (tDBDF) superfamily, having a flavin adenine dinucleotide, FAD, as prosthetic group and NAD(P)H as substrate. The establishment of a Charge-Transfer Complex (CTC) between the isoalloxazine ring of the reduced flavin and the nicotinamide ring of NAD+ in NDH-2 was described, and in this work we explored its role in the kinetic mechanism using different electron donors and electron acceptors. We observed that CTC slows down the rate of the second half reaction (quinone reduction) and determines the effect of HQNO, an inhibitor. Also, protonation equilibrium simulations clearly indicate that the protonation probability of an important residue for proton transfer to the active site (D302) is influenced by the presence of the CTC. We propose that CTC is critical for the overall mechanism of NDH-2 and possibly relevant to keep a low quinol/quinone ratio and avoid excessive ROS production in vivo.
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Affiliation(s)
- Filipa V Sena
- Instituto de Tecnologia Química e Biológica - António Xavier, Universidade Nova de Lisboa, Av. da Republica EAN, 2780-157 Oeiras, Portugal
| | - Filipe M Sousa
- Instituto de Tecnologia Química e Biológica - António Xavier, Universidade Nova de Lisboa, Av. da Republica EAN, 2780-157 Oeiras, Portugal
| | - A Sofia F Oliveira
- School of Biochemistry, University of Bristol, University Walk, Bristol BS8 1TD, UK
| | - Cláudio M Soares
- Instituto de Tecnologia Química e Biológica - António Xavier, Universidade Nova de Lisboa, Av. da Republica EAN, 2780-157 Oeiras, Portugal
| | - Teresa Catarino
- Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - Manuela M Pereira
- Instituto de Tecnologia Química e Biológica - António Xavier, Universidade Nova de Lisboa, Av. da Republica EAN, 2780-157 Oeiras, Portugal; University of Lisbon, Faculty of Sciences, BioISI - Biosystems & Integrative Sciences Institute, Campo Grande, C8, 1749-016 Lisboa, Portugal.
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23
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Duan HD, Lubner CE, Tokmina-Lukaszewska M, Gauss GH, Bothner B, King PW, Peters JW, Miller AF. Distinct properties underlie flavin-based electron bifurcation in a novel electron transfer flavoprotein FixAB from Rhodopseudomonas palustris. J Biol Chem 2018; 293:4688-4701. [PMID: 29462786 DOI: 10.1074/jbc.ra117.000707] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Revised: 02/08/2018] [Indexed: 11/06/2022] Open
Abstract
A newly recognized third fundamental mechanism of energy conservation in biology, electron bifurcation, uses free energy from exergonic redox reactions to drive endergonic redox reactions. Flavin-based electron bifurcation furnishes low-potential electrons to demanding chemical reactions, such as reduction of dinitrogen to ammonia. We employed the heterodimeric flavoenzyme FixAB from the diazotrophic bacterium Rhodopseudomonas palustris to elucidate unique properties that underpin flavin-based electron bifurcation. FixAB is distinguished from canonical electron transfer flavoproteins (ETFs) by a second FAD that replaces the AMP of canonical ETF. We exploited near-UV-visible CD spectroscopy to resolve signals from the different flavin sites in FixAB and to interrogate the putative bifurcating FAD. CD aided in assigning the measured reduction midpoint potentials (E° values) to individual flavins, and the E° values tested the accepted model regarding the redox properties required for bifurcation. We found that the higher-E° flavin displays sequential one-electron (1-e-) reductions to anionic semiquinone and then to hydroquinone, consistent with the reactivity seen in canonical ETFs. In contrast, the lower-E° flavin displayed a single two-electron (2-e-) reduction without detectable accumulation of semiquinone, consistent with unstable semiquinone states, as required for bifurcation. This is the first demonstration that a FixAB protein possesses the thermodynamic prerequisites for bifurcating activity, and the separation of distinct optical signatures for the two flavins lays a foundation for mechanistic studies to learn how electron flow can be directed in a protein environment. We propose that a novel optical signal observed at long wavelength may reflect electron delocalization between the two flavins.
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Affiliation(s)
- H Diessel Duan
- Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506
| | | | | | - George H Gauss
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717
| | - Brian Bothner
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717
| | - Paul W King
- National Renewable Energy Laboratory, Golden, Colorado 80401
| | - John W Peters
- Institute of Biological Chemistry, Washington State University, Pullman, Washington 99163
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24
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Powell, III RW, Buteler MP, Lenka S, Crotti M, Santangelo S, Burg MJ, Bruner S, Brenna E, Roitberg AE, Stewart JD. Investigating Saccharomyces cerevisiae alkene reductase OYE 3 by substrate profiling, X-ray crystallography and computational methods. Catal Sci Technol 2018. [DOI: 10.1039/c8cy00440d] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Saccharomyces cerevisiae OYE 3 and OYE 1 share 80% sequence identity, but sometimes differ in stereoselectivities.
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Affiliation(s)
| | - M. Pilar Buteler
- Department of Chemistry
- 126 Sisler Hall
- University of Florida
- Gainesville
- USA
| | - Sunidhi Lenka
- Department of Chemistry
- 126 Sisler Hall
- University of Florida
- Gainesville
- USA
| | - Michele Crotti
- Dipartimento di Chimica
- Materiali ed Ingegneria Chimica “Giulio Natta” Politecnico di Milano
- Milano
- Italy
| | - Sara Santangelo
- Dipartimento di Chimica
- Materiali ed Ingegneria Chimica “Giulio Natta” Politecnico di Milano
- Milano
- Italy
| | - Matthew J. Burg
- Department of Chemistry
- 126 Sisler Hall
- University of Florida
- Gainesville
- USA
| | - Steven Bruner
- Department of Chemistry
- 126 Sisler Hall
- University of Florida
- Gainesville
- USA
| | - Elisabetta Brenna
- Dipartimento di Chimica
- Materiali ed Ingegneria Chimica “Giulio Natta” Politecnico di Milano
- Milano
- Italy
| | - Adrian E. Roitberg
- Department of Chemistry
- 126 Sisler Hall
- University of Florida
- Gainesville
- USA
| | - Jon D. Stewart
- Department of Chemistry
- 126 Sisler Hall
- University of Florida
- Gainesville
- USA
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25
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Werther T, Wahlefeld S, Salewski J, Kuhlmann U, Zebger I, Hildebrandt P, Dobbek H. Redox-dependent substrate-cofactor interactions in the Michaelis-complex of a flavin-dependent oxidoreductase. Nat Commun 2017. [PMCID: PMC5519977 DOI: 10.1038/ncomms16084] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
How an enzyme activates its substrate for turnover is fundamental for catalysis but incompletely understood on a structural level. With redox enzymes one typically analyses structures of enzyme–substrate complexes in the unreactive oxidation state of the cofactor, assuming that the interaction between enzyme and substrate is independent of the cofactors oxidation state. Here, we investigate the Michaelis complex of the flavoenzyme xenobiotic reductase A with the reactive reduced cofactor bound to its substrates by X-ray crystallography and resonance Raman spectroscopy and compare it to the non-reactive oxidized Michaelis complex mimics. We find that substrates bind in different orientations to the oxidized and reduced flavin, in both cases flattening its structure. But only authentic Michaelis complexes display an unexpected rich vibrational band pattern uncovering a strong donor–acceptor complex between reduced flavin and substrate. This interaction likely activates the catalytic ground state of the reduced flavin, accelerating the reaction within a compressed cofactor–substrate complex. Due to their transient nature, enzyme-substrate complexes are difficult to characterize structurally. Here, the authors capture the reactive reduced form of xenobiotic reductase A bound to its substrate and show that the oxidation state of the flavin cofactor affects the interaction of the substrate with the enzyme.
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26
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Hoben JP, Lubner CE, Ratzloff MW, Schut GJ, Nguyen DMN, Hempel KW, Adams MWW, King PW, Miller AF. Equilibrium and ultrafast kinetic studies manipulating electron transfer: A short-lived flavin semiquinone is not sufficient for electron bifurcation. J Biol Chem 2017; 292:14039-14049. [PMID: 28615449 DOI: 10.1074/jbc.m117.794214] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Revised: 06/11/2017] [Indexed: 11/06/2022] Open
Abstract
Flavin-based electron transfer bifurcation is emerging as a fundamental and powerful mechanism for conservation and deployment of electrochemical energy in enzymatic systems. In this process, a pair of electrons is acquired at intermediate reduction potential (i.e. intermediate reducing power), and each electron is passed to a different acceptor, one with lower and the other with higher reducing power, leading to "bifurcation." It is believed that a strongly reducing semiquinone species is essential for this process, and it is expected that this species should be kinetically short-lived. We now demonstrate that the presence of a short-lived anionic flavin semiquinone (ASQ) is not sufficient to infer the existence of bifurcating activity, although such a species may be necessary for the process. We have used transient absorption spectroscopy to compare the rates and mechanisms of decay of ASQ generated photochemically in bifurcating NADH-dependent ferredoxin-NADP+ oxidoreductase and the non-bifurcating flavoproteins nitroreductase, NADH oxidase, and flavodoxin. We found that different mechanisms dominate ASQ decay in the different protein environments, producing lifetimes ranging over 2 orders of magnitude. Capacity for electron transfer among redox cofactors versus charge recombination with nearby donors can explain the range of ASQ lifetimes that we observe. Our results support a model wherein efficient electron propagation can explain the short lifetime of the ASQ of bifurcating NADH-dependent ferredoxin-NADP+ oxidoreductase I and can be an indication of capacity for electron bifurcation.
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Affiliation(s)
- John P Hoben
- From the Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506
| | | | | | - Gerrit J Schut
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602
| | - Diep M N Nguyen
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602
| | - Karl W Hempel
- From the Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506
| | - Michael W W Adams
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602
| | - Paul W King
- National Renewable Energy Laboratory, Golden, Colorado 80401
| | - Anne-Frances Miller
- From the Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506.
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27
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Turrini NG, Eger E, Reiter TC, Faber K, Hall M. Sequential Enzymatic Conversion of α-Angelica Lactone to γ-Valerolactone through Hydride-Independent C=C Bond Isomerization. CHEMSUSCHEM 2016; 9:3393-3396. [PMID: 27885835 PMCID: PMC5574032 DOI: 10.1002/cssc.201601363] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Indexed: 06/06/2023]
Abstract
A case of hydride-independent reaction catalyzed by flavin-dependent ene-reductases from the Old Yellow Enzyme (OYE) family was identified. α-Angelica lactone was isomerized to the conjugated β-isomer in a nicotinamide-free and hydride-independent process. The catalytic cycle of C=C bond isomerization appears to be flavin-independent and to rely solely on a deprotonation-reprotonation sequence through acid-base catalysis. Key residues in the enzyme active site were mutated and provided insight on important mechanistic features. The isomerization of α-angelica lactone by OYE2 in aqueous buffer furnished 6.3 mm β-isomer in 15 min at 30 °C. In presence of nicotinamide adenine dinucleotide (NADH), the latter could be further reduced to γ-valerolactone. This enzymatic tool was successfully applied on semi-preparative scale and constitutes a sustainable process for the valorization of platform chemicals from renewable resources.
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Affiliation(s)
| | - Elisabeth Eger
- Department of ChemistryUniversity of GrazHeinrichstrasse 288010GrazAustria
| | - Tamara C. Reiter
- Department of ChemistryUniversity of GrazHeinrichstrasse 288010GrazAustria
- ACIB GmbH, Department of ChemistryUniversity of GrazHeinrichstrasse 288010GrazAustria
| | - Kurt Faber
- Department of ChemistryUniversity of GrazHeinrichstrasse 288010GrazAustria
| | - Mélanie Hall
- Department of ChemistryUniversity of GrazHeinrichstrasse 288010GrazAustria
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28
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Lawhorn BG, Philp J, Graves AP, Holt DA, Gatto GJ, Kallander LS. Substituent Effects on Drug–Receptor H-bond Interactions: Correlations Useful for the Design of Kinase Inhibitors. J Med Chem 2016; 59:10629-10641. [DOI: 10.1021/acs.jmedchem.6b01342] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Brian G. Lawhorn
- Heart Failure Discovery Performance Unit and ‡Platform Technology
and Sciences, GlaxoSmithKline, 709 Swedeland Road, King of Prussia, Pennsylvania 19406, United States
| | - Joanne Philp
- Heart Failure Discovery Performance Unit and ‡Platform Technology
and Sciences, GlaxoSmithKline, 709 Swedeland Road, King of Prussia, Pennsylvania 19406, United States
| | - Alan P. Graves
- Heart Failure Discovery Performance Unit and ‡Platform Technology
and Sciences, GlaxoSmithKline, 709 Swedeland Road, King of Prussia, Pennsylvania 19406, United States
| | - Dennis A. Holt
- Heart Failure Discovery Performance Unit and ‡Platform Technology
and Sciences, GlaxoSmithKline, 709 Swedeland Road, King of Prussia, Pennsylvania 19406, United States
| | - Gregory J. Gatto
- Heart Failure Discovery Performance Unit and ‡Platform Technology
and Sciences, GlaxoSmithKline, 709 Swedeland Road, King of Prussia, Pennsylvania 19406, United States
| | - Lara S. Kallander
- Heart Failure Discovery Performance Unit and ‡Platform Technology
and Sciences, GlaxoSmithKline, 709 Swedeland Road, King of Prussia, Pennsylvania 19406, United States
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29
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Dennig A, Busto E, Kroutil W, Faber K. Biocatalytic One-Pot Synthesis of l-Tyrosine Derivatives from Monosubstituted Benzenes, Pyruvate, and Ammonia. ACS Catal 2015. [DOI: 10.1021/acscatal.5b02129] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Alexander Dennig
- Department of Chemistry,
Organic and Bioorganic Chemistry, University of Graz, Heinrichstrasse
28, A-8010 Graz, Austria
| | - Eduardo Busto
- Department of Chemistry,
Organic and Bioorganic Chemistry, University of Graz, Heinrichstrasse
28, A-8010 Graz, Austria
| | - Wolfgang Kroutil
- Department of Chemistry,
Organic and Bioorganic Chemistry, University of Graz, Heinrichstrasse
28, A-8010 Graz, Austria
| | - Kurt Faber
- Department of Chemistry,
Organic and Bioorganic Chemistry, University of Graz, Heinrichstrasse
28, A-8010 Graz, Austria
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30
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Riedel A, Mehnert M, Paul CE, Westphal AH, van Berkel WJH, Tischler D. Functional characterization and stability improvement of a 'thermophilic-like' ene-reductase from Rhodococcus opacus 1CP. Front Microbiol 2015; 6:1073. [PMID: 26483784 PMCID: PMC4589676 DOI: 10.3389/fmicb.2015.01073] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Accepted: 09/18/2015] [Indexed: 01/26/2023] Open
Abstract
Ene-reductases (ERs) are widely applied for the asymmetric synthesis of relevant industrial chemicals. A novel ER OYERo2 was found within a set of 14 putative old yellow enzymes (OYEs) obtained by genome mining of the actinobacterium Rhodococcus opacus 1CP. Multiple sequence alignment suggested that the enzyme belongs to the group of 'thermophilic-like' OYEs. OYERo2 was produced in Escherichia coli and biochemically characterized. The enzyme is strongly NADPH dependent and uses non-covalently bound FMNH2 for the reduction of activated α,β-unsaturated alkenes. In the active form OYERo2 is a dimer. Optimal catalysis occurs at pH 7.3 and 37°C. OYERo2 showed highest specific activities (45-50 U mg(-1)) on maleimides, which are efficiently converted to the corresponding succinimides. The OYERo2-mediated reduction of prochiral alkenes afforded the (R)-products with excellent optical purity (ee > 99%). OYERo2 is not as thermo-resistant as related OYEs. Introduction of a characteristic intermolecular salt bridge by site-specific mutagenesis raised the half-life of enzyme inactivation at 32°C from 28 to 87 min and improved the tolerance toward organic co-solvents. The suitability of OYERo2 for application in industrial biocatalysis is discussed.
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Affiliation(s)
- Anika Riedel
- Interdisciplinary Ecological Center, Environmental Microbiology Group, Institute of Biosciences, Technical University Bergakademie Freiberg Freiberg, Germany ; Laboratory of Biochemistry, Wageningen University Wageningen, Netherlands
| | - Marika Mehnert
- Interdisciplinary Ecological Center, Environmental Microbiology Group, Institute of Biosciences, Technical University Bergakademie Freiberg Freiberg, Germany
| | - Caroline E Paul
- Department of Biotechnology, Delft University of Technology Delft, Netherlands
| | - Adrie H Westphal
- Laboratory of Biochemistry, Wageningen University Wageningen, Netherlands
| | | | - Dirk Tischler
- Interdisciplinary Ecological Center, Environmental Microbiology Group, Institute of Biosciences, Technical University Bergakademie Freiberg Freiberg, Germany ; Laboratory of Biochemistry, Wageningen University Wageningen, Netherlands
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31
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Mishanina TV, Yadav PK, Ballou DP, Banerjee R. Transient Kinetic Analysis of Hydrogen Sulfide Oxidation Catalyzed by Human Sulfide Quinone Oxidoreductase. J Biol Chem 2015; 290:25072-80. [PMID: 26318450 DOI: 10.1074/jbc.m115.682369] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Indexed: 11/06/2022] Open
Abstract
The first step in the mitochondrial sulfide oxidation pathway is catalyzed by sulfide quinone oxidoreductase (SQR), which belongs to the family of flavoprotein disulfide oxidoreductases. During the catalytic cycle, the flavin cofactor is intermittently reduced by sulfide and oxidized by ubiquinone, linking H2S oxidation to the electron transfer chain and to energy metabolism. Human SQR can use multiple thiophilic acceptors, including sulfide, sulfite, and glutathione, to form as products, hydrodisulfide, thiosulfate, and glutathione persulfide, respectively. In this study, we have used transient kinetics to examine the mechanism of the flavin reductive half-reaction and have determined the redox potential of the bound flavin to be -123 ± 7 mV. We observe formation of an unusually intense charge-transfer (CT) complex when the enzyme is exposed to sulfide and unexpectedly, when it is exposed to sulfite. In the canonical reaction, sulfide serves as the sulfur donor and sulfite serves as the acceptor, forming thiosulfate. We show that thiosulfate is also formed when sulfide is added to the sulfite-induced CT intermediate, representing a new mechanism for thiosulfate formation. The CT complex is formed at a kinetically competent rate by reaction with sulfide but not with sulfite. Our study indicates that sulfide addition to the active site disulfide is preferred under normal turnover conditions. However, under pathological conditions when sulfite concentrations are high, sulfite could compete with sulfide for addition to the active site disulfide, leading to attenuation of SQR activity and to an alternate route for thiosulfate formation.
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Affiliation(s)
- Tatiana V Mishanina
- From the Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan 48109-0600
| | - Pramod K Yadav
- From the Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan 48109-0600
| | - David P Ballou
- From the Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan 48109-0600
| | - Ruma Banerjee
- From the Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan 48109-0600
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32
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Bergner T, Pavkov-Keller T, Kreuzer K, Kowaliuk J, Plank M, Runggatscher K, Turrini NG, Zucol B, Wallner S, Faber K, Gruber K, Macheroux P. Anthranoyl-CoA monooxygenase/reductase from Azoarcus evansii possesses both FMN and FAD in two distinct and independent active sites. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1854:890-6. [PMID: 25843773 DOI: 10.1016/j.bbapap.2015.03.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Revised: 03/10/2015] [Accepted: 03/26/2015] [Indexed: 10/23/2022]
Abstract
Anthranoyl-CoA monooxygenase/reductase (ACMR) participates in an unusual pathway for the degradation of aromatic compounds in Azoarcus evansii. It catalyzes the monooxygenation of anthranoyl-CoA to 5-hydroxyl-2-aminobenzoyl-CoA and the subsequent reduction to the dearomatized product 2-amino-5-oxo-cyclohex-1-ene-1-carbonyl-CoA. The two reactions occur in separate domains, termed the monooxygenase and reductase domain. Both domains were reported to utilize FAD as a cofactor for hydroxylation and reduction, respectively. We have heterologously expressed ACMR in Escherichia coli BL21 and found that the monooxygenase domain contains FAD. However, the reductase domain utilizes FMN and not FAD for the reduction of the intermediate 5-hydroxyl-2-aminobenzoyl-CoA. A homology model for the reductase domain predicted a topology similar to the Old Yellow Enzyme family, which exclusively bind FMN, in accordance with our results. Binding studies with 2-aminobenzoyl-CoA (AbCoA) and p-hydroxybenzaldehyde (pHB) as probes for the monooxygenase and reductase domain, respectively, indicated that two functionally distinct and independent active sites exist. Given the homodimeric quartenary structure of ACMR and the compact shape of the dimer as determined by small-angle X-ray scattering experiments we propose that the monooxygenase and reductase domain of opposite peptide chains are involved in the transformation of anthranoyl-CoA to 2-amino-5-oxo-cyclohex-1-ene-1-carbonyl-CoA.
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Affiliation(s)
- Thomas Bergner
- Institute of Biochemistry, Graz University of Technology, A-8010 Graz, Austria
| | - Tea Pavkov-Keller
- ACIB-Austrian Centre of Industrial Biotechnology, A-8010 Graz, Austria
| | - Katharina Kreuzer
- Institute of Biochemistry, Graz University of Technology, A-8010 Graz, Austria
| | - Jakob Kowaliuk
- Institute of Biochemistry, Graz University of Technology, A-8010 Graz, Austria
| | - Markus Plank
- Institute of Biochemistry, Graz University of Technology, A-8010 Graz, Austria
| | | | | | - Benjamin Zucol
- Institute of Biochemistry, Graz University of Technology, A-8010 Graz, Austria
| | - Silvia Wallner
- Institute of Biochemistry, Graz University of Technology, A-8010 Graz, Austria
| | - Kurt Faber
- Institute of Chemistry, University of Graz, A-8010 Graz, Austria
| | - Karl Gruber
- Institute of Molecular Biosciences, University of Graz, A-8010 Graz, Austria
| | - Peter Macheroux
- Institute of Biochemistry, Graz University of Technology, A-8010 Graz, Austria.
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33
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Patterson-Orazem A, Sullivan B, Stewart JD. Pichia stipitis OYE 2.6 variants with improved catalytic efficiencies from site-saturation mutagenesis libraries. Bioorg Med Chem 2014; 22:5628-32. [PMID: 25087048 DOI: 10.1016/j.bmc.2014.07.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2014] [Revised: 06/23/2014] [Accepted: 07/01/2014] [Indexed: 01/25/2023]
Abstract
An earlier directed evolution project using alkene reductase OYE 2.6 from Pichia stipitis yielded 13 active site variants with improved properties toward three homologous Baylis-Hillman adducts. Here, we probed the generality of these improvements by testing the wild-type and all 13 variants against a panel of 16 structurally-diverse electron-deficient alkenes. Several substrates were sterically demanding, and as hoped, creating additional active site volume yielded better conversions for these alkenes. The most impressive improvement was found for 2-butylidenecyclohexanone. The wild-type provided less than 20% conversion after 24h; a triple mutant afforded more than 60% conversion in the same time period. Moreover, even wild-type OYE 2.6 can reduce cyclohexenones with very bulky 4-substituents efficiently.
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Affiliation(s)
| | - Bradford Sullivan
- Department of Chemistry, University of Florida, 126 Sisler Hall, Gainesville, FL 32611, USA
| | - Jon D Stewart
- Department of Chemistry, University of Florida, 126 Sisler Hall, Gainesville, FL 32611, USA.
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34
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Steinkellner G, Gruber CC, Pavkov-Keller T, Binter A, Steiner K, Winkler C, Łyskowski A, Schwamberger O, Oberer M, Schwab H, Faber K, Macheroux P, Gruber K. Identification of promiscuous ene-reductase activity by mining structural databases using active site constellations. Nat Commun 2014; 5:4150. [PMID: 24954722 PMCID: PMC4083419 DOI: 10.1038/ncomms5150] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Accepted: 05/15/2014] [Indexed: 12/03/2022] Open
Abstract
The exploitation of catalytic promiscuity and the application of de novo design have recently opened the access to novel, non-natural enzymatic activities. Here we describe a structural bioinformatic method for predicting catalytic activities of enzymes based on three-dimensional constellations of functional groups in active sites ('catalophores'). As a proof-of-concept we identify two enzymes with predicted promiscuous ene-reductase activity (reduction of activated C-C double bonds) and compare them with known ene-reductases, that is, members of the Old Yellow Enzyme family. Despite completely different amino acid sequences, overall structures and protein folds, high-resolution crystal structures reveal equivalent binding modes of typical Old Yellow Enzyme substrates and ligands. Biochemical and biocatalytic data show that the two enzymes indeed possess ene-reductase activity and reveal an inverted stereopreference compared with Old Yellow Enzymes for some substrates. This method could thus be a tool for the identification of viable starting points for the development and engineering of novel biocatalysts.
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Affiliation(s)
- Georg Steinkellner
- ACIB GmbH, Petersgasse 14, 8010 Graz, Austria
- These authors contributed equally to this work
| | - Christian C. Gruber
- ACIB GmbH, Petersgasse 14, 8010 Graz, Austria
- These authors contributed equally to this work
| | | | | | | | - Christoph Winkler
- Department of Chemistry, University of Graz, Heinrichstrasse 28, 8010 Graz, Austria
| | | | - Orsolya Schwamberger
- ACIB GmbH, Petersgasse 14, 8010 Graz, Austria
- Institute of Molecular Biosciences, University of Graz, Humboldtstrasse 50, 8010 Graz, Austria
| | - Monika Oberer
- Institute of Molecular Biosciences, University of Graz, Humboldtstrasse 50, 8010 Graz, Austria
| | - Helmut Schwab
- ACIB GmbH, Petersgasse 14, 8010 Graz, Austria
- Institute of Molecular Biotechnology, Graz University of Technology, Petersgasse 14, 8010 Graz, Austria
| | - Kurt Faber
- ACIB GmbH, Petersgasse 14, 8010 Graz, Austria
- Department of Chemistry, University of Graz, Heinrichstrasse 28, 8010 Graz, Austria
| | - Peter Macheroux
- ACIB GmbH, Petersgasse 14, 8010 Graz, Austria
- Institute of Biochemistry, Graz University of Technology, Petersgasse 12, 8010 Graz, Austria
| | - Karl Gruber
- ACIB GmbH, Petersgasse 14, 8010 Graz, Austria
- Institute of Molecular Biosciences, University of Graz, Humboldtstrasse 50, 8010 Graz, Austria
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35
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Winkler CK, Clay D, Entner M, Plank M, Faber K. NAD(P)H-independent asymmetric C=C bond reduction catalyzed by ene reductases by using artificial co-substrates as the hydrogen donor. Chemistry 2014; 20:1403-9. [PMID: 24382795 PMCID: PMC4413776 DOI: 10.1002/chem.201303897] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2013] [Indexed: 11/12/2022]
Abstract
To develop a nicotinamide-independent single flavoenzyme system for the asymmetric bioreduction of C=C bonds, four types of hydrogen donor, encompassing more than 50 candidates, were investigated. Six highly potent, cheap, and commercially available co-substrates were identified that (under the optimized conditions) resulted in conversions and enantioselectivities comparable with, or even superior to, those obtained with traditional two-enzyme nicotinamide adenine dinucleotide phosphate (NAD(P)H)-recycling systems.
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Affiliation(s)
- Christoph K Winkler
- Department of Chemistry, Organic and Bioorganic Chemistry, University of GrazHeinrichstrasse 28, 8010 Graz (Austria) Fax: (+43) 316-380-9840
| | - Dorina Clay
- Department of Chemistry, Organic and Bioorganic Chemistry, University of GrazHeinrichstrasse 28, 8010 Graz (Austria) Fax: (+43) 316-380-9840
| | - Marcello Entner
- Department of Chemistry, Organic and Bioorganic Chemistry, University of GrazHeinrichstrasse 28, 8010 Graz (Austria) Fax: (+43) 316-380-9840
| | - Markus Plank
- Department of Chemistry, Organic and Bioorganic Chemistry, University of GrazHeinrichstrasse 28, 8010 Graz (Austria) Fax: (+43) 316-380-9840
| | - Kurt Faber
- Department of Chemistry, Organic and Bioorganic Chemistry, University of GrazHeinrichstrasse 28, 8010 Graz (Austria) Fax: (+43) 316-380-9840
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36
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Pompeu YA, Sullivan B, Stewart JD. X-ray Crystallography Reveals How Subtle Changes Control the Orientation of Substrate Binding in an Alkene Reductase. ACS Catal 2013. [DOI: 10.1021/cs400622e] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yuri A. Pompeu
- Department
of Chemistry, University of Florida, 126 Sisler Hall, Gainesville, Florida 32611, United States
| | - Bradford Sullivan
- Department
of Chemistry, University of Florida, 126 Sisler Hall, Gainesville, Florida 32611, United States
| | - Jon D. Stewart
- Department
of Chemistry, University of Florida, 126 Sisler Hall, Gainesville, Florida 32611, United States
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37
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Daugherty AB, Govindarajan S, Lutz S. Improved biocatalysts from a synthetic circular permutation library of the flavin-dependent oxidoreductase old yellow enzyme. J Am Chem Soc 2013; 135:14425-32. [PMID: 23987134 DOI: 10.1021/ja4074886] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Members of the old yellow enzyme (OYE) family are widely used, effective biocatalysts for the stereoselective trans-hydrogenation of activated alkenes. To further expand their substrate scope and improve catalytic performance, we have applied a protein engineering strategy called circular permutation (CP) to enhance the function of OYE1 from Saccharomyces pastorianus. CP can influence a biocatalyst's function by altering protein backbone flexibility and active site accessibility, both critical performance features because the catalytic cycle for OYE1 is thought to involve rate-limiting conformational changes. To explore the impact of CP throughout the OYE1 protein sequence, we implemented a highly efficient approach for cell-free cpOYE library preparation by combining whole-gene synthesis with in vitro transcription/translation. The versatility of such an ex vivo system was further demonstrated by the rapid and reliable functional evaluation of library members under variable environmental conditions with three reference substrates ketoisophorone, cinnamaldehyde, and (S)-carvone. Library analysis identified over 70 functional OYE1 variants with several biocatalysts exhibiting over an order of magnitude improved catalytic activity. Although catalytic gains of individual cpOYE library members vary by substrate, the locations of new protein termini in functional variants for all tested substates fall within the same four distinct loop/lid regions near the active site. Our findings demonstrate the importance of these structural elements in enzyme function and support the hypothesis of conformational flexibility as a limiting factor for catalysis in wild type OYE.
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Affiliation(s)
- Ashley B Daugherty
- Department of Chemistry, Emory University , 1515 Dickey Drive, Atlanta, Georgia 30084, United States
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38
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Winkler CK, Clay D, van Heerden E, Faber K. Overcoming co-product inhibition in the nicotinamide independent asymmetric bioreduction of activated C=C-bonds using flavin-dependent ene-reductases. Biotechnol Bioeng 2013; 110:3085-92. [PMID: 23794404 PMCID: PMC4034509 DOI: 10.1002/bit.24981] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2013] [Revised: 05/24/2013] [Accepted: 06/10/2013] [Indexed: 11/16/2022]
Abstract
Eleven flavoproteins from the old yellow enzyme family were found to catalyze the disproportionation (“dismutation”) of conjugated enones. Incomplete conversions, which were attributed to enzyme inhibition by the co-product phenol could be circumvented via in situ co-product removal by scavenging the phenol using the polymeric adsorbent MP-carbonate. The optimized system allowed to reduce an alkene activated by ester groups in a “coupled-substrate” approach via nicotinamide-free hydrogen transfer with >90% conversion and complete stereoselectivity.
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Affiliation(s)
- Christoph K Winkler
- Department of Chemistry, Organic and Bioorganic Chemistry, University of Graz, Heinrichstrasse 28, A-8010, Graz, Austria
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39
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Iqbal N, Rudroff F, Brigé A, Van Beeumen J, Mihovilovic MD. Asymmetric bioreduction of activated carbon-carbon double bonds using Shewanella yellow enzyme (SYE-4) as novel enoate reductase. Tetrahedron 2012; 68:7619-7623. [PMID: 22991485 PMCID: PMC3415682 DOI: 10.1016/j.tet.2012.05.092] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2012] [Revised: 05/03/2012] [Accepted: 05/22/2012] [Indexed: 12/01/2022]
Abstract
Shewanella yellow enzyme (SYE-4), a novel recombinant enoate reductase, was screened against a variety of different substrates bearing an activated double bond, such as unsaturated cyclic ketones, diesters, and substituted imides. Dimethyl- and ethyl esters of 2-methylmaleic acid were selectively reduced to (R)-configured succinic acid derivatives and various N-substituted maleimides furnished the desired (R)-products in up to >99% enantiomeric excess. Naturally occurring (+)-carvone was selectively reduced to (−)-cis-dihydrocarvone and (−)-carvone was converted to the diastereomeric product, respectively. Overall SYE-4 proved to be a useful biocatalyst for the selective reduction of activated C
Created by potrace 1.16, written by Peter Selinger 2001-2019
]]>C double bonds and complements the pool of synthetic valuable enoate reductases.
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Affiliation(s)
- Naseem Iqbal
- Institute of Applied Synthetic Chemistry, Vienna University of Technology, Getreidemarkt 9, 163-OC, A-1060 Vienna, Austria
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40
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Hernández-Ortega A, Lucas F, Ferreira P, Medina M, Guallar V, Martínez AT. Role of Active Site Histidines in the Two Half-Reactions of the Aryl-Alcohol Oxidase Catalytic Cycle. Biochemistry 2012; 51:6595-608. [DOI: 10.1021/bi300505z] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | - Fátima Lucas
- Joint BSC-IRB
Research Program
in Computational Biology, Barcelona Supercomputing Center, Jordi Girona 29, E-08034 Barcelona, Spain
| | - Patricia Ferreira
- Department of Biochemistry and
Molecular and Cellular Biology and Institute of Biocomputation and
Physics of Complex Systems, University of Zaragoza, E-50009 Zaragoza, Spain
| | - Milagros Medina
- Department of Biochemistry and
Molecular and Cellular Biology and Institute of Biocomputation and
Physics of Complex Systems, University of Zaragoza, E-50009 Zaragoza, Spain
| | - Victor Guallar
- Joint BSC-IRB
Research Program
in Computational Biology, Barcelona Supercomputing Center, Jordi Girona 29, E-08034 Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluís Companys 23, E-08010 Barcelona, Spain
| | - Angel T. Martínez
- Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, E-28040
Madrid, Spain
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41
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Pompeu YA, Sullivan B, Walton AZ, Stewart JD. Structural and Catalytic Characterization of Pichia stipitis OYE 2.6, a Useful Biocatalyst for Asymmetric Alkene Reductions. Adv Synth Catal 2012. [DOI: 10.1002/adsc.201200213] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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42
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Okamoto N, Yamaguchi K, Mizohata E, Tokuoka K, Uchiyama N, Sugiyama S, Matsumura H, Inaka K, Urade Y, Inoue T. Structural insight into the stereoselective production of PGF2α by Old Yellow Enzyme from Trypanosoma cruzi. J Biochem 2011; 150:563-8. [PMID: 21840922 DOI: 10.1093/jb/mvr096] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Old yellow enzyme (OYE) is an NADPH oxidoreductase capable of reducing a variety of compounds. It contains flavin mononucleotide (FMN) as a prosthetic group. A ternary complex structure of OYE from Trypanosoma cruzi (TcOYE) with FMN and one of the substrates, p-hydroxybenzaldehyde, shows a striking movement around the active site upon binding of the substrate. From a structural comparison of other OYE complexed with 12-oxophytodienoate, we have constructed a complex structure with another substrate, prostaglandin H(2) (PGH(2)), to provide a proposed stereoselective reaction mechanism for the reduction of PGH(2) to prostaglandin F(2α) by TcOYE.
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Affiliation(s)
- Naoki Okamoto
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, Yamada-Oka, Suita, Japan
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43
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Toogood HS, Fryszkowska A, Hulley M, Sakuma M, Mansell D, Stephens GM, Gardiner JM, Scrutton NS. A Site-Saturated Mutagenesis Study of Pentaerythritol Tetranitrate Reductase Reveals that Residues 181 and 184 Influence Ligand Binding, Stereochemistry and Reactivity. Chembiochem 2011; 12:738-49. [DOI: 10.1002/cbic.201000662] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2010] [Indexed: 11/09/2022]
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44
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Toogood H, Gardiner J, Scrutton N. Biocatalytic Reductions and Chemical Versatility of the Old Yellow Enzyme Family of Flavoprotein Oxidoreductases. ChemCatChem 2010. [DOI: 10.1002/cctc.201000094] [Citation(s) in RCA: 250] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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45
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Spiegelhauer O, Mende S, Dickert F, Knauer SH, Ullmann GM, Dobbek H. Cysteine as a modulator residue in the active site of xenobiotic reductase A: a structural, thermodynamic and kinetic study. J Mol Biol 2010; 398:66-82. [PMID: 20206186 DOI: 10.1016/j.jmb.2010.02.044] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2009] [Revised: 02/20/2010] [Accepted: 02/24/2010] [Indexed: 11/18/2022]
Abstract
Xenobiotic reductase A (XenA) from Pseudomonas putida 86 catalyzes the NADH/NADPH-dependent reduction of various substrates, including 2-cyclohexenone and 8-hydroxycoumarin. XenA is a member of the old yellow enzyme (OYE) family of flavoproteins and is structurally and functionally similar to other bacterial members of this enzyme class. A characteristic feature of XenA is the presence of a cysteine residue (Cys25) in the active site, where in most members of the OYE family a threonine residue is found that modulates the reduction potential of the FMN/FMNH(-) couple. We investigated the role of Cys25 by studying two variants in which the residue has been exchanged for a serine and an alanine residue. While the exchange against alanine has a remarkably small effect on the reduction potential, the reactivity and the structure of XenA, the exchange against serine increases the reduction potential by +82 mV, increases the rate constant of the reductive half-reaction and decreases the rate constant in the oxidative half-reaction. We determined six crystal structures at high to true atomic resolution (d(min) 1.03-1.80 A) of the three XenA variants with and without the substrate coumarin bound in the active site. The atomic resolution structure of XenA in complex with coumarin reveals a compressed active site geometry in which the isoalloxazine ring is sandwiched between coumarin and the protein backbone. The structures further reveal that the conformation of the active site and substrate interactions are preserved in the two variants, indicating that the observed changes are due to local effects only. We propose that Cys25 and the residues in its place determine which of the two half-reactions is rate limiting, depending on the substrate couple. This might help to explain why the genome of Pseudomonas putida encodes multiple xenobiotic reductases containing either cysteine, threonine or alanine in the active site.
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Affiliation(s)
- Olivia Spiegelhauer
- Bioinorganic Chemistry, Universität Bayreuth, Universitätsstrasse 30, 95447 Bayreuth, Germany
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Stueckler C, Reiter TC, Baudendistel N, Faber K. Nicotinamide-independent asymmetric bioreduction of CC-bonds via disproportionation of enones catalyzed by enoate reductases. Tetrahedron 2010; 66:663-667. [PMID: 21270958 PMCID: PMC3007678 DOI: 10.1016/j.tet.2009.11.065] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2009] [Revised: 11/11/2009] [Accepted: 11/12/2009] [Indexed: 11/17/2022]
Abstract
The asymmetric bioreduction of activated CC-bonds catalyzed by a single flavoprotein was achieved via direct hydrogen transfer from a sacrificial 2-enone or 1,4-dione as hydrogen donor without requirement of a nicotinamide cofactor. Due to its simplicity, this system has clear advantages over conventional FAD-recycling systems.
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Affiliation(s)
- Clemens Stueckler
- Department of Chemistry, Organic & Bioorganic Chemistry, University of Graz, Heinrichstrasse 28, A-8010 Graz, Austria
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Elegheert J, van den Hemel D, Dix I, Stout J, Van Beeumen J, Brigé A, Savvides SN. Towards structural studies of the old yellow enzyme homologue SYE4 from Shewanella oneidensis and its complexes at atomic resolution. Acta Crystallogr Sect F Struct Biol Cryst Commun 2009; 66:85-90. [PMID: 20057079 DOI: 10.1107/s1744309109050386] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2009] [Accepted: 11/23/2009] [Indexed: 11/10/2022]
Abstract
Shewanella oneidensis is an environmentally versatile Gram-negative gamma-proteobacterium that is endowed with an unusually large proteome of redox proteins. Of the four old yellow enzyme (OYE) homologues found in S. oneidensis, SYE4 is the homologue most implicated in resistance to oxidative stress. SYE4 was recombinantly expressed in Escherichia coli, purified and crystallized using the hanging-drop vapour-diffusion method. The crystals belonged to the orthorhombic space group P2(1)2(1)2(1) and were moderately pseudo-merohedrally twinned, emulating a P422 metric symmetry. The native crystals of SYE4 were of exceptional diffraction quality and provided complete data to 1.10 A resolution using synchrotron radiation, while crystals of the reduced enzyme and of the enzyme in complex with a wide range of ligands typically led to high-quality complete data sets to 1.30-1.60 A resolution, thus providing a rare opportunity to dissect the structure-function relationships of a good-sized enzyme (40 kDa) at true atomic resolution. Here, the attainment of a number of experimental milestones in the crystallographic studies of SYE4 and its complexes are reported, including isolation of the elusive hydride-Meisenheimer complex.
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Affiliation(s)
- Jonathan Elegheert
- Department of Biochemistry and Microbiology, Laboratory for Protein Biochemistry and Biomolecular Engineering (L-ProBE), Ghent University, K. L. Ledeganckstraat 35, 9000 Ghent, Belgium
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Spiegelhauer O, Dickert F, Mende S, Niks D, Hille R, Ullmann M, Dobbek H. Kinetic characterization of xenobiotic reductase A from Pseudomonas putida 86. Biochemistry 2009; 48:11412-20. [PMID: 19839648 DOI: 10.1021/bi901370u] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Xenobiotic reductase A (XenA) from Pseudomonas putida is a member of the old-yellow-enzyme family of flavin-containing enzymes and catalyzes the NADH/NADPH-dependent reduction of various substrates, including 8-hydroxycoumarin and 2-cyclohexenone. Here we present a kinetic and thermodynamic analysis of XenA. In the reductive half-reaction, complexes of oxidized XenA with NADH or NADPH form charge-transfer (CT) intermediates with increased absorption around 520-560 nm, which occurs with a second-order rate constant of 9.4 x 10(5) M(-1) s(-1) with NADH and 6.4 x 10(5) M(-1) s(-1) with NADPH, while its disappearance is controlled by a rate constant of 210-250 s(-1) with both substrates. Transfer of hydride from NADPH proceeds 24 times more rapidly than from NADH. This modest kinetic preference of XenA for NADPH is unlike the typical discrimination between NADH and NADPH by binding affinity. Docking studies combined with electrostatic energy calculations indicate that the 2'-phosphate group attached to the adenine moiety of NADPH is responsible for this difference. The reductions of 2-cyclohexenone and coumarin in the oxidative half-reaction are both concentration-dependent under the assay conditions and reveal a more than 50-fold larger limiting rate constant for the reduction of 2-cyclohexenone compared to that of coumarin. Our work corroborates the link between XenA and other members of the old-yellow-enzyme family but demonstrates several differences in the reactivity of these enzymes.
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Structural basis of substrate specificity of plant 12-oxophytodienoate reductases. J Mol Biol 2009; 392:1266-77. [PMID: 19660473 DOI: 10.1016/j.jmb.2009.07.087] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2009] [Revised: 07/27/2009] [Accepted: 07/29/2009] [Indexed: 11/24/2022]
Abstract
12-Oxophytodienoate reductase 3 (OPR3) is a FMN-dependent oxidoreductase that catalyzes the reduction of the cyclopentenone (9S,13S)-12-oxophytodienoate [(9S,13S)-OPDA] to the corresponding cyclopentanone in the biosynthesis of the plant hormone jasmonic acid. In vitro, however, OPR3 reduces the jasmonic acid precursor (9S,13S)-OPDA as well as the enantiomeric (9R,13R)-OPDA, while its isozyme OPR1 is highly selective, accepting only (9R,13R)-OPDA as a substrate. To uncover the molecular determinants of this remarkable enantioselectivity, we determined the crystal structures of OPR1 and OPR3 in complex with the ligand p-hydroxybenzaldehyde. Structural comparison with the OPR1:(9R,13R)-OPDA complex and further biochemical and mutational analyses revealed that two active-site residues, Tyr78 and Tyr246 in OPR1 and Phe74 and His244 in OPR3, are critical for substrate filtering. The relatively smaller OPR3 residues allow formation of a wider substrate binding pocket that is less enantio-restrictive. Substitution of Phe74 and His244 by the corresponding OPR1 tyrosines resulted in an OPR3 mutant showing enhanced, OPR1-like substrate selectivity. Moreover, sequence analysis of the OPR family supports the filtering function of Tyr78 and Tyr246 and allows predictions with respect to substrate specificity and biological function of thus far uncharacterized OPR isozymes. The discovered structural features may also be relevant for other stereoselective proteins and guide the rational design of stereospecific enzymes for biotechnological applications.
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Wei L, Makowski T, Martinez C, Ghosh A. Efficient synthesis of (R)-3-amino-1,1,1-trifluoropropan-2-ol via a Dakin–West reaction followed by enantioselective reduction. ACTA ACUST UNITED AC 2008. [DOI: 10.1016/j.tetasy.2008.12.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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