1
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Taylor A, Zhang S, Johannissen LO, Sakuma M, Phillips RS, Green AP, Hay S, Heyes DJ, Scrutton NS. Mechanistic implications of the ternary complex structural models for the photoenzyme protochlorophyllide oxidoreductase. FEBS J 2024; 291:1404-1421. [PMID: 38060334 DOI: 10.1111/febs.17025] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 11/13/2023] [Accepted: 12/05/2023] [Indexed: 04/04/2024]
Abstract
The photoenzyme protochlorophyllide oxidoreductase (POR) is an important enzyme for understanding biological H-transfer mechanisms. It uses light to catalyse the reduction of protochlorophyllide to chlorophyllide, a key step in chlorophyll biosynthesis. Although a wealth of spectroscopic data have provided crucial mechanistic insight, a structural rationale for POR photocatalysis has proved challenging and remains hotly debated. Recent structural models of the ternary enzyme-substrate complex, derived from crystal and electron microscopy data, show differences in the orientation of the protochlorophyllide substrate and the architecture of the POR active site, with significant implications for the catalytic mechanism. Here, we use a combination of computational and experimental approaches to investigate the compatibility of each structural model with the hypothesised reaction mechanisms and propose an alternative structural model for the cyanobacterial POR ternary complex. We show that a strictly conserved tyrosine, previously proposed to act as the proton donor in POR photocatalysis, is unlikely to be involved in this step of the reaction but is crucial for Pchlide binding. Instead, an active site cysteine is important for both hydride and proton transfer reactions in POR and is proposed to act as the proton donor, either directly or through a water-mediated network. Moreover, a conserved glutamine is important for Pchlide binding and ensuring efficient photochemistry by tuning its electronic properties, likely by interacting with the central Mg atom of the substrate. This optimal 'binding pose' for the POR ternary enzyme-substrate complex illustrates how light energy can be harnessed to facilitate enzyme catalysis by this unique enzyme.
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Affiliation(s)
- Aoife Taylor
- Manchester Institute of Biotechnology and Department of Chemistry, School of Natural Sciences, Faculty of Science and Engineering, The University of Manchester, UK
| | - Shaowei Zhang
- Manchester Institute of Biotechnology and Department of Chemistry, School of Natural Sciences, Faculty of Science and Engineering, The University of Manchester, UK
| | - Linus O Johannissen
- Manchester Institute of Biotechnology and Department of Chemistry, School of Natural Sciences, Faculty of Science and Engineering, The University of Manchester, UK
| | - Michiyo Sakuma
- Manchester Institute of Biotechnology and Department of Chemistry, School of Natural Sciences, Faculty of Science and Engineering, The University of Manchester, UK
| | - Robert S Phillips
- Departments of Chemistry and Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA
| | - Anthony P Green
- Manchester Institute of Biotechnology and Department of Chemistry, School of Natural Sciences, Faculty of Science and Engineering, The University of Manchester, UK
| | - Sam Hay
- Manchester Institute of Biotechnology and Department of Chemistry, School of Natural Sciences, Faculty of Science and Engineering, The University of Manchester, UK
| | - Derren J Heyes
- Manchester Institute of Biotechnology and Department of Chemistry, School of Natural Sciences, Faculty of Science and Engineering, The University of Manchester, UK
| | - Nigel S Scrutton
- Manchester Institute of Biotechnology and Department of Chemistry, School of Natural Sciences, Faculty of Science and Engineering, The University of Manchester, UK
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2
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Liu R, Wang L, Meng Y, Tian Y, Li F, Lu H. Theoretical and Experimental Studies on Plant Light-Dependent Protochlorophyllide Oxidoreductase as a Novel Target for Searching Potential Herbicides. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023. [PMID: 37467369 DOI: 10.1021/acs.jafc.3c01783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/21/2023]
Abstract
Herbicide resistance is a prevalent problem that has posed a foremost challenge to crop production worldwide. Light-dependent enzyme NADPH: protochlorophyllide oxidoreductase (LPOR) in plants is a metabolic target that could satisfy this unmet demand. Herein, for the first time, we embarked on proposing a new mode of action of herbicides by performing structure-based virtual screening targeting multiple LPOR binding sites, with the determination of further bioactivity on the lead series. The feasibility of exploiting high selectivity and safety herbicides targeting LPOR was discussed from the perspective of the origin and phylogeny. Besides, we revealed the structural rearrangement and the selection key for NADPH cofactor binding to LPOR. Based on these, multitarget virtual screening was performed and the result identified compounds 2 affording micromolar inhibition, in which the IC50 reached 4.74 μM. Transcriptome analysis revealed that compound 2 induced more genes related to chlorophyll synthesis in Arabidopsis thaliana, especially the LPOR genes. Additionally, we clarified that these compounds binding to the site enhanced the overall stability and local rigidity of the complex systems from molecular dynamics simulation. This study delivers a guideline on how to assess activity-determining features of inhibitors to LPOR and how to translate this knowledge into the design of novel and effective inhibitors against malignant weed that act by targeting LPOR.
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Affiliation(s)
- Ruiyuan Liu
- College of Science, China Agricultural University, Beijing 100193, China
| | - Leng Wang
- College of Science, China Agricultural University, Beijing 100193, China
| | - Yue Meng
- College of Science, China Agricultural University, Beijing 100193, China
| | - Yiyi Tian
- College of Science, China Agricultural University, Beijing 100193, China
| | - Fang Li
- College of Science, China Agricultural University, Beijing 100193, China
| | - Huizhe Lu
- College of Science, China Agricultural University, Beijing 100193, China
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3
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Taylor A, Heyes DJ, Scrutton NS. Catalysis by Nature's photoenzymes. Curr Opin Struct Biol 2022; 77:102491. [PMID: 36323132 DOI: 10.1016/j.sbi.2022.102491] [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: 03/18/2022] [Revised: 08/22/2022] [Accepted: 10/01/2022] [Indexed: 12/14/2022]
Abstract
Photoenzymes use light to initiate biochemical reactions. Although rarely found in nature, their study has advanced understanding of how light energy can be harnessed to facilitate enzyme catalysis, which is also of importance to the design and engineering of man-made photocatalysts. Natural photoenzymes can be assigned to one of two families, based broadly on the nature of the light-sensing chromophores used, those being chlorophyll-like tetrapyrroles or flavins. In all cases, light absorption leads to excited state electron transfer, which in turn initiates photocatalysis. Reviewed here are recent findings relating to the structures and mechanisms of known photoenzymes. We highlight recent advances that have deepened understanding of mechanisms in biological photocatalysis.
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Affiliation(s)
- Aoife Taylor
- Future Biomanufacturing Research Hub, Manchester Institute of Biotechnology and Department of Chemistry, School of Natural Sciences, The University of Manchester, M1 7DN, United Kingdom
| | - Derren J Heyes
- Future Biomanufacturing Research Hub, Manchester Institute of Biotechnology and Department of Chemistry, School of Natural Sciences, The University of Manchester, M1 7DN, United Kingdom. https://twitter.com/DerrenHeyes
| | - Nigel S Scrutton
- Future Biomanufacturing Research Hub, Manchester Institute of Biotechnology and Department of Chemistry, School of Natural Sciences, The University of Manchester, M1 7DN, United Kingdom.
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4
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Li C, Hu B, Cao Y, Li Y. Unveiling the dehydrogenation mechanism of dihydrogen‐bonded phenol‐borane‐dimethylamine complex in the ground and excited states. J PHYS ORG CHEM 2022. [DOI: 10.1002/poc.4415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Chaozheng Li
- School of Mechanical and Electrical Engineering Henan Institute of Science and Technology Xinxiang China
| | - Bo Hu
- School of Mechanical and Electrical Engineering Henan Institute of Science and Technology Xinxiang China
| | - Yonghua Cao
- School of Mechanical and Electrical Engineering Henan Institute of Science and Technology Xinxiang China
| | - Yongfeng Li
- School of Mechanical and Electrical Engineering Henan Institute of Science and Technology Xinxiang China
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5
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Johannissen LO, Taylor A, Hardman SJ, Heyes DJ, Scrutton NS, Hay S. How Photoactivation Triggers Protochlorophyllide Reduction: Computational Evidence of a Stepwise Hydride Transfer during Chlorophyll Biosynthesis. ACS Catal 2022; 12:4141-4148. [PMID: 35574213 PMCID: PMC9098174 DOI: 10.1021/acscatal.2c00866] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 03/08/2022] [Indexed: 12/28/2022]
Abstract
![]()
The
photochemical reaction catalyzed by enzyme protochlorophyllide
oxidoreductase (POR), a rare example of a photoactivated enzyme, is
a crucial step during chlorophyll biosynthesis and involves the fastest
known biological hydride transfer. Structures of the enzyme with bound
substrate protochlorophyllide (PChlide) and coenzyme nicotinamide
adenine dinucleotide phosphate (NADPH) have recently been published,
opening up the possibility of using computational approaches to provide
a comprehensive understanding of the excited state chemistry. Herein,
we propose a complete mechanism for the photochemistry between PChlide
and NADPH based on density functional theory (DFT) and time-dependent
DFT calculations that is consistent with recent experimental data.
In this multi-step mechanism, photoexcitation of PChlide leads to
electron transfer from NADPH to PChlide, which in turn facilitates
hydrogen atom transfer by weakening the breaking C–H bond.
This work rationalizes how photoexcitation facilitates hydride transfer
in POR and has more general implications for biological hydride transfer
reactions.
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Affiliation(s)
- Linus O. Johannissen
- Manchester Institute of Biotechnology and Department of Chemistry, The University of Manchester, Manchester M1 7DN, U.K
| | - Aoife Taylor
- Manchester Institute of Biotechnology and Department of Chemistry, The University of Manchester, Manchester M1 7DN, U.K
| | - Samantha J.O. Hardman
- Manchester Institute of Biotechnology and Department of Chemistry, The University of Manchester, Manchester M1 7DN, U.K
| | - Derren J. Heyes
- Manchester Institute of Biotechnology and Department of Chemistry, The University of Manchester, Manchester M1 7DN, U.K
| | - Nigel S. Scrutton
- Manchester Institute of Biotechnology and Department of Chemistry, The University of Manchester, Manchester M1 7DN, U.K
| | - Sam Hay
- Manchester Institute of Biotechnology and Department of Chemistry, The University of Manchester, Manchester M1 7DN, U.K
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6
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Silva PJ, Cheng Q. An Alternative Proposal for the Reaction Mechanism of Light-Dependent Protochlorophyllide Oxidoreductase. ACS Catal 2022; 12:2589-2605. [PMID: 36568346 PMCID: PMC9778109 DOI: 10.1021/acscatal.1c05351] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Light-dependent protochlorophyllide oxidoreductase is one of the few known enzymes that require a quantum of light to start their catalytic cycle. Upon excitation, it uses NADPH to reduce the C17-C18 in its substrate (protochlorophyllide) through a complex mechanism that has heretofore eluded precise determination. Isotopic labeling experiments have shown that the hydride-transfer step is very fast, with a small barrier close to 9 kcal mol-1, and is followed by a proton-transfer step, which has been postulated to be the protonation of the product by the strictly conserved Tyr189 residue. Since the structure of the enzyme-substrate complex has not yet been experimentally determined, we first used modeling techniques to discover the actual substrate binding mode. Two possible binding modes were found, both yielding stable binding (as ascertained through molecular dynamics simulations) but only one of which placed the critical C17=C18 bond consistently close to the NADPH pro-S hydrogen and to Tyr189. This binding pose was then used as a starting point for the testing of previous mechanistic proposals using time-dependent density functional theory. The quantum-chemical computations clearly showed that such mechanisms have prohibitively high activation energies. Instead, these computations showed the feasibility of an alternative mechanism initiated by excited-state electron transfer from the key Tyr189 to the substrate. This mechanism appears to agree with the extant experimental data and reinterprets the final protonation step as a proton transfer to the active site itself rather than to the product, aiming at regenerating it for another round of catalysis.
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Affiliation(s)
- Pedro J. Silva
- FP-I3ID/Fac.
de Ciências da Saúde, Universidade
Fernando Pessoa, 4200-150 Porto, Portugal,UCIBIO@REQUIMTE,
BioSIM, Departamento de Biomedicina, Faculdade de Medicina, Universidade do Porto, 4200-319 Porto, Portugal,
| | - Qi Cheng
- Department
of Biochemistry, College of Life Sciences, Hebei Agricultural University, Baoding, Hebei 071000, China,State
Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, Hebei 071000, China,
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7
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Sameer H, Victor G, Katalin S, Henrik A. Elucidation of ligand binding and dimerization of NADPH:protochlorophyllide (Pchlide) oxidoreductase from pea (Pisum sativum L.) by structural analysis and simulations. Proteins 2021; 89:1300-1314. [PMID: 34021929 DOI: 10.1002/prot.26151] [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: 09/09/2020] [Revised: 02/18/2021] [Accepted: 05/11/2021] [Indexed: 11/07/2022]
Abstract
NADPH:protochlorophyllide (Pchlide) oxidoreductase (POR) is a key enzyme of chlorophyll biosynthesis in angiosperms. It is one of few known photoenzymes, which catalyzes the light-activated trans-reduction of the C17-C18 double bond of Pchlide's porphyrin ring. Due to the light requirement, dark-grown angiosperms cannot synthesize chlorophyll. No crystal structure of POR is available, so to improve understanding of the protein's three-dimensional structure, its dimerization, and binding of ligands (both the cofactor NADPH and substrate Pchlide), we computationally investigated the sequence and structural relationships among homologous proteins identified through database searches. The results indicate that α4 and α7 helices of monomers form the interface of POR dimers. On the basis of conserved residues, we predicted 11 functionally important amino acids that play important roles in POR binding to NADPH. Structural comparison of available crystal structures revealed that they participate in formation of binding pockets that accommodate the Pchlide ligand, and that five atoms of the closed tetrapyrrole are involved in non-bonding interactions. However, we detected no clear pattern in the physico-chemical characteristics of the amino acids they interact with. Thus, we hypothesize that interactions of these atoms in the Pchlide porphyrin ring are important to hold the ligand within the POR binding site. Analysis of Pchlide binding in POR by molecular docking and PELE simulations revealed that the orientation of the nicotinamide group is important for Pchlide binding. These findings highlight the complexity of interactions of porphyrin-containing ligands with proteins, and we suggest that fit-inducing processes play important roles in POR-Pchlide interactions.
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Affiliation(s)
- Hassan Sameer
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
| | - Guallar Victor
- ICREA, Passeig Lluís Companys 23, Barcelona, Spain
- Barcelona Supercomputing Center (BSC), Barcelona, Spain
| | - Solymosi Katalin
- Department of Plant Anatomy, Institute of Biology, Eötvös Loránd University, Budapest, Hungary
| | - Aronsson Henrik
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
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8
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Li C, Hu B, Cao Y, Li Y. Elaborating the excited-state double proton transfer mechanism and multiple fluorescent characteristics of 3,5-bis(2-hydroxypheny)-1H-1,2,4-triazole. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2021; 258:119854. [PMID: 33933943 DOI: 10.1016/j.saa.2021.119854] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 02/28/2021] [Accepted: 04/15/2021] [Indexed: 06/12/2023]
Abstract
Recently, Krishnamoorthy and coworkers reported a new type of proton transfer, which was labeled as 'proton transfer triggered proton transfer', in 3,5-bis(2-hydroxypheny)-1H-1,2,4-triazole (bis-HPTA). In this work, the excited-state double proton transfer (ESDPT) mechanism and multiple fluorescent characteristics of bis-HPTA were investigated. Upon photo-excitation, the intramolecular hydrogen bonding strength changed and the electron density of bis-HPTA redistributed. These changes will affect the proton transfer process. In S0 state, the proton transfer processes of bis-HPTA were prohibited on the stepwise and concerted pathways. After vertical excitation to the S1 state, the ESIPT-II process was more likely to occur than the ESIPT-I process, which was contrary to the conclusion that the ESIPT-II process is blocked and the ESIPT-II process takes place after the ESIPT-I process proposed by Krishnamoorthy and coworkers. When the K2 tautomer was formed through the ESIPT-II process, the second proton transfer process on the stepwise pathway was prohibited. On another stepwise pathway, after the ESIPT-I process (form the K1 tautomer), the second proton transfer process should overcome a higher potential barrier than the ESIPT-I process to form ESDPT tautomer. On the concerted pathway, the bis-HPTA can synchronous transfer double protons to form the ESDPT tautomer. The ESDPT tautomer was unstable and immediately converted to the K2 tautomer via a barrierless reverse proton transfer process. Thus, the fluorescent maximum at 465 nm from the ESDPT tautomer reported by Krishnamoorthy and coworkers was ascribed to the K2 tautomer. Most of the fluorophores show dual fluorescent properties, while the bis-HPTA undergoing ESDPT process exhibited three well-separated fluorescent peaks, corresponding to its normal form (438 nm), K1 tautomer (462 nm) and K2 tautomer (450 nm), respectively.
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Affiliation(s)
- Chaozheng Li
- School of Mechanical and Electrical Engineering, Henan Institute of Science and Technology, Xinxiang 453003, China.
| | - Bo Hu
- School of Mechanical and Electrical Engineering, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - Yonghua Cao
- School of Mechanical and Electrical Engineering, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - Yongfeng Li
- School of Mechanical and Electrical Engineering, Henan Institute of Science and Technology, Xinxiang 453003, China
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9
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Zeng Y, Liu L, Chen B, Zhang W. Light-Driven Enzymatic Decarboxylation of Dicarboxylic Acids. ChemistryOpen 2021; 10:553-559. [PMID: 33945237 PMCID: PMC8095292 DOI: 10.1002/open.202100039] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Revised: 04/06/2021] [Indexed: 11/24/2022] Open
Abstract
Photodecarboxylase from Chlorella variabillis (CvFAP) is one of the three known light-activated enzymes that catalyzes the decarboxylation of fatty acids into the corresponding C1-shortened alkanes. Although the substrate scope of CvFAP has been altered by protein engineering and decoy molecules, it is still limited to mono-fatty acids. Our studies demonstrate for the first time that long chain dicarboxylic acids can be converted by CvFAP. Notably, the conversion of dicarboxylic acids to alkanes still represents a chemically very challenging reaction. Herein, the light-driven enzymatic decarboxylation of dicarboxylic acids to the corresponding (C2-shortened) alkanes using CvFAP is described. A series of dicarboxylic acids is decarboxylated into alkanes in good yields by means of this approach, even for the preparative scales. Reaction pathway studies show that mono-fatty acids are formed as the intermediate products before the final release of C2-shortened alkanes. In addition, the thermostability, storage stability, and recyclability of CvFAP for decarboxylation of dicarboxylic acids are well evaluated. These results represent an advancement over the current state-of-the-art.
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Affiliation(s)
- Yong‐Yi Zeng
- School of Marine SciencesSun Yat-Sen UniversityZhuhai519082P. R. China
| | - Lan Liu
- School of Marine SciencesSun Yat-Sen UniversityZhuhai519082P. R. China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)Zhuhai519082P. R. China
| | - Bi‐Shuang Chen
- School of Marine SciencesSun Yat-Sen UniversityZhuhai519082P. R. China
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal EngineeringZhuhai519082P. R. China
| | - Wuyuan Zhang
- Tianjin Institute of Industrial BiotechnologyChinese Academy of SciencesWest 7th AvenueTianjin300308P. R. China
- National Technology Innovation Center of Synthetic Biology32 West 7th AvenueTianjin300308P. R. China
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10
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Solymosi K, Mysliwa-Kurdziel B. The Role of Membranes and Lipid-Protein Interactions in the Mg-Branch of Tetrapyrrole Biosynthesis. FRONTIERS IN PLANT SCIENCE 2021; 12:663309. [PMID: 33995458 PMCID: PMC8113382 DOI: 10.3389/fpls.2021.663309] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 03/22/2021] [Indexed: 05/31/2023]
Abstract
Chlorophyll (Chl) is essential for photosynthesis and needs to be produced throughout the whole plant life, especially under changing light intensity and stress conditions which may result in the destruction and elimination of these pigments. All steps of the Mg-branch of tetrapyrrole biosynthesis leading to Chl formation are carried out by enzymes associated with plastid membranes. Still the significance of these protein-membrane and protein-lipid interactions in Chl synthesis and chloroplast differentiation are not very well-understood. In this review, we provide an overview on Chl biosynthesis in angiosperms with emphasis on its association with membranes and lipids. Moreover, the last steps of the pathway including the reduction of protochlorophyllide (Pchlide) to chlorophyllide (Chlide), the biosynthesis of the isoprenoid phytyl moiety and the esterification of Chlide are also summarized. The unique biochemical and photophysical properties of the light-dependent NADPH:protochlorophyllide oxidoreductase (LPOR) enzyme catalyzing Pchlide photoreduction and located to peculiar tubuloreticular prolamellar body (PLB) membranes of light-deprived tissues of angiosperms and to envelope membranes, as well as to thylakoids (especially grana margins) are also reviewed. Data about the factors influencing tubuloreticular membrane formation within cells, the spectroscopic properties and the in vitro reconstitution of the native LPOR enzyme complexes are also critically discussed.
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Affiliation(s)
- Katalin Solymosi
- Department of Plant Anatomy, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Beata Mysliwa-Kurdziel
- Department of Plant Physiology and Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
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11
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Sorigué D, Hadjidemetriou K, Blangy S, Gotthard G, Bonvalet A, Coquelle N, Samire P, Aleksandrov A, Antonucci L, Benachir A, Boutet S, Byrdin M, Cammarata M, Carbajo S, Cuiné S, Doak RB, Foucar L, Gorel A, Grünbein M, Hartmann E, Hienerwadel R, Hilpert M, Kloos M, Lane TJ, Légeret B, Legrand P, Li-Beisson Y, Moulin SLY, Nurizzo D, Peltier G, Schirò G, Shoeman RL, Sliwa M, Solinas X, Zhuang B, Barends TRM, Colletier JP, Joffre M, Royant A, Berthomieu C, Weik M, Domratcheva T, Brettel K, Vos MH, Schlichting I, Arnoux P, Müller P, Beisson F. Mechanism and dynamics of fatty acid photodecarboxylase. Science 2021; 372:372/6538/eabd5687. [PMID: 33833098 DOI: 10.1126/science.abd5687] [Citation(s) in RCA: 81] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 02/17/2021] [Indexed: 12/21/2022]
Abstract
Fatty acid photodecarboxylase (FAP) is a photoenzyme with potential green chemistry applications. By combining static, time-resolved, and cryotrapping spectroscopy and crystallography as well as computation, we characterized Chlorella variabilis FAP reaction intermediates on time scales from subpicoseconds to milliseconds. High-resolution crystal structures from synchrotron and free electron laser x-ray sources highlighted an unusual bent shape of the oxidized flavin chromophore. We demonstrate that decarboxylation occurs directly upon reduction of the excited flavin by the fatty acid substrate. Along with flavin reoxidation by the alkyl radical intermediate, a major fraction of the cleaved carbon dioxide unexpectedly transformed in 100 nanoseconds, most likely into bicarbonate. This reaction is orders of magnitude faster than in solution. Two strictly conserved residues, R451 and C432, are essential for substrate stabilization and functional charge transfer.
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Affiliation(s)
- D Sorigué
- Aix-Marseille University, CEA, CNRS, Institute of Biosciences and Biotechnologies, BIAM Cadarache, 13108 Saint-Paul-lez-Durance, France
| | - K Hadjidemetriou
- Université Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale, 38000 Grenoble, France
| | - S Blangy
- Aix-Marseille University, CEA, CNRS, Institute of Biosciences and Biotechnologies, BIAM Cadarache, 13108 Saint-Paul-lez-Durance, France
| | - G Gotthard
- European Synchrotron Radiation Facility, 38043 Grenoble, France
| | - A Bonvalet
- LOB, CNRS, INSERM, Ecole Polytechnique, Institut Polytechnique de Paris, 91128 Palaiseau, France
| | - N Coquelle
- Large-Scale Structures Group, Institut Laue Langevin, 38042 Grenoble Cedex 9, France
| | - P Samire
- Aix-Marseille University, CEA, CNRS, Institute of Biosciences and Biotechnologies, BIAM Cadarache, 13108 Saint-Paul-lez-Durance, France.,Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - A Aleksandrov
- LOB, CNRS, INSERM, Ecole Polytechnique, Institut Polytechnique de Paris, 91128 Palaiseau, France
| | - L Antonucci
- LOB, CNRS, INSERM, Ecole Polytechnique, Institut Polytechnique de Paris, 91128 Palaiseau, France
| | - A Benachir
- LOB, CNRS, INSERM, Ecole Polytechnique, Institut Polytechnique de Paris, 91128 Palaiseau, France
| | - S Boutet
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - M Byrdin
- Université Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale, 38000 Grenoble, France
| | - M Cammarata
- Department of Physics, UMR UR1-CNRS 6251, University of Rennes 1, F-Rennes, France.
| | - S Carbajo
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - S Cuiné
- Aix-Marseille University, CEA, CNRS, Institute of Biosciences and Biotechnologies, BIAM Cadarache, 13108 Saint-Paul-lez-Durance, France
| | - R B Doak
- Max-Planck-Institut für medizinische Forschung, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - L Foucar
- Max-Planck-Institut für medizinische Forschung, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - A Gorel
- Max-Planck-Institut für medizinische Forschung, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - M Grünbein
- Max-Planck-Institut für medizinische Forschung, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - E Hartmann
- Max-Planck-Institut für medizinische Forschung, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - R Hienerwadel
- Aix-Marseille University, CEA, CNRS, Institute of Biosciences and Biotechnologies, BIAM Cadarache, 13108 Saint-Paul-lez-Durance, France
| | - M Hilpert
- Max-Planck-Institut für medizinische Forschung, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - M Kloos
- Max-Planck-Institut für medizinische Forschung, Jahnstrasse 29, 69120 Heidelberg, Germany.
| | - T J Lane
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - B Légeret
- Aix-Marseille University, CEA, CNRS, Institute of Biosciences and Biotechnologies, BIAM Cadarache, 13108 Saint-Paul-lez-Durance, France
| | - P Legrand
- Synchrotron SOLEIL. L'Orme des Merisiers Saint-Aubin, BP 48, 91192 Gif-sur-Yvette, France
| | - Y Li-Beisson
- Aix-Marseille University, CEA, CNRS, Institute of Biosciences and Biotechnologies, BIAM Cadarache, 13108 Saint-Paul-lez-Durance, France
| | - S L Y Moulin
- Aix-Marseille University, CEA, CNRS, Institute of Biosciences and Biotechnologies, BIAM Cadarache, 13108 Saint-Paul-lez-Durance, France
| | - D Nurizzo
- European Synchrotron Radiation Facility, 38043 Grenoble, France
| | - G Peltier
- Aix-Marseille University, CEA, CNRS, Institute of Biosciences and Biotechnologies, BIAM Cadarache, 13108 Saint-Paul-lez-Durance, France
| | - G Schirò
- Université Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale, 38000 Grenoble, France
| | - R L Shoeman
- Max-Planck-Institut für medizinische Forschung, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - M Sliwa
- Univ. Lille, CNRS, UMR 8516, LASIRE, LAboratoire de Spectroscopie pour les Interactions, la Réactivité et l'Environnement, 59000 Lille, France
| | - X Solinas
- LOB, CNRS, INSERM, Ecole Polytechnique, Institut Polytechnique de Paris, 91128 Palaiseau, France
| | - B Zhuang
- LOB, CNRS, INSERM, Ecole Polytechnique, Institut Polytechnique de Paris, 91128 Palaiseau, France.,Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - T R M Barends
- Max-Planck-Institut für medizinische Forschung, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - J-P Colletier
- Université Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale, 38000 Grenoble, France
| | - M Joffre
- LOB, CNRS, INSERM, Ecole Polytechnique, Institut Polytechnique de Paris, 91128 Palaiseau, France
| | - A Royant
- Université Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale, 38000 Grenoble, France.,European Synchrotron Radiation Facility, 38043 Grenoble, France
| | - C Berthomieu
- Aix-Marseille University, CEA, CNRS, Institute of Biosciences and Biotechnologies, BIAM Cadarache, 13108 Saint-Paul-lez-Durance, France.
| | - M Weik
- Université Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale, 38000 Grenoble, France.
| | - T Domratcheva
- Max-Planck-Institut für medizinische Forschung, Jahnstrasse 29, 69120 Heidelberg, Germany. .,Department of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russia
| | - K Brettel
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - M H Vos
- LOB, CNRS, INSERM, Ecole Polytechnique, Institut Polytechnique de Paris, 91128 Palaiseau, France.
| | - I Schlichting
- Max-Planck-Institut für medizinische Forschung, Jahnstrasse 29, 69120 Heidelberg, Germany.
| | - P Arnoux
- Aix-Marseille University, CEA, CNRS, Institute of Biosciences and Biotechnologies, BIAM Cadarache, 13108 Saint-Paul-lez-Durance, France.
| | - P Müller
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France.
| | - F Beisson
- Aix-Marseille University, CEA, CNRS, Institute of Biosciences and Biotechnologies, BIAM Cadarache, 13108 Saint-Paul-lez-Durance, France.
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12
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Heyes DJ, Zhang S, Taylor A, Johannissen LO, Hardman SJO, Hay S, Scrutton NS. Photocatalysis as the 'master switch' of photomorphogenesis in early plant development. NATURE PLANTS 2021; 7:268-276. [PMID: 33686224 DOI: 10.1038/s41477-021-00866-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 01/29/2021] [Indexed: 06/12/2023]
Abstract
Enzymatic photocatalysis is seldom used in biology. Photocatalysis by light-dependent protochlorophyllide oxidoreductase (LPOR)-one of only a few natural light-dependent enzymes-is an exception, and is responsible for the conversion of protochlorophyllide to chlorophyllide in chlorophyll biosynthesis. Photocatalysis by LPOR not only regulates the biosynthesis of the most abundant pigment on Earth but it is also a 'master switch' in photomorphogenesis in early plant development. Following illumination, LPOR promotes chlorophyll production, plastid membranes are transformed and the photosynthetic apparatus is established. Given these remarkable, light-induced pigment and morphological changes, the LPOR-catalysed reaction has been extensively studied from catalytic, physiological and plant development perspectives, highlighting vital, and multiple, cellular roles of this intriguing enzyme. Here, we offer a perspective in which the link between LPOR photocatalysis and plant photomorphogenesis is explored. Notable breakthroughs in LPOR structural biology have uncovered the structural-mechanistic basis of photocatalysis. These studies have clarified how photon absorption by the pigment protochlorophyllide-bound in a ternary LPOR-protochlorophyllide-NADPH complex-triggers photocatalysis and a cascade of complex molecular and cellular events that lead to plant morphological changes. Photocatalysis is therefore the master switch responsible for early-stage plant development and ultimately life on Earth.
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Affiliation(s)
- Derren J Heyes
- Manchester Institute of Biotechnology, Department of Chemistry, School of Natural Sciences, The University of Manchester, Manchester, UK.
| | - Shaowei Zhang
- Manchester Institute of Biotechnology, Department of Chemistry, School of Natural Sciences, The University of Manchester, Manchester, UK
| | - Aoife Taylor
- Manchester Institute of Biotechnology, Department of Chemistry, School of Natural Sciences, The University of Manchester, Manchester, UK
| | - Linus O Johannissen
- Manchester Institute of Biotechnology, Department of Chemistry, School of Natural Sciences, The University of Manchester, Manchester, UK
| | - Samantha J O Hardman
- Manchester Institute of Biotechnology, Department of Chemistry, School of Natural Sciences, The University of Manchester, Manchester, UK
| | - Sam Hay
- Manchester Institute of Biotechnology, Department of Chemistry, School of Natural Sciences, The University of Manchester, Manchester, UK
| | - Nigel S Scrutton
- Manchester Institute of Biotechnology, Department of Chemistry, School of Natural Sciences, The University of Manchester, Manchester, UK.
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13
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Dhillon P, Scrutton NS. In conversation with Nigel Scrutton. FEBS J 2020; 288:1728-1733. [PMID: 33373117 DOI: 10.1111/febs.15632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 11/15/2020] [Indexed: 11/30/2022]
Abstract
Nigel Scrutton FRS is Professor of Molecular Enzymology and Biophysical Chemistry at the University of Manchester and former Director of the Manchester Institute of Biotechnology (MIB). He obtained a first degree in Biochemistry from King's College London and followed this with a PhD at the University of Cambridge. His doctoral research, undertaken in Richard Perham's laboratory, yielded fundamental breakthroughs in enzyme redesign that have stood the test of time. Nigel was awarded a ScD degree by the University of Cambridge in 2003. After faculty positions at the University of Leicester, Nigel was appointed Professor at the University of Manchester in 2005. Over the last 15 years, he has cemented his reputation as a world leader in the fields of enzyme engineering and biocatalysis, synthetic biology, biophysics and biomanufacturing, notably by establishing and directing the Synthetic Biology Research Centre 'SYNBIOCHEM' and UK Future Biomanufacturing Research Hub. In recognition of his scientific contributions, he has received many academic awards and accolades, including being elected as Fellow of the Royal Society earlier this year. In this interview, he highlights how fundamental studies of enzymatic catalysis and mechanisms are driving key advances in biotechnology and biomanufacturing, and describes how the experiences and mentors of his formative years helped to shape his successful career at the interface between discovery and application-focused science.
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Affiliation(s)
| | - Nigel S Scrutton
- Manchester Institute of Biotechnology, University of Manchester, UK
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14
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Zhang S, Godwin ARF, Taylor A, Hardman SJO, Jowitt TA, Johannissen LO, Hay S, Baldock C, Heyes DJ, Scrutton NS. Dual role of the active site 'lid' regions of protochlorophyllide oxidoreductase in photocatalysis and plant development. FEBS J 2020; 288:175-189. [PMID: 32866986 DOI: 10.1111/febs.15542] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 08/15/2020] [Accepted: 08/24/2020] [Indexed: 11/29/2022]
Abstract
Protochlorophyllide oxidoreductase (POR) catalyses reduction of protochlorophyllide (Pchlide) to chlorophyllide, a light-dependent reaction of chlorophyll biosynthesis. POR is also important in plant development as it is the main constituent of prolamellar bodies in etioplast membranes. Prolamellar bodies are highly organised, paracrystalline structures comprising aggregated oligomeric structures of POR-Pchlide-NADPH complexes. How these oligomeric structures are formed and the role of Pchlide in oligomerisation remains unclear. POR crystal structures highlight two peptide regions that form a 'lid' to the active site, and undergo conformational change on binding Pchlide. Here, we show that Pchlide binding triggers formation of large oligomers of POR using size exclusion chromatography. A POR 'octamer' has been isolated and its structure investigated by cryo-electron microscopy at 7.7 Å resolution. This structure shows that oligomer formation is most likely driven by the interaction of amino acid residues in the highly conserved lid regions. Computational modelling indicates that Pchlide binding stabilises exposure of hydrophobic surfaces formed by the lid regions, which supports POR dimerisation and ultimately oligomer formation. Studies with variant PORs demonstrate that lid residues are involved in substrate binding and photocatalysis. These highly conserved lid regions therefore have a dual function. The lid residues position Pchlide optimally to enable photocatalysis. Following Pchlide binding, they also enable POR oligomerisation - a process that is reversed through subsequent photocatalysis in the early stages of chloroplast development.
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Affiliation(s)
- Shaowei Zhang
- Manchester Institute of Biotechnology, The University of Manchester, UK.,Department of Chemistry, Faculty of Science and Engineering, School of Natural Sciences, The University of Manchester, UK
| | - Alan R F Godwin
- Wellcome Centre for Cell-Matrix Research, University of Manchester, UK.,Division of Cell-Matrix Biology and Regenerative Medicine, Faculty of Biology, Medicine and Health, School of Biological Sciences, Manchester Academic Health Science Centre, University of Manchester, UK
| | - Aoife Taylor
- Manchester Institute of Biotechnology, The University of Manchester, UK.,Department of Chemistry, Faculty of Science and Engineering, School of Natural Sciences, The University of Manchester, UK
| | - Samantha J O Hardman
- Manchester Institute of Biotechnology, The University of Manchester, UK.,Department of Chemistry, Faculty of Science and Engineering, School of Natural Sciences, The University of Manchester, UK
| | - Thomas A Jowitt
- Wellcome Centre for Cell-Matrix Research, University of Manchester, UK.,Division of Cell-Matrix Biology and Regenerative Medicine, Faculty of Biology, Medicine and Health, School of Biological Sciences, Manchester Academic Health Science Centre, University of Manchester, UK
| | - Linus O Johannissen
- Manchester Institute of Biotechnology, The University of Manchester, UK.,Department of Chemistry, Faculty of Science and Engineering, School of Natural Sciences, The University of Manchester, UK
| | - Sam Hay
- Manchester Institute of Biotechnology, The University of Manchester, UK.,Department of Chemistry, Faculty of Science and Engineering, School of Natural Sciences, The University of Manchester, UK
| | - Clair Baldock
- Wellcome Centre for Cell-Matrix Research, University of Manchester, UK.,Division of Cell-Matrix Biology and Regenerative Medicine, Faculty of Biology, Medicine and Health, School of Biological Sciences, Manchester Academic Health Science Centre, University of Manchester, UK
| | - Derren J Heyes
- Manchester Institute of Biotechnology, The University of Manchester, UK.,Department of Chemistry, Faculty of Science and Engineering, School of Natural Sciences, The University of Manchester, UK
| | - Nigel S Scrutton
- Manchester Institute of Biotechnology, The University of Manchester, UK.,Department of Chemistry, Faculty of Science and Engineering, School of Natural Sciences, The University of Manchester, UK
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15
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Heyes DJ, Lakavath B, Hardman SJO, Sakuma M, Hedison TM, Scrutton NS. Photochemical Mechanism of Light-Driven Fatty Acid Photodecarboxylase. ACS Catal 2020; 10:6691-6696. [PMID: 32905273 PMCID: PMC7469136 DOI: 10.1021/acscatal.0c01684] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 05/18/2020] [Indexed: 01/06/2023]
Abstract
![]()
Fatty
acid photodecarboxylase (FAP) is a promising target for the
production of biofuels and fine chemicals. It contains a flavin adenine
dinucleotide cofactor and catalyzes the blue-light-dependent decarboxylation
of fatty acids to generate the corresponding alkane. However, little
is known about the catalytic mechanism of FAP, or how light is used
to drive enzymatic decarboxylation. Here, we have used a combination
of time-resolved and cryogenic trapping UV–visible absorption
spectroscopy to characterize a red-shifted flavin intermediate observed
in the catalytic cycle of FAP. We show that this intermediate can
form below the “glass transition” temperature of proteins,
whereas the subsequent decay of the species proceeds only at higher
temperatures, implying a role for protein motions in the decay of
the intermediate. Solvent isotope effect measurements, combined with
analyses of selected site-directed variants of FAP, suggest that the
formation of the red-shifted flavin species is directly coupled with
hydrogen atom transfer from a nearby active site cysteine residue,
yielding the final alkane product. Our study suggests that this cysteine
residue forms a thiolate-flavin charge-transfer species, which is
assigned as the red-shifted flavin intermediate. Taken together, our
data provide insights into light-dependent decarboxylase mechanisms
catalyzed by FAP and highlight important considerations in the (re)design
of flavin-based photoenzymes.
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Affiliation(s)
- Derren J. Heyes
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
| | - Balaji Lakavath
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
| | - Samantha J. O. Hardman
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
| | - Michiyo Sakuma
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
| | - Tobias M. Hedison
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
| | - Nigel S. Scrutton
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
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16
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Crystal structures of cyanobacterial light-dependent protochlorophyllide oxidoreductase. Proc Natl Acad Sci U S A 2020; 117:8455-8461. [PMID: 32234783 DOI: 10.1073/pnas.1920244117] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The reduction of protochlorophyllide (Pchlide) to chlorophyllide (Chlide) is the penultimate step of chlorophyll biosynthesis. In oxygenic photosynthetic bacteria, algae, and plants, this reaction can be catalyzed by the light-dependent Pchlide oxidoreductase (LPOR), a member of the short-chain dehydrogenase superfamily sharing a conserved Rossmann fold for NAD(P)H binding and the catalytic activity. Whereas modeling and simulation approaches have been used to study the catalytic mechanism of this light-driven reaction, key details of the LPOR structure remain unclear. We determined the crystal structures of LPOR from two cyanobacteria, Synechocystis sp. PCC 6803 and Thermosynechococcus elongatus Structural analysis defines the LPOR core fold, outlines the LPOR-NADPH interaction network, identifies the residues forming the substrate cavity and the proton-relay path, and reveals the role of the LPOR-specific loop. These findings provide a basis for understanding the structure-function relationships of the light-driven Pchlide reduction.
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17
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Structural basis for enzymatic photocatalysis in chlorophyll biosynthesis. Nature 2019; 574:722-725. [PMID: 31645759 DOI: 10.1038/s41586-019-1685-2] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Accepted: 09/25/2019] [Indexed: 12/26/2022]
Abstract
The enzyme protochlorophyllide oxidoreductase (POR) catalyses a light-dependent step in chlorophyll biosynthesis that is essential to photosynthesis and, ultimately, all life on Earth1-3. POR, which is one of three known light-dependent enzymes4,5, catalyses reduction of the photosensitizer and substrate protochlorophyllide to form the pigment chlorophyllide. Despite its biological importance, the structural basis for POR photocatalysis has remained unknown. Here we report crystal structures of cyanobacterial PORs from Thermosynechococcus elongatus and Synechocystis sp. in their free forms, and in complex with the nicotinamide coenzyme. Our structural models and simulations of the ternary protochlorophyllide-NADPH-POR complex identify multiple interactions in the POR active site that are important for protochlorophyllide binding, photosensitization and photochemical conversion to chlorophyllide. We demonstrate the importance of active-site architecture and protochlorophyllide structure in driving POR photochemistry in experiments using POR variants and protochlorophyllide analogues. These studies reveal how the POR active site facilitates light-driven reduction of protochlorophyllide by localized hydride transfer from NADPH and long-range proton transfer along structurally defined proton-transfer pathways.
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18
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Schneidewind J, Krause F, Bocola M, Stadler AM, Davari MD, Schwaneberg U, Jaeger KE, Krauss U. Consensus model of a cyanobacterial light-dependent protochlorophyllide oxidoreductase in its pigment-free apo-form and photoactive ternary complex. Commun Biol 2019; 2:351. [PMID: 31583285 PMCID: PMC6761149 DOI: 10.1038/s42003-019-0590-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 08/29/2019] [Indexed: 12/02/2022] Open
Abstract
Photosynthetic organisms employ two different enzymes for the reduction of the C17 = C18 double bond of protochlorophyllide (Pchlide), yielding the chlorophyll precursor chlorophyllide. First, a nitrogenase-like, light-independent (dark-operative) Pchlide oxidoreductase and secondly, a light-dependent Pchlide oxidoreductase (LPOR). For the latter enzyme, despite decades of research, no structural information is available. Here, we use protein structure modelling, molecular dynamics (MD) simulations combined with multi-wavelength analytical ultracentrifugation (MWA-AUC) and small angle X-ray scattering (SAXS) experiments to derive a consensus model of the LPOR apoprotein and the substrate/cofactor/LPOR ternary complex. MWA-AUC and SAXS experiments independently demonstrate that the apoprotein is monomeric, while ternary complex formation induces dimerization. SAXS-guided modelling studies provide a full-length model of the apoprotein and suggest a tentative mode of dimerization for the LPOR ternary complex, supported by published cross-link constraints. Our study provides a first impression of the LPOR structural organization.
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Affiliation(s)
- Judith Schneidewind
- Institut für Molekulare Enzymtechnologie, Heinrich-Heine-Universität Düsseldorf, Forschungszentrum Jülich GmbH, D-52425 Jülich, Germany
| | - Frank Krause
- Nanolytics, Gesellschaft für Kolloidanalytik GmbH, Am Mühlenberg 11, 14476 Potsdam, Germany
| | - Marco Bocola
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany
| | - Andreas Maximilian Stadler
- Jülich Centre for Neutron Science (JCNS-1) and Institute for Complex Systems (ICS-1), Forschungszentrum Jülich GmbH, D-52425 Jülich, Germany
- Institute of Physical Chemistry, RWTH Aachen University, Landoltweg 2, 52056 Aachen, Germany
| | - Mehdi D. Davari
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany
| | - Ulrich Schwaneberg
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany
- DWI-Leibniz Institut für Interaktive Materialien, Forckenbeckstraße 50, 52056 Aachen, Germany
| | - Karl-Erich Jaeger
- Institut für Molekulare Enzymtechnologie, Heinrich-Heine-Universität Düsseldorf, Forschungszentrum Jülich GmbH, D-52425 Jülich, Germany
- IBG-1: Biotechnologie, Forschungszentrum Jülich GmbH, D-52425 Jülich, Germany
| | - Ulrich Krauss
- Institut für Molekulare Enzymtechnologie, Heinrich-Heine-Universität Düsseldorf, Forschungszentrum Jülich GmbH, D-52425 Jülich, Germany
- IBG-1: Biotechnologie, Forschungszentrum Jülich GmbH, D-52425 Jülich, Germany
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19
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Stadler AM, Schneidewind J, Zamponi M, Knieps-Grünhagen E, Gholami S, Schwaneberg U, Rivalta I, Garavelli M, Davari MD, Jaeger KE, Krauss U. Ternary Complex Formation and Photoactivation of a Photoenzyme Results in Altered Protein Dynamics. J Phys Chem B 2019; 123:7372-7384. [PMID: 31380636 DOI: 10.1021/acs.jpcb.9b06608] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The interplay between protein dynamics and catalysis remains a fundamental question in enzymology. We here investigate the ns-timescale dynamics of a light-dependent NADPH:protochlorophyllide oxidoreductase (LPOR), a photoenzyme crucial for chlorophyll synthesis. LPORs catalyze the light-triggered trans addition of a hydride and a proton across the C17═C18 double bond of the chlorophyll precursor protochlorophyllide (Pchlide). Because of the lack of an LPOR structure, the global structural and dynamic consequences of LPOR/Pchlide/NADPH ternary complex formation remain elusive. Moreover, photoactivation of LPORs by low-light preillumination is controversially discussed as unequivocal proof for this phenomenon is lacking. By employing quasielastic neutron spectroscopy (QENS), we show that the formation of the ternary holoprotein complex as well as photoactivation lead to progressive rigidification of the protein. These findings are supported by thermostability measurements, which reveal different melting behavior and thermostabilities for the apo- and holoprotein ternary complexes. Molecular dynamics simulations in good agreement with the experimental QENS results suggest that the increased flexibility observed for the apoprotein stems from structural fluctuations of the NADPH and Pchlide substrate binding sites of the enzyme. On the basis of our results, in conjunction with activity and stability measurements, we provide independent proof for LPOR photoactivation, defined as a process that modifies the protein structure and dynamics, resulting in an increased substrate turnover. Our findings advance the structural and dynamic understanding of LPORs and provide a first link between protein dynamics and catalysis for this enzyme class.
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Affiliation(s)
| | | | - Michaela Zamponi
- Jülich Centre for Neutron Science (JCNS) at Heinz Maier-Leibnitz Zentrum (MLZ) , Forschungszentrum Jülich GmbH , Lichtenbergstr. 1 , 85748 Garching , Germany
| | | | - Samira Gholami
- Dipartimento di Chimica Industriale , Università degli Studi di Bologna , Viale del Risorgimento 4 , I-40136 Bologna , Italy
| | - Ulrich Schwaneberg
- Institute of Biotechnology , RWTH Aachen University , Worringer Weg 3 , D-52074 Aachen , Germany.,DWI-Leibniz Institute for Interactive Materials , Forckenbeckstraße 50 , 52056 Aachen , Germany
| | - Ivan Rivalta
- Université de Lyon, École Normale Supérieure de Lyon, CNRS, Université Claude Bernard Lyon 1, Laboratoire de Chimie UMR 5182 , F-69342 Lyon , France
| | - Marco Garavelli
- Dipartimento di Chimica Industriale , Università degli Studi di Bologna , Viale del Risorgimento 4 , I-40136 Bologna , Italy.,École Normale Supérieure de Lyon, CNRS, Laboratoire de Chimie UMR 5182, Université de Lyon , 46 Allée d'Italie , F-69364 Lyon Cedex 07 , France
| | - Mehdi D Davari
- Institute of Biotechnology , RWTH Aachen University , Worringer Weg 3 , D-52074 Aachen , Germany
| | - Karl-Erich Jaeger
- IBG-1: Biotechnologie , Forschungszentrum Jülich GmbH , D-52425 Jülich , Germany
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20
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Huijbers MME, Zhang W, Tonin F, Hollmann F. Lichtgetriebene enzymatische Decarboxylierung von Fettsäuren. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201807119] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Mieke M. E. Huijbers
- Department of Biotechnology; Delft University of Technology; Van der Maasweg 9 2629 HZ Delft Niederlande
| | - Wuyuan Zhang
- Department of Biotechnology; Delft University of Technology; Van der Maasweg 9 2629 HZ Delft Niederlande
| | - Fabio Tonin
- Department of Biotechnology; Delft University of Technology; Van der Maasweg 9 2629 HZ Delft Niederlande
| | - Frank Hollmann
- Department of Biotechnology; Delft University of Technology; Van der Maasweg 9 2629 HZ Delft Niederlande
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21
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Huijbers MME, Zhang W, Tonin F, Hollmann F. Light-Driven Enzymatic Decarboxylation of Fatty Acids. Angew Chem Int Ed Engl 2018; 57:13648-13651. [PMID: 30106504 PMCID: PMC6197046 DOI: 10.1002/anie.201807119] [Citation(s) in RCA: 86] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 08/13/2018] [Indexed: 11/10/2022]
Abstract
The photoenzymatic decarboxylation of fatty acids to alkanes is proposed as an alternative approach for the synthesis of biodiesel. By using a recently discovered photodecarboxylase from Chlorella variabilis NC64A (CvFAP) we demonstrate the irreversible preparation of alkanes from fatty acids and triglycerides. Several fatty acids and their triglycerides are converted by CvFAP in near‐quantitative yield and exclusive selectivity upon illumination with blue light. Very promising turnover numbers of up to 8000 were achieved in this proof‐of‐concept study.
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Affiliation(s)
- Mieke M E Huijbers
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629, HZ, Delft, The Netherlands
| | - Wuyuan Zhang
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629, HZ, Delft, The Netherlands
| | - Fabio Tonin
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629, HZ, Delft, The Netherlands
| | - Frank Hollmann
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629, HZ, Delft, The Netherlands
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22
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Archipowa N, Kutta RJ, Heyes DJ, Scrutton NS. Stepwise Hydride Transfer in a Biological System: Insights into the Reaction Mechanism of the Light-Dependent Protochlorophyllide Oxidoreductase. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201712729] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Nataliya Archipowa
- Manchester Institute of Biotechnology and School of Chemistry; The University of Manchester; 131 Princess Street Manchester M1 7DN UK
| | - Roger J. Kutta
- Manchester Institute of Biotechnology and School of Chemistry; The University of Manchester; 131 Princess Street Manchester M1 7DN UK
- Current address: Institut für Physikalische und Theoretische Chemie; Universität Regensburg; Universitätsstr. 31 93053 Regensburg Germany
| | - Derren J. Heyes
- Manchester Institute of Biotechnology and School of Chemistry; The University of Manchester; 131 Princess Street Manchester M1 7DN UK
| | - Nigel S. Scrutton
- Manchester Institute of Biotechnology and School of Chemistry; The University of Manchester; 131 Princess Street Manchester M1 7DN UK
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23
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Archipowa N, Kutta RJ, Heyes DJ, Scrutton NS. Stepwise Hydride Transfer in a Biological System: Insights into the Reaction Mechanism of the Light-Dependent Protochlorophyllide Oxidoreductase. Angew Chem Int Ed Engl 2018; 57:2682-2686. [PMID: 29363234 PMCID: PMC5861667 DOI: 10.1002/anie.201712729] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 01/22/2018] [Indexed: 11/24/2022]
Abstract
Hydride transfer plays a crucial role in a wide range of biological systems. However, its mode of action (concerted or stepwise) is still under debate. Light‐dependent NADPH: protochlorophyllide oxidoreductase (POR) catalyzes the stereospecific trans addition of a hydride anion and a proton across the C17−C18 double bond of protochlorophyllide. Time‐resolved absorption and emission spectroscopy were used to investigate the hydride transfer mechanism in POR. Apart from excited states of protochlorophyllide, three discrete intermediates were resolved, consistent with a stepwise mechanism that involves an initial electron transfer from NADPH. A subsequent proton‐coupled electron transfer followed by a proton transfer yield distinct different intermediates for wild type and the C226S variant, that is, initial hydride attaches to either C17 or C18, but ends in the same chlorophyllide stereoisomer. This work provides the first evidence of a stepwise hydride transfer in a biological system.
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Affiliation(s)
- Nataliya Archipowa
- Manchester Institute of Biotechnology and School of Chemistry, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Roger J Kutta
- Manchester Institute of Biotechnology and School of Chemistry, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.,Current address: Institut für Physikalische und Theoretische Chemie, Universität Regensburg, Universitätsstr. 31, 93053, Regensburg, Germany
| | - Derren J Heyes
- Manchester Institute of Biotechnology and School of Chemistry, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Nigel S Scrutton
- Manchester Institute of Biotechnology and School of Chemistry, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
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24
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Rajagopal V, Stokes C, Ferzoco A. A Linear Ion Trap with an Expanded Inscribed Diameter to Improve Optical Access for Fluorescence Spectroscopy. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2018; 29:260-269. [PMID: 28822082 DOI: 10.1007/s13361-017-1763-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Revised: 07/17/2017] [Accepted: 07/18/2017] [Indexed: 06/07/2023]
Abstract
We report a custom-geometry linear ion trap designed for fluorescence spectroscopy of gas-phase ions at ambient to cryogenic temperatures. Laser-induced fluorescence from trapped ions is collected from between the trapping rods, orthogonal to the excitation laser that runs along the axis of the linear ion trap. To increase optical access to the ion cloud, the diameter of the round trapping rods is 80% of the inscribed diameter, rather than the roughly 110% used to approximate purely quadrupolar electric fields. To encompass as much of the ion cloud as possible, the first collection optic has a 25.4 mm diameter and a numerical aperture of 0.6. The choice of geometry and collection optics yields 107 detected photons/s from trapped rhodamine 6G ions. The trap is coupled to a closed-cycle helium refrigerator, which in combination with two 50 Ohm heaters enables temperature control to below 25 K on the rod electrodes. The purpose of the instrument is to broaden the applicability of fluorescence spectroscopy of gas-phase ions to cases where photon emission is a minority relaxation pathway. Such studies are important to understand how the microenvironment of a chromophore influences excited state charge transfer processes. Graphical Abstract ᅟ.
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Affiliation(s)
| | - Chris Stokes
- The Rowland Institute at Harvard University, Cambridge, MA, 02142, USA
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25
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26
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Brandariz-de-Pedro G, Heyes DJ, Hardman SJO, Shanmugam M, Jones AR, Weber S, Nohr D, Scrutton NS, Fielding AJ. Direct Evidence of an Excited-State Triplet Species upon Photoactivation of the Chlorophyll Precursor Protochlorophyllide. J Phys Chem Lett 2017; 8:1219-1223. [PMID: 28244763 DOI: 10.1021/acs.jpclett.7b00200] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
The chlorophyll precursor protochlorophyllide (Pchlide), which is the substrate for the light-driven enzyme protochlorophyllide oxidoreductase, has unique excited-state properties that facilitate photocatalysis. Previous time-resolved spectroscopy measurements have implied that a long-lived triplet state is formed during the excited-state relaxation of Pchlide, although direct evidence of its existence is still lacking. Here we use time-resolved electron paramagnetic resonance (EPR) in combination with time-resolved absorption measurements at a range of temperatures (10-290 K), solvents, and oxygen concentrations to provide a detailed characterization of the triplet state of Pchlide. The triplet decays in a biphasic, oxygen-dependent manner, while the first reported EPR signature of a Pchlide triplet displays both emissive and absorptive features and an antisymmetric spectrum similar to other porphyrin triplet states. This work demonstrates that the Pchlide triplet is accessible to various cryogenic spectroscopic probes over a range of time scales and paves the way for understanding its potential role in catalysis.
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Affiliation(s)
- Guillem Brandariz-de-Pedro
- School of Chemistry and the Photon Science Institute, University of Manchester , Oxford Road, Manchester M13 9PL, United Kingdom
- Manchester Institute of Biotechnology, University of Manchester , 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Derren J Heyes
- Manchester Institute of Biotechnology, University of Manchester , 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Samantha J O Hardman
- Manchester Institute of Biotechnology, University of Manchester , 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Muralidharan Shanmugam
- Manchester Institute of Biotechnology, University of Manchester , 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Alex R Jones
- School of Chemistry and the Photon Science Institute, University of Manchester , Oxford Road, Manchester M13 9PL, United Kingdom
- Manchester Institute of Biotechnology, University of Manchester , 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Stefan Weber
- Institute of Physical Chemistry, Albert-Ludwigs-Universität Freiburg , 79104 Freiburg, Germany
| | - Daniel Nohr
- Institute of Physical Chemistry, Albert-Ludwigs-Universität Freiburg , 79104 Freiburg, Germany
| | - Nigel S Scrutton
- Manchester Institute of Biotechnology, University of Manchester , 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Alistair J Fielding
- School of Chemistry and the Photon Science Institute, University of Manchester , Oxford Road, Manchester M13 9PL, United Kingdom
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27
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Heyes DJ, Hardman SJO, Mansell D, Ní Cheallaigh A, Gardiner JM, Johannissen LO, Greetham GM, Towrie M, Scrutton NS. Excited-State Properties of Protochlorophyllide Analogues and Implications for Light-Driven Synthesis of Chlorophyll. J Phys Chem B 2017; 121:1312-1320. [PMID: 28117585 DOI: 10.1021/acs.jpcb.7b00528] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Protochlorophyllide (Pchlide), an intermediate in the biosynthesis of chlorophyll, is the substrate for the light-driven enzyme protochlorophyllide oxidoreductase. Pchlide has excited-state properties that allow it to initiate photochemistry in the enzyme active site, which involves reduction of Pchlide by sequential hydride and proton transfer. The basis of this photochemical behavior has been investigated here using a combination of time-resolved spectroscopies and density functional theory calculations of a number of Pchlide analogues with modifications to various substituent groups. A keto group on ring E is essential for excited-state charge separation in the molecule, which is the driving force for the photoreactivity of the pigment. Vibrational "fingerprints" of specific regions of the Pchlide chromophore have been assigned, allowing identification of the modes that are crucial for excited-state chemistry in the enzyme. This work provides an understanding of the structural determinants of Pchlide that are important for harnessing light energy.
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Affiliation(s)
- Derren J Heyes
- Manchester Institute of Biotechnology and School of Chemistry, The University of Manchester , 131 Princess Street, Manchester M1 7DN, U.K
| | - Samantha J O Hardman
- Manchester Institute of Biotechnology and School of Chemistry, The University of Manchester , 131 Princess Street, Manchester M1 7DN, U.K
| | - David Mansell
- Manchester Institute of Biotechnology and School of Chemistry, The University of Manchester , 131 Princess Street, Manchester M1 7DN, U.K
| | - Aisling Ní Cheallaigh
- Manchester Institute of Biotechnology and School of Chemistry, The University of Manchester , 131 Princess Street, Manchester M1 7DN, U.K
| | - John M Gardiner
- Manchester Institute of Biotechnology and School of Chemistry, The University of Manchester , 131 Princess Street, Manchester M1 7DN, U.K
| | - Linus O Johannissen
- Manchester Institute of Biotechnology and School of Chemistry, The University of Manchester , 131 Princess Street, Manchester M1 7DN, U.K
| | - Gregory M Greetham
- Central Laser Facility, Research Complex at Harwell, Science and Technology Facilities Council , Harwell Oxford, Didcot OX11 0QX, U.K
| | - Michael Towrie
- Central Laser Facility, Research Complex at Harwell, Science and Technology Facilities Council , Harwell Oxford, Didcot OX11 0QX, U.K
| | - Nigel S Scrutton
- Manchester Institute of Biotechnology and School of Chemistry, The University of Manchester , 131 Princess Street, Manchester M1 7DN, U.K
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28
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Menon BRK, Hardman SJO, Scrutton NS, Heyes DJ. Multiple active site residues are important for photochemical efficiency in the light-activated enzyme protochlorophyllide oxidoreductase (POR). JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2016; 161:236-43. [PMID: 27285815 PMCID: PMC4970445 DOI: 10.1016/j.jphotobiol.2016.05.029] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Figures] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Revised: 05/17/2016] [Accepted: 05/30/2016] [Indexed: 11/22/2022]
Abstract
Protochlorophyllide oxidoreductase (POR) catalyzes the light-driven reduction of protochlorophyllide (Pchlide), an essential, regulatory step in chlorophyll biosynthesis. The unique requirement of the enzyme for light has provided the opportunity to investigate how light energy can be harnessed to power biological catalysis and enzyme dynamics. Excited state interactions between the Pchlide molecule and the protein are known to drive the subsequent reaction chemistry. However, the structural features of POR and active site residues that are important for photochemistry and catalysis are currently unknown, because there is no crystal structure for POR. Here, we have used static and time-resolved spectroscopic measurements of a number of active site variants to study the role of a number of residues, which are located in the proposed NADPH/Pchlide binding site based on previous homology models, in the reaction mechanism of POR. Our findings, which are interpreted in the context of a new improved structural model, have identified several residues that are predicted to interact with the coenzyme or substrate. Several of the POR variants have a profound effect on the photochemistry, suggesting that multiple residues are important in stabilizing the excited state required for catalysis. Our work offers insight into how the POR active site geometry is finely tuned by multiple active site residues to support enzyme-mediated photochemistry and reduction of Pchlide, both of which are crucial to the existence of life on Earth. Identified several active site residues that can interact with coenzyme/substrate Multiple residues are important in excited state POR–protochlorophyllide interactions. New structural model for T. elongatus POR to rationalize mutagenesis outcomes POR active site geometry is finely-tuned to support photochemistry.
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Affiliation(s)
- Binuraj R K Menon
- Centre for Synthetic Biology of Fine and Speciality Chemicals, Manchester Institute of Biotechnology, School of Chemistry, The University of Manchester, Manchester, M1 7DN, UK
| | - Samantha J O Hardman
- Centre for Synthetic Biology of Fine and Speciality Chemicals, Manchester Institute of Biotechnology, School of Chemistry, The University of Manchester, Manchester, M1 7DN, UK
| | - Nigel S Scrutton
- Centre for Synthetic Biology of Fine and Speciality Chemicals, Manchester Institute of Biotechnology, School of Chemistry, The University of Manchester, Manchester, M1 7DN, UK.
| | - Derren J Heyes
- Centre for Synthetic Biology of Fine and Speciality Chemicals, Manchester Institute of Biotechnology, School of Chemistry, The University of Manchester, Manchester, M1 7DN, UK.
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29
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Greetham GM, Donaldson PM, Nation C, Sazanovich IV, Clark IP, Shaw DJ, Parker AW, Towrie M. A 100 kHz Time-Resolved Multiple-Probe Femtosecond to Second Infrared Absorption Spectrometer. APPLIED SPECTROSCOPY 2016; 70:645-653. [PMID: 26887988 DOI: 10.1177/0003702816631302] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Accepted: 08/05/2015] [Indexed: 06/05/2023]
Abstract
We present a dual-amplifier laser system for time-resolved multiple-probe infrared (IR) spectroscopy based on the ytterbium potassium gadolinium tungstate (Yb:KGW) laser medium. Comparisons are made between the ytterbium-based technology and titanium sapphire laser systems for time-resolved IR spectroscopy measurements. The 100 kHz probing system provides new capability in time-resolved multiple-probe experiments, as more information is obtained from samples in a single experiment through multiple-probing. This method uses the high repetition-rate probe pulses to repeatedly measure spectra at 10 µs intervals following excitation allowing extended timescales to be measured routinely along with ultrafast data. Results are presented showing the measurement of molecular dynamics over >10 orders of magnitude in timescale, out to 20 ms, with an experimental time response of <200 fs. The power of multiple-probing is explored through principal component analysis of repeating probe measurements as a novel method for removing noise and measurement artifacts.
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Affiliation(s)
- Gregory M Greetham
- Central Laser Facility, Science and Technology Facilities Council, Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, UK
| | - Paul M Donaldson
- Central Laser Facility, Science and Technology Facilities Council, Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, UK
| | - Charlie Nation
- Central Laser Facility, Science and Technology Facilities Council, Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, UK
| | - Igor V Sazanovich
- Central Laser Facility, Science and Technology Facilities Council, Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, UK
| | - Ian P Clark
- Central Laser Facility, Science and Technology Facilities Council, Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, UK
| | - Daniel J Shaw
- Central Laser Facility, Science and Technology Facilities Council, Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, UK Department of Physics, University of Strathclyde, SUPA, Glasgow, UK
| | - Anthony W Parker
- Central Laser Facility, Science and Technology Facilities Council, Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, UK
| | - Michael Towrie
- Central Laser Facility, Science and Technology Facilities Council, Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, UK
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30
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Hoeven R, Hardman SJO, Heyes DJ, Scrutton NS. Cross-Species Analysis of Protein Dynamics Associated with Hydride and Proton Transfer in the Catalytic Cycle of the Light-Driven Enzyme Protochlorophyllide Oxidoreductase. Biochemistry 2016; 55:903-13. [DOI: 10.1021/acs.biochem.5b01355] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Robin Hoeven
- Centre for Synthetic Biology
of Fine and Speciality Chemicals, Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
| | - Samantha J. O. Hardman
- Centre for Synthetic Biology
of Fine and Speciality Chemicals, Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
| | - Derren J. Heyes
- Centre for Synthetic Biology
of Fine and Speciality Chemicals, Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
| | - Nigel S. Scrutton
- Centre for Synthetic Biology
of Fine and Speciality Chemicals, Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
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31
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Gabruk M, Mysliwa-Kurdziel B. Light-Dependent Protochlorophyllide Oxidoreductase: Phylogeny, Regulation, and Catalytic Properties. Biochemistry 2015; 54:5255-62. [PMID: 26230427 DOI: 10.1021/acs.biochem.5b00704] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
This Current Topic focuses on light-dependent protochlorophyllide oxidoreductase (POR, EC 1.3.1.33). POR catalyzes the penultimate reaction of chlorophyll biosynthesis, i.e., the light-triggered reduction of protochlorophyllide to chlorophyllide. In this reaction, the chlorin ring of the chlorophyll molecule is formed, which is crucial for photosynthesis. POR is one of very few enzymes that are driven by light; however, it is unique in the need for its substrate to absorb photons to induce the conformational changes in the enzyme, which are required for its catalytic activation. Moreover, the enzyme is also involved in the negative feedback of the chlorophyll biosynthesis pathway and controls chlorophyll content via its light-dependent activity. Even though it has been almost 70 years since the first isolation of active POR complexes, our knowledge of them has markedly advanced in recent years. In this review, we summarize the current state of knowledge of POR, including the phylogenetic roots of POR, the mechanisms of the regulation of POR genes expression, the regulation of POR activity, the import of POR into plastids, the role of POR in PLB formation, and the molecular mechanism of protochlorophyllide reduction by POR. To the best of our knowledge, no previous review has compiled such a broad set of recent findings about POR.
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Affiliation(s)
- Michal Gabruk
- Department of Plant Physiology and Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University , Gronostajowa 7, 30-387 Krakow, Poland
| | - Beata Mysliwa-Kurdziel
- Department of Plant Physiology and Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University , Gronostajowa 7, 30-387 Krakow, Poland
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