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Nicoll CR, Alvigini L, Gottinger A, Cecchini D, Mannucci B, Corana F, Mascotti ML, Mattevi A. In vitro construction of the COQ metabolon unveils the molecular determinants of coenzyme Q biosynthesis. Nat Catal 2024; 7:148-160. [PMID: 38425362 PMCID: PMC7615680 DOI: 10.1038/s41929-023-01087-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 11/20/2023] [Indexed: 03/02/2024]
Abstract
Metabolons are protein assemblies that perform a series of reactions in a metabolic pathway. However, the general importance and aptitude of metabolons for enzyme catalysis remain poorly understood. In animals, biosynthesis of coenzyme Q is currently attributed to ten different proteins, with COQ3, COQ4, COQ5, COQ6, COQ7 and COQ9 forming the iconic COQ metabolon. Yet several reaction steps conducted by the metabolon remain enigmatic. To elucidate the prerequisites for animal coenzyme Q biosynthesis, we sought to construct the entire metabolon in vitro. Here we show that this approach, rooted in ancestral sequence reconstruction, reveals the enzymes responsible for the uncharacterized steps and captures the biosynthetic pathway in vitro. We demonstrate that COQ8, a kinase, increases and streamlines coenzyme Q production. Our findings provide crucial insight into how biocatalytic efficiency is regulated and enhanced by these biosynthetic engines in the context of the cell.
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Affiliation(s)
- Callum R. Nicoll
- Department of Biology and Biotechnology ‘Lazzaro Spallanzani’, University of Pavia, Pavia, Italy
| | - Laura Alvigini
- Department of Biology and Biotechnology ‘Lazzaro Spallanzani’, University of Pavia, Pavia, Italy
| | - Andrea Gottinger
- Department of Biology and Biotechnology ‘Lazzaro Spallanzani’, University of Pavia, Pavia, Italy
| | - Domiziana Cecchini
- Department of Biology and Biotechnology ‘Lazzaro Spallanzani’, University of Pavia, Pavia, Italy
| | | | - Federica Corana
- ’Centro Grandi Strumenti’, University of Pavia, Pavia, Italy
| | - María Laura Mascotti
- Molecular Enzymology Group, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
- IMIBIO-SL CONICET, Facultad de Química Bioquímica y Farmacia, Universidad Nacional de San Luis, San Luis, Argentina
| | - Andrea Mattevi
- Department of Biology and Biotechnology ‘Lazzaro Spallanzani’, University of Pavia, Pavia, Italy
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Mascotti ML, Juri Ayub M, Fraaije MW. On the diversity of F 420 -dependent oxidoreductases: A sequence- and structure-based classification. Proteins 2021; 89:1497-1507. [PMID: 34216160 PMCID: PMC8518648 DOI: 10.1002/prot.26170] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 03/30/2021] [Accepted: 06/26/2021] [Indexed: 11/05/2022]
Abstract
The F420 deazaflavin cofactor is an intriguing molecule as it structurally resembles the canonical flavin cofactor, although behaves as a nicotinamide cofactor due to its obligate hydride-transfer reactivity and similar low redox potential. Since its discovery, numerous enzymes relying on it have been described. The known deazaflavoproteins are taxonomically restricted to Archaea and Bacteria. The biochemistry of the deazaflavoenzymes is diverse and they exhibit great structural variability. In this study a thorough sequence and structural homology evolutionary analysis was performed in order to generate an overarching classification of the F420 -dependent oxidoreductases. Five different deazaflavoenzyme Classes (I-V) are described according to their structural folds as follows: Class I encompassing the TIM-barrel F420 -dependent enzymes; Class II including the Rossmann fold F420 -dependent enzymes; Class III comprising the β-roll F420 -dependent enzymes; Class IV which exclusively gathers the SH3 barrel F420 -dependent enzymes and Class V including the three layer ββα sandwich F420 -dependent enzymes. This classification provides a framework for the identification and biochemical characterization of novel deazaflavoenzymes.
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Affiliation(s)
- María Laura Mascotti
- Molecular Enzymology Group, University of Groningen, Groningen, The Netherlands.,IMIBIO-SL CONICET, Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis, San Luis, Argentina
| | - Maximiliano Juri Ayub
- IMIBIO-SL CONICET, Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis, San Luis, Argentina
| | - Marco W Fraaije
- Molecular Enzymology Group, University of Groningen, Groningen, The Netherlands
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Bailleul G, Nicoll CR, Mascotti ML, Mattevi A, Fraaije MW. Ancestral reconstruction of mammalian FMO1 enables structural determination, revealing unique features that explain its catalytic properties. J Biol Chem 2020; 296:100221. [PMID: 33759784 PMCID: PMC7948450 DOI: 10.1074/jbc.ra120.016297] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 12/17/2020] [Accepted: 12/21/2020] [Indexed: 11/09/2022] Open
Abstract
Mammals rely on the oxidative flavin-containing monooxygenases (FMOs) to detoxify numerous and potentially deleterious xenobiotics; this activity extends to many drugs, giving FMOs high pharmacological relevance. However, our knowledge regarding these membrane-bound enzymes has been greatly impeded by the lack of structural information. We anticipated that ancestral-sequence reconstruction could help us identify protein sequences that are more amenable to structural analysis. As such, we hereby reconstructed the mammalian ancestral protein sequences of both FMO1 and FMO4, denoted as ancestral flavin-containing monooxygenase (AncFMO)1 and AncFMO4, respectively. AncFMO1, sharing 89.5% sequence identity with human FMO1, was successfully expressed as a functional enzyme. It displayed typical FMO activities as demonstrated by oxygenating benzydamine, tamoxifen, and thioanisole, drug-related compounds known to be also accepted by human FMO1, and both NADH and NADPH cofactors could act as electron donors, a feature only described for the FMO1 paralogs. AncFMO1 crystallized as a dimer and was structurally resolved at 3.0 Å resolution. The structure harbors typical FMO aspects with the flavin adenine dinucleotide and NAD(P)H binding domains and a C-terminal transmembrane helix. Intriguingly, AncFMO1 also contains some unique features, including a significantly porous and exposed active site, and NADPH adopting a new conformation with the 2’-phosphate being pushed inside the NADP+ binding domain instead of being stretched out in the solvent. Overall, the ancestrally reconstructed mammalian AncFMO1 serves as the first structural model to corroborate and rationalize the catalytic properties of FMO1.
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Affiliation(s)
- Gautier Bailleul
- Molecular Enzymology Group, University of Groningen, Groningen, the Netherlands
| | - Callum R Nicoll
- Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, Pavia, Italy
| | - María Laura Mascotti
- Molecular Enzymology Group, University of Groningen, Groningen, the Netherlands; IMIBIO-SL CONICET, Facultad de Química Bioquímica y Farmacia, Universidad Nacional de San Luis, San Luis, Argentina
| | - Andrea Mattevi
- Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, Pavia, Italy.
| | - Marco W Fraaije
- Molecular Enzymology Group, University of Groningen, Groningen, the Netherlands.
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Magallanes-Noguera C, Cecati FM, Mascotti ML, Reta GF, Agostini E, Orden AA, Kurina-Sanz M. Plant tissue cultures as sources of new ene- and ketoreductase activities. J Biotechnol 2017; 251:14-20. [PMID: 28359867 DOI: 10.1016/j.jbiotec.2017.03.023] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Revised: 02/22/2017] [Accepted: 03/22/2017] [Indexed: 11/16/2022]
Abstract
While many redox enzymes are nowadays available for synthetic applications, the toolbox of ene-reductases is still limited. Consequently, the screening for these enzymes from diverse sources in the search of new biocatalyst suitable for green chemistry approaches is needed. Among 13 plant tissue cultures, Medicago sativa and Tessaria absinthioides calli, as well as Capsicum annuum hairy roots, were selected due to their ability to hydrogenate the CC double bond of the model substrate 2-cyclohexene-1-one. The three axenic plant cultures showed more preference toward highly activated molecules such as nitrostyrene and maleimide rather than the classical substrates of the well-known Old Yellow Enzymes, resembling the skills of the NAD(P)H-dependent flavin-independent enzymes. When the three biocatalytic systems were applied in the reduction of chalcones, T. absinthioides showed high chemoselectivity toward the CC double bond whereas the other two demonstrated abilities to biohydrogenate the CC double bounds and the carbonyl groups in a sequential fashion.
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Affiliation(s)
- Cynthia Magallanes-Noguera
- INTEQUI-CONICET, Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis, Chacabuco y Pedernera, CP 5700 San Luis, Argentina
| | - Francisco M Cecati
- INTEQUI-CONICET, Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis, Chacabuco y Pedernera, CP 5700 San Luis, Argentina
| | - María Laura Mascotti
- IMIBIO-CONICET, Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis, Chacabuco y Pedernera, Argentina
| | - Guillermo F Reta
- INTEQUI-CONICET, Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis, Chacabuco y Pedernera, CP 5700 San Luis, Argentina
| | - Elizabeth Agostini
- Departamento de Biología Molecular, FCEFQN, Universidad Nacional de Río Cuarto, Ruta 36 Km 601, CP 5800 Río Cuarto, Córdoba, Argentina
| | - Alejandro A Orden
- INTEQUI-CONICET, Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis, Chacabuco y Pedernera, CP 5700 San Luis, Argentina.
| | - Marcela Kurina-Sanz
- INTEQUI-CONICET, Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis, Chacabuco y Pedernera, CP 5700 San Luis, Argentina.
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Mascotti ML, Kurina-Sanz M, Juri Ayub M, Fraaije MW. Insights in the kinetic mechanism of the eukaryotic Baeyer-Villiger monooxygenase BVMOAf1 from Aspergillus fumigatus Af293. Biochimie 2014; 107 Pt B:270-6. [PMID: 25230086 DOI: 10.1016/j.biochi.2014.09.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Accepted: 09/05/2014] [Indexed: 12/23/2022]
Abstract
This work reports a detailed kinetic study of the recently discovered BVMOAf1 from Aspergillus fumigatus Af293. By performing steady state and pre-steady state kinetic analyses, it was demonstrated that the rate of catalysis is partially limited by the NADPH-mediated reduction of the flavin cofactor, a unique hallmark of BVMOAf1. In addition, the oxygenating C4a-(hydro)peroxyflavin intermediate could be spectrophotometrically detected and it was found to be the most stable among all analyzed BVMOs. To assess the possible influence of some residues on the kinetic features, model-inspired site-directed mutagenesis was performed. Among the mutants, the Q436A variant showed a slightly broader substrate scope and a better catalytic efficiency. In summary, this study describes for the first time the kinetic parameters for an eukaryotic BVMO.
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Affiliation(s)
- María Laura Mascotti
- INTEQUI-CONICET, Facultad de Química Bioquímica y Farmacia, Universidad Nacional de San Luis, CP 5700 San Luis, Argentina.
| | - Marcela Kurina-Sanz
- INTEQUI-CONICET, Facultad de Química Bioquímica y Farmacia, Universidad Nacional de San Luis, CP 5700 San Luis, Argentina
| | - Maximiliano Juri Ayub
- IMIBIO-SL CONICET, Facultad de Química Bioquímica y Farmacia, Universidad Nacional de San Luis, CP 5700 San Luis, Argentina
| | - Marco W Fraaije
- Molecular Enzymology Group, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
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Mascotti ML, Orden AA, Bisogno FR, de Gonzalo G, Kurina-Sanz M. Aspergillus genus as a source of new catalysts for sulfide oxidation. ACTA ACUST UNITED AC 2012. [DOI: 10.1016/j.molcatb.2012.05.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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