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Soualmia F, Cherrier MV, Chauviré T, Mauger M, Tatham P, Guillot A, Guinchard X, Martin L, Amara P, Mouesca JM, Daghmoum M, Benjdia A, Gambarelli S, Berteau O, Nicolet Y. Radical S-Adenosyl-l-Methionine Enzyme PylB: A C-Centered Radical to Convert l-Lysine into (3 R)-3-Methyl-d-Ornithine. J Am Chem Soc 2024; 146:6493-6505. [PMID: 38426440 DOI: 10.1021/jacs.3c03747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2024]
Abstract
PylB is a radical S-adenosyl-l-methionine (SAM) enzyme predicted to convert l-lysine into (3R)-3-methyl-d-ornithine, a precursor in the biosynthesis of the 22nd proteogenic amino acid pyrrolysine. This protein highly resembles that of the radical SAM tyrosine and tryptophan lyases, which activate their substrate by abstracting a H atom from the amino-nitrogen position. Here, combining in vitro assays, analytical methods, electron paramagnetic resonance spectroscopy, and theoretical methods, we demonstrated that instead, PylB activates its substrate by abstracting a H atom from the Cγ position of l-lysine to afford the radical-based β-scission. Strikingly, we also showed that PylB catalyzes the reverse reaction, converting (3R)-3-methyl-d-ornithine into l-lysine and using catalytic amounts of the 5'-deoxyadenosyl radical. Finally, we identified significant in vitro production of 5'-thioadenosine, an unexpected shunt product that we propose to result from the quenching of the 5'-deoxyadenosyl radical species by the nearby [Fe4S4] cluster.
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Affiliation(s)
- Feryel Soualmia
- Université Paris-Saclay, Micalis Institute, ChemSyBio, Université Paris-Saclay, INRAE, AgroParisTech, 78350 Jouy-en-Josas, France
| | - Mickael V Cherrier
- Univ. Grenoble Alpes, CEA, CNRS, IBS, Metalloproteins Unit, F-38000 Grenoble, France
| | - Timothée Chauviré
- Univ. Grenoble Alpes, CEA, CNRS, IRIG-DIESE-SyMMES-CAMPE, F-38000 Grenoble, France
| | - Mickaël Mauger
- Université Paris-Saclay, Micalis Institute, ChemSyBio, Université Paris-Saclay, INRAE, AgroParisTech, 78350 Jouy-en-Josas, France
| | - Philip Tatham
- Université Paris-Saclay, Micalis Institute, ChemSyBio, Université Paris-Saclay, INRAE, AgroParisTech, 78350 Jouy-en-Josas, France
| | - Alain Guillot
- Université Paris-Saclay, Micalis Institute, ChemSyBio, Université Paris-Saclay, INRAE, AgroParisTech, 78350 Jouy-en-Josas, France
| | - Xavier Guinchard
- Université Paris-Saclay, CNRS, Institut de Chimie des Substances Naturelles, UPR 2301, 91198 Gif-sur-Yvette, France
| | - Lydie Martin
- Univ. Grenoble Alpes, CEA, CNRS, IBS, Metalloproteins Unit, F-38000 Grenoble, France
| | - Patricia Amara
- Univ. Grenoble Alpes, CEA, CNRS, IBS, Metalloproteins Unit, F-38000 Grenoble, France
| | - Jean-Marie Mouesca
- Univ. Grenoble Alpes, CEA, CNRS, IRIG-DIESE-SyMMES-CAMPE, F-38000 Grenoble, France
| | - Meriem Daghmoum
- Université Paris-Saclay, CNRS, Institut de Chimie des Substances Naturelles, UPR 2301, 91198 Gif-sur-Yvette, France
| | - Alhosna Benjdia
- Université Paris-Saclay, Micalis Institute, ChemSyBio, Université Paris-Saclay, INRAE, AgroParisTech, 78350 Jouy-en-Josas, France
| | - Serge Gambarelli
- Univ. Grenoble Alpes, CEA, CNRS, IRIG-DIESE-SyMMES-CAMPE, F-38000 Grenoble, France
| | - Olivier Berteau
- Université Paris-Saclay, Micalis Institute, ChemSyBio, Université Paris-Saclay, INRAE, AgroParisTech, 78350 Jouy-en-Josas, France
| | - Yvain Nicolet
- Univ. Grenoble Alpes, CEA, CNRS, IBS, Metalloproteins Unit, F-38000 Grenoble, France
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Omeiri J, Martin L, Usclat A, Cherrier MV, Nicolet Y. Maturation of the [FeFe]-Hydrogenase: Direct Transfer of the (κ 3 -cysteinate)Fe II (CN)(CO) 2 Complex B from HydG to HydE. Angew Chem Int Ed Engl 2023; 62:e202314819. [PMID: 37962296 DOI: 10.1002/anie.202314819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Revised: 11/13/2023] [Accepted: 11/14/2023] [Indexed: 11/15/2023]
Abstract
[FeFe]-hydrogenases efficiently catalyze the reversible oxidation of molecular hydrogen. Their prowess stems from the intricate H-cluster, combining a [Fe4 S4 ] center with a binuclear iron center ([2Fe]H ). In the latter, each iron atom is coordinated by a CO and CN ligand, connected by a CO and an azadithiolate ligand. The synthesis of this active site involves a unique multiprotein assembly, featuring radical SAM proteins HydG and HydE. HydG initiates the transformation of L-tyrosine into cyanide and carbon monoxide to generate complex B, which is subsequently transferred to HydE to continue the biosynthesis of the [2Fe]H -subcluster. Due to its instability, complex B isolation for structural or spectroscopic characterization has been elusive thus far. Nevertheless, the use of a biomimetic analogue of complex B allowed circumvention of the need for the HydG protein during in vitro functional investigations, implying a similar structure for complex B. Herein, we used the HydE protein as a nanocage to encapsulate and stabilize the complex B product generated by HydG. Using X-ray crystallography, we successfully determined its structure at 1.3 Å resolution. Furthermore, we demonstrated that complex B is directly transferred from HydG to HydE, thus not being released into the solution post-synthesis, highlighting a transient interaction between the two proteins.
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Affiliation(s)
- Juneina Omeiri
- Univ. Grenoble-Alpes, CEA, CNRS, IBS, Metalloproteins Unit, 38000, Grenoble, France
| | - Lydie Martin
- Univ. Grenoble-Alpes, CEA, CNRS, IBS, Metalloproteins Unit, 38000, Grenoble, France
| | - Anthony Usclat
- Univ. Grenoble-Alpes, CEA, CNRS, IBS, Metalloproteins Unit, 38000, Grenoble, France
| | - Mickael V Cherrier
- Univ. Grenoble-Alpes, CEA, CNRS, IBS, Metalloproteins Unit, 38000, Grenoble, France
| | - Yvain Nicolet
- Univ. Grenoble-Alpes, CEA, CNRS, IBS, Metalloproteins Unit, 38000, Grenoble, France
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3
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Abstract
This Review focuses on the structure-function relationship of radical S-adenosyl-l-methionine (SAM) enzymes involved in the assembly of metallocofactors corresponding to the active sites of [FeFe]-hydrogenase and nitrogenase [MoFe]-protein. It does not claim to correspond to an extensive review on the assembly machineries of these enzyme active sites, for which many good reviews are already available, but instead deals with the contribution of structural data to the understanding of their chemical mechanism (Buren et al. Chem. Rev.2020, 142 ( (25), ) 11006-11012; Britt et al. Chem. Sci.2020, 11 ( (38), ), 10313-10323). Hence, we will present the history and current knowledge about the radical SAM maturases HydE, HydG, and NifB as well as what, in our opinion, should be done in the near future to overcome the existing barriers in our understanding of this fascinating chemistry that intertwine organic radicals and organometallic complexes.
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Affiliation(s)
- Yvain Nicolet
- Univ. Grenoble Alpes, CEA, CNRS, IBS, Metalloproteins Unit, F-38000 Grenoble, France
| | - Mickael V. Cherrier
- Univ. Grenoble Alpes, CEA, CNRS, IBS, Metalloproteins Unit, F-38000 Grenoble, France
| | - Patricia Amara
- Univ. Grenoble Alpes, CEA, CNRS, IBS, Metalloproteins Unit, F-38000 Grenoble, France
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4
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Abstract
The nitrogenase MoFe protein contains two different FeS centers, the P-cluster and the iron–molybdenum cofactor (FeMo-co). The former is a [Fe8S7] center responsible for conveying electrons to the latter, a [MoFe7S9C-(R)-homocitrate] species, where N2 reduction takes place. NifB is arguably the key enzyme in FeMo-co assembly as it catalyzes the fusion of two [Fe4S4] clusters and the insertion of carbide and sulfide ions to build NifB-co, a [Fe8S9C] precursor to FeMo-co. Recently, two crystal structures of NifB proteins were reported, one containing two out of three [Fe4S4] clusters coordinated by the protein which is likely to correspond to an early stage of the reaction mechanism. The other one was fully complemented with the three [Fe4S4] clusters (RS, K1 and K2), but was obtained at lower resolution and a satisfactory model was not obtained. Here we report improved processing of this crystallographic data. At odds with what was previously reported, this structure contains a unique [Fe8S8] cluster, likely to be a NifB-co precursor resulting from the fusion of K1- and K2-clusters. Strikingly, this new [Fe8S8] cluster has both a structure and coordination sphere geometry reminiscent of the fully reduced P-cluster (PN-state) with an additional μ2-bridging sulfide ion pointing toward the RS cluster. Comparison of available NifB structures further unveils the plasticity of this protein and suggests how ligand reorganization would accommodate cluster loading and fusion in the time-course of NifB-co synthesis. The K-cluster of NifB as a key intermediate in the synthesis of the nitrogenase active site supports [Fe4S4] cluster fusion occurs before carbide and sulfide insertion and displays ligand spatial arrangement reminiscent to that of the P-cluster.![]()
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Affiliation(s)
- Leon P Jenner
- Univ. Grenoble Alpes, CEA, CNRS, IBS, Metalloproteins Unit F-38000 Grenoble France
| | - Mickael V Cherrier
- Univ. Grenoble Alpes, CEA, CNRS, IBS, Metalloproteins Unit F-38000 Grenoble France
| | - Patricia Amara
- Univ. Grenoble Alpes, CEA, CNRS, IBS, Metalloproteins Unit F-38000 Grenoble France
| | - Luis M Rubio
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria Pozuelo de Alarcón 28223 Madrid Spain
| | - Yvain Nicolet
- Univ. Grenoble Alpes, CEA, CNRS, IBS, Metalloproteins Unit F-38000 Grenoble France
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5
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Arhab Y, Rahier R, Noiriel A, Cherrier MV, Abousalham A. Expression and Purification of Recombinant Vigna unguiculata Phospholipase D in Pichia pastoris for Structural Studies. Methods Mol Biol 2018; 1835:191-201. [PMID: 30109653 DOI: 10.1007/978-1-4939-8672-9_10] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The production of pure enzymes in high quantities is a proven strategy to study the catalytic mechanism as well as the solving of structure at the atomic scale for therapeutic or industrial purposes. Phospholipase D (PLD, EC 3.1.4.4) is found in a wide majority of living organisms and has been shown to be involved in signal transduction, vesicle trafficking, and membrane metabolism processes. Located at the membrane-cytoplasm interface, plant PLDs are soluble but also bear an evident hydrophobic aspect making challenging its expression and its purification in large quantity. So far there is no high-resolution three-dimensional structure for a eukaryotic PLD. The protocols herein describe the cloning of the eukaryotic recombinant PLDα of Vigna unguiculata (cowpea) into the yeast expression system Pichia pastoris and its two-step purification process. This allowed us to purify to homogeneity hundreds of micrograms of highly pure protein to conduct in fine structural studies.
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Affiliation(s)
- Yani Arhab
- Univ Lyon, Université Lyon 1, Institut de Chimie et de Biochimie Moléculaires et Supramoléculaires, UMR 5246 CNRS, Métabolisme, Enzymes et Mécanismes Moléculaires (MEM²), Villeurbanne Cedex, 69622, France
| | - Renaud Rahier
- Univ Lyon, Université Lyon 1, Institut de Chimie et de Biochimie Moléculaires et Supramoléculaires, UMR 5246 CNRS, Métabolisme, Enzymes et Mécanismes Moléculaires (MEM²), Villeurbanne Cedex, 69622, France
| | - Alexandre Noiriel
- Univ Lyon, Université Lyon 1, Institut de Chimie et de Biochimie Moléculaires et Supramoléculaires, UMR 5246 CNRS, Métabolisme, Enzymes et Mécanismes Moléculaires (MEM²), Villeurbanne Cedex, 69622, France
| | - Mickael V Cherrier
- UMR 5086 Molecular Microbiology and Structural Biochemistry, Université de Lyon-CNRS, Institut de Biologie et Chimie des Protéines, Lyon Cedex 07, France
- Univ. Grenoble Alpes, CEA, CNRS, IBS, Grenoble, France
| | - Abdelkarim Abousalham
- Univ Lyon, Université Lyon 1, Institut de Chimie et de Biochimie Moléculaires et Supramoléculaires, UMR 5246 CNRS, Métabolisme, Enzymes et Mécanismes Moléculaires (MEM²), Villeurbanne Cedex, 69622, France.
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6
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Gennari M, Brazzolotto D, Pécaut J, Cherrier MV, Pollock CJ, DeBeer S, Retegan M, Pantazis DA, Neese F, Rouzières M, Clérac R, Duboc C. Dioxygen Activation and Catalytic Reduction to Hydrogen Peroxide by a Thiolate-Bridged Dimanganese(II) Complex with a Pendant Thiol. J Am Chem Soc 2015; 137:8644-53. [DOI: 10.1021/jacs.5b04917] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Marcello Gennari
- CNRS
UMR 5250, DCM, Université Grenoble Alpes, F-38000 Grenoble, France
| | | | - Jacques Pécaut
- INAC-SCIB, Université Grenoble Alpes, F-38000 Grenoble, France
- Reconnaissance Ionique et Chimie de Coordination, CEA, INAC-SCIB, F-38000 Grenoble, France
| | - Mickael V. Cherrier
- Metalloproteins
Unit, Institut de Biologie Structurale Jean-Pierre Ebel, CEA, CNRS
UMR 5075, Université Grenoble Alpes, 41 rue Horowitz, 38027 Grenoble Cedex 1, France
- Université de Lyon, F-69622 Lyon, France
- Université Claude Bernard Lyon 1, F-69622 Villeurbanne, France
- CNRS,
UMR 5086 Bases Moléculaires et Structurales de Systèmes
Infectieux, Institut de Biologie et Chimie des Protéines, 7 Passage du Vercors, F-69367 Lyon, France
| | - Christopher J. Pollock
- Max-Planck-Institut für Chemische Energie Konversion, Stiftstrasse 34-36, D-45470 Mülheim an der Ruhr, Germany
| | - Serena DeBeer
- Max-Planck-Institut für Chemische Energie Konversion, Stiftstrasse 34-36, D-45470 Mülheim an der Ruhr, Germany
- Department
of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Marius Retegan
- Max-Planck-Institut für Chemische Energie Konversion, Stiftstrasse 34-36, D-45470 Mülheim an der Ruhr, Germany
| | - Dimitrios A. Pantazis
- Max-Planck-Institut für Chemische Energie Konversion, Stiftstrasse 34-36, D-45470 Mülheim an der Ruhr, Germany
| | - Frank Neese
- Max-Planck-Institut für Chemische Energie Konversion, Stiftstrasse 34-36, D-45470 Mülheim an der Ruhr, Germany
| | - Mathieu Rouzières
- CNRS, CRPP, UPR 8641, F-33600 Pessac, France
- CRPP,
UPR 8641, Université Bordeaux, F-33600 Pessac, France
| | - Rodolphe Clérac
- CNRS, CRPP, UPR 8641, F-33600 Pessac, France
- CRPP,
UPR 8641, Université Bordeaux, F-33600 Pessac, France
| | - Carole Duboc
- CNRS
UMR 5250, DCM, Université Grenoble Alpes, F-38000 Grenoble, France
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7
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Chevalley A, Cherrier MV, Fontecilla-Camps JC, Ghasemi M, Salmain M. Artificial metalloenzymes derived from bovine β-lactoglobulin for the asymmetric transfer hydrogenation of an aryl ketone – synthesis, characterization and catalytic activity. Dalton Trans 2014; 43:5482-9. [DOI: 10.1039/c3dt53253d] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Protein hybrids resulting from the supramolecular anchoring to bovine β-lactoglobulin of fatty acid-derived Rh(iii) diimine complexes catalysed the asymmetric transfer hydrogenation of trifluoroacetophenone with up to 32% ee.
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Affiliation(s)
- Alice Chevalley
- Chimie ParisTech (Ecole Nationale Supérieure de Chimie de Paris)
- Laboratoire Charles Friedel
- 75231 Paris cedex 05, France
- CNRS
- UMR 7223
| | - Mickael V. Cherrier
- Metalloproteins Unit
- Institut de Biologie Structurale Jean-Pierre Ebel
- UMR 5075
- CEA
- CNRS
| | | | - Mahsa Ghasemi
- Chimie ParisTech (Ecole Nationale Supérieure de Chimie de Paris)
- Laboratoire Charles Friedel
- 75231 Paris cedex 05, France
- CNRS
- UMR 7223
| | - Michèle Salmain
- Chimie ParisTech (Ecole Nationale Supérieure de Chimie de Paris)
- Laboratoire Charles Friedel
- 75231 Paris cedex 05, France
- CNRS
- UMR 7223
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