1
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Fernández I, Saunders N, Duquerroy S, Bolland WH, Arbabian A, Baquero E, Blanc C, Lafaye P, Haouz A, Buchrieser J, Schwartz O, Rey FA. Structural basis of TMPRSS2 zymogen activation and recognition by the HKU1 seasonal coronavirus. Cell 2024; 187:4246-4260.e16. [PMID: 38964326 DOI: 10.1016/j.cell.2024.06.007] [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: 02/14/2024] [Revised: 03/16/2024] [Accepted: 06/05/2024] [Indexed: 07/06/2024]
Abstract
The human seasonal coronavirus HKU1-CoV, which causes common colds worldwide, relies on the sequential binding to surface glycans and transmembrane serine protease 2 (TMPRSS2) for entry into target cells. TMPRSS2 is synthesized as a zymogen that undergoes autolytic activation to process its substrates. Several respiratory viruses, in particular coronaviruses, use TMPRSS2 for proteolytic priming of their surface spike protein to drive membrane fusion upon receptor binding. We describe the crystal structure of the HKU1-CoV receptor binding domain in complex with TMPRSS2, showing that it recognizes residues lining the catalytic groove. Combined mutagenesis of interface residues and comparison across species highlight positions 417 and 469 as determinants of HKU1-CoV host tropism. The structure of a receptor-blocking nanobody in complex with zymogen or activated TMPRSS2 further provides the structural basis of TMPRSS2 activating conformational change, which alters loops recognized by HKU1-CoV and dramatically increases binding affinity.
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Affiliation(s)
- Ignacio Fernández
- Institut Pasteur, Université de Paris Cité, CNRS UMR 3569, Structural Virology Unit, 75015 Paris, France
| | - Nell Saunders
- Institut Pasteur, Université de Paris Cité, CNRS UMR 3569, Virus & Immunity Unit, 75015 Paris, France
| | - Stéphane Duquerroy
- Institut Pasteur, Université de Paris Cité, CNRS UMR 3569, Structural Virology Unit, 75015 Paris, France; Université Paris-Saclay, Faculté des Sciences, Orsay, France
| | - William H Bolland
- Institut Pasteur, Université de Paris Cité, CNRS UMR 3569, Virus & Immunity Unit, 75015 Paris, France
| | - Atousa Arbabian
- Institut Pasteur, Université de Paris Cité, CNRS UMR 3569, Structural Virology Unit, 75015 Paris, France
| | - Eduard Baquero
- Institut Pasteur, Université de Paris Cité, INSERM U1222, Nanoimaging core, 75015 Paris, France
| | - Catherine Blanc
- Institut Pasteur, Université de Paris Cité, Pasteur-TheraVectys Joint Lab, Paris, France
| | - Pierre Lafaye
- Institut Pasteur, Université Paris Cité, CNRS UMR 3528, Antibody Engineering Facility-C2RT, 75015 Paris, France
| | - Ahmed Haouz
- Institut Pasteur, Université Paris Cité, CNRS UMR 3528, Crystalogenesis Facility-C2RT, 75015 Paris, France
| | - Julian Buchrieser
- Institut Pasteur, Université de Paris Cité, CNRS UMR 3569, Virus & Immunity Unit, 75015 Paris, France
| | - Olivier Schwartz
- Institut Pasteur, Université de Paris Cité, CNRS UMR 3569, Virus & Immunity Unit, 75015 Paris, France; Vaccine Research Institute, Créteil, France.
| | - Félix A Rey
- Institut Pasteur, Université de Paris Cité, CNRS UMR 3569, Structural Virology Unit, 75015 Paris, France.
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2
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Kubiak X, Polsinelli I, Chavas LMG, Fyfe CD, Guillot A, Fradale L, Brewee C, Grimaldi S, Gerbaud G, Thureau A, Legrand P, Berteau O, Benjdia A. Structural and mechanistic basis for RiPP epimerization by a radical SAM enzyme. Nat Chem Biol 2024; 20:382-391. [PMID: 38158457 DOI: 10.1038/s41589-023-01493-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 10/30/2023] [Indexed: 01/03/2024]
Abstract
D-Amino acid residues, found in countless peptides and natural products including ribosomally synthesized and post-translationally modified peptides (RiPPs), are critical for the bioactivity of several antibiotics and toxins. Recently, radical S-adenosyl-L-methionine (SAM) enzymes have emerged as the only biocatalysts capable of installing direct and irreversible epimerization in RiPPs. However, the mechanism underpinning this biochemical process is ill-understood and the structural basis for this post-translational modification remains unknown. Here we report an atomic-resolution crystal structure of a RiPP-modifying radical SAM enzyme in complex with its substrate properly positioned in the active site. Crystallographic snapshots, size-exclusion chromatography-small-angle x-ray scattering, electron paramagnetic resonance spectroscopy and biochemical analyses reveal how epimerizations are installed in RiPPs and support an unprecedented enzyme mechanism for peptide epimerization. Collectively, our study brings unique perspectives on how radical SAM enzymes interact with RiPPs and catalyze post-translational modifications in natural products.
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Affiliation(s)
- Xavier Kubiak
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, ChemSyBio, Jouy-en-Josas, France
| | - Ivan Polsinelli
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, ChemSyBio, Jouy-en-Josas, France
| | | | - Cameron D Fyfe
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, ChemSyBio, Jouy-en-Josas, France
| | - Alain Guillot
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, ChemSyBio, Jouy-en-Josas, France
| | - Laura Fradale
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, ChemSyBio, Jouy-en-Josas, France
| | - Clémence Brewee
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, ChemSyBio, Jouy-en-Josas, France
| | | | | | - Aurélien Thureau
- Synchrotron SOLEIL, HelioBio Group, L'Orme des Merisiers, Saint-Aubin, France
| | - Pierre Legrand
- Synchrotron SOLEIL, HelioBio Group, L'Orme des Merisiers, Saint-Aubin, France
| | - Olivier Berteau
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, ChemSyBio, Jouy-en-Josas, France.
| | - Alhosna Benjdia
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, ChemSyBio, Jouy-en-Josas, France.
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3
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Zecchin P, Pecqueur L, Oltmanns J, Velours C, Schünemann V, Fontecave M, Golinelli‐Pimpaneau B. Structure-based insights into the mechanism of [4Fe-4S]-dependent sulfur insertase LarE. Protein Sci 2024; 33:e4874. [PMID: 38100250 PMCID: PMC10806937 DOI: 10.1002/pro.4874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 11/28/2023] [Accepted: 12/12/2023] [Indexed: 12/17/2023]
Abstract
Several essential cellular metabolites, such as enzyme cofactors, contain sulfur atoms and their biosynthesis requires specific thiolation enzymes. LarE is an ATP-dependent sulfur insertase, which catalyzes the sequential conversion of the two carboxylate groups of the precursor of the lactate racemase cofactor into thiocarboxylates. Two types of LarE enzymes are known, one that uses a catalytic cysteine as a sacrificial sulfur donor, and the other one that uses a [4Fe-4S] cluster as a cofactor. Only the crystal structure of LarE from Lactobacillus plantarum (LpLarE) from the first class has been solved. We report here the crystal structure of LarE from Methanococcus maripaludis (MmLarE), belonging to the second class, in the cluster-free (apo-) and cluster-bound (holo-) forms. The structure of holo-MmLarE shows that the [4Fe-4S] cluster is chelated by three cysteines only, leaving an open coordination site on one Fe atom. Moreover, the fourth nonprotein-bonded iron atom was able to bind an anionic ligand such as a phosphate group or a chloride ion. Together with the spectroscopic analysis of holo-MmLarE and the previously reported biochemical investigations of holo-LarE from Thermotoga maritima, these crystal structures support the hypothesis of a reaction mechanism, in which the [4Fe-4S] cluster binds a hydrogenosulfide ligand in place of the chloride anion, thus generating a [4Fe-5S] intermediate, and transfers it to the substrate, as in the case of [4Fe-4S]-dependent tRNA thiolation enzymes.
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Affiliation(s)
- Paolo Zecchin
- Laboratoire de Chimie des Processus Biologiques, Collège de France, CNRS UMR 8829Sorbonne UniversitéParis cedex 05France
| | - Ludovic Pecqueur
- Laboratoire de Chimie des Processus Biologiques, Collège de France, CNRS UMR 8829Sorbonne UniversitéParis cedex 05France
| | - Jonathan Oltmanns
- Universität of Kaiserslautern‐LandauDepartment of PhysicsKaiserslauternGermany
| | - Christophe Velours
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRSUniversité Paris‐SaclayGif‐sur‐Yvette cedexFrance
- Present address:
Fundamental Microbiology and Pathogenicity LaboratoryUMR 5234 CNRS‐University of Bordeaux, SFR TransBioMedBordeauxFrance
| | - Volker Schünemann
- Universität of Kaiserslautern‐LandauDepartment of PhysicsKaiserslauternGermany
| | - Marc Fontecave
- Laboratoire de Chimie des Processus Biologiques, Collège de France, CNRS UMR 8829Sorbonne UniversitéParis cedex 05France
| | - Béatrice Golinelli‐Pimpaneau
- Laboratoire de Chimie des Processus Biologiques, Collège de France, CNRS UMR 8829Sorbonne UniversitéParis cedex 05France
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4
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Ozgulbas DY, Jensen D, Butler R, Vescovi R, Foster IT, Irvin M, Nakaye Y, Chu M, Dufresne EM, Seifert S, Babnigg G, Ramanathan A, Zhang Q. Robotic pendant drop: containerless liquid for μs-resolved, AI-executable XPCS. LIGHT, SCIENCE & APPLICATIONS 2023; 12:196. [PMID: 37596264 PMCID: PMC10439219 DOI: 10.1038/s41377-023-01233-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 06/30/2023] [Accepted: 07/15/2023] [Indexed: 08/20/2023]
Abstract
The dynamics and structure of mixed phases in a complex fluid can significantly impact its material properties, such as viscoelasticity. Small-angle X-ray Photon Correlation Spectroscopy (SA-XPCS) can probe the spontaneous spatial fluctuations of the mixed phases under various in situ environments over wide spatiotemporal ranges (10-6-103 s /10-10-10-6 m). Tailored material design, however, requires searching through a massive number of sample compositions and experimental parameters, which is beyond the bandwidth of the current coherent X-ray beamline. Using 3.7-μs-resolved XPCS synchronized with the clock frequency at the Advanced Photon Source, we demonstrated the consistency between the Brownian dynamics of ~100 nm diameter colloidal silica nanoparticles measured from an enclosed pendant drop and a sealed capillary. The electronic pipette can also be mounted on a robotic arm to access different stock solutions and create complex fluids with highly-repeatable and precisely controlled composition profiles. This closed-loop, AI-executable protocol is applicable to light scattering techniques regardless of the light wavelength and optical coherence, and is a first step towards high-throughput, autonomous material discovery.
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Affiliation(s)
- Doga Yamac Ozgulbas
- Data Science and Learning Division, Argonne National Laboratory, Lemont, IL, 60439, USA
| | - Don Jensen
- X-ray Science Division, Argonne National Laboratory, Lemont, IL, 60439, USA
| | - Rory Butler
- Departement of Computer Science, University of Chicago, 5801 S Ellis Ave, Chicago, IL, 60637, USA
| | - Rafael Vescovi
- Data Science and Learning Division, Argonne National Laboratory, Lemont, IL, 60439, USA
| | - Ian T Foster
- Data Science and Learning Division, Argonne National Laboratory, Lemont, IL, 60439, USA
| | - Michael Irvin
- Data Science and Learning Division, Argonne National Laboratory, Lemont, IL, 60439, USA
| | - Yasukazu Nakaye
- XRD Design and Engineering Department, Rigaku Corporation 3-9-12 Matsubara-cho, Akishima-shi, Tokyo, 196-8666, Japan
| | - Miaoqi Chu
- X-ray Science Division, Argonne National Laboratory, Lemont, IL, 60439, USA
| | - Eric M Dufresne
- X-ray Science Division, Argonne National Laboratory, Lemont, IL, 60439, USA
| | - Soenke Seifert
- X-ray Science Division, Argonne National Laboratory, Lemont, IL, 60439, USA
| | - Gyorgy Babnigg
- Bioscience Division, Argonne National Laboratory, Lemont, IL, 60439, USA
| | - Arvind Ramanathan
- Data Science and Learning Division, Argonne National Laboratory, Lemont, IL, 60439, USA.
| | - Qingteng Zhang
- X-ray Science Division, Argonne National Laboratory, Lemont, IL, 60439, USA.
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5
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Madru C, Martínez-Carranza M, Laurent S, Alberti AC, Chevreuil M, Raynal B, Haouz A, Le Meur RA, Delarue M, Henneke G, Flament D, Krupovic M, Legrand P, Sauguet L. DNA-binding mechanism and evolution of replication protein A. Nat Commun 2023; 14:2326. [PMID: 37087464 PMCID: PMC10122647 DOI: 10.1038/s41467-023-38048-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 04/13/2023] [Indexed: 04/24/2023] Open
Abstract
Replication Protein A (RPA) is a heterotrimeric single stranded DNA-binding protein with essential roles in DNA replication, recombination and repair. Little is known about the structure of RPA in Archaea, the third domain of life. By using an integrative structural, biochemical and biophysical approach, we extensively characterize RPA from Pyrococcus abyssi in the presence and absence of DNA. The obtained X-ray and cryo-EM structures reveal that the trimerization core and interactions promoting RPA clustering on ssDNA are shared between archaea and eukaryotes. However, we also identified a helical domain named AROD (Acidic Rpa1 OB-binding Domain), and showed that, in Archaea, RPA forms an unanticipated tetrameric supercomplex in the absence of DNA. The four RPA molecules clustered within the tetramer could efficiently coat and protect stretches of ssDNA created by the advancing replisome. Finally, our results provide insights into the evolution of this primordial replication factor in eukaryotes.
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Affiliation(s)
- Clément Madru
- Architecture and Dynamics of Biological Macromolecules, Institut Pasteur, Université Paris Cité, CNRS, UMR 3528, Paris, France
| | - Markel Martínez-Carranza
- Architecture and Dynamics of Biological Macromolecules, Institut Pasteur, Université Paris Cité, CNRS, UMR 3528, Paris, France
| | - Sébastien Laurent
- Univ Brest, Ifremer, CNRS, Biologie et Ecologie des Ecoystèmes marins profonds (BEEP), F-29280, Plouzané, France
| | - Alessandra C Alberti
- Architecture and Dynamics of Biological Macromolecules, Institut Pasteur, Université Paris Cité, CNRS, UMR 3528, Paris, France
| | - Maelenn Chevreuil
- Molecular Biophysics Platform, C2RT, Institut Pasteur, Université Paris Cité, CNRS, UMR 3528, Paris, France
| | - Bertrand Raynal
- Molecular Biophysics Platform, C2RT, Institut Pasteur, Université Paris Cité, CNRS, UMR 3528, Paris, France
| | - Ahmed Haouz
- Crystallography Platform, C2RT, Institut Pasteur, Université Paris Cité, CNRS, UMR 3528, Paris, France
| | - Rémy A Le Meur
- Biological NMR Platform & HDX, C2RT, Institut Pasteur, Université Paris Cité, CNRS, UMR 3528, Paris, France
| | - Marc Delarue
- Architecture and Dynamics of Biological Macromolecules, Institut Pasteur, Université Paris Cité, CNRS, UMR 3528, Paris, France
| | - Ghislaine Henneke
- Univ Brest, Ifremer, CNRS, Biologie et Ecologie des Ecoystèmes marins profonds (BEEP), F-29280, Plouzané, France
| | - Didier Flament
- Univ Brest, Ifremer, CNRS, Biologie et Ecologie des Ecoystèmes marins profonds (BEEP), F-29280, Plouzané, France
| | - Mart Krupovic
- Archaeal Virology Unit, Institut Pasteur, Université Paris Cité, CNRS, UMR 6047, Paris, France
| | - Pierre Legrand
- Architecture and Dynamics of Biological Macromolecules, Institut Pasteur, Université Paris Cité, CNRS, UMR 3528, Paris, France
- Synchrotron SOLEIL, HelioBio group, L'Orme des Merisiers, 91190, Saint-Aubin, France
| | - Ludovic Sauguet
- Architecture and Dynamics of Biological Macromolecules, Institut Pasteur, Université Paris Cité, CNRS, UMR 3528, Paris, France.
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6
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Fernández I, Dynesen LT, Coquin Y, Pederzoli R, Brun D, Haouz A, Gessain A, Rey FA, Buseyne F, Backovic M. The crystal structure of a simian Foamy Virus receptor binding domain provides clues about entry into host cells. Nat Commun 2023; 14:1262. [PMID: 36878926 PMCID: PMC9988990 DOI: 10.1038/s41467-023-36923-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 02/21/2023] [Indexed: 03/08/2023] Open
Abstract
The surface envelope glycoprotein (Env) of all retroviruses mediates virus binding to cells and fusion of the viral and cellular membranes. A structure-function relationship for the HIV Env that belongs to the Orthoretrovirus subfamily has been well established. Structural information is however largely missing for the Env of Foamy viruses (FVs), the second retroviral subfamily. In this work we present the X-ray structure of the receptor binding domain (RBD) of a simian FV Env at 2.57 Å resolution, revealing two subdomains and an unprecedented fold. We have generated a model for the organization of the RBDs within the trimeric Env, which indicates that the upper subdomains form a cage-like structure at the apex of the Env, and identified residues K342, R343, R359 and R369 in the lower subdomain as key players for the interaction of the RBD and viral particles with heparan sulfate.
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Affiliation(s)
- Ignacio Fernández
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, Unité de Virologie Structurale, 75015, Paris, France
| | - Lasse Toftdal Dynesen
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, Unité d'Épidémiologie et Physiopathologie des Virus Oncogènes, 75015, Paris, France
| | - Youna Coquin
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, Unité d'Épidémiologie et Physiopathologie des Virus Oncogènes, 75015, Paris, France
| | - Riccardo Pederzoli
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, Unité de Virologie Structurale, 75015, Paris, France
| | - Delphine Brun
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, Unité de Virologie Structurale, 75015, Paris, France
| | - Ahmed Haouz
- Institut Pasteur, Université Paris Cité, Plateforme de cristallographie-C2RT, CNRS UMR 3528, 75015, Paris, France
| | - Antoine Gessain
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, Unité d'Épidémiologie et Physiopathologie des Virus Oncogènes, 75015, Paris, France
| | - Félix A Rey
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, Unité de Virologie Structurale, 75015, Paris, France
| | - Florence Buseyne
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, Unité d'Épidémiologie et Physiopathologie des Virus Oncogènes, 75015, Paris, France
| | - Marija Backovic
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, Unité de Virologie Structurale, 75015, Paris, France.
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7
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Vasireddi R, Gardais A, Chavas LMG. Manufacturing of Ultra-Thin X-ray-Compatible COC Microfluidic Devices for Optimal In Situ Macromolecular Crystallography Experiments. MICROMACHINES 2022; 13:1365. [PMID: 36014287 PMCID: PMC9416059 DOI: 10.3390/mi13081365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 08/11/2022] [Accepted: 08/19/2022] [Indexed: 06/15/2023]
Abstract
Cyclic-olefin-copolymer (COC)-based microfluidic devices are increasingly becoming the center of highly valuable research for in situ X-ray measurements due to their compatibility with X-rays, biological compounds, chemical resistance, optical properties, low cost, and simplified handling. COC microfluidic devices present potential solutions to challenging biological applications such as protein binding, folding, nucleation, growth kinetics, and structural changes. In recent years, the techniques applied to manufacturing and handling these devices have capitalized on enormous progress toward small-scale sample probing. Here, we describe the new and innovative design aspects, fabrication, and experimental implementation of low-cost and micron-sized X-ray-compatible microfluidic sample environments that address diffusion-based crystal formation for crystallographic characterization. The devices appear fully compatible with crystal growth and subsequent X-ray diffraction experiments, resulting in remarkably low background data recording. The results highlighted in this research demonstrate how the engineered microfluidic devices allow the recording of accurate crystallographic data at room temperature and structure determination at high resolution.
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Affiliation(s)
| | - Antonin Gardais
- Synchrotron SOLEIL, L’Orme des Merisier, Saint-Aubin, 91192 Gif-sur-Yvette, France
| | - Leonard M. G. Chavas
- Department of Applied Physics, Nagoya University, Nagoya 464-8603, Japan
- Synchrotron Radiation Research Center, Nagoya University, Nagoya 464-8603, Japan
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8
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Chaussavoine I, Isabet T, Lener R, Montaville P, Vasireddi R, Chavas LMG. Implementation of wedged-serial protein crystallography at PROXIMA-1. JOURNAL OF SYNCHROTRON RADIATION 2022; 29:439-446. [PMID: 35254307 PMCID: PMC8900848 DOI: 10.1107/s1600577521013242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 12/14/2021] [Indexed: 06/14/2023]
Abstract
An approach for serial crystallography experiments based on wedged-data collection is described. This is an alternative method for recording in situ X-ray diffraction data on crystalline samples efficiently loaded in an X-ray compatible microfluidic chip. Proper handling of the microfluidic chip places crystalline samples at geometrically known positions with respect to the focused X-ray interaction area for serial data collection of small wedges. The integration of this strategy takes advantage of the greatly modular sample environment available on the endstation, which allows access to both in situ and more classical cryo-crystallography with minimum time loss. The method represents another optional data collection approach that adds up to the already large set of methods made available to users. Coupled with the advances in processing serial crystallography data, the wedged-data collection strategy proves highly efficient in minimizing the amount of required sample crystals for recording a complete dataset. From the advances in microfluidic technology presented here, high-throughput room-temperature crystallography experiments may become routine and should be easily extended to industrial use.
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Affiliation(s)
| | | | - Robin Lener
- Synchrotron SOLEIL, 91192 Gif-sur-Yvette, France
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9
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Crystallographic snapshots of a B 12-dependent radical SAM methyltransferase. Nature 2022; 602:336-342. [PMID: 35110733 PMCID: PMC8828468 DOI: 10.1038/s41586-021-04355-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 12/15/2021] [Indexed: 01/01/2023]
Abstract
By catalysing the microbial formation of methane, methyl-coenzyme M reductase has a central role in the global levels of this greenhouse gas1,2. The activity of methyl-coenzyme M reductase is profoundly affected by several unique post-translational modifications3–6, such as a unique C-methylation reaction catalysed by methanogenesis marker protein 10 (Mmp10), a radical S-adenosyl-l-methionine (SAM) enzyme7,8. Here we report the spectroscopic investigation and atomic resolution structure of Mmp10 from Methanosarcina acetivorans, a unique B12 (cobalamin)-dependent radical SAM enzyme9. The structure of Mmp10 reveals a unique enzyme architecture with four metallic centres and critical structural features involved in the control of catalysis. In addition, the structure of the enzyme–substrate complex offers a glimpse into a B12-dependent radical SAM enzyme in a precatalytic state. By combining electron paramagnetic resonance spectroscopy, structural biology and biochemistry, our study illuminates the mechanism by which the emerging superfamily of B12-dependent radical SAM enzymes catalyse chemically challenging alkylation reactions and identifies distinctive active site rearrangements to provide a structural rationale for the dual use of the SAM cofactor for radical and nucleophilic chemistry. Structural and spectroscopic studies show how a B12-dependent radical SAM enzyme catalyses unique and challenging alkylation chemistry, including protein post-translational modification required for methane biosynthesis.
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