1
|
Bennett SP, Crack JC, Puglisi R, Pastore A, Le Brun NE. Native mass spectrometric studies of IscSU reveal a concerted, sulfur-initiated mechanism of iron-sulfur cluster assembly. Chem Sci 2022; 14:78-95. [PMID: 36605734 PMCID: PMC9769115 DOI: 10.1039/d2sc04169c] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 11/13/2022] [Indexed: 11/16/2022] Open
Abstract
Iron-sulfur (Fe-S) clusters are cofactors essential for life. Though the proteins that function in the assembly of Fe-S clusters are well known, details of the molecular mechanism are less well established. The Isc (iron-sulfur cluster) biogenesis apparatus is widespread in bacteria and is the closest homologue to the human system. Mutations in certain components of the human system lead to disease, and so further studies of this system could be important for developing strategies for medical treatments. We have studied two core components of the Isc biogenesis system: IscS, a cysteine desulfurase; and IscU, a scaffold protein on which clusters are built before subsequent transfer onto recipient apo-proteins. Fe2+-binding, sulfur transfer, and formation of a [2Fe-2S] was followed by a range of techniques, including time-resolved mass spectrometry, and intermediate and product species were unambiguously identified through isotopic substitution experiments using 57Fe and 34S. Under cluster synthesis conditions, sulfur adducts and the [2Fe-2S] cluster product readily accumulated on IscU, but iron adducts (other than the cluster itself) were not observed at physiologically relevant Fe2+ concentrations. Our data indicate that either Fe2+ or sulfur transfer can occur first, but that the transfer of sulfane sulfur (S0) to IscU must occur first if Zn2+ is bound to IscU, suggesting that it is the key step that initiates cluster assembly. Following this, [2Fe-2S] cluster formation is a largely concerted reaction once Fe2+ is introduced.
Collapse
Affiliation(s)
- Sophie P. Bennett
- Centre for Molecular and Structural Biochemistry, School of Chemistry, University of East AngliaNorwich Research ParkNorwichNR4 7TJUK
| | - Jason C. Crack
- Centre for Molecular and Structural Biochemistry, School of Chemistry, University of East AngliaNorwich Research ParkNorwichNR4 7TJUK
| | - Rita Puglisi
- The Wohl Institute, King's College London, Denmark Hill CampusLondon SE5 8AFUK
| | - Annalisa Pastore
- The Wohl Institute, King's College London, Denmark Hill CampusLondon SE5 8AFUK
| | - Nick E. Le Brun
- Centre for Molecular and Structural Biochemistry, School of Chemistry, University of East AngliaNorwich Research ParkNorwichNR4 7TJUK
| |
Collapse
|
2
|
The Redox Active [2Fe-2S] Clusters: Key-Components of a Plethora of Enzymatic Reactions—Part I: Archaea. INORGANICS 2022. [DOI: 10.3390/inorganics10010014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The earliest forms of life (i.e., Archaea, Bacteria, and Eukarya) appeared on our planet about ten billion years after its formation. Although Archaea do not seem to possess the multiprotein machinery constituted by the NIF (Nitrogen Fixation), ISC (Iron Sulfur Cluster), SUF (sulfur mobilization) enzymes, typical of Bacteria and Eukarya, some of them are able to encode Fe-S proteins. Here we discussed the multiple enzymatic reactions triggered by the up-to-date structurally characterized members of the archaeal family that require the crucial presence of structurally characterized [2Fe-2S] assemblies, focusing on their biological functions and, when available, on their electrochemical behavior.
Collapse
|
3
|
Benoit SL, Agudelo S, Maier RJ. A two-hybrid system reveals previously uncharacterized protein-protein interactions within the Helicobacter pylori NIF iron-sulfur maturation system. Sci Rep 2021; 11:10794. [PMID: 34031459 PMCID: PMC8144621 DOI: 10.1038/s41598-021-90003-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 04/26/2021] [Indexed: 11/10/2022] Open
Abstract
Iron-sulfur (Fe-S) proteins play essential roles in all living organisms. The gastric pathogen Helicobacter pylori relies exclusively on the NIF system for biosynthesis and delivery of Fe-S clusters. Previously characterized components include two essential proteins, NifS (cysteine desulfurase) and NifU (scaffold protein), and a dispensable Fe-S carrier, Nfu. Among 38 proteins previously predicted to coordinate Fe-S clusters, two proteins, HP0207 (a member of the Nbp35/ApbC ATPase family) and HP0277 (previously annotated as FdxA, a member of the YfhL ferredoxin-like family) were further studied, using a bacterial two-hybrid system approach to identify protein-protein interactions. ApbC was found to interact with 30 proteins, including itself, NifS, NifU, Nfu and FdxA, and alteration of the conserved ATPase motif in ApbC resulted in a significant (50%) decrease in the number of protein interactions, suggesting the ATpase activity is needed for some ApbC-target protein interactions. FdxA was shown to interact with 21 proteins, including itself, NifS, ApbC and Nfu, however no interactions between NifU and FdxA were detected. By use of cross-linking studies, a 51-kDa ApbC-Nfu heterodimer complex was identified. Attempts to generate apbC chromosomal deletion mutants in H. pylori were unsuccessful, therefore indirectly suggesting the hp0207 gene is essential. In contrast, mutants in the fdxA gene were obtained, albeit only in one parental strain (26695). Taken together, these results suggest both ApbC and FdxA are important players in the H. pylori NIF maturation system.
Collapse
Affiliation(s)
- Stéphane L Benoit
- Department of Microbiology, The University of Georgia, 30602, Athens, Georgia.,Center for Metalloenzyme Studies, The University of Georgia, 30602, Athens, Georgia
| | - Stephanie Agudelo
- Department of Microbiology, The University of Georgia, 30602, Athens, Georgia
| | - Robert J Maier
- Department of Microbiology, The University of Georgia, 30602, Athens, Georgia. .,Center for Metalloenzyme Studies, The University of Georgia, 30602, Athens, Georgia.
| |
Collapse
|
4
|
Deciphering the role of sulfonamides and molecular basis of thioredoxin domain dynamics through comparative simulations. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2020.114797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
|
5
|
Nakamura R, Hikita M, Ogawa S, Takahashi Y, Fujishiro T. Snapshots of PLP‐substrate and PLP‐product external aldimines as intermediates in two types of cysteine desulfurase enzymes. FEBS J 2019; 287:1138-1154. [DOI: 10.1111/febs.15081] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 08/11/2019] [Accepted: 10/01/2019] [Indexed: 11/27/2022]
Affiliation(s)
- Ryosuke Nakamura
- Department of Biochemistry and Molecular Biology Graduate School of Science and Engineering Saitama University Saitama Japan
| | - Masahide Hikita
- Structural Biology Research Center, Photon Factory Institute of Materials Structure Science High Energy Accelerator Research Organization Tsukuba Japan
| | - Shoko Ogawa
- Department of Biochemistry and Molecular Biology Graduate School of Science and Engineering Saitama University Saitama Japan
| | - Yasuhiro Takahashi
- Department of Biochemistry and Molecular Biology Graduate School of Science and Engineering Saitama University Saitama Japan
| | - Takashi Fujishiro
- Department of Biochemistry and Molecular Biology Graduate School of Science and Engineering Saitama University Saitama Japan
| |
Collapse
|
6
|
Puglisi R, Pastore A. The role of chaperones in iron-sulfur cluster biogenesis. FEBS Lett 2018; 592:4011-4019. [PMID: 30194723 PMCID: PMC6506825 DOI: 10.1002/1873-3468.13245] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 09/03/2018] [Accepted: 09/05/2018] [Indexed: 11/10/2022]
Abstract
Iron–sulfur cluster biogenesis is a complex process mediated by numerous proteins among which two from bacteria chaperones, called HscB and HscA in bacteria. They are highly conserved up to eukaryotes and homologous to DnaJ and DnaK, respectively, but with specific differences. As compared with other chaperones, HscB and HscA have escaped attention and relatively little is known about their functions. After briefly introducing the various chaperone families, we reviewed here the current structural and functional knowledge HscA and HscB and on their role in cluster formation. We critically evaluated the literature and highlighted the weak aspects which will require more attention in the future. We sincerely hope that this study will inspire new interest on this important and interesting system.
Collapse
Affiliation(s)
- Rita Puglisi
- UK Dementia Research Institute at King's College London, London, UK.,The Wohl Institute at King's College London, London, UK
| | - Annalisa Pastore
- UK Dementia Research Institute at King's College London, London, UK.,The Wohl Institute at King's College London, London, UK.,Department of Molecular Medicine, University of Pavia, Pavia, Italy
| |
Collapse
|
7
|
Cysteine Desulfurase IscS2 Plays a Role in Oxygen Resistance in Clostridium difficile. Infect Immun 2018; 86:IAI.00326-18. [PMID: 29866903 DOI: 10.1128/iai.00326-18] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Accepted: 05/25/2018] [Indexed: 11/20/2022] Open
Abstract
Clostridium difficile is an anaerobic, spore-forming bacterium capable of colonizing the gastrointestinal tract of humans following disruption of the normal microbiota, typically from antibiotic therapy for an unrelated infection. With approximately 500,000 confirmed infections leading to 29,000 deaths per year in the United States, C. difficile infection (CDI) is an urgent public health threat. We previously determined that C. difficile survives in up to 3% oxygen. Low levels of oxygen are present in the intestinal tract, with the higher concentrations being associated with the epithelial cell surface. Additionally, antibiotic treatment, the greatest risk factor for CDI, increases the intestinal oxygen concentration. Therefore, we hypothesized that the C. difficile genome encodes mechanisms for survival during oxidative stress. Previous data have shown that cysteine desulfurases involved in iron-sulfur cluster assembly are involved in protecting bacteria from oxidative stress. In this study, deletion of a putative cysteine desulfurase (Cd630_12790/IscS2) involved in the iron-sulfur cluster (Isc) system caused a severe growth defect in the presence of 2% oxygen. Additionally, this mutant delayed colonization in a conventional mouse model of CDI and failed to colonize in a germfree model, which has higher intestinal oxygen levels. These data imply an undefined role for this cysteine desulfurase in protecting C. difficile from low levels of oxygen in the gut.
Collapse
|
8
|
Abdizadeh H, Atilgan AR, Atilgan C, Dedeoglu B. Computational approaches for deciphering the equilibrium and kinetic properties of iron transport proteins. Metallomics 2018; 9:1513-1533. [PMID: 28967944 DOI: 10.1039/c7mt00216e] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
With the advances in three-dimensional structure determination techniques, high quality structures of the iron transport proteins transferrin and the bacterial ferric binding protein (FbpA) have been deposited in the past decade. These are proteins of relatively large size, and developments in hardware and software have only recently made it possible to study their dynamics using standard computational resources. We review computational techniques towards understanding the equilibrium and kinetic properties of iron transport proteins under different environmental conditions. At the level of detail that requires quantum chemical treatments, the octahedral geometry around iron has been scrutinized and it has been established that the iron coordinating tyrosines are in an unusual deprotonated state. At the atomistic level, both the N-lobe and the full bilobal structure of transferrin have been studied under varying conditions of pH, ionic strength and binding of other metal ions by molecular dynamics (MD) simulations. These studies have allowed questions to be answered, among others, on the function of second shell residues in iron release, the role of synergistic anions in preparing the active site for iron binding, and the differences between the kinetics of the N- and the C-lobe. MD simulations on FbpA have led to the detailed observation of the binding kinetics of phosphate to the apo form, and to the conformational preferences of the holo form under conditions mimicking the environmental niches provided by the periplasmic space. To study the dynamics of these proteins with their receptors, one must resort to coarse-grained methodologies, since these systems are prohibitively large for atomistic simulations. A study of the complex of human transferrin (hTf) with its pathogenic receptor by such methods has revealed a potential mechanistic explanation for the defense mechanism that arises in evolutionary warfare. Meanwhile, the motions in the transferrin receptor bound hTf have been shown to disfavor apo hTf dissociation, explaining why the two proteins remain in complex during the recycling process from the endosome to the cell surface. Open problems and possible technological applications related to metal ion binding-release in iron transport proteins that may be handled by hybrid use of quantum mechanical, MD and coarse-grained approaches are discussed.
Collapse
Affiliation(s)
- H Abdizadeh
- Faculty of Engineering and Natural Sciences, Sabancı University, Orhanlı 34956, Tuzla, Istanbul, Turkey.
| | | | | | | |
Collapse
|
9
|
Benoit SL, Holland AA, Johnson MK, Maier RJ. Iron-sulfur protein maturation in Helicobacter pylori: identifying a Nfu-type cluster carrier protein and its iron-sulfur protein targets. Mol Microbiol 2018; 108:379-396. [PMID: 29498770 DOI: 10.1111/mmi.13942] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/23/2018] [Indexed: 01/03/2023]
Abstract
Helicobacter pylori is anomalous among non nitrogen-fixing bacteria in containing an incomplete NIF system for Fe-S cluster assembly comprising two essential proteins, NifS (cysteine desulfurase) and NifU (scaffold protein). Although nifU deletion strains cannot be obtained via the conventional gene replacement, a NifU-depleted strain was constructed and shown to be more sensitive to oxidative stress compared to wild-type (WT) strains. The hp1492 gene, encoding a putative Nfu-type Fe-S cluster carrier protein, was disrupted in three different H. pylori strains, indicating that it is not essential. However, Δnfu strains have growth deficiency, are more sensitive to oxidative stress and are unable to colonize mouse stomachs. Moreover, Δnfu strains have lower aconitase activity but higher hydrogenase activity than the WT. Recombinant Nfu was found to bind either one [2Fe-2S] or [4Fe-4S] cluster/dimer, based on analytical, UV-visible absorption/CD and resonance Raman studies. A bacterial two-hybrid system was used to ascertain interactions between Nfu, NifS, NifU and each of 36 putative Fe-S-containing target proteins. Nfu, NifS and NifU were found to interact with 15, 6 and 29 putative Fe-S proteins respectively. The results indicate that Nfu, NifS and NifU play a major role in the biosynthesis and/or delivery of Fe-S clusters in H. pylori.
Collapse
Affiliation(s)
- Stéphane L Benoit
- Department of Microbiology and Center for Metalloenzyme Studies, University of Georgia, Athens, GA 30602, USA
| | - Ashley A Holland
- Department of Chemistry and Center for Metalloenzyme Studies, University of Georgia, Athens, GA 30602, USA
| | - Michael K Johnson
- Department of Chemistry and Center for Metalloenzyme Studies, University of Georgia, Athens, GA 30602, USA
| | - Robert J Maier
- Department of Microbiology and Center for Metalloenzyme Studies, University of Georgia, Athens, GA 30602, USA
| |
Collapse
|
10
|
Adinolfi S, Puglisi R, Crack JC, Iannuzzi C, Dal Piaz F, Konarev PV, Svergun DI, Martin S, Le Brun NE, Pastore A. The Molecular Bases of the Dual Regulation of Bacterial Iron Sulfur Cluster Biogenesis by CyaY and IscX. Front Mol Biosci 2018; 4:97. [PMID: 29457004 PMCID: PMC5801593 DOI: 10.3389/fmolb.2017.00097] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Accepted: 12/22/2017] [Indexed: 12/11/2022] Open
Abstract
IscX (or YfhJ) is a protein of unknown function which takes part in the iron-sulfur cluster assembly machinery, a highly specialized and essential metabolic pathway. IscX binds to iron with low affinity and interacts with IscS, the desulfurase central to cluster assembly. Previous studies have suggested a competition between IscX and CyaY, the bacterial ortholog of frataxin, for the same binding surface of IscS. This competition could suggest a link between the two proteins with a functional significance. Using a hybrid approach based on nuclear magnetic resonance, small angle scattering and biochemical methods, we show here that IscX is a modulator of the inhibitory properties of CyaY: by competing for the same site on IscS, the presence of IscX rescues the rates of enzymatic cluster formation which are inhibited by CyaY. The effect is stronger at low iron concentrations, whereas it becomes negligible at high iron concentrations. These results strongly suggest the mechanism of the dual regulation of iron sulfur cluster assembly under the control of iron as the effector.
Collapse
Affiliation(s)
| | - Rita Puglisi
- The Wohl Institute, King's College London, London, United Kingdom
| | - Jason C Crack
- School of Chemistry, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Clara Iannuzzi
- The Wohl Institute, King's College London, London, United Kingdom.,DBBGP, Università degli Studi della Campania "L. Vanvitelli,", Naples, Italy
| | - Fabrizio Dal Piaz
- Dipartimento di Medicina, Chirurgia e Odontoiatria "Scuola Medica Salernitana"/DIPMED, Universita' di Salerno, Fisciano, Italy
| | - Petr V Konarev
- A.V. Shubnikov Institute of Crystallography of Federal Scientific Research Centre "Crystallography and Photonics" of Russian Academy of Sciences, Moscow, Russia.,National Research Centre "Kurchatov Institute, ", Moscow, Russia
| | | | | | - Nick E Le Brun
- School of Chemistry, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Annalisa Pastore
- The Wohl Institute, King's College London, London, United Kingdom.,Department of Molecular Medicine, University of Pavia, Pavia, Italy
| |
Collapse
|
11
|
Noguera ME, Aran M, Smal C, Vazquez DS, Herrera MG, Roman EA, Alaimo N, Gallo M, Santos J. Insights on the conformational dynamics of human frataxin through modifications of loop-1. Arch Biochem Biophys 2017; 636:123-137. [PMID: 29097312 DOI: 10.1016/j.abb.2017.10.022] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2017] [Revised: 10/20/2017] [Accepted: 10/28/2017] [Indexed: 02/07/2023]
Abstract
Human frataxin (FXN) is a highly conserved mitochondrial protein involved in iron homeostasis and activation of the iron-sulfur cluster assembly. FXN deficiency causes the neurodegenerative disease Friedreich's Ataxia. Here, we investigated the effect of alterations in loop-1, a stretch presumably essential for FXN function, on the conformational stability and dynamics of the native state. We generated four loop-1 variants, carrying substitutions, insertions and deletions. All of them were stable and well-folded proteins. Fast local motions (ps-ns) and slower long-range conformational dynamics (μs-ms) were altered in some mutants as judged by NMR. Particularly, loop-1 modifications impact on the dynamics of a distant region that includes residues from the β-sheet, helix α1 and the C-terminal. Remarkably, all the mutants retain the ability to activate cysteine desulfurase, even when two of them exhibit a strong decrease in iron binding, revealing a differential sensitivity of these functional features to loop-1 perturbation. Consequently, we found that even for a small and relatively rigid protein, engineering a loop segment enables to alter conformational dynamics through a long-range effect, preserving the native-state structure and important aspects of function.
Collapse
Affiliation(s)
- Martín E Noguera
- Instituto de Química y Físico-Química Biológicas, University of Buenos Aires, Junín 956, 1113AAD, Buenos Aires, Argentina
| | - Martín Aran
- The Leloir Institute Foundation and IIBBA-CONICET, Av. Patricias Argentinas 435, 1405 Buenos Aires, Argentina
| | - Clara Smal
- The Leloir Institute Foundation and IIBBA-CONICET, Av. Patricias Argentinas 435, 1405 Buenos Aires, Argentina
| | - Diego S Vazquez
- Instituto de Química y Físico-Química Biológicas, University of Buenos Aires, Junín 956, 1113AAD, Buenos Aires, Argentina
| | - María Georgina Herrera
- Instituto de Química y Físico-Química Biológicas, University of Buenos Aires, Junín 956, 1113AAD, Buenos Aires, Argentina
| | - Ernesto A Roman
- Instituto de Química y Físico-Química Biológicas, University of Buenos Aires, Junín 956, 1113AAD, Buenos Aires, Argentina
| | - Nadine Alaimo
- Dipartimento di Scienze e Tecnologie Chimiche, University of Rome "Tor Vergata", Via della Ricerca Scientifica snc, 00133 Roma, Italy
| | - Mariana Gallo
- Dipartimento di Scienze e Tecnologie Chimiche, University of Rome "Tor Vergata", Via della Ricerca Scientifica snc, 00133 Roma, Italy; IRBM Science Park S.p.A., Via Pontina km 30,600., 00071 Pomezia (RM), Italy.
| | - Javier Santos
- Instituto de Química y Físico-Química Biológicas, University of Buenos Aires, Junín 956, 1113AAD, Buenos Aires, Argentina.
| |
Collapse
|
12
|
Abstract
The biogenesis of iron-sulfur (Fe/S) proteins in eukaryotes is a multistage, multicompartment process that is essential for a broad range of cellular functions, including genome maintenance, protein translation, energy conversion, and the antiviral response. Genetic and cell biological studies over almost 2 decades have revealed some 30 proteins involved in the synthesis of cellular [2Fe-2S] and [4Fe-4S] clusters and their incorporation into numerous apoproteins. Mechanistic aspects of Fe/S protein biogenesis continue to be elucidated by biochemical and ultrastructural investigations. Here, we review recent developments in the pursuit of constructing a comprehensive model of Fe/S protein assembly in the mitochondrion.
Collapse
Affiliation(s)
- Joseph J Braymer
- Institut für Zytobiologie und Zytopathologie, Philipps-Universität Marburg, Robert-Koch-Strasse 6, 35032 Marburg
| | - Roland Lill
- Institut für Zytobiologie und Zytopathologie, Philipps-Universität Marburg, Robert-Koch-Strasse 6, 35032 Marburg; LOEWE Zentrum für Synthetische Mikrobiologie SynMikro, Hans-Meerwein-Strasse, 35043 Marburg, Germany.
| |
Collapse
|
13
|
Hammond RG, Tan X, Johnson MA. SARS-unique fold in the Rousettus bat coronavirus HKU9. Protein Sci 2017; 26:1726-1737. [PMID: 28580734 PMCID: PMC5563143 DOI: 10.1002/pro.3208] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Revised: 05/26/2017] [Accepted: 05/26/2017] [Indexed: 12/28/2022]
Abstract
The coronavirus nonstructural protein 3 (nsp3) is a multifunctional protein that comprises multiple structural domains. This protein assists viral polyprotein cleavage, host immune interference, and may play other roles in genome replication or transcription. Here, we report the solution NMR structure of a protein from the “SARS‐unique region” of the bat coronavirus HKU9. The protein contains a frataxin fold or double‐wing motif, which is an α + β fold that is associated with protein/protein interactions, DNA binding, and metal ion binding. High structural similarity to the human severe acute respiratory syndrome (SARS) coronavirus nsp3 is present. A possible functional site that is conserved among some betacoronaviruses has been identified using bioinformatics and biochemical analyses. This structure provides strong experimental support for the recent proposal advanced by us and others that the “SARS‐unique” region is not unique to the human SARS virus, but is conserved among several different phylogenetic groups of coronaviruses and provides essential functions. PDB Code(s): 5UTV
Collapse
Affiliation(s)
- Robert G Hammond
- Department of Chemistry, University of Alabama at Birmingham, Birmingham, Alabama, 35294
| | - Xuan Tan
- Department of Chemistry, University of Alabama at Birmingham, Birmingham, Alabama, 35294
| | - Margaret A Johnson
- Department of Chemistry, University of Alabama at Birmingham, Birmingham, Alabama, 35294
| |
Collapse
|
14
|
Fantini M, Malinverni D, De Los Rios P, Pastore A. New Techniques for Ancient Proteins: Direct Coupling Analysis Applied on Proteins Involved in Iron Sulfur Cluster Biogenesis. Front Mol Biosci 2017; 4:40. [PMID: 28664160 PMCID: PMC5471300 DOI: 10.3389/fmolb.2017.00040] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2017] [Accepted: 05/24/2017] [Indexed: 12/01/2022] Open
Abstract
Direct coupling analysis (DCA) is a powerful statistical inference tool used to study protein evolution. It was introduced to predict protein folds and protein-protein interactions, and has also been applied to the prediction of entire interactomes. Here, we have used it to analyze three proteins of the iron-sulfur biogenesis machine, an essential metabolic pathway conserved in all organisms. We show that DCA can correctly reproduce structural features of the CyaY/frataxin family (a protein involved in the human disease Friedreich's ataxia) despite being based on the relatively small number of sequences allowed by its genomic distribution. This result gives us confidence in the method. Its application to the iron-sulfur cluster scaffold protein IscU, which has been suggested to function both as an ordered and a disordered form, allows us to distinguish evolutionary traces of the structured species, suggesting that, if present in the cell, the disordered form has not left evolutionary imprinting. We observe instead, for the first time, direct indications of how the protein can dimerize head-to-head and bind 4Fe4S clusters. Analysis of the alternative scaffold protein IscA provides strong support to a coordination of the cluster by a dimeric form rather than a tetramer, as previously suggested. Our analysis also suggests the presence in solution of a mixture of monomeric and dimeric species, and guides us to the prevalent one. Finally, we used DCA to analyze interactions between some of these proteins, and discuss the potentials and limitations of the method.
Collapse
Affiliation(s)
- Marco Fantini
- BioSNS, Faculty of Mathematical and Natural Sciences, Scuola Normale SuperiorePisa, Italy
| | - Duccio Malinverni
- Institute of Physics, School of Basic Sciences, and Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de LausanneLausanne, Switzerland
| | - Paolo De Los Rios
- Institute of Physics, School of Basic Sciences, and Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de LausanneLausanne, Switzerland
| | - Annalisa Pastore
- Maurice Wohl Institute, King's CollegeLondon, United Kingdom.,Molecular Medicine Department, University of PaviaPavia, Italy
| |
Collapse
|
15
|
Prischi F, Pastore A. Hybrid Methods in Iron-Sulfur Cluster Biogenesis. Front Mol Biosci 2017; 4:12. [PMID: 28349052 PMCID: PMC5346568 DOI: 10.3389/fmolb.2017.00012] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Accepted: 02/23/2017] [Indexed: 11/13/2022] Open
Abstract
Hybrid methods, which combine and integrate several biochemical and biophysical techniques, have rapidly caught up in the last twenty years to provide a way to obtain a fuller description of proteins and molecular complexes with sizes and complexity otherwise not easily affordable. Here, we review the use of a robust hybrid methodology based on a mixture of NMR, SAXS, site directed mutagenesis and molecular docking which we have developed to determine the structure of weakly interacting molecular complexes. We applied this technique to gain insights into the structure of complexes formed amongst proteins involved in the molecular machine, which produces the essential iron-sulfur cluster prosthetic groups. Our results were validated both by X-ray structures and by other groups who adopted the same approach. We discuss the advantages and the limitations of our methodology and propose new avenues, which could improve it.
Collapse
Affiliation(s)
- Filippo Prischi
- School of Biological Sciences, University of Essex Colchester, UK
| | - Annalisa Pastore
- Maurice Wohl Institute, King's College LondonLondon, UK; Molecular Medicine Department, University of PaviaPavia, Italy
| |
Collapse
|