1
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Shi R, Hou W, Wang ZQ, Xu X. Biogenesis of Iron-Sulfur Clusters and Their Role in DNA Metabolism. Front Cell Dev Biol 2021; 9:735678. [PMID: 34660592 PMCID: PMC8514734 DOI: 10.3389/fcell.2021.735678] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Accepted: 09/06/2021] [Indexed: 12/02/2022] Open
Abstract
Iron–sulfur (Fe/S) clusters (ISCs) are redox-active protein cofactors that their synthesis, transfer, and insertion into target proteins require many components. Mitochondrial ISC assembly is the foundation of all cellular ISCs in eukaryotic cells. The mitochondrial ISC cooperates with the cytosolic Fe/S protein assembly (CIA) systems to accomplish the cytosolic and nuclear Fe/S clusters maturation. ISCs are needed for diverse cellular functions, including nitrogen fixation, oxidative phosphorylation, mitochondrial respiratory pathways, and ribosome assembly. Recent research advances have confirmed the existence of different ISCs in enzymes that regulate DNA metabolism, including helicases, nucleases, primases, DNA polymerases, and glycosylases. Here we outline the synthesis of mitochondrial, cytosolic and nuclear ISCs and highlight their functions in DNA metabolism.
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Affiliation(s)
- Ruifeng Shi
- Shenzhen University-Friedrich Schiller Universität Jena Joint Ph.D. Program in Biomedical Sciences, Shenzhen University School of Medicine, Shenzhen, China.,Guangdong Key Laboratory for Genome Stability and Disease Prevention and Marshall Laboratory of Biomedical Engineering, Shenzhen University School of Medicine, Shenzhen, China
| | - Wenya Hou
- Guangdong Key Laboratory for Genome Stability and Disease Prevention and Marshall Laboratory of Biomedical Engineering, Shenzhen University School of Medicine, Shenzhen, China
| | - Zhao-Qi Wang
- Leibniz Institute on Aging-Fritz Lipmann Institute (FLI), Jena, Germany.,Faculty of Biological Sciences, Friedrich-Schiller-University Jena, Jena, Germany
| | - Xingzhi Xu
- Shenzhen University-Friedrich Schiller Universität Jena Joint Ph.D. Program in Biomedical Sciences, Shenzhen University School of Medicine, Shenzhen, China.,Guangdong Key Laboratory for Genome Stability and Disease Prevention and Marshall Laboratory of Biomedical Engineering, Shenzhen University School of Medicine, Shenzhen, China
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2
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Van Stappen C, Decamps L, Cutsail GE, Bjornsson R, Henthorn JT, Birrell JA, DeBeer S. The Spectroscopy of Nitrogenases. Chem Rev 2020; 120:5005-5081. [PMID: 32237739 PMCID: PMC7318057 DOI: 10.1021/acs.chemrev.9b00650] [Citation(s) in RCA: 111] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Indexed: 01/08/2023]
Abstract
Nitrogenases are responsible for biological nitrogen fixation, a crucial step in the biogeochemical nitrogen cycle. These enzymes utilize a two-component protein system and a series of iron-sulfur clusters to perform this reaction, culminating at the FeMco active site (M = Mo, V, Fe), which is capable of binding and reducing N2 to 2NH3. In this review, we summarize how different spectroscopic approaches have shed light on various aspects of these enzymes, including their structure, mechanism, alternative reactivity, and maturation. Synthetic model chemistry and theory have also played significant roles in developing our present understanding of these systems and are discussed in the context of their contributions to interpreting the nature of nitrogenases. Despite years of significant progress, there is still much to be learned from these enzymes through spectroscopic means, and we highlight where further spectroscopic investigations are needed.
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Affiliation(s)
- Casey Van Stappen
- Max Planck Institute for
Chemical Energy Conversion, Stiftstrasse 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Laure Decamps
- Max Planck Institute for
Chemical Energy Conversion, Stiftstrasse 34-36, 45470 Mülheim an der Ruhr, Germany
| | - George E. Cutsail
- Max Planck Institute for
Chemical Energy Conversion, Stiftstrasse 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Ragnar Bjornsson
- Max Planck Institute for
Chemical Energy Conversion, Stiftstrasse 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Justin T. Henthorn
- Max Planck Institute for
Chemical Energy Conversion, Stiftstrasse 34-36, 45470 Mülheim an der Ruhr, Germany
| | - James A. Birrell
- Max Planck Institute for
Chemical Energy Conversion, Stiftstrasse 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Serena DeBeer
- Max Planck Institute for
Chemical Energy Conversion, Stiftstrasse 34-36, 45470 Mülheim an der Ruhr, Germany
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3
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Zanello P. Structure and electrochemistry of proteins harboring iron-sulfur clusters of different nuclearities. Part V. Nitrogenases. Coord Chem Rev 2019. [DOI: 10.1016/j.ccr.2019.07.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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4
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Cai R, Abdellaoui S, Kitt JP, Irvine C, Harris JM, Minteer SD, Korzeniewski C. Confocal Raman Microscopy for the Determination of Protein and Quaternary Ammonium Ion Loadings in Biocatalytic Membranes for Electrochemical Energy Conversion and Storage. Anal Chem 2017; 89:13290-13298. [DOI: 10.1021/acs.analchem.7b03380] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Rong Cai
- Department
of Chemistry, University of Utah, 315 S 1400, Salt Lake City, Utah 84112, United States
| | - Sofiene Abdellaoui
- Department
of Chemistry, University of Utah, 315 S 1400, Salt Lake City, Utah 84112, United States
| | - Jay P. Kitt
- Department
of Chemistry, University of Utah, 315 S 1400, Salt Lake City, Utah 84112, United States
| | - Cullen Irvine
- Department
of Chemistry, University of Utah, 315 S 1400, Salt Lake City, Utah 84112, United States
| | - Joel M. Harris
- Department
of Chemistry, University of Utah, 315 S 1400, Salt Lake City, Utah 84112, United States
| | - Shelley D. Minteer
- Department
of Chemistry, University of Utah, 315 S 1400, Salt Lake City, Utah 84112, United States
| | - Carol Korzeniewski
- Department
of Chemistry, University of Utah, 315 S 1400, Salt Lake City, Utah 84112, United States
- Department
of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79416, United States
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5
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Ollagnier de Choudens S, Barras F. Genetic, Biochemical, and Biophysical Methods for Studying FeS Proteins and Their Assembly. Methods Enzymol 2017; 595:1-32. [PMID: 28882198 DOI: 10.1016/bs.mie.2017.07.015] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
FeS clusters containing proteins are structurally and functionally diverse and present in most organisms. Our understanding of FeS cluster production and insertion into polypeptides has benefited from collaborative efforts between in vitro and in vivo studies. The former allows a detailed description of FeS-containing protein and a deep understanding of the molecular mechanisms catalyzing FeS cluster assembly. The second allows to include metabolic and environmental constraints within the analysis of FeS homeostasis. The interplay and the cross talk between the two approaches have been a key strategy to reach a multileveled integrated understanding of FeS cluster homeostasis. In this chapter, we describe the genetic and biochemical/biophysical strategies that were used in the field of FeS cluster biogenesis, with the aim of providing the reader with a critical view of both approaches. In addition to the description of classic tricks and a series of recommendations, we will also discuss models as well as spectroscopic techniques useful to characterize FeS clusters such as UV-visible, Mössbauer, electronic paramagnetic resonance, resonance Raman, circular dichroism, and nuclear magnetic resonance.
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Affiliation(s)
- Sandrine Ollagnier de Choudens
- Université Grenoble Alpes, Laboratoire de Chimie et Biologie des Métaux, BioCat, Grenoble, France; CNRS, Laboratoire de Chimie et Biologie des Métaux, BioCat, UMR, Grenoble, France; CEA-Grenoble, DRF/BIG/CBM, Grenoble, France.
| | - Frédéric Barras
- Laboratoire Chimie Bactérienne, Université Aix-Marseille, CNRS, Marseille, France.
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6
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Artz JH, Zadvornyy OA, Mulder DW, King PW, Peters JW. Structural Characterization of Poised States in the Oxygen Sensitive Hydrogenases and Nitrogenases. Methods Enzymol 2017; 595:213-259. [PMID: 28882202 DOI: 10.1016/bs.mie.2017.07.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The crystallization of FeS cluster-containing proteins has been challenging due to their oxygen sensitivity, and yet these enzymes are involved in many critical catalytic reactions. The last few years have seen a wealth of innovative experiments designed to elucidate not just structural but mechanistic insights into FeS cluster enzymes. Here, we focus on the crystallization of hydrogenases, which catalyze the reversible reduction of protons to hydrogen, and nitrogenases, which reduce dinitrogen to ammonia. A specific focus is given to the different experimental parameters and strategies that are used to trap distinct enzyme states, specifically, oxidants, reductants, and gas treatments. Other themes presented here include the recent use of Cryo-EM, and how coupling various spectroscopies to crystallization is opening up new approaches for structural and mechanistic analysis.
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Affiliation(s)
- Jacob H Artz
- Institute of Biological Chemistry, Washington State University, Pullman, WA, United States
| | - Oleg A Zadvornyy
- Institute of Biological Chemistry, Washington State University, Pullman, WA, United States
| | - David W Mulder
- National Renewable Energy Laboratory, Biosciences Center, Golden, CO, United States
| | - Paul W King
- National Renewable Energy Laboratory, Biosciences Center, Golden, CO, United States
| | - John W Peters
- Institute of Biological Chemistry, Washington State University, Pullman, WA, United States.
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7
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Pence N, Tokmina-Lukaszewska M, Yang ZY, Ledbetter RN, Seefeldt LC, Bothner B, Peters JW. Unraveling the interactions of the physiological reductant flavodoxin with the different conformations of the Fe protein in the nitrogenase cycle. J Biol Chem 2017; 292:15661-15669. [PMID: 28784660 DOI: 10.1074/jbc.m117.801548] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2017] [Revised: 08/02/2017] [Indexed: 01/21/2023] Open
Abstract
Nitrogenase reduces dinitrogen (N2) to ammonia in biological nitrogen fixation. The nitrogenase Fe protein cycle involves a transient association between the reduced, MgATP-bound Fe protein and the MoFe protein and includes electron transfer, ATP hydrolysis, release of Pi, and dissociation of the oxidized, MgADP-bound Fe protein from the MoFe protein. The cycle is completed by reduction of oxidized Fe protein and nucleotide exchange. Recently, a kinetic study of the nitrogenase Fe protein cycle involving the physiological reductant flavodoxin reported a major revision of the rate-limiting step from MoFe protein and Fe protein dissociation to release of Pi Because the Fe protein cannot interact with flavodoxin and the MoFe protein simultaneously, knowledge of the interactions between flavodoxin and the different nucleotide states of the Fe protein is critically important for understanding the Fe protein cycle. Here we used time-resolved limited proteolysis and chemical cross-linking to examine nucleotide-induced structural changes in the Fe protein and their effects on interactions with flavodoxin. Differences in proteolytic cleavage patterns and chemical cross-linking patterns were consistent with known nucleotide-induced structural differences in the Fe protein and indicated that MgATP-bound Fe protein resembles the structure of the Fe protein in the stabilized nitrogenase complex structures. Docking models and cross-linking patterns between the Fe protein and flavodoxin revealed that the MgADP-bound state of the Fe protein has the most complementary docking interface with flavodoxin compared with the MgATP-bound state. Together, these findings provide new insights into the control mechanisms in protein-protein interactions during the Fe protein cycle.
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Affiliation(s)
- Natasha Pence
- From the Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164.,the Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717, and
| | | | - Zhi-Yong Yang
- the Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322
| | - Rhesa N Ledbetter
- the Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322
| | - Lance C Seefeldt
- the Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322
| | - Brian Bothner
- the Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717, and
| | - John W Peters
- From the Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164, .,the Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717, and
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8
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Liu J, Chakraborty S, Hosseinzadeh P, Yu Y, Tian S, Petrik I, Bhagi A, Lu Y. Metalloproteins containing cytochrome, iron-sulfur, or copper redox centers. Chem Rev 2014; 114:4366-469. [PMID: 24758379 PMCID: PMC4002152 DOI: 10.1021/cr400479b] [Citation(s) in RCA: 549] [Impact Index Per Article: 54.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Indexed: 02/07/2023]
Affiliation(s)
- Jing Liu
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Saumen Chakraborty
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Parisa Hosseinzadeh
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Yang Yu
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Shiliang Tian
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Igor Petrik
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Ambika Bhagi
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Yi Lu
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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9
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Hoffman BM, Lukoyanov D, Yang ZY, Dean DR, Seefeldt LC. Mechanism of nitrogen fixation by nitrogenase: the next stage. Chem Rev 2014; 114:4041-62. [PMID: 24467365 PMCID: PMC4012840 DOI: 10.1021/cr400641x] [Citation(s) in RCA: 969] [Impact Index Per Article: 96.9] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Brian M Hoffman
- Department of Chemistry and Biochemistry, Utah State University , 0300 Old Main Hill, Logan, Utah 84322, United States
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10
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Gao H, Subramanian S, Couturier J, Naik SG, Kim SK, Leustek T, Knaff DB, Wu HC, Vignols F, Huynh BH, Rouhier N, Johnson MK. Arabidopsis thaliana Nfu2 accommodates [2Fe-2S] or [4Fe-4S] clusters and is competent for in vitro maturation of chloroplast [2Fe-2S] and [4Fe-4S] cluster-containing proteins. Biochemistry 2013; 52:6633-45. [PMID: 24032747 DOI: 10.1021/bi4007622] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Nfu-type proteins are essential in the biogenesis of iron-sulfur (Fe-S) clusters in numerous organisms. A number of phenotypes including low levels of Fe-S cluster incorporation are associated with the deletion of the gene encoding a chloroplast-specific Nfu-type protein, Nfu2 from Arabidopsis thaliana (AtNfu2). Here, we report that recombinant AtNfu2 is able to assemble both [2Fe-2S] and [4Fe-4S] clusters. Analytical data and gel filtration studies support cluster/protein stoichiometries of one [2Fe-2S] cluster/homotetramer and one [4Fe-4S] cluster/homodimer. The combination of UV-visible absorption and circular dichroism and resonance Raman and Mössbauer spectroscopies has been employed to investigate the nature, properties, and transfer of the clusters assembled on Nfu2. The results are consistent with subunit-bridging [2Fe-2S](2+) and [4Fe-4S](2+) clusters coordinated by the cysteines in the conserved CXXC motif. The results also provided insight into the specificity of Nfu2 for the maturation of chloroplastic Fe-S proteins via intact, rapid, and quantitative cluster transfer. [2Fe-2S] cluster-bound Nfu2 is shown to be an effective [2Fe-2S](2+) cluster donor for glutaredoxin S16 but not glutaredoxin S14. Moreover, [4Fe-4S] cluster-bound Nfu2 is shown to be a very rapid and efficient [4Fe-4S](2+) cluster donor for adenosine 5'-phosphosulfate reductase (APR1), and yeast two-hybrid studies indicate that APR1 forms a complex with Nfu2 but not with Nfu1 and Nfu3, the two other chloroplastic Nfu proteins. This cluster transfer is likely to be physiologically relevant and is particularly significant for plant metabolism as APR1 catalyzes the second step in reductive sulfur assimilation, which ultimately results in the biosynthesis of cysteine, methionine, glutathione, and Fe-S clusters.
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Affiliation(s)
- Huanyao Gao
- Department of Chemistry and Center for Metalloenzyme Studies, University of Georgia , Athens, Georgia, 30602, United States
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11
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Mitra D, George SJ, Guo Y, Kamali S, Keable S, Peters JW, Pelmenschikov V, Case DA, Cramer SP. Characterization of [4Fe-4S] cluster vibrations and structure in nitrogenase Fe protein at three oxidation levels via combined NRVS, EXAFS, and DFT analyses. J Am Chem Soc 2013; 135:2530-43. [PMID: 23282058 DOI: 10.1021/ja307027n] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Azotobacter vinelandii nitrogenase Fe protein (Av2) provides a rare opportunity to investigate a [4Fe-4S] cluster at three oxidation levels in the same protein environment. Here, we report the structural and vibrational changes of this cluster upon reduction using a combination of NRVS and EXAFS spectroscopies and DFT calculations. Key to this work is the synergy between these three techniques as each generates highly complementary information and their analytical methodologies are interdependent. Importantly, the spectroscopic samples contained no glassing agents. NRVS and DFT reveal a systematic 10-30 cm(-1) decrease in Fe-S stretching frequencies with each added electron. The "oxidized" [4Fe-4S](2+) state spectrum is consistent with and extends previous resonance Raman spectra. For the "reduced" [4Fe-4S](1+) state in Fe protein, and for any "all-ferrous" [4Fe-4S](0) cluster, these NRVS spectra are the first available vibrational data. NRVS simulations also allow estimation of the vibrational disorder for Fe-S and Fe-Fe distances, constraining the EXAFS analysis and allowing structural disorder to be estimated. For oxidized Av2, EXAFS and DFT indicate nearly equal Fe-Fe distances, while addition of one electron decreases the cluster symmetry. However, addition of the second electron to form the all-ferrous state induces significant structural change. EXAFS data recorded to k = 21 Å(-1) indicates a 1:1 ratio of Fe-Fe interactions at 2.56 Å and 2.75 Å, a result consistent with DFT. Broken symmetry (BS) DFT rationalizes the interplay between redox state and the Fe-S and Fe-Fe distances as predominantly spin-dependent behavior inherent to the [4Fe-4S] cluster and perturbed by the Av2 protein environment.
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Affiliation(s)
- Devrani Mitra
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois 60637, USA
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12
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Mulder DW, Peters JW. Small angle x-ray scattering spectroscopy. Methods Mol Biol 2011; 766:177-189. [PMID: 21833868 DOI: 10.1007/978-1-61779-194-9_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Conformational changes imposed upon the Fe protein during binding and hydrolysis of Mg·ATP are key to initiating the cycle of interactions within the nitrogenase complex that result in gated electron transfer and the eventual multiple electron reduction of dinitrogen to ammonia. Wonderful insights into how nitrogenase accomplishes this have been gleaned from a number of very nice crystal structures, but conformational changes can only be inferred in a very superficial manner, and a number of key conformations relevant to fully understanding conformational changes have eluded this approach. Alternatively, small angle x-ray scattering (SAXS) has proven to be a helpful method for complimenting x-ray crystallography and determining solution structures of various nucleotide-bound states.
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Affiliation(s)
- David W Mulder
- Department of Chemistry and Biochemistry, Astrobiology Biogeocatalysis Research Center, Montana State University, Bozeman, MT 59717, USA.
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13
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Abstract
Nitrogenase is the enzyme responsible for biological reduction of dinitrogen (N(2)) to ammonia, a form usable for life. Playing a central role in the global biogeochemical nitrogen cycle, this enzyme has been the focus of intensive research for over 60 years. This chapter provides an overview of the features of nitrogenase as a background to the subsequent chapters of this volume that detail the many methods that have been applied in an attempt to gain a deeper understanding of this complex enzyme.
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Affiliation(s)
- Zhi-Yong Yang
- Department of Chemistry and Biochemistry, Utah State University, Logan, UT 84322, USA.
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14
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Abstract
The cleavage of [4Fe-4S]-type clusters is thought to be important in proteins such as Fe-S scaffold proteins and nitrogenase. However, most [4Fe-4S](2+) clusters in proteins have two antiferromagnetically coupled high-spin layers in which a minority spin is delocalized in each layer, thus forming a symmetric Fe(2.5+)-Fe(2.5+) pair, and how cleavage occurs between the irons is puzzling because of the shared electron. Previously, we proposed a novel mechanism for the fission of a [4Fe-4S] core into two [2Fe-2S] cores in which the minority spin localizes on one iron, thus breaking the symmetry and creating a transition state with two Fe(3+)-Fe(2+) pairs. Cleavage first through the weak Fe(2+)-S bonds lowers the activation energy. Here, we propose a test of this mechanism: break the symmetry of the cluster by changing the ligands to promote spin localization, which should enhance reactivity. The cleavage reactions for the homoligand [Fe(4)S(4)L(4)](2-) (L = SCH(3), Cl, H) and heteroligand [Fe(4)S(4)(SCH(3))(2)L(2)](2-) (L = Cl, H) clusters in the gas phase were examined via broken-symmetry density functional theory calculations. In the heteroligand clusters, the minority spin localized on the iron coordinated by the weaker electron-donor ligand, and the reaction energy and activation barrier of the cleavage were lowered, which is in accord with our proposed mechanism and consistent with photoelectron spectroscopy and collision-induced dissociation experiments. These studies suggest that proteins requiring facile fission of their [4Fe-4S] cluster in their biological function might have spin-localized [4Fe-4S] clusters.
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Affiliation(s)
- Shuqiang Niu
- Department of Chemistry, Georgetown University, Washington, D.C. 20057-1227, USA
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15
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Abstract
Nitrogen-fixing bacteria catalyze the reduction of dinitrogen (N(2)) to two ammonia molecules (NH(3)), the major contribution of fixed nitrogen to the biogeochemical nitrogen cycle. The most widely studied nitrogenase is the molybdenum (Mo)-dependent enzyme. The reduction of N(2) by this enzyme involves the transient interaction of two component proteins, designated the iron (Fe) protein and the MoFe protein, and minimally requires 16 magnesium ATP (MgATP), eight protons, and eight electrons. The current state of knowledge on how these proteins and small molecules together effect the reduction of N(2) to ammonia is reviewed. Included is a summary of the roles of the Fe protein and MgATP hydrolysis, information on the roles of the two metal clusters contained in the MoFe protein in catalysis, insights gained from recent success in trapping substrates and inhibitors at the active-site metal cluster FeMo cofactor, and finally, considerations of the mechanism of N(2) reduction catalyzed by nitrogenase.
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Affiliation(s)
- Lance C Seefeldt
- Department of Chemistry and Biochemistry, Utah State University, Logan, UT 84322, USA.
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16
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Structural basis for VO2+-inhibition of nitrogenase activity: (B) pH-sensitive inner-sphere rearrangements in the 1H-environment of the metal coordination site of the nitrogenase Fe–protein identified by ENDOR spectroscopy. J Biol Inorg Chem 2008; 13:637-50. [DOI: 10.1007/s00775-008-0364-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2007] [Accepted: 03/05/2008] [Indexed: 11/25/2022]
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17
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Bandyopadhyay S, Naik SG, O'Carroll IP, Huynh BH, Dean DR, Johnson MK, Dos Santos PC. A proposed role for the Azotobacter vinelandii NfuA protein as an intermediate iron-sulfur cluster carrier. J Biol Chem 2008; 283:14092-9. [PMID: 18339629 DOI: 10.1074/jbc.m709161200] [Citation(s) in RCA: 93] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Iron-sulfur clusters ([Fe-S] clusters) are assembled on molecular scaffolds and subsequently used for maturation of proteins that require [Fe-S] clusters for their functions. Previous studies have shown that Azotobacter vinelandii produces at least two [Fe-S] cluster assembly scaffolds: NifU, required for the maturation of nitrogenase, and IscU, required for the general maturation of other [Fe-S] proteins. A. vinelandii also encodes a protein designated NfuA, which shares amino acid sequence similarity with the C-terminal region of NifU. The activity of aconitase, a [4Fe-4S] cluster-containing enzyme, is markedly diminished in a strain containing an inactivated nfuA gene. This inactivation also results in a null-growth phenotype when the strain is cultivated under elevated oxygen concentrations. NifU has a limited ability to serve the function of NfuA, as its expression at high levels corrects the defect of the nfuA-disrupted strain. Spectroscopic and analytical studies indicate that one [4Fe-4S] cluster can be assembled in vitro within a dimeric form of NfuA. The resultant [4Fe-4S] cluster-loaded form of NfuA is competent for rapid in vitro activation of apo-aconitase. Based on these results a model is proposed where NfuA could represent a class of intermediate [Fe-S] cluster carriers involved in [Fe-S] protein maturation.
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18
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Sarma R, Mulder DW, Brecht E, Szilagyi RK, Seefeldt LC, Tsuruta H, Peters JW. Probing the MgATP-bound conformation of the nitrogenase Fe protein by solution small-angle X-ray scattering. Biochemistry 2007; 46:14058-66. [PMID: 18001132 PMCID: PMC3289971 DOI: 10.1021/bi700446s] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The MgATP-bound conformation of the Fe protein of nitrogenase from Azotobacter vinelandii has been examined in solution by small-angle X-ray scattering (SAXS) and compared to existing crystallographically characterized Fe protein conformations. The results of the analysis of the crystal structure of an Fe protein variant with a Switch II single-amino acid deletion recently suggested that the MgATP-bound state of the Fe protein may exist in a conformation that involves a large-scale reorientation of the dimer subunits, resulting in an overall elongated structure relative to the more compact structure of the MgADP-bound state. It was hypothesized that the Fe protein variant may be a conformational mimic of the MgATP-bound state of the native Fe protein largely on the basis of the observation that the spectroscopic properties of the [4Fe-4S] cluster of the variant mimicked in part the spectroscopic signatures of the native nitrogenase Fe protein in the MgATP-bound state. In this work, SAXS studies reveal that the large-scale conformational differences between the native Fe protein and the variant observed by X-ray crystallography are also observed in solution. In addition, comparison of the SAXS curves of the Fe protein nucleotide-bound states to the nucleotide-free states indicates that the conformation of the MgATP-bound state in solution does not resemble the structure of the variant as initially proposed, but rather, at the resolution of this experiment, it resembles the structure of the nucleotide-free state. These results provide insights into the Fe protein conformations that define the role of MgATP in nitrogenase catalysis.
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Affiliation(s)
- Ranjana Sarma
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717
| | - David W. Mulder
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717
| | - Eric Brecht
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717
| | - Robert K. Szilagyi
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717
| | | | | | - John W. Peters
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717
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19
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Meyer J. Iron-sulfur protein folds, iron-sulfur chemistry, and evolution. J Biol Inorg Chem 2007; 13:157-70. [PMID: 17992543 DOI: 10.1007/s00775-007-0318-7] [Citation(s) in RCA: 173] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2007] [Accepted: 10/25/2007] [Indexed: 11/28/2022]
Abstract
An inventory of unique local protein folds around Fe-S clusters has been derived from the analysis of protein structure databases. Nearly 50 such folds have been identified, and over 90% of them harbor low-potential [2Fe-2S](2+,+) or [4Fe-4S](2+,+) clusters. In contrast, high-potential Fe-S clusters, notwithstanding their structural diversity, occur in only three different protein folds. These observations suggest that the extant population of Fe-S protein folds has to a large extent been shaped in the reducing iron- and sulfur-rich environment that is believed to have predominated on this planet until approximately two billion years ago. High-potential active sites are then surmised to be rarer because they emerged later, in a more oxidizing biosphere, in conditions where iron and sulfide had become poorly available, Fe-S clusters were less stable, and in addition faced competition from heme iron and copper active sites. Among the low-potential Fe-S active sites, protein folds hosting [4Fe-4S](2+,+) clusters outnumber those with [2Fe-2S](2+,+) ones by a factor of 3 at least. This is in keeping with the higher chemical stability and versatility of the tetranuclear clusters, compared with the binuclear ones. It is therefore suggested that, at least while novel Fe-S sites are evolving within proteins, the intrinsic chemical stability of the inorganic moiety may be more important than the stabilizing effect of the polypeptide chain. The discovery rate of novel Fe-S-containing protein folds underwent a sharp increase around 1995, and has remained stable to this day. The current trend suggests that the mapping of the Fe-S fold space is not near completion, in agreement with predictions made for protein folds in general. Altogether, the data collected and analyzed here suggest that the extant structural landscape of Fe-S proteins has been shaped to a large extent by primeval geochemical conditions on one hand, and iron-sulfur chemistry on the other.
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Affiliation(s)
- Jacques Meyer
- Commissariat à l'Energie Atomique, Université Joseph Fourier, UMR5249, CEA-Grenoble, 38054, Grenoble, France.
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20
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Wilson PE, Nyborg AC, Kenealey J, Lowery TJ, Crawford K, King CR, Engan AJ, Johnson JL, Watt GD. Evidence for a synergistic salt-protein interaction -- complex patterns of activation vs. inhibition of nitrogenase by salt. Biophys Chem 2006; 122:184-94. [PMID: 16603308 DOI: 10.1016/j.bpc.2006.03.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2005] [Revised: 03/16/2006] [Accepted: 03/19/2006] [Indexed: 11/26/2022]
Abstract
The molybdenum nitrogenase enzyme system, comprised of the MoFe protein and the Fe protein, catalyzes the reduction of atmospheric N(2) to NH(3). Interactions between these two proteins and between Fe protein and nucleotides (MgADP and MgATP) are crucial to catalysis. It is well established that salts are inhibitors of nitrogenase catalysis that target these interactions. However, the implications of salt effects are often overlooked. We have reexamined salt effects in light of a comprehensive framework for nitrogenase interactions to offer an in-depth analysis of the sources of salt inhibition and underlying apparent cooperativity. More importantly, we have identified patterns of salt activation of nitrogenase that correspond to at least two mechanisms. One of these mechanisms is that charge screening of MoFe protein-Fe protein interactions in the nitrogenase complex accelerates the rate of nitrogenase complex dissociation, which is the rate-limiting step of catalysis. This kind of salt activation operates under conditions of high catalytic activity and low salt concentrations that may resemble those found in vivo. While simple kinetic arguments are strong evidence for this kind of salt activation, further confirmation was sought by demonstrating that tight complexes that have previously displayed little or no activity due to the inability of Fe protein to dissociate from the complex are activated by the presence of salt. This occurs for the combination Azotobacter vinelandii MoFe protein with: (a) the L127Delta Fe protein; and (b) Clostridium pasteurianum Fe protein. The curvature of activation vs. salt implies a synergistic salt-protein interaction.
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Affiliation(s)
- Phillip E Wilson
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 84602, USA
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21
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Sen S, Peters JW. The thermal adaptation of the nitrogenase Fe protein from thermophilic Methanobacter thermoautotrophicus. Proteins 2006; 62:450-60. [PMID: 16315272 DOI: 10.1002/prot.20765] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The nitrogenase Fe protein is a key component of the biochemical machinery responsible for the process of biological nitrogen fixation. The Fe protein is a member of a class of nucleotide-binding proteins that couple the binding and hydrolysis of nucleoside triphosphates to conformational changes. The nucleotide-dependent conformational changes modulate the formation of a macromolecular complex, and some members of the class include Galpha, EF-Tu, and myosin. The members of this class are highly interesting model systems for the analysis of aspects of thermal adaptability, since their mechanisms involve protein conformational change and protein-protein interactions. In this study, we have used our extensive knowledge of the structure of the Azotobacter vinelandii nitrogenase Fe protein in multiple structural conformations, and standard homology modeling approaches have been used to generate reliable models of the Fe protein from thermophilic Methanobacter thermoautotrophicus in the analogous structural conformations. The resulting structural comparison reveals that thermal adaptation of the M. thermoautotrophicus Fe protein is conferred by a number of factors, including increased structural rigidity that results from various structural changes within the protein interior. The analysis of hypothetical docking models and nitrogenase complex structures provides insights into the thermal adaptation of the protein-protein interactions that support macromolecular complex formation and catalysis at higher temperatures.
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Affiliation(s)
- Sanchayita Sen
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717, USA
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22
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Sen S, Krishnakumar A, McClead J, Johnson MK, Seefeldt LC, Szilagyi RK, Peters JW. Insights into the role of nucleotide-dependent conformational change in nitrogenase catalysis: Structural characterization of the nitrogenase Fe protein Leu127 deletion variant with bound MgATP. J Inorg Biochem 2006; 100:1041-52. [PMID: 16616373 DOI: 10.1016/j.jinorgbio.2006.02.016] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2005] [Revised: 02/11/2006] [Accepted: 02/13/2006] [Indexed: 11/16/2022]
Abstract
In the present work, determination of the structure of the nitrogenase Leu 127 deletion variant Fe protein with MgATP bound is presented, along with density functional theory calculations, to provide insights into the roles of MgATP in the nitrogenase reaction mechanism. Comparison of the MgATP-bound structure of this Fe protein to the nucleotide-free form indicates that the binding of MgATP does not alter the overall structure of the variant significantly with only small differences in the conformation of amino acids in direct contact with the two bound MgATP molecules being seen. The earlier observation of splitting of the [4Fe-4S] cluster into two [2Fe-2S] clusters was observed to be unaltered upon binding MgATP. Density functional theory was used to probe the assignment of ligands to the two [2Fe-2S] rhombs. The Mg(2+) environment in the MgATP-bound structure of the Leu127 deletion Fe protein is similar to that observed for the Fe protein in the nitrogenase Fe protein: MoFe protein complex stabilized by MgADP and tetrafluoroaluminate suggesting that large scale conformational change implicated for the Fe protein may not be mediated by changes in the Mg(2+) coordination. The results presented here indicated that MgATP may enhance the stability of an open conformation and prohibit intersubunit interactions, which have been implicated in promoting nucleotide hydrolysis. This could be critical to the tight control of MgATP hydrolysis observed within the nitrogenase complex and may be important for maintaining unidirectional electron flow toward substrate reduction.
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Affiliation(s)
- Sanchayita Sen
- Department of Chemistry and Biochemistry, Montana State University, 108 Gaines Hall, Bozeman, MT 59717, USA
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23
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Peters JW, Szilagyi RK. Exploring new frontiers of nitrogenase structure and mechanism. Curr Opin Chem Biol 2006; 10:101-8. [PMID: 16510305 DOI: 10.1016/j.cbpa.2006.02.019] [Citation(s) in RCA: 106] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2005] [Accepted: 02/17/2006] [Indexed: 11/30/2022]
Abstract
The mechanism of the complex enzyme nitrogenase has long been one of the most challenging problems in bioinorganic chemistry. The complexity of the metal centers of nitrogenase has stretched the boundaries of biochemical, physical and computational tools for providing insights into its structure and chemical function. Recently, there have been several key advances in crystallography and spectroscopy that have impacted the way the nitrogenase mechanism is approached. These advances have opened new frontiers in nitrogenase research, which has started to reveal novel details about the molecular structure, substrate binding and reduction. Here, we discuss these recent advances and their implications on the future of nitrogenase research.
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Affiliation(s)
- John W Peters
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717, USA.
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24
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Rees DC, Akif Tezcan F, Haynes CA, Walton MY, Andrade S, Einsle O, Howard JB. Structural basis of biological nitrogen fixation. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2005; 363:971-84; discussion 1035-40. [PMID: 15901546 DOI: 10.1098/rsta.2004.1539] [Citation(s) in RCA: 194] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Biological nitrogen fixation is mediated by the nitrogenase enzyme system that catalyses the ATP dependent reduction of atmospheric dinitrogen to ammonia. Nitrogenase consists of two component metalloproteins, the MoFe-protein with the FeMo-cofactor that provides the active site for substrate reduction, and the Fe-protein that couples ATP hydrolysis to electron transfer. An overview of the nitrogenase system is presented that emphasizes the structural organization of the proteins and associated metalloclusters that have the remarkable ability to catalyse nitrogen fixation under ambient conditions. Although the mechanism of ammonia formation by nitrogenase remains enigmatic, mechanistic inferences motivated by recent developments in the areas of nitrogenase biochemistry, spectroscopy, model chemistry and computational studies are discussed within this structural framework.
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Affiliation(s)
- Douglas C Rees
- Division of Chemistry and Chemical Engineering, 114-96, California Institute of Technology, Pasadena, CA 91125, USA.
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