1
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Schüren AO, Ridgway BM, Di Salvo F, Carella LM, Gramm VK, Metzger E, Doctorovich F, Rentschler E, Schünemann V, Ruschewitz U, Klein A. Structural insight into halide-coordinated [Fe 4S 4X nY 4-n] 2- clusters (X, Y = Cl, Br, I) by XRD and Mössbauer spectroscopy. Dalton Trans 2023; 52:1277-1290. [PMID: 36621931 DOI: 10.1039/d2dt03203a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Iron sulphur halide clusters [Fe4S4Br4]2- and [Fe4S4X2Y2]2- (X, Y = Cl, Br, I) were obtained in excellent yields (77 to 78%) and purity from [Fe(CO)5], elemental sulphur, I2 and benzyltrimethylammonium (BTMA+) iodide, bromide and chloride. Single crystals of (BTMA)2[Fe4S4Br4] (1), (BTMA)2[Fe4S4Br2Cl2] (2), (BTMA)2[Fe4S4Cl2I2] (3), and (BTMA)2[Fe4S4Br2I2] (4) were isostructural to the previously reported (BTMA)2[Fe4S4I4] (5) (monoclinic, Cc). Instead of the chloride cubane cluster [Fe4S4Cl4]2-, we found the prismane-shaped cluster (BTMA)3[Fe6S6Cl6] (6) (P1̄). 57Fe Mössbauer spectroscopy indicates complete delocalisation with Fe2.5+ oxidation states for all iron atoms. Magnetic measurements showed small χMT values at 298 K ranging from 1.12 to 1.54 cm3 K mol-1, indicating the dominant antiferromagnetic exchange interactions. With decreasing temperature, the χMT values decreased to reach a plateau at around 100 K. From about 20 K, the values drop significantly. Fitting the data in the Heisenberg-Dirac-van Vleck (HDvV) as well as the Heisenberg Double Exchange (HDE) formalism confirmed the delocalisation and antiferromagnetic coupling assumed from Mössbauer spectroscopy.
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Affiliation(s)
- Andreas O Schüren
- Universität zu Köln, Mathematisch-Naturwissenschaftliche Fakultät, Department für Chemie, Institut für Anorganische Chemie, Greinstraße 6, D-50939 Köln, Germany. .,INQUIMAE-CONICET-Universidad de Buenos Aires, Intendente Güiraldes 2160, Pabellón 2, Piso 3, C1428EGA, Buenos Aires, Argentina
| | - Benjamin M Ridgway
- INQUIMAE-CONICET-Universidad de Buenos Aires, Intendente Güiraldes 2160, Pabellón 2, Piso 3, C1428EGA, Buenos Aires, Argentina
| | - Florencia Di Salvo
- INQUIMAE-CONICET-Universidad de Buenos Aires, Intendente Güiraldes 2160, Pabellón 2, Piso 3, C1428EGA, Buenos Aires, Argentina.,Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Química Inorgánica, Analítica y Química Física, Intendente Güiraldes 2160, Pabellón 2, Piso 3, C1428EGA, Buenos Aires, Argentina
| | - Luca M Carella
- Johannes Gutenberg Universität Mainz, Department Chemie, Duesbergweg 10-14, 55128 Mainz, Germany
| | - Verena K Gramm
- Universität zu Köln, Mathematisch-Naturwissenschaftliche Fakultät, Department für Chemie, Institut für Anorganische Chemie, Greinstraße 6, D-50939 Köln, Germany.
| | - Elisa Metzger
- TU Kaiserlautern Department of Physics, 67663 Kaiserlautern, Germany
| | - Fabio Doctorovich
- INQUIMAE-CONICET-Universidad de Buenos Aires, Intendente Güiraldes 2160, Pabellón 2, Piso 3, C1428EGA, Buenos Aires, Argentina.,Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Química Inorgánica, Analítica y Química Física, Intendente Güiraldes 2160, Pabellón 2, Piso 3, C1428EGA, Buenos Aires, Argentina
| | - Eva Rentschler
- Johannes Gutenberg Universität Mainz, Department Chemie, Duesbergweg 10-14, 55128 Mainz, Germany
| | - Volker Schünemann
- TU Kaiserlautern Department of Physics, 67663 Kaiserlautern, Germany
| | - Uwe Ruschewitz
- Universität zu Köln, Mathematisch-Naturwissenschaftliche Fakultät, Department für Chemie, Institut für Anorganische Chemie, Greinstraße 6, D-50939 Köln, Germany.
| | - Axel Klein
- Universität zu Köln, Mathematisch-Naturwissenschaftliche Fakultät, Department für Chemie, Institut für Anorganische Chemie, Greinstraße 6, D-50939 Köln, Germany.
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2
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Abstract
Synthetic iron-sulfur cubanes are models for biological cofactors, which are essential to delineate oxidation states in the more complex enzymatic systems. However, a complete series of [Fe4S4]n complexes spanning all redox states accessible by 1-electron transformations of the individual iron atoms (n = 0-4+) has never been prepared, deterring the methodical comparison of structure and spectroscopic signature. Here, we demonstrate that the use of a bulky arylthiolate ligand promoting the encapsulation of alkali-metal cations in the vicinity of the cubane enables the synthesis of such a series. Characterization by EPR, 57Fe Mössbauer spectroscopy, UV-visible electronic absorption, variable-temperature X-ray diffraction analysis, and cyclic voltammetry reveals key trends for the geometry of the Fe4S4 core as well as for the Mössbauer isomer shift, which both correlate systematically with oxidation state. Furthermore, we confirm the S = 4 electronic ground state of the most reduced member of the series, [Fe4S4]0, and provide electrochemical evidence that it is accessible within 0.82 V from the [Fe4S4]2+ state, highlighting its relevance as a mimic of the nitrogenase iron protein cluster.
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3
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Abstract
Nitrogenase is the only enzyme capable of reducing N2 to NH3. This challenging reaction requires the coordinated transfer of multiple electrons from the reductase, Fe-protein, to the catalytic component, MoFe-protein, in an ATP-dependent fashion. In the last two decades, there have been significant advances in our understanding of how nitrogenase orchestrates electron transfer (ET) from the Fe-protein to the catalytic site of MoFe-protein and how energy from ATP hydrolysis transduces the ET processes. In this review, we summarize these advances, with focus on the structural and thermodynamic redox properties of nitrogenase component proteins and their complexes, as well as on new insights regarding the mechanism of ET reactions during catalysis and how they are coupled to ATP hydrolysis. We also discuss recently developed chemical, photochemical, and electrochemical methods for uncoupling substrate reduction from ATP hydrolysis, which may provide new avenues for studying the catalytic mechanism of nitrogenase.
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Affiliation(s)
- Hannah L Rutledge
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - F Akif Tezcan
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
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4
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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: 105] [Impact Index Per Article: 26.3] [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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5
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Seefeldt LC, Yang ZY, Lukoyanov DA, Harris DF, Dean DR, Raugei S, Hoffman BM. Reduction of Substrates by Nitrogenases. Chem Rev 2020; 120:5082-5106. [PMID: 32176472 DOI: 10.1021/acs.chemrev.9b00556] [Citation(s) in RCA: 169] [Impact Index Per Article: 42.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Nitrogenase is the enzyme that catalyzes biological N2 reduction to NH3. This enzyme achieves an impressive rate enhancement over the uncatalyzed reaction. Given the high demand for N2 fixation to support food and chemical production and the heavy reliance of the industrial Haber-Bosch nitrogen fixation reaction on fossil fuels, there is a strong need to elucidate how nitrogenase achieves this difficult reaction under benign conditions as a means of informing the design of next generation synthetic catalysts. This Review summarizes recent progress in addressing how nitrogenase catalyzes the reduction of an array of substrates. New insights into the mechanism of N2 and proton reduction are first considered. This is followed by a summary of recent gains in understanding the reduction of a number of other nitrogenous compounds not considered to be physiological substrates. Progress in understanding the reduction of a wide range of C-based substrates, including CO and CO2, is also discussed, and remaining challenges in understanding nitrogenase substrate reduction are considered.
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Affiliation(s)
- Lance C Seefeldt
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322, United States
| | - Zhi-Yong Yang
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322, United States
| | - Dmitriy A Lukoyanov
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Derek F Harris
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322, United States
| | - Dennis R Dean
- Biochemistry Department, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Simone Raugei
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Brian M Hoffman
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
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6
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Hassan A, Macedo LJA, Souza JCPD, Lima FCDA, Crespilho FN. A combined Far-FTIR, FTIR Spectromicroscopy, and DFT Study of the Effect of DNA Binding on the [4Fe4S] Cluster Site in EndoIII. Sci Rep 2020; 10:1931. [PMID: 32029762 PMCID: PMC7005299 DOI: 10.1038/s41598-020-58531-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 11/04/2019] [Indexed: 11/28/2022] Open
Abstract
Endonuclease III (EndoIII) is a DNA glycosylase that contains the [4Fe4S] cluster, which is essential for the protein to bind to damaged DNA in a process called base excision repair (BER). Here we propose that the change in the covalency of Fe–S bonds of the [4Fe4S] cluster caused by double-stranded (ds)-DNA binding is accompanied by a change in their strength, which is due to alterations of the electronic structure of the cluster. Micro-FTIR spectroscopy in the mid-IR region and FTIR spectroscopy in the far IR (450 and 300 cm−1) were used independently to study the structural changes in EndoIII and the behavior of the [4Fe4S] cluster it contains, in the native form and upon its binding to ds-DNA. Structural changes in the DNA itself were also examined. The characteristics vibrational modes, corresponding to Fe–S (sulfide) and Fe–S (thiolate) bonds were identified in the cluster through far IR spectroscopy as well through quantum chemistry calculations. Based on the experimental results, these vibrational modes shift in their spectral positions caused by negatively charged DNA in the vicinity of the cluster. Modifications of the Fe–S bond lengths upon DNA binding, both of the Fe–S (sulfide) and Fe–S (thiolate) bonds in the [4Fe4S] cluster of EndoIII are responsible for the stabilization of the cluster towards higher oxidation state (3+), and hence its redox communication along the ds-DNA helix.
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Affiliation(s)
- Ayaz Hassan
- São Carlos Institute of Chemistry, University of São Paulo, 13560-970, São Paulo, Brazil.
| | - Lucyano J A Macedo
- São Carlos Institute of Chemistry, University of São Paulo, 13560-970, São Paulo, Brazil
| | - João C P de Souza
- Goiano Federal Institute of Education, Science and Technology, Campus Rio Verde, 75901-970, Goiás, Brazil
| | - Filipe C D A Lima
- Federal Institute of Education, Science, and Technology of São Paulo, Campus Matão, 15991-502, São Paulo, Brazil
| | - Frank N Crespilho
- São Carlos Institute of Chemistry, University of São Paulo, 13560-970, São Paulo, Brazil.
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7
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Dance I. Computational Investigations of the Chemical Mechanism of the Enzyme Nitrogenase. Chembiochem 2020; 21:1671-1709. [DOI: 10.1002/cbic.201900636] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Indexed: 12/15/2022]
Affiliation(s)
- Ian Dance
- School of Chemistry UNSW Sydney Sydney 2052 Australia
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8
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Wittkamp F, Mishra N, Wang H, Wille HC, Steinbrügge R, Kaupp M, Cramer SP, Apfel UP, Pelmenschikov V. Insights from 125Te and 57Fe nuclear resonance vibrational spectroscopy: a [4Fe-4Te] cluster from two points of view. Chem Sci 2019; 10:7535-7541. [PMID: 31588304 PMCID: PMC6761874 DOI: 10.1039/c9sc02025j] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Accepted: 06/22/2019] [Indexed: 11/21/2022] Open
Abstract
Can sulfur-to-tellurium exchange serve as a method to understand iron–sulfur clusters of enzymatic systems?
Iron–sulfur clusters are common building blocks for electron transport and active sites of metalloproteins. Their comprehensive investigation is crucial for understanding these enzymes, which play important roles in modern biomimetic catalysis and biotechnology applications. We address this issue by utilizing (Et4N)3[Fe4Te4(SPh)4], a tellurium modified version of a conventional reduced [4Fe–4S]+ cluster, and performed both 57Fe- and 125Te-NRVS to reveal its characteristic vibrational features. Our analysis exposed major differences in the resulting 57Fe spectrum profile as compared to that of the respective [4Fe–4S] cluster, and between the 57Fe and 125Te profiles. DFT calculations are applied to rationalize structural, electronic, vibrational, and redox-dependent properties of the [4Fe–4Te]+ core. We herein highlight the potential of sulfur/tellurium exchange as a method to isolate the iron-only motion in enzymatic systems.
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Affiliation(s)
- Florian Wittkamp
- Department of Chemistry and Biochemistry , Inorganic Chemistry I , Ruhr-Universität Bochum , Universitätsstraße 150 , 44801 Bochum , Germany .
| | - Nakul Mishra
- Department of Chemistry , University of California , Davis, One Shields Avenue , Davis , California 95616 , USA .
| | - Hongxin Wang
- Department of Chemistry , University of California , Davis, One Shields Avenue , Davis , California 95616 , USA .
| | - Hans-Christian Wille
- Deutsches Elektronen-Synchrotron DESY , Notkestraße 85 , 22607 Hamburg , Germany
| | - René Steinbrügge
- Deutsches Elektronen-Synchrotron DESY , Notkestraße 85 , 22607 Hamburg , Germany
| | - Martin Kaupp
- Institute of Chemistry , Theoretical Chemistry/Quantum Chemistry , Technical University of Berlin , Sekr. C7, Straße des 17. Juni 135 , 10623 Berlin , Germany .
| | - Stephen P Cramer
- Department of Chemistry , University of California , Davis, One Shields Avenue , Davis , California 95616 , USA .
| | - Ulf-Peter Apfel
- Department of Chemistry and Biochemistry , Inorganic Chemistry I , Ruhr-Universität Bochum , Universitätsstraße 150 , 44801 Bochum , Germany . .,Fraunhofer UMSICHT , Osterfelder Straße 3 , 46047 Oberhausen , Germany
| | - Vladimir Pelmenschikov
- Institute of Chemistry , Theoretical Chemistry/Quantum Chemistry , Technical University of Berlin , Sekr. C7, Straße des 17. Juni 135 , 10623 Berlin , Germany .
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9
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Chen X, Li Q, Gong Y. Coordination Structures of the Uranyl(VI)–Diamide Complexes: A Combined Mass Spectrometric, EXAFS Spectroscopic, and Theoretical Study. Inorg Chem 2019; 58:5695-5702. [DOI: 10.1021/acs.inorgchem.9b00047] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Xiuting Chen
- Department of Radiochemistry, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
- School of Nuclear Science and Technology, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qingnuan Li
- Department of Radiochemistry, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Yu Gong
- Department of Radiochemistry, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
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10
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Carrillo-Campos J, Riveros-Rosas H, Rodríguez-Sotres R, Muñoz-Clares RA. Bona fide choline monoxygenases evolved in Amaranthaceae plants from oxygenases of unknown function: Evidence from phylogenetics, homology modeling and docking studies. PLoS One 2018; 13:e0204711. [PMID: 30256846 PMCID: PMC6157903 DOI: 10.1371/journal.pone.0204711] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 09/12/2018] [Indexed: 12/25/2022] Open
Abstract
Few land plants can synthesize and accumulate the osmoprotectant glycine betaine (GB) even though this metabolic trait has major adaptive importance given the prevalence of drought, hypersaline soils or cold. GB is synthesized from choline in two reactions catalyzed by choline monooxygenases (CMOs) and enzymes of the family 10 of aldehyde dehydrogenases (ALDH10s) that gained betaine aldehyde dehydrogenase activity (BADH). Homolog genes encoding CMO and ALDH10 enzymes are present in all known land plant genomes, but since GB-non-accumulators plants lack the BADH-type ALDH10 isozyme, they would be expected to also lack the CMO activity to avoid accumulation of the toxic betaine aldehyde. To explore CMOs substrate specificity, we performed amino acid sequence alignments, phylogenetic analysis, homology modeling and docking simulations. We found that plant CMOs form a monophyletic subfamily within the Rieske/mononuclear non-heme oxygenases family with two clades: CMO1 and CMO2, the latter diverging from CMO1 after gene duplication. CMO1 enzymes are present in all plants; CMO2s only in the Amaranthaceae high-GB-accumulators plants. CMO2s, and particularly their mononuclear non-heme iron domain where the active site is located, evolved at a faster rate than CMO1s, which suggests positive selection. The homology model and docking simulations of the spinach CMO2 enzyme showed at the active site three aromatic residues forming a box with which the trimethylammonium group of choline could interact through cation-π interactions, and a glutamate, which also may interact with the trimethylammonium group through a charge-charge interaction. The aromatic box and the carboxylate have been shown to be critical for choline binding in other proteins. Interestingly, these residues are conserved in CMO2 proteins but not in CMO1 proteins, where two of these aromatic residues are leucine and the glutamate is asparagine. These findings reinforce our proposal that the CMO1s physiological substrate is not choline but a still unknown metabolite.
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Affiliation(s)
- Javier Carrillo-Campos
- Departamento de Bioquímica, Facultad de Química, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Héctor Riveros-Rosas
- Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Rogelio Rodríguez-Sotres
- Departamento de Bioquímica, Facultad de Química, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Rosario A. Muñoz-Clares
- Departamento de Bioquímica, Facultad de Química, Universidad Nacional Autónoma de México, Ciudad de México, México
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11
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Lupan A, Silaghi-Dumitrescu R, King RB. Tetracapped tetrahedral ruthenium-sulfur clusters related to iron-sulfur structural units in metalloenzymes. Inorganica Chim Acta 2018. [DOI: 10.1016/j.ica.2017.10.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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12
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Carlson MR, Gray DL, Richers CP, Wang W, Zhao PH, Rauchfuss TB, Pelmenschikov V, Pham CC, Gee LB, Wang H, Cramer SP. Sterically Stabilized Terminal Hydride of a Diiron Dithiolate. Inorg Chem 2018; 57:1988-2001. [PMID: 29384371 DOI: 10.1021/acs.inorgchem.7b02903] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The kinetically robust hydride [t-HFe2(Me2pdt)(CO)2(dppv)2]+ ([t-H1]+) (Me2pdt2- = Me2C(CH2S-)2; dppv = cis-1,2-C2H2(PPh2)2) and related derivatives were prepared with 57Fe enrichment for characterization by NMR, FT-IR, and NRVS. The experimental results were rationalized using DFT molecular modeling and spectral simulations. The spectroscopic analysis was aimed at supporting assignments of Fe-H vibrational spectra as they relate to recent measurements on [FeFe]-hydrogenase enzymes. The combination of bulky Me2pdt2- and dppv ligands stabilizes the terminal hydride with respect to its isomerization to the 5-16 kcal/mol more stable bridging hydride ([μ-H1]+) with t1/2(313.3 K) = 19.3 min. In agreement with the nOe experiments, the calculations predict that one methyl group in [t-H1]+ interacts with the hydride with a computed CH···HFe distance of 1.7 Å. Although [t-H571]+ exhibits multiple NRVS features in the 720-800 cm-1 region containing the bending Fe-H modes, the deuterated [t-D571]+ sample exhibits a unique Fe-D/CO band at ∼600 cm-1. In contrast, the NRVS spectra for [μ-H571]+ exhibit weaker bands near 670-700 cm-1 produced by the Fe-H-Fe wagging modes coupled to Me2pdt2- and dppv motions.
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Affiliation(s)
- Michaela R Carlson
- School of Chemical Sciences, University of Illinois , Urbana, Illinois 61801, United States
| | - Danielle L Gray
- School of Chemical Sciences, University of Illinois , Urbana, Illinois 61801, United States
| | - Casseday P Richers
- School of Chemical Sciences, University of Illinois , Urbana, Illinois 61801, United States
| | - Wenguang Wang
- School of Chemical Sciences, University of Illinois , Urbana, Illinois 61801, United States
| | - Pei-Hua Zhao
- School of Chemical Sciences, University of Illinois , Urbana, Illinois 61801, United States
| | - Thomas B Rauchfuss
- School of Chemical Sciences, University of Illinois , Urbana, Illinois 61801, United States
| | | | - Cindy C Pham
- Department of Chemistry, University of California , Davis, California 95616, United States
| | - Leland B Gee
- Department of Chemistry, University of California , Davis, California 95616, United States
| | - Hongxin Wang
- Department of Chemistry, University of California , Davis, California 95616, United States
| | - Stephen P Cramer
- Department of Chemistry, University of California , Davis, California 95616, United States
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13
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Abstract
For over 20 years, nuclear resonance vibrational spectroscopy (NRVS) has been used to study vibrational dynamics of iron-containing materials. With the only selection rule being iron motion, 57Fe NRVS has become an excellent tool to study iron-containing enzymes. Over the past decade, considerable progress has been made in the study of complex metalloenzymes using NRVS. Iron cofactors in heme-containing globins; [2Fe2S], [3Fe4S], [4Fe4S] proteins; the [NiFe] and [FeFe] hydrogenases; and nitrogenases have been explored in a fashion not possible through traditional vibrational spectroscopy. In this chapter, we discuss the basics of NRVS, a strategy to perform NRVS, and a discussion of the application of NRVS on rubredoxin and [FeFe] hydrogenase.
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Affiliation(s)
- Leland B Gee
- University of California, Davis, Davis, CA, United States.
| | - Hongxin Wang
- University of California, Davis, Davis, CA, United States
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14
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Antuch M, Millet P, Iwase A, Kudo A, Grigoriev SA, Voloshin YZ. Characterization of Rh:SrTiO3 photoelectrodes surface-modified with a cobalt clathrochelate and their application to the hydrogen evolution reaction. Electrochim Acta 2017. [DOI: 10.1016/j.electacta.2017.10.018] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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15
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Pelmenschikov V, Birrell JA, Pham CC, Mishra N, Wang H, Sommer C, Reijerse E, Richers CP, Tamasaku K, Yoda Y, Rauchfuss TB, Lubitz W, Cramer SP. Reaction Coordinate Leading to H 2 Production in [FeFe]-Hydrogenase Identified by Nuclear Resonance Vibrational Spectroscopy and Density Functional Theory. J Am Chem Soc 2017; 139:16894-16902. [PMID: 29054130 PMCID: PMC5699932 DOI: 10.1021/jacs.7b09751] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
[FeFe]-hydrogenases are metalloenzymes that reversibly reduce protons to molecular hydrogen at exceptionally high rates. We have characterized the catalytically competent hydride state (Hhyd) in the [FeFe]-hydrogenases from both Chlamydomonas reinhardtii and Desulfovibrio desulfuricans using 57Fe nuclear resonance vibrational spectroscopy (NRVS) and density functional theory (DFT). H/D exchange identified two Fe-H bending modes originating from the binuclear iron cofactor. DFT calculations show that these spectral features result from an iron-bound terminal hydride, and the Fe-H vibrational frequencies being highly dependent on interactions between the amine base of the catalytic cofactor with both hydride and the conserved cysteine terminating the proton transfer chain to the active site. The results indicate that Hhyd is the catalytic state one step prior to H2 formation. The observed vibrational spectrum, therefore, provides mechanistic insight into the reaction coordinate for H2 bond formation by [FeFe]-hydrogenases.
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Affiliation(s)
- Vladimir Pelmenschikov
- Institut für Chemie, Technische Universität Berlin , Strasse des 17 Juni 135, 10623 Berlin, Germany
| | - James A Birrell
- Max-Planck-Institut für Chemische Energiekonversion , Stiftstrasse 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Cindy C Pham
- Department of Chemistry, University of California, Davis , One Shields Avenue, Davis, California 95616, United States
| | - Nakul Mishra
- Department of Chemistry, University of California, Davis , One Shields Avenue, Davis, California 95616, United States
| | - Hongxin Wang
- Department of Chemistry, University of California, Davis , One Shields Avenue, Davis, California 95616, United States
| | - Constanze Sommer
- Max-Planck-Institut für Chemische Energiekonversion , Stiftstrasse 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Edward Reijerse
- Max-Planck-Institut für Chemische Energiekonversion , Stiftstrasse 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Casseday P Richers
- School of Chemical Sciences, University of Illinois , 600 S. Mathews Avenue, Urbana, Illinois 61801, United States
| | - Kenji Tamasaku
- JASRI , Spring-8, 1-1-1 Kouto, Mikazuki-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - Yoshitaka Yoda
- JASRI , Spring-8, 1-1-1 Kouto, Mikazuki-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - Thomas B Rauchfuss
- School of Chemical Sciences, University of Illinois , 600 S. Mathews Avenue, Urbana, Illinois 61801, United States
| | - Wolfgang Lubitz
- Max-Planck-Institut für Chemische Energiekonversion , Stiftstrasse 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Stephen P Cramer
- Department of Chemistry, University of California, Davis , One Shields Avenue, Davis, California 95616, United States
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16
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Zhang Y, Mei T, Yang D, Zhang Y, Wang B, Qu J. Synthesis and reactivity of thiolate-bridged multi-iron complexes supported by cyclic (alkyl)(amino)carbene. Dalton Trans 2017; 46:15888-15896. [PMID: 29116275 DOI: 10.1039/c7dt03353b] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The combined utilization of Me2-cAAC (Me2-cAAC = :C(CH2)(CMe2)2N-2,6-iPr2C6H3) and thiolates as supporting ligands enables the access of unprecedented carbene coordinated thiolate-bridged diiron(ii) complexes [(Me2-cAAC)Fe(μ-SR)(Br)]2 (R = Me, 3; R = Et, 4). The coordination environment of each tetrahedral iron(ii) center in complexes 3 and 4 is composed of one terminal bromide atom, one carbene carbon atom and two thiolate sulfur atoms, which is similar to the carbide-containing sulfur-rich environment of iron centers in the belt region of the FeMo-cofactor. Interestingly, when NaSCPh3 was chosen as the thiolate ligand, C-S bond homolysis occurred to form a rare [3 : 1] site-differentiated cubane-type cluster [(Me2-cAAC)Fe4S4(Br)3][Me2-cAACH] (5). Furthermore, complexes 3 and 4 exhibit good exchange reactivity toward the azide anion to give novel thiolate-bridged diiron complexes with two azido ligands in a trans arrangement.
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Affiliation(s)
- Yanpeng Zhang
- State Key Laboratory of Fine Chemicals, Dalian University of Technology, Dalian 116024, P. R. China
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17
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Zanello P. The competition between chemistry and biology in assembling iron–sulfur derivatives. Molecular structures and electrochemistry. Part V. {[Fe4S4](SCysγ)4} proteins. Coord Chem Rev 2017. [DOI: 10.1016/j.ccr.2016.10.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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18
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Can M, Giles LJ, Ragsdale SW, Sarangi R. X-ray Absorption Spectroscopy Reveals an Organometallic Ni-C Bond in the CO-Treated Form of Acetyl-CoA Synthase. Biochemistry 2017; 56:1248-1260. [PMID: 28186407 DOI: 10.1021/acs.biochem.6b00983] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Acetyl-CoA synthase (ACS) is a key enzyme in the Wood-Ljungdahl pathway of anaerobic CO2 fixation, which has long been proposed to operate by a novel mechanism involving a series of protein-bound organometallic (Ni-CO, methyl-Ni, and acetyl-Ni) intermediates. Here we report the first direct structural evidence of the proposed metal-carbon bond. We describe the preparation of the highly active metal-replete enzyme and near-quantitative generation of the kinetically competent carbonylated intermediate. This advance has allowed a combination of Ni and Fe K-edge X-ray absorption spectroscopy and extended X-ray absorption fine structure experiments along with density functional theory calculations. The data reveal that CO binds to the proximal Ni of the six-metal metallocenter at the active site and undergoes dramatic structural and electronic perturbation in forming this organometallic Ni-CO intermediate. This direct identification of a Ni-carbon bond in the catalytically competent CO-bound form of the A cluster of ACS provides definitive experimental structural evidence supporting the proposed organometallic mechanism of anaerobic acetyl-CoA synthesis.
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Affiliation(s)
- Mehmet Can
- Department of Biological Chemistry, University of Michigan , Ann Arbor, Michigan 48109-0606, United States
| | - Logan J Giles
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory , Menlo Park, California 94025, United States.,Department of Chemistry, Stanford University , Stanford, California 94306, United States
| | - Stephen W Ragsdale
- Department of Biological Chemistry, University of Michigan , Ann Arbor, Michigan 48109-0606, United States
| | - Ritimukta Sarangi
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory , Menlo Park, California 94025, United States
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19
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Lauterbach L, Gee LB, Pelmenschikov V, Jenney FE, Kamali S, Yoda Y, Adams MWW, Cramer SP. Characterization of the [3Fe-4S](0/1+) cluster from the D14C variant of Pyrococcus furiosus ferredoxin via combined NRVS and DFT analyses. Dalton Trans 2016; 45:7215-9. [PMID: 27063792 PMCID: PMC4940129 DOI: 10.1039/c5dt04760a] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The D14C variant of Pyrococcus furiosus ferredoxin provides an extraordinary framework to investigate a [3Fe-4S] cluster at two oxidation levels and compare the results to its physiologic [4Fe-4S] counterpart in the very same protein. Our spectroscopic and computational study reveals vibrational property changes related to the electronic and structural aspects of both Fe-S clusters.
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Affiliation(s)
- Lars Lauterbach
- Department of Chemistry, University of California, Davis, CA 95616, USA and Institut für Chemie, Technische Universität Berlin, 10623 Berlin, Germany.
| | - Leland B Gee
- Department of Chemistry, University of California, Davis, CA 95616, USA
| | | | - Francis E Jenney
- Georgia Campus, Philadelphia College of Osteopathic Medicine, Suwanee, GA 30024, USA
| | - Saeed Kamali
- Department of Chemistry, University of California, Davis, CA 95616, USA and Department of Mechanical, Aerospace and Biomedical Engineering, University of Tennessee Space Institute, Tullahoma, TN 37388, USA
| | | | - Michael W W Adams
- Department of Biochemistry & Molecular Biology, Life Sciences Building, University of Georgia, Athens, GA 30602, USA
| | - Stephen P Cramer
- Department of Chemistry, University of California, Davis, CA 95616, USA and Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
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20
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Aussignargues C, Pandelia ME, Sutter M, Plegaria JS, Zarzycki J, Turmo A, Huang J, Ducat DC, Hegg EL, Gibney BR, Kerfeld CA. Structure and Function of a Bacterial Microcompartment Shell Protein Engineered to Bind a [4Fe-4S] Cluster. J Am Chem Soc 2016; 138:5262-70. [DOI: 10.1021/jacs.5b11734] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | - Maria-Eirini Pandelia
- Department
of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Markus Sutter
- Physical
Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | | | | | | | | | | | | | - Brian R. Gibney
- Department
of Chemistry, Brooklyn College, Brooklyn, New York 11210, United States
- Ph.D.
Programs in Chemistry and Biochemistry, The Graduate Center of the City University of New York, New York, New York 10016, United States
| | - Cheryl A. Kerfeld
- Physical
Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Department
of Plant and Microbial Biology, University of California, Berkeley, California 94720, United States
- Berkeley Synthetic Biology Institute, Berkeley, California 94720, United States
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21
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Schüren AO, Gramm VK, Dürr M, Foi A, Ivanović-Burmazović I, Doctorovich F, Ruschewitz U, Klein A. Halide coordinated homoleptic [Fe4S4X4](2-) and heteroleptic [Fe4S4X2Y2](2-) clusters (X, Y = Cl, Br, I)--alternative preparations, structural analogies and spectroscopic properties in solution and solid state. Dalton Trans 2016; 45:361-75. [PMID: 26618565 DOI: 10.1039/c5dt02769a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
New facile methods to prepare iron sulphur halide clusters [Fe4S4X4](2-) from [Fe(CO)5] and elemental sulphur were elaborated. Reactions of ferrous precursors like tetrahalidoferrates(ii) or simple ferrous halides with [Fe(CO)5] and sulphur turned out to be efficient methods to prepare homoleptic [Fe4S4X4](2-) (X = Cl, Br) and heteroleptic clusters [Fe4S4X4-nYn](2-) (X = Cl, Br; Y = Br, I). Solid materials were obtained as salts of BTMA(+) (= benzyltrimethylammonium); the new compounds containing [Fe4S4Br4](2-) and [Fe4S4X2Y2](2-) (X, Y = Cl, Br, I) were all isostructural to (BTMA)2[Fe4S4I4] (monoclinic, Cc) as inferred from synchrotron X-ray powder diffraction. While the solid materials contain defined heteroleptic clusters with a halide X : Y ratio of 2 : 2, dissolving these compounds leads to rapid scrambling of the halide ligands forming mixtures of all five possible [Fe4S4X4-nYn](2-) clusters as could be shown by UHR-ESI MS. The variation of X and Y allowed assignment of the absorption bands in the visible and NIR; the long-wavelength bands around 1100 nm were tentatively assigned to intervalence charge transfer (IVCT) transitions.
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Affiliation(s)
- Andreas O Schüren
- Department für Chemie, Institut für Anorganische Chemie, Universität zu Köln, Greinstraße 6, 50939 Köln, Germany. and Departamento de Química Inorgánica, Analítica, y Química Física, Facultad de Ciencias Exactas y Naturales, INQUIMAE-CONICET, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, Piso 3, C1428EHA Buenos Aires, Argentina
| | - Verena K Gramm
- Department für Chemie, Institut für Anorganische Chemie, Universität zu Köln, Greinstraße 6, 50939 Köln, Germany.
| | - Maximilian Dürr
- Department Chemie und Pharmazie, Lehrstuhl für Bioanorgansiche Chemie, Friedrich-Alexander-Universität Erlangen-Nürnberg, Egerlandstraße 1, 91058 Erlangen, Germany
| | - Ana Foi
- Departamento de Química Inorgánica, Analítica, y Química Física, Facultad de Ciencias Exactas y Naturales, INQUIMAE-CONICET, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, Piso 3, C1428EHA Buenos Aires, Argentina
| | - Ivana Ivanović-Burmazović
- Department Chemie und Pharmazie, Lehrstuhl für Bioanorgansiche Chemie, Friedrich-Alexander-Universität Erlangen-Nürnberg, Egerlandstraße 1, 91058 Erlangen, Germany
| | - Fabio Doctorovich
- Departamento de Química Inorgánica, Analítica, y Química Física, Facultad de Ciencias Exactas y Naturales, INQUIMAE-CONICET, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, Piso 3, C1428EHA Buenos Aires, Argentina
| | - Uwe Ruschewitz
- Department für Chemie, Institut für Anorganische Chemie, Universität zu Köln, Greinstraße 6, 50939 Köln, Germany.
| | - Axel Klein
- Department für Chemie, Institut für Anorganische Chemie, Universität zu Köln, Greinstraße 6, 50939 Köln, Germany.
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22
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Trasviña-Arenas CH, Lopez-Castillo LM, Sanchez-Sandoval E, Brieba LG. Dispensability of the [4Fe-4S] cluster in novel homologues of adenine glycosylase MutY. FEBS J 2016; 283:521-40. [PMID: 26613369 DOI: 10.1111/febs.13608] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2015] [Revised: 11/15/2015] [Accepted: 11/24/2015] [Indexed: 01/31/2023]
Abstract
7,8-Dihydro-8-deoxyguanine (8oG) is one of the most common oxidative lesions in DNA. DNA polymerases misincorporate an adenine across from this lesion. Thus, 8oG is a highly mutagenic lesion responsible for G:C→T:A transversions. MutY is an adenine glycosylase, part of the base excision repair pathway that removes adenines, when mispaired with 8oG or guanine. Its catalytic domain includes a [4Fe-4S] cluster motif coordinated by cysteinyl ligands. When this cluster is absent, MutY activity is depleted and several studies concluded that the [4Fe-4S] cluster motif is an indispensable component for DNA binding, substrate recognition and enzymatic activity. In the present study, we identified 46 MutY homologues that lack the canonical cysteinyl ligands, suggesting an absence of the [4Fe-4S] cluster. A phylogenetic analysis groups these novel MutYs into two different clades. One clade is exclusive of the order Lactobacillales and another clade has a mixed composition of anaerobic and microaerophilic bacteria and species from the protozoan genus Entamoeba. Structural modeling and sequence analysis suggests that the loss of the [4Fe-4S] cluster is compensated by a convergent solution in which bulky amino acids substitute the [4Fe-4S] cluster. We functionally characterized MutYs from Lactobacillus brevis and Entamoeba histolytica as representative members from each clade and found that both enzymes are active adenine glycosylases. Furthermore, chimeric glycosylases, in which the [4Fe-4S] cluster of Escherichia coli MutY is replaced by the corresponding amino acids of LbY and EhY, are also active. Our data indicates that the [4Fe-4S] cluster plays a structural role in MutYs and evidences the existence of alternative functional solutions in nature.
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Affiliation(s)
- Carlos H Trasviña-Arenas
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Irapuato, Guanajuato, México
| | - Laura M Lopez-Castillo
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Irapuato, Guanajuato, México
| | - Eugenia Sanchez-Sandoval
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Irapuato, Guanajuato, México
| | - Luis G Brieba
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Irapuato, Guanajuato, México
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23
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Chakraborty S, Reed J, Sage JT, Branagan NC, Petrik ID, Miner KD, Hu MY, Zhao J, Alp EE, Lu Y. Recent advances in biosynthetic modeling of nitric oxide reductases and insights gained from nuclear resonance vibrational and other spectroscopic studies. Inorg Chem 2015; 54:9317-29. [PMID: 26274098 PMCID: PMC4677664 DOI: 10.1021/acs.inorgchem.5b01105] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
This Forum Article focuses on recent
advances in structural and spectroscopic studies of biosynthetic models
of nitric oxide reductases (NORs). NORs are complex metalloenzymes
found in the denitrification pathway of Earth’s nitrogen cycle
where they catalyze the proton-dependent two-electron reduction of
nitric oxide (NO) to nitrous oxide (N2O). While much progress
has been made in biochemical and biophysical studies of native NORs
and their variants, a clear mechanistic understanding of this important
metalloenzyme related to its function is still elusive. We report
herein UV–vis and nuclear resonance vibrational spectroscopy
(NRVS) studies of mononitrosylated intermediates of the NOR reaction
of a biosynthetic model. The ability to selectively substitute metals
at either heme or nonheme metal sites allows the introduction of independent 57Fe probe atoms at either site, as well as allowing the preparation
of analogues of stable reaction intermediates by replacing either
metal with a redox inactive metal. Together with previous structural
and spectroscopic results, we summarize insights gained from studying
these biosynthetic models toward understanding structural features
responsible for the NOR activity and its mechanism. The outlook on
NOR modeling is also discussed, with an emphasis on the design of
models capable of catalytic turnovers designed based on close mimics
of the secondary coordination sphere of native NORs. New insights into nitric oxide reductases (NORs) are obtained. Using
nuclear resonance vibrational spectroscopy, we probe both iron atoms
in mononitrosylated intermediates of the NOR reaction in a biosynthetic
protein model that reveal new insights into the structural and electronic
features responsible for the NOR activity and its likely mechanism.
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Affiliation(s)
| | | | - J Timothy Sage
- Department of Physics, Northeastern University , Boston, Massachusetts 02115, United States
| | - Nicole C Branagan
- Department of Physics, Northeastern University , Boston, Massachusetts 02115, United States
| | | | | | - Michael Y Hu
- Advanced Photon Source, Argonne National Laboratory , Argonne, Illinois 60439, United States
| | - Jiyong Zhao
- Advanced Photon Source, Argonne National Laboratory , Argonne, Illinois 60439, United States
| | - E Ercan Alp
- Advanced Photon Source, Argonne National Laboratory , Argonne, Illinois 60439, United States
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24
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Hydride bridge in [NiFe]-hydrogenase observed by nuclear resonance vibrational spectroscopy. Nat Commun 2015; 6:7890. [PMID: 26259066 PMCID: PMC4531378 DOI: 10.1038/ncomms8890] [Citation(s) in RCA: 78] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Accepted: 06/18/2015] [Indexed: 11/28/2022] Open
Abstract
The metabolism of many anaerobes relies on [NiFe]-hydrogenases, whose characterization when bound to substrates has proven non-trivial. Presented here is direct evidence for a hydride bridge in the active site of the 57Fe-labelled fully reduced Ni-R form of Desulfovibrio vulgaris Miyazaki F [NiFe]-hydrogenase. A unique ‘wagging' mode involving H− motion perpendicular to the Ni(μ-H)57Fe plane was studied using 57Fe-specific nuclear resonance vibrational spectroscopy and density functional theory (DFT) calculations. On Ni(μ-D)57Fe deuteride substitution, this wagging causes a characteristic perturbation of Fe–CO/CN bands. Spectra have been interpreted by comparison with Ni(μ-H/D)57Fe enzyme mimics [(dppe)Ni(μ-pdt)(μ-H/D)57Fe(CO)3]+ and DFT calculations, which collectively indicate a low-spin Ni(II)(μ-H)Fe(II) core for Ni-R, with H− binding Ni more tightly than Fe. The present methodology is also relevant to characterizing Fe–H moieties in other important natural and synthetic catalysts. Understanding the catalytic mechanism of redox-active hydrogenases is a key to efficient hydrogen production and consumption. Here, the authors use nuclear resonance vibrational spectroscopy to study [NiFe]-hydrogenase, and observe a bridging hydride structure in an EPR silent intermediate.
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25
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Machala L, Procházka V, Miglierini M, Sharma VK, Marušák Z, Wille HC, Zbořil R. Direct evidence of Fe(V) and Fe(IV) intermediates during reduction of Fe(VI) to Fe(III): a nuclear forward scattering of synchrotron radiation approach. Phys Chem Chem Phys 2015; 17:21787-90. [PMID: 26248056 DOI: 10.1039/c5cp03784k] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Identification of unstable high-valent iron species in electron transfer reactions of ferrate(VI) (Fe(VI)O4(2-), Fe(VI)) has been an important challenge in advancing the understanding of the oxidative mechanisms of ferrates. This paper presents the first example of distinguishing various phases differing in the valence state of iron in the solid state reduction of Fe(VI) to Fe(III) oxides at 235 °C using hyperfine parameters, isomer shift and hyperfine magnetic field, obtained from nuclear forward scattering of synchrotron radiation (NFS). The NFS technique enables a fast data accumulation resulting in high time resolution of in situ experiments. The results suggest a reaction mechanism, involving Fe(V) and Fe(IV) species, in the thermal decomposition of K2FeO4 to KFeO2. The present study opens up an approach to exploring the unambiguous identification of Fe(VI), Fe(V), Fe(IV), and Fe(III) in electron-transfer reaction mechanisms of ferrates in solid and aqueous phase systems.
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Affiliation(s)
- Libor Machala
- Regional Centre of Advanced Technologies and Materials, Departments of Experimental Physics and Physical Chemistry, Faculty of Science, Palacký University, Šlechtitelů 11, 783 71 Olomouc, Czech Republic.
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26
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Maiuri M, Delfino I, Cerullo G, Manzoni C, Pelmenschikov V, Guo Y, Wang H, Gee LB, Dapper CH, Newton WE, Cramer SP. Low frequency dynamics of the nitrogenase MoFe protein via femtosecond pump probe spectroscopy - Observation of a candidate promoting vibration. J Inorg Biochem 2015; 153:128-135. [PMID: 26343576 DOI: 10.1016/j.jinorgbio.2015.07.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Revised: 06/18/2015] [Accepted: 07/09/2015] [Indexed: 11/28/2022]
Abstract
We have used femtosecond pump-probe spectroscopy (FPPS) to study the FeMo-cofactor within the nitrogenase (N2ase) MoFe protein from Azotobacter vinelandii. A sub-20-fs visible laser pulse was used to pump the sample to an excited electronic state, and a second sub-10-fs pulse was used to probe changes in transmission as a function of probe wavelength and delay time. The excited protein relaxes to the ground state with a ~1.2ps time constant. With the short laser pulse we coherently excited the vibrational modes associated with the FeMo-cofactor active site, which are then observed in the time domain. Superimposed on the relaxation dynamics, we distinguished a variety of oscillation frequencies with the strongest band peaks at ~84, 116, 189, and 226cm(-1). Comparison with data from nuclear resonance vibrational spectroscopy (NRVS) shows that the latter pair of signals comes predominantly from the FeMo-cofactor. The frequencies obtained from the FPPS experiment were interpreted with normal mode calculations using both an empirical force field (EFF) and density functional theory (DFT). The FPPS data were also compared with the first reported resonance Raman (RR) spectrum of the N2ase MoFe protein. This approach allows us to outline and assign vibrational modes having relevance to the catalytic activity of N2ase. In particular, the 226cm(-1) band is assigned as a potential 'promoting vibration' in the H-atom transfer (or proton-coupled electron transfer) processes that are an essential feature of N2ase catalysis. The results demonstrate that high-quality room-temperature solution data can be obtained on the MoFe protein by the FPPS technique and that these data provide added insight to the motions and possible operation of this protein and its catalytic prosthetic group.
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Affiliation(s)
- Margherita Maiuri
- IFN-CNR, Dipartimento di Fisica, Politecnico di Milano, Piazza Leonardo da Vinci 32, I-20133 Milano, Italy
| | - Ines Delfino
- Dipartimento di Scienze Ecologiche e Biologiche, Università della Tuscia, Largo dell'Università, I-01100 Viterbo, Italy
| | - Giulio Cerullo
- IFN-CNR, Dipartimento di Fisica, Politecnico di Milano, Piazza Leonardo da Vinci 32, I-20133 Milano, Italy
| | - Cristian Manzoni
- IFN-CNR, Dipartimento di Fisica, Politecnico di Milano, Piazza Leonardo da Vinci 32, I-20133 Milano, Italy
| | - Vladimir Pelmenschikov
- Institut für Chemie, Technische Universität Berlin, Strasse des 17 Juni 135, 10623 Berlin, Germany
| | - Yisong Guo
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, PA 15213, United States
| | - Hongxin Wang
- Department of Chemistry, University of California, Davis, CA 95616, United States
| | - Leland B Gee
- Department of Chemistry, University of California, Davis, CA 95616, United States
| | - Christie H Dapper
- Department of Biochemistry, Virginia Polytechnic Institute & State University, Blacksburg, VA 24061, United States
| | - William E Newton
- Department of Biochemistry, Virginia Polytechnic Institute & State University, Blacksburg, VA 24061, United States
| | - Stephen P Cramer
- Department of Chemistry, University of California, Davis, CA 95616, United States; Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States.
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27
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Fuss JO, Tsai CL, Ishida JP, Tainer JA. Emerging critical roles of Fe-S clusters in DNA replication and repair. BIOCHIMICA ET BIOPHYSICA ACTA 2015; 1853:1253-71. [PMID: 25655665 PMCID: PMC4576882 DOI: 10.1016/j.bbamcr.2015.01.018] [Citation(s) in RCA: 130] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Revised: 01/13/2015] [Accepted: 01/26/2015] [Indexed: 10/24/2022]
Abstract
Fe-S clusters are partners in the origin of life that predate cells, acetyl-CoA metabolism, DNA, and the RNA world. The double helix solved the mystery of DNA replication by base pairing for accurate copying. Yet, for genome stability necessary to life, the double helix has equally important implications for damage repair. Here we examine striking advances that uncover Fe-S cluster roles both in copying the genetic sequence by DNA polymerases and in crucial repair processes for genome maintenance, as mutational defects cause cancer and degenerative disease. Moreover, we examine an exciting, controversial role for Fe-S clusters in a third element required for life - the long-range coordination and regulation of replication and repair events. By their ability to delocalize electrons over both Fe and S centers, Fe-S clusters have unbeatable features for protein conformational control and charge transfer via double-stranded DNA that may fundamentally transform our understanding of life, replication, and repair. This article is part of a Special Issue entitled: Fe/S proteins: Analysis, structure, function, biogenesis and diseases.
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Affiliation(s)
- Jill O Fuss
- Life Sciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA.
| | - Chi-Lin Tsai
- Life Sciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Justin P Ishida
- Life Sciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - John A Tainer
- Life Sciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA; Department of Molecular and Cellular Oncology, The University of Texas M. D. Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX 77030, USA.
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28
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Lauterbach L, Wang H, Horch M, Gee LB, Yoda Y, Tanaka Y, Zebger I, Lenz O, Cramer SP. Nuclear resonance vibrational spectroscopy reveals the FeS cluster composition and active site vibrational properties of an O 2-tolerant NAD +-reducing [NiFe] hydrogenase. Chem Sci 2015; 6:1055-1060. [PMID: 25678951 PMCID: PMC4321745 DOI: 10.1039/c4sc02982h] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Nuclear resonance vibrational spectroscopy is used to characterize all Fe-containing cofactors in a complex multicofactor enzyme.
Hydrogenases are complex metalloenzymes that catalyze the reversible splitting of molecular hydrogen into protons and electrons essentially without overpotential. The NAD+-reducing soluble hydrogenase (SH) from Ralstonia eutropha is capable of H2 conversion even in the presence of usually toxic dioxygen. The molecular details of the underlying reactions are largely unknown, mainly because of limited knowledge of the structure and function of the various metal cofactors present in the enzyme. Here, all iron-containing cofactors of the SH were investigated by 57Fe specific nuclear resonance vibrational spectroscopy (NRVS). Our data provide experimental evidence for one [2Fe2S] center and four [4Fe4S] clusters, which is consistent with the amino acid sequence composition. Only the [2Fe2S] cluster and one of the four [4Fe4S] clusters were reduced upon incubation of the SH with NADH. This finding explains the discrepancy between the large number of FeS clusters and the small amount of FeS cluster-related signals as detected by electron paramagnetic resonance spectroscopic analysis of several NAD+-reducing hydrogenases. For the first time, Fe–CO and Fe–CN modes derived from the [NiFe] active site could be distinguished by NRVS through selective 13C labeling of the CO ligand. This strategy also revealed the molecular coordinates that dominate the individual Fe–CO modes. The present approach explores the complex vibrational signature of the Fe–S clusters and the hydrogenase active site, thereby showing that NRVS represents a powerful tool for the elucidation of complex biocatalysts containing multiple cofactors.
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Affiliation(s)
- Lars Lauterbach
- Institute of Chemistry, Technische Universität Berlin, Straße des 17, Juni 135, 10623 Berlin, Germany ; Department of Chemistry, University of California, One Shields Ave, Davis CA 95616, USA
| | - Hongxin Wang
- Department of Chemistry, University of California, One Shields Ave, Davis CA 95616, USA ; Physical Biosciences Division, Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley CA 94720, USA
| | - Marius Horch
- Institute of Chemistry, Technische Universität Berlin, Straße des 17, Juni 135, 10623 Berlin, Germany
| | - Leland B Gee
- Department of Chemistry, University of California, One Shields Ave, Davis CA 95616, USA
| | - Yoshitaka Yoda
- JASRI, SPring-8, 1-1-1 Kouto, Mikazuki-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - Yoshihito Tanaka
- RIKEN, SPring-8, 1-1-1 Kouto, Mikazuki-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - Ingo Zebger
- Institute of Chemistry, Technische Universität Berlin, Straße des 17, Juni 135, 10623 Berlin, Germany
| | - Oliver Lenz
- Institute of Chemistry, Technische Universität Berlin, Straße des 17, Juni 135, 10623 Berlin, Germany
| | - Stephen P Cramer
- Department of Chemistry, University of California, One Shields Ave, Davis CA 95616, USA ; Physical Biosciences Division, Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley CA 94720, USA
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Liu K, Rykov AI, Wang J, Zhang T. Recent Advances in the Application of Mößbauer Spectroscopy in Heterogeneous Catalysis. ADVANCES IN CATALYSIS 2015. [DOI: 10.1016/bs.acat.2015.09.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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30
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Scott A, Pelmenschikov V, Guo Y, Yan L, Wang H, George SJ, Dapper CH, Newton WE, Yoda Y, Tanaka Y, Cramer SP. Structural characterization of CO-inhibited Mo-nitrogenase by combined application of nuclear resonance vibrational spectroscopy, extended X-ray absorption fine structure, and density functional theory: new insights into the effects of CO binding and the role of the interstitial atom. J Am Chem Soc 2014; 136:15942-54. [PMID: 25275608 PMCID: PMC4235365 DOI: 10.1021/ja505720m] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Indexed: 01/21/2023]
Abstract
The properties of CO-inhibited Azotobacter vinelandii (Av) Mo-nitrogenase (N2ase) have been examined by the combined application of nuclear resonance vibrational spectroscopy (NRVS), extended X-ray absorption fine structure (EXAFS), and density functional theory (DFT). Dramatic changes in the NRVS are seen under high-CO conditions, especially in a 188 cm(-1) mode associated with symmetric breathing of the central cage of the FeMo-cofactor. Similar changes are reproduced with the α-H195Q N2ase variant. In the frequency region above 450 cm(-1), additional features are seen that are assigned to Fe-CO bending and stretching modes (confirmed by (13)CO isotope shifts). The EXAFS for wild-type N2ase shows evidence for a significant cluster distortion under high-CO conditions, most dramatically in the splitting of the interaction between Mo and the shell of Fe atoms originally at 5.08 Å in the resting enzyme. A DFT model with both a terminal -CO and a partially reduced -CHO ligand bound to adjacent Fe sites is consistent with both earlier FT-IR experiments, and the present EXAFS and NRVS observations for the wild-type enzyme. Another DFT model with two terminal CO ligands on the adjacent Fe atoms yields Fe-CO bands consistent with the α-H195Q variant NRVS. The calculations also shed light on the vibrational "shake" modes of the interstitial atom inside the central cage, and their interaction with the Fe-CO modes. Implications for the CO and N2 reactivity of N2ase are discussed.
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Affiliation(s)
- Aubrey
D. Scott
- Department
of Chemistry, University of California, Davis, California 95616, United States
| | | | - Yisong Guo
- Department
of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Lifen Yan
- Department
of Chemistry, University of California, Davis, California 95616, United States
| | - Hongxin Wang
- Department
of Chemistry, University of California, Davis, California 95616, United States
- Physical
Biosciences Division, Lawrence Berkeley
National Laboratory, Berkeley, California 94720, United States
| | - Simon J. George
- Department
of Chemistry, University of California, Davis, California 95616, United States
| | - Christie H. Dapper
- Department
of Biochemistry, Virginia Polytechnic Institute
& State University, Blacksburg, Virginia 24061, United States
| | - William E. Newton
- Department
of Biochemistry, Virginia Polytechnic Institute
& State University, Blacksburg, Virginia 24061, United States
| | - Yoshitaka Yoda
- Research
and Utilization Division, SPring-8/JASRI, 1-1-1 Kouto, Sayo, Hyogo 679-5198, Japan
| | - Yoshihito Tanaka
- SR
Materials Science Instrumentation Unit, RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
| | - Stephen P. Cramer
- Department
of Chemistry, University of California, Davis, California 95616, United States
- Physical
Biosciences Division, Lawrence Berkeley
National Laboratory, Berkeley, California 94720, United States
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31
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Rupnik K, Lee CC, Wiig JA, Hu Y, Ribbe MW, Hales BJ. Nonenzymatic synthesis of the P-cluster in the nitrogenase MoFe protein: evidence of the involvement of all-ferrous [Fe4S4](0) intermediates. Biochemistry 2014; 53:1108-16. [PMID: 24520862 PMCID: PMC3970913 DOI: 10.1021/bi401699u] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
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The
P-cluster in the nitrogenase MoFe protein is a [Fe8S7] cluster and represents the most complex FeS cluster
found in Nature. To date, the exact mechanism of the in vivo synthesis of the P-cluster remains unclear. What is known is that
the precursor to the P-cluster is a pair of neighboring [Fe4S4]-like clusters found on the ΔnifH MoFe protein, a protein expressed in the absence of the nitrogenase
Fe protein (NifH). Moreover, incubation of the ΔnifH MoFe protein with NifH and MgATP results in the synthesis of the
MoFe protein P-clusters. To improve our understanding of the mechanism
of this reaction, we conducted a magnetic circular dichroism (MCD)
spectroscopic study of the [Fe4S4]-like clusters
on the ΔnifH MoFe protein. Reducing the ΔnifH MoFe protein with Ti(III) citrate results in the quenching
of the S = 1/2 electron paramagnetic
resonance signal
associated with the [Fe4S4]+ state
of the clusters. MCD spectroscopy reveals this reduction results in
all four 4Fe clusters being converted into the unusual, all-ferrous
[Fe4S4]0 state. Subsequent increases
of the redox potential generate new clusters. Most significantly,
one of these newly formed clusters is the P-cluster, which represents
approximately 20–25% of the converted Fe concentration. The
other two clusters are an
X cluster, of unknown structure, and a classic [Fe4S4] cluster, which represents approximately 30–35% of
the Fe concentration. Diamagnetic FeS clusters may also have
been generated but, because of their low spectral intensity, would
not have been identified. These results demonstrate that the nitrogenase
P-cluster can be generated in the absence of NifH and MgATP.
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Affiliation(s)
- Kresimir Rupnik
- Department of Chemistry, Louisiana State University , Baton Rouge, Louisiana 70808, United States
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32
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Rizzello L, Pompa PP. Nanosilver-based antibacterial drugs and devices: mechanisms, methodological drawbacks, and guidelines. Chem Soc Rev 2013; 43:1501-18. [PMID: 24292075 DOI: 10.1039/c3cs60218d] [Citation(s) in RCA: 450] [Impact Index Per Article: 40.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Despite the current advancement in drug discovery and pharmaceutical biotechnology, infection diseases induced by bacteria continue to be one of the greatest health problems worldwide, afflicting millions of people annually. Almost all microorganisms have, in fact, an intrinsic outstanding ability to flout many therapeutic interventions, thanks to their fast and easy-to-occur evolutionary genetic mechanisms. At the same time, big pharmaceutical companies are losing interest in new antibiotics development, shifting their capital investments in much more profitable research and development fields. New smart solutions are, thus, required to overcome such concerns, and should combine the feasibility of industrial production processes with cheapness and effectiveness. In this framework, nanotechnology-based solutions, and in particular silver nanoparticles (AgNPs), have recently emerged as promising candidates in the market as new antibacterial agents. AgNPs display, in fact, enhanced broad-range antibacterial/antiviral properties, and their synthesis procedures are quite cost effective. However, despite their increasing impact on the market, many relevant issues are still open. These include the molecular mechanisms governing the AgNPs-bacteria interactions, the physico-chemical parameters underlying their toxicity to prokaryotes, the lack of standardized methods and materials, and the uncertainty in the definition of general strategies to develop smart antibacterial drugs and devices based on nanosilver. In this review, we analyze the experimental data on the bactericidal effects of AgNPs, discussing the complex scenario and presenting the potential drawbacks and limitations in the techniques and methods employed. Moreover, after analyzing in depth the main mechanisms involved, we provide some general strategies/procedures to perform antibacterial tests of AgNPs, and propose some general guidelines for the design of antibacterial nanosystems and devices based on silver/nanosilver.
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Affiliation(s)
- Loris Rizzello
- Istituto Italiano di Tecnologia (IIT), Center for Bio-Molecular Nanotechnologies@UniLe, Via Barsanti, 73010 Arnesano (Lecce), Italy.
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33
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Jain R, Vanamee ES, Dzikovski BG, Buku A, Johnson RE, Prakash L, Prakash S, Aggarwal AK. An iron-sulfur cluster in the polymerase domain of yeast DNA polymerase ε. J Mol Biol 2013; 426:301-8. [PMID: 24144619 DOI: 10.1016/j.jmb.2013.10.015] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2013] [Accepted: 10/08/2013] [Indexed: 10/26/2022]
Abstract
DNA polymerase ε (Polε) is a multi-subunit polymerase that contributes to genomic stability via its roles in leading strand replication and the repair of damaged DNA. Polε from Saccharomyces cerevisiae is composed of four subunits--Pol2, Dpb2, Dpb3, and Dpb4. Here, we report the presence of a [Fe-S] cluster directly within the active polymerase domain of Pol2 (residues 1-1187). We show that binding of the [Fe-S] cluster is mediated by cysteines in an insertion (Pol2(ins)) that is conserved in Pol2 orthologs but is absent in the polymerase domains of Polα, Polδ, and Polζ. We also show that the [Fe-S] cluster is required for Pol2 polymerase activity but not for its exonuclease activity. Collectively, our work suggests that Polε is perhaps more sensitive than other DNA polymerases to changes in oxidative stress in eukaryotic cells.
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Affiliation(s)
- Rinku Jain
- Department of Structural and Chemical Biology, Mount Sinai School of Medicine, Box 1677, 1425 Madison Avenue, New York, NY 10029, USA
| | - Eva S Vanamee
- Department of Structural and Chemical Biology, Mount Sinai School of Medicine, Box 1677, 1425 Madison Avenue, New York, NY 10029, USA
| | - Boris G Dzikovski
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Angeliki Buku
- Department of Structural and Chemical Biology, Mount Sinai School of Medicine, Box 1677, 1425 Madison Avenue, New York, NY 10029, USA
| | - Robert E Johnson
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, 301 University Boulevard, Galveston, TX 77755-1061, USA
| | - Louise Prakash
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, 301 University Boulevard, Galveston, TX 77755-1061, USA
| | - Satya Prakash
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, 301 University Boulevard, Galveston, TX 77755-1061, USA
| | - Aneel K Aggarwal
- Department of Structural and Chemical Biology, Mount Sinai School of Medicine, Box 1677, 1425 Madison Avenue, New York, NY 10029, USA.
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