1
|
Brown AC, Suess DLM. An Iron-Sulfur Cluster with a Highly Pyramidalized Three-Coordinate Iron Center and a Negligible Affinity for Dinitrogen. J Am Chem Soc 2023; 145:20088-20096. [PMID: 37656961 PMCID: PMC10824254 DOI: 10.1021/jacs.3c07677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/03/2023]
Abstract
Attempts to generate open coordination sites for N2 binding at synthetic Fe-S clusters often instead result in cluster oligomerization. Recently, it was shown for Mo-Fe-S clusters that such oligomerization reactions can be prevented through the use of sterically protective supporting ligands, thereby enabling N2 complex formation. Here, this strategy is extended to Fe-only Fe-S clusters. One-electron reduction of (IMes)3Fe4S4Cl (IMes = 1,3-dimesitylimidazol-2-ylidene) forms the transiently stable edge-bridged double cubane (IMes)6Fe8S8, which loses two IMes ligands to form the face-bridged double-cubane, (IMes)4Fe8S8. The finding that the three supporting IMes ligands do not confer sufficient protection to curtail cluster oligomerization prompted the design of a new N-heterocyclic carbene, SIArMe,iPr (1,3-bis(3,5-diisopropyl-2,6-dimethylphenyl)-2-imidazolidinylidene; abbreviated as SIAr), that features bulky groups strategically placed in remote positions. When the reduction of (SIAr)3Fe4S4Cl or [(SIAr)3Fe4S4(THF)]+ is conducted in the presence of SIAr, the formation of (SIAr)4Fe8S8 is indeed suppressed, permitting characterization of the reduced [Fe4S4]0 product. Surprisingly, rather than being an N2 complex, the product is simply (SIAr)3Fe4S4: a cluster with a three-coordinate Fe site that adopts an unusually pyramidalized geometry. Although (SIAr)3Fe4S4 does not coordinate N2 to any appreciable extent under the surveyed conditions, it does bind CO to form (SIAr)3Fe4S4(CO). This finding demonstates that the binding pocket at the unique Fe is not too small for N2; instead, the exceptionally weak affinity for N2 can be attributed to weak Fe-N2 bonding. The differences in the N2 coordination chemistry between sterically protected Mo-Fe-S clusters and Fe-only Fe-S clusters are discussed.
Collapse
Affiliation(s)
- Alexandra C Brown
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Daniel L M Suess
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| |
Collapse
|
2
|
Abstract
The Fischer-Tropsch (FT) process converts a mixture of CO and H2 into liquid hydrocarbons as a major component of the gas-to-liquid technology for the production of synthetic fuels. Contrary to the energy-demanding chemical FT process, the enzymatic FT-type reactions catalyzed by nitrogenase enzymes, their metalloclusters, and synthetic mimics utilize H+ and e- as the reducing equivalents to reduce CO, CO2, and CN- into hydrocarbons under ambient conditions. The C1 chemistry exemplified by these FT-type reactions is underscored by the structural and electronic properties of the nitrogenase-associated metallocenters, and recent studies have pointed to the potential relevance of this reactivity to nitrogenase mechanism, prebiotic chemistry, and biotechnological applications. This review will provide an overview of the features of nitrogenase enzymes and associated metalloclusters, followed by a detailed discussion of the activities of various nitrogenase-derived FT systems and plausible mechanisms of the enzymatic FT reactions, highlighting the versatility of this unique reactivity while providing perspectives onto its mechanistic, evolutionary, and biotechnological implications.
Collapse
Affiliation(s)
- Yilin Hu
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine 92697-3900, USA
| | - Chi Chung Lee
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine 92697-3900, USA
| | - Mario Grosch
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine 92697-3900, USA
| | - Joseph B. Solomon
- Department of Chemistry, University of California, Irvine, CA 92697-2025, USA
| | - Wolfgang Weigand
- Institute of Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - Markus W. Ribbe
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine 92697-3900, USA
- Department of Chemistry, University of California, Irvine, CA 92697-2025, USA
| |
Collapse
|
3
|
Eight Unexpected Selenoprotein Families in Organometallic Biochemistry in Clostridium difficile, in ABC Transport, and in Methylmercury Biosynthesis. J Bacteriol 2023; 205:e0025922. [PMID: 36598231 PMCID: PMC9879109 DOI: 10.1128/jb.00259-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The bioinformatics of a nine-gene locus, designated selenocysteine-assisted organometallic (SAO), was investigated after identifying six new selenoprotein families and constructing hidden Markov models (HMMs) that find and annotate members of those families. Four are selenoproteins in most SAO loci, including Clostridium difficile. They include two ABC transporter subunits, namely, permease SaoP, with selenocysteine (U) at the channel-gating position, and substrate-binding subunit SaoB. Cytosolic selenoproteins include SaoL, homologous to MerB organomercurial lyases from mercury resistance loci, and SaoT, related to thioredoxins. SaoL, SaoB, and surface protein SaoC (an occasional selenoprotein) share an unusual CU dipeptide motif, which is something rare in selenoproteins but found in selenoprotein variants of mercury resistance transporter subunit MerT. A nonselenoprotein, SaoE, shares homology with Cu/Zn efflux and arsenical efflux pumps. The organization of the SAO system suggests substrate interaction with surface-exposed selenoproteins, followed by import, metabolism that may cleave a carbon-to-heavy metal bond, and finally metal efflux. A novel type of mercury resistance is possible, but SAO instead may support fermentative metabolism, with selenocysteine-mediated formation of organometallic intermediates, followed by import, degradation, and metal efflux. Phylogenetic profiling shows SOA loci consistently co-occur with Stickland fermentation markers but even more consistently with 8Fe-9S cofactor-type double-cubane proteins. Hypothesizing that the SAO system forms organometallic intermediates, we investigated the known methylmercury formation protein families HgcA and HgcB. Both families contained overlooked selenoproteins. Most HgcAs have a CU motif N terminal to their previously accepted start sites. Seeking additional rare and overlooked selenoproteins may help reveal more cryptic aspects of microbial biochemistry. IMPORTANCE This work adds 8 novel prokaryotic selenoproteins to the 80 or so families previously known. It describes the SAO (selenocysteine-assisted organometallic) locus, with the most selenoproteins of any known system. The rare CU motif recurs throughout, suggesting the formation and degradation of organometallic compounds. That suggestion triggered a reexamination of HgcA and HcgB, which are methylmercury formation proteins that can adversely impact food safety. Both are selenoproteins, once corrected, with HgcA again showing a CU motif. The SAO system is plausibly a mercury resistance locus for selenium-dependent anaerobes. But instead, it may exploit heavy metals as cofactors in organometallic intermediate-forming pathways that circumvent high activation energies and facilitate the breakdown of otherwise poorly accessible nutrients. SAO could provide an edge that helps Clostridium difficile, an important pathogen, establish disease.
Collapse
|
4
|
Ribbe MW, Górecki K, Grosch M, Solomon JB, Quechol R, Liu YA, Lee CC, Hu Y. Nitrogenase Fe Protein: A Multi-Tasking Player in Substrate Reduction and Metallocluster Assembly. Molecules 2022; 27:molecules27196743. [PMID: 36235278 PMCID: PMC9571451 DOI: 10.3390/molecules27196743] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 10/05/2022] [Accepted: 10/06/2022] [Indexed: 11/18/2022] Open
Abstract
The Fe protein of nitrogenase plays multiple roles in substrate reduction and metallocluster assembly. Best known for its function to transfer electrons to its catalytic partner during nitrogenase catalysis, the Fe protein is also a key player in the biosynthesis of the complex metalloclusters of nitrogenase. In addition, it can function as a reductase on its own and affect the ambient reduction of CO2 or CO to hydrocarbons. This review will provide an overview of the properties and functions of the Fe protein, highlighting the relevance of this unique FeS enzyme to areas related to the catalysis, biosynthesis, and applications of the fascinating nitrogenase system.
Collapse
Affiliation(s)
- Markus W. Ribbe
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697-3900, USA
- Department of Chemistry, University of California, Irvine, CA 92697-2025, USA
- Correspondence: (M.W.R.); (Y.H.)
| | - Kamil Górecki
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697-3900, USA
| | - Mario Grosch
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697-3900, USA
| | - Joseph B. Solomon
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697-3900, USA
- Department of Chemistry, University of California, Irvine, CA 92697-2025, USA
| | - Robert Quechol
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697-3900, USA
| | - Yiling A. Liu
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697-3900, USA
| | - Chi Chung Lee
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697-3900, USA
| | - Yilin Hu
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697-3900, USA
- Correspondence: (M.W.R.); (Y.H.)
| |
Collapse
|
5
|
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.
Collapse
|
6
|
Brown AC, Thompson NB, Suess DLM. Evidence for Low-Valent Electronic Configurations in Iron-Sulfur Clusters. J Am Chem Soc 2022; 144:9066-9073. [PMID: 35575703 DOI: 10.1021/jacs.2c01872] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Although biological iron-sulfur (Fe-S) clusters perform some of the most difficult redox reactions in nature, they are thought to be composed exclusively of Fe2+ and Fe3+ ions, as well as mixed-valent pairs with average oxidation states of Fe2.5+. We herein show that Fe-S clusters formally composed of these valences can access a wider range of electronic configurations─in particular, those featuring low-valent Fe1+ centers. We demonstrate that CO binding to a synthetic [Fe4S4]0 cluster supported by N-heterocyclic carbene ligands induces the generation of Fe1+ centers via intracluster electron transfer, wherein a neighboring pair of Fe2+ sites reduces the CO-bound site to a low-valent Fe1+ state. Similarly, CO binding to an [Fe4S4]+ cluster induces electron delocalization with a neighboring Fe site to form a mixed-valent Fe1.5+Fe2.5+ pair in which the CO-bound site adopts partial low-valent character. These low-valent configurations engender remarkable C-O bond activation without having to traverse highly negative and physiologically inaccessible [Fe4S4]0/[Fe4S4]- redox couples.
Collapse
Affiliation(s)
- Alexandra C Brown
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Niklas B Thompson
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Daniel L M Suess
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| |
Collapse
|
7
|
Monkcom EC, Negenman HA, Masferrer-Rius E, Lutz M, Ye S, Bill E, Klein Gebbink RJ. 2H1C Mimicry: Bioinspired Iron and Zinc Complexes Supported by N,N,O Phenolate Ligands. Eur J Inorg Chem 2022. [DOI: 10.1002/ejic.202101046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Emily C. Monkcom
- Utrecht University: Universiteit Utrecht Organic Chemistry and Catalysis Universiteitsweg 99 3584CG Utrecht NETHERLANDS
| | - Hidde A. Negenman
- Utrecht University: Universiteit Utrecht Organic Chemistry and Catalysis Universiteitsweg 99 3584CG Utrecht NETHERLANDS
| | - Eduard Masferrer-Rius
- Utrecht University: Universiteit Utrecht Organic Chemistry and Catalysis Universiteitsweg 99 3584CG Utrecht NETHERLANDS
| | - Martin Lutz
- Utrecht University: Universiteit Utrecht Crystal and Structural Chemistry Universiteitsweg 99 3584CG Utrecht NETHERLANDS
| | - Shengfa Ye
- Chinese Academy of Sciences Institute of Chemistry 457 Zhongshan Road 116023 Dalian CHINA
| | - Eckhard Bill
- Max Planck Institute of Coal Research: Max-Planck-Institut fur Kohlenforschung Inorganic Spectroscopy Kaiser-Wilhelm-Platz 1 45470 Mülheim an der Ruhr GERMANY
| | | |
Collapse
|
8
|
Abstract
57Fe Mӧssbauer spectroscopy is unparalleled in the study of Fe-S cluster-containing proteins because of its unique ability to detect all forms of iron. Enrichment of biological samples with the 57Fe isotope and manipulation of experimental parameters such as temperature and magnetic field allow for elucidation of the number of Fe-S clusters present in a given protein, their nuclearity, oxidation state, geometry, and ligation environment, as well as any transient states relevant to enzyme chemistry. This chapter is arranged in five sections to help navigate an experimentalist to utilize 57Fe Mӧssbauer spectroscopy for delineating the role and structure of biological Fe-S clusters. The first section lays out the tools and technical considerations for the preparation of 57Fe-labeled samples. The choice of experimental parameters and their effects on the Mӧssbauer spectra are presented in the following two sections. The last two sections provide a theoretical and practical guide on spectral acquisition and analysis relevant to Fe-S centers.
Collapse
|
9
|
Guo L, Zhang D, Fu S, Zhang J, Zhang X, He J, Peng C, Zhang Y, Qiu Y, Ye C, Liu Y, Wu Z, Hu CAA. Metagenomic Sequencing Analysis of the Effects of Colistin Sulfate on the Pig Gut Microbiome. Front Vet Sci 2021; 8:663820. [PMID: 34277753 PMCID: PMC8282896 DOI: 10.3389/fvets.2021.663820] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 05/25/2021] [Indexed: 12/14/2022] Open
Abstract
The gut microbiome plays important roles in maintaining host health, and inappropriate use of antibiotics can cause imbalance, which may contribute to serious disease. However, despite its promise, using metagenomic sequencing to explore the effects of colistin on gut microbiome composition in pig has not been reported. Herein, we evaluated the roles of colistin in gut microbiome modulation in pigs. Metagenomic analysis demonstrated that overall microbial diversity was higher in the colistin group compared with the control group. Antibiotic Resistance Genes Database analysis demonstrated that following colistin treatment, expression levels of tsnr, ant6ia, tetq, oleb, norm, ant3ia, and mexh were significantly upregulated, indicating that colistin may induce transformation of antibiotic resistance genes. Colistin also affected the microbiome distribution patterns at both genus and phylum levels. In addition, at the species level, colistin significantly reduced the abundance of Prevotella copri, Phascolarctobacterium succinatutens, and Prevotella stercorea and enhanced the abundance of Treponema succinifaciens and Acidaminococcus fermentans compared to the control group. Gene Ontology analysis demonstrated that following treatment with colistin, metabolic process, cellular process, and single-organism process were the dominant affected terms. Kyoto Encyclopedia of Genes and Genomes analysis showed that oxidative phosphorylation, protein processing in endoplasmic reticulum, various types of N-glycan biosynthesis, protein processing in endoplasmic reticulum, pathogenic Escherichia coli infection, and mitogen-activated protein kinase signaling pathway–yeast were the dominant signaling pathways in the colistin group. Overall, our results suggested that colistin affects microbial diversity and may modulate gut microbiome composition in pig, potentially providing novel strategy or antibiotic rationalization pertinent to human and animal health.
Collapse
Affiliation(s)
- Ling Guo
- Hubei Key Laboratory of Animal Nutrition and Feed Science, Wuhan Polytechnic University, Wuhan, China.,Hubei Collaborative Innovation Center for Animal Nutrition and Feed Safety, Wuhan, China
| | - Dan Zhang
- Hubei Key Laboratory of Animal Nutrition and Feed Science, Wuhan Polytechnic University, Wuhan, China.,Hubei Collaborative Innovation Center for Animal Nutrition and Feed Safety, Wuhan, China
| | - Shulin Fu
- Hubei Key Laboratory of Animal Nutrition and Feed Science, Wuhan Polytechnic University, Wuhan, China.,Hubei Collaborative Innovation Center for Animal Nutrition and Feed Safety, Wuhan, China
| | - Jiacheng Zhang
- Hubei Key Laboratory of Animal Nutrition and Feed Science, Wuhan Polytechnic University, Wuhan, China.,Hubei Collaborative Innovation Center for Animal Nutrition and Feed Safety, Wuhan, China
| | - Xiaofang Zhang
- Hubei Key Laboratory of Animal Nutrition and Feed Science, Wuhan Polytechnic University, Wuhan, China.,Hubei Collaborative Innovation Center for Animal Nutrition and Feed Safety, Wuhan, China
| | - Jing He
- Hubei Key Laboratory of Animal Nutrition and Feed Science, Wuhan Polytechnic University, Wuhan, China.,Hubei Collaborative Innovation Center for Animal Nutrition and Feed Safety, Wuhan, China
| | - Chun Peng
- Hubei Key Laboratory of Animal Nutrition and Feed Science, Wuhan Polytechnic University, Wuhan, China.,Hubei Collaborative Innovation Center for Animal Nutrition and Feed Safety, Wuhan, China
| | - Yunfei Zhang
- Hubei Key Laboratory of Animal Nutrition and Feed Science, Wuhan Polytechnic University, Wuhan, China.,Hubei Collaborative Innovation Center for Animal Nutrition and Feed Safety, Wuhan, China
| | - Yinsheng Qiu
- Hubei Key Laboratory of Animal Nutrition and Feed Science, Wuhan Polytechnic University, Wuhan, China.,Hubei Collaborative Innovation Center for Animal Nutrition and Feed Safety, Wuhan, China
| | - Chun Ye
- Hubei Key Laboratory of Animal Nutrition and Feed Science, Wuhan Polytechnic University, Wuhan, China.,Hubei Collaborative Innovation Center for Animal Nutrition and Feed Safety, Wuhan, China
| | - Yu Liu
- Hubei Key Laboratory of Animal Nutrition and Feed Science, Wuhan Polytechnic University, Wuhan, China.,Hubei Collaborative Innovation Center for Animal Nutrition and Feed Safety, Wuhan, China
| | - Zhongyuan Wu
- Hubei Key Laboratory of Animal Nutrition and Feed Science, Wuhan Polytechnic University, Wuhan, China.,Hubei Collaborative Innovation Center for Animal Nutrition and Feed Safety, Wuhan, China
| | - Chien-An Andy Hu
- Hubei Key Laboratory of Animal Nutrition and Feed Science, Wuhan Polytechnic University, Wuhan, China.,Biochemistry and Molecular Biology, University of New Mexico School of Medicine, Albuquerque, NM, United States
| |
Collapse
|
10
|
Li Manni G, Dobrautz W, Bogdanov NA, Guther K, Alavi A. Resolution of Low-Energy States in Spin-Exchange Transition-Metal Clusters: Case Study of Singlet States in [Fe(III) 4S 4] Cubanes. J Phys Chem A 2021; 125:4727-4740. [PMID: 34048648 PMCID: PMC8201447 DOI: 10.1021/acs.jpca.1c00397] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
![]()
Polynuclear transition-metal
(PNTM) clusters owe their catalytic
activity to numerous energetically low-lying spin states and stable
oxidation states. The characterization of their electronic structure
represents one of the greatest challenges of modern chemistry. We
propose a theoretical framework that enables the resolution of targeted
electronic states with ease and apply it to two [Fe(III)4S4] cubanes. Through direct access to their many-body
wave functions, we identify important correlation mechanisms and their
interplay with the geometrical distortions observed in these clusters,
which are core properties in understanding their catalytic activity.
The simulated magnetic coupling constants predicted by our strategy
allow us to make qualitative connections between spin interactions
and geometrical distortions, demonstrating its predictive power. Moreover,
despite its simplicity, the strategy provides magnetic coupling constants
in good agreement with the available experimental ones. The complexes
are intrinsically frustrated anti-ferromagnets, and the obtained spin
structures together with the geometrical distortions represent two
possible ways to release spin frustration (spin-driven Jahn–Teller
distortion). Our paradigm provides a simple, yet rigorous, route to
uncover the electronic structure of PNTM clusters and may be applied
to a wide variety of such clusters.
Collapse
Affiliation(s)
- Giovanni Li Manni
- Department of Electronic Structure Theory, Max Planck Institute for Solid State Research, Heisenbergstraße 1, 70569 Stuttgart, Germany
| | - Werner Dobrautz
- Department of Electronic Structure Theory, Max Planck Institute for Solid State Research, Heisenbergstraße 1, 70569 Stuttgart, Germany
| | - Nikolay A Bogdanov
- Department of Electronic Structure Theory, Max Planck Institute for Solid State Research, Heisenbergstraße 1, 70569 Stuttgart, Germany
| | - Kai Guther
- Department of Electronic Structure Theory, Max Planck Institute for Solid State Research, Heisenbergstraße 1, 70569 Stuttgart, Germany
| | - Ali Alavi
- Department of Electronic Structure Theory, Max Planck Institute for Solid State Research, Heisenbergstraße 1, 70569 Stuttgart, Germany.,Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| |
Collapse
|
11
|
Bím D, Alonso-Gil S, Srnec M. From Synthetic to Biological Fe 4 S 4 Complexes: Redox Properties Correlated to Function of Radical S-Adenosylmethionine Enzymes. Chempluschem 2020; 85:2534-2541. [PMID: 33245201 DOI: 10.1002/cplu.202000663] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 11/02/2020] [Indexed: 11/10/2022]
Abstract
By employing the computational protocol for calculation of reduction potentials of the Fe4 S4 -containing species validated using a representative series of well-defined synthetic complexes, we focused on redox properties of two prototypical radical SAM enzymes to reveal how they transform SAM into the reactive 5'-deoxyadenosyl radical, and how they tune this radical for its proper biological function. We found the reduction potential of SAM is indeed elevated by 0.3-0.4 V upon coordination to Fe4 S4 , which was previously speculated in the literature. This makes a generation of 5'-deoxyadenosyl radical from SAM less endergonic (by ca. 7-9 kcal mol-1 ) and hence more feasible in both enzymes as compared to the identical process in water. Furthermore, our calculations indicate that the enzyme-bound 5'-deoxyadenosyl radical has a significantly lower reduction potential than in referential aqueous solution, which may help the enzymes to suppress potential side redox reactions and simultaneously elevate its proton-philic character, which may, in turn, promote the radical hydrogen-atom abstraction ability.
Collapse
Affiliation(s)
- Daniel Bím
- J. Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, Dolejškova 3, Prague, 8 182 23, Czech Republic
| | - Santiago Alonso-Gil
- J. Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, Dolejškova 3, Prague, 8 182 23, Czech Republic
| | - Martin Srnec
- J. Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, Dolejškova 3, Prague, 8 182 23, Czech Republic
| |
Collapse
|
12
|
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.
Collapse
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
| |
Collapse
|
13
|
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.
Collapse
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
| |
Collapse
|
14
|
Jeoung JH, Martins BM, Dobbek H. Double-Cubane [8Fe9S] Clusters: A Novel Nitrogenase-Related Cofactor in Biology. Chembiochem 2020; 21:1710-1716. [PMID: 32187824 PMCID: PMC7317905 DOI: 10.1002/cbic.202000016] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 02/14/2020] [Indexed: 12/20/2022]
Abstract
Three different types of electron-transferring metallo-ATPases are able to couple ATP hydrolysis to the reduction of low-potential metal sites, thereby energizing an electron. Besides the Fe-protein known from nitrogenase and homologous enzymes, two other kinds of ATPase with different scaffolds and cofactors are used to achieve a unidirectional, energetic, uphill electron transfer to either reduce inactive Co-corrinoid-containing proteins (RACE-type activators) or a second iron-sulfur cluster-containing enzyme of a unique radical enzymes family (archerases). We have found a new cofactor in the latter enzyme family, that is, a double-cubane cluster with two [4Fe4S] subclusters bridged by a sulfido ligand. An enzyme containing this cofactor catalyzes the ATP-dependent reduction of small molecules, including acetylene. Thus, enzymes containing the double-cubane cofactor are analogous in function and share some structural features with nitrogenases.
Collapse
Affiliation(s)
- Jae-Hun Jeoung
- Institut für Biologie, Strukturbiologie/Biochemie, Humboldt-Universität zu Berlin, Unter den Linden 6, 10099, Berlin, Germany
| | - Berta M Martins
- Institut für Biologie, Strukturbiologie/Biochemie, Humboldt-Universität zu Berlin, Unter den Linden 6, 10099, Berlin, Germany
| | - Holger Dobbek
- Institut für Biologie, Strukturbiologie/Biochemie, Humboldt-Universität zu Berlin, Unter den Linden 6, 10099, Berlin, Germany
| |
Collapse
|
15
|
Rettberg LA, Stiebritz MT, Kang W, Lee CC, Ribbe MW, Hu Y. Structural and Mechanistic Insights into CO 2 Activation by Nitrogenase Iron Protein. Chemistry 2019; 25:13078-13082. [PMID: 31402524 DOI: 10.1002/chem.201903387] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 08/06/2019] [Indexed: 11/09/2022]
Abstract
The Fe protein of nitrogenase catalyzes the ambient reduction of CO2 when its cluster is present in the all-ferrous, [Fe4 S4 ]0 oxidation state. Here, we report a combined structural and theoretical study that probes the unique reactivity of the all-ferrous Fe protein toward CO2 . Structural comparisons of the Azotobacter vinelandii Fe protein in the [Fe4 S4 ]0 and [Fe4 S4 ]+ states point to a possible asymmetric functionality of a highly conserved Arg pair in CO2 binding and reduction. Density functional theory (DFT) calculations provide further support for the asymmetric coordination of O by the "proximal" Arg and binding of C to a unique Fe atom of the all-ferrous cluster, followed by donation of protons by the proximate guanidinium group of Arg that eventually results in the scission of a C-O bond. These results provide important mechanistic and structural insights into CO2 activation by a surface-exposed, scaffold-held [Fe4 S4 ] cluster.
Collapse
Affiliation(s)
- Lee A Rettberg
- Department of Molecular Biology & Biochemistry, University of California, Irvine, CA, 92697-3900, USA
| | - Martin T Stiebritz
- Department of Molecular Biology & Biochemistry, University of California, Irvine, CA, 92697-3900, USA
| | - Wonchull Kang
- Department of Molecular Biology & Biochemistry, University of California, Irvine, CA, 92697-3900, USA
| | - Chi Chung Lee
- Department of Molecular Biology & Biochemistry, University of California, Irvine, CA, 92697-3900, USA
| | - Markus W Ribbe
- Department of Molecular Biology & Biochemistry, University of California, Irvine, CA, 92697-3900, USA.,Department Chemistry, University of California, Irvine, Irvine, CA, 92697-2025, USA
| | - Yilin Hu
- Department of Molecular Biology & Biochemistry, University of California, Irvine, CA, 92697-3900, USA
| |
Collapse
|
16
|
Buckel W. Enzymatic Reactions Involving Ketyls: From a Chemical Curiosity to a General Biochemical Mechanism. Biochemistry 2019; 58:5221-5233. [PMID: 30995029 DOI: 10.1021/acs.biochem.9b00171] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Ketyls are radical anions with nucleophilic properties. Ketyls obtained by enzymatic one-electron reduction of thioesters were proposed as intermediates for the dehydration of (R)-2-hydroxyacyl-CoA to (E)-2-enoyl-CoA. This concept was extended to the Birch-like reduction of benzoyl-CoA to 1,5-cyclohexadienecarboxyl-CoA. Nature uses two methods to achieve the therefore required low reduction potentials of less than -600 mV, either by an ATP-driven electron transfer similar to that catalyzed by the iron protein of nitrogenase or by electron bifurcation. Ketyls formed by thiyl radical-initiated oxidation of alcohols followed by deprotonation are involved in coenzyme B12-independent diol dehydratases, other glycyl radical enzymes mediating key reactions in the degradations of choline, taurine, and 4-hydroxyproline, and all three classes of ribonucleotide reductases. A special case is the dehydration of 4-hydroxybutyryl-CoA to crotonyl-CoA, which most likely proceeds via an oxidation to an allylic ketyl but requires neither a strong reductant nor an external radical generator.
Collapse
Affiliation(s)
- Wolfgang Buckel
- Fachbereich Biologie , Philipps-Universität , 35032 Marburg , Germany
| |
Collapse
|
17
|
Abstract
Covering: up to the end of 2017 The human body is composed of an equal number of human and microbial cells. While the microbial community inhabiting the human gastrointestinal tract plays an essential role in host health, these organisms have also been connected to various diseases. Yet, the gut microbial functions that modulate host biology are not well established. In this review, we describe metabolic functions of the human gut microbiota that involve metalloenzymes. These activities enable gut microbial colonization, mediate interactions with the host, and impact human health and disease. We highlight cases in which enzyme characterization has advanced our understanding of the gut microbiota and examples that illustrate the diverse ways in which metalloenzymes facilitate both essential and unique functions of this community. Finally, we analyze Human Microbiome Project sequencing datasets to assess the distribution of a prominent family of metalloenzymes in human-associated microbial communities, guiding future enzyme characterization efforts.
Collapse
|
18
|
Moula G, Matsumoto T, Miehlich ME, Meyer K, Tatsumi K. Synthesis of an All-Ferric Cuboidal Iron-Sulfur Cluster [Fe III4 S 4 (SAr) 4 ]. Angew Chem Int Ed Engl 2018; 57:11594-11597. [PMID: 29775229 DOI: 10.1002/anie.201803679] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Indexed: 11/11/2022]
Abstract
An unprecedented, super oxidized all-ferric iron-sulfur cubanoid cluster with all terminal thiolates, Fe4 S4 (STbt)4 (3) [Tbt=2,4,6-tris{bis(trimethylsilyl)methyl}phenyl], has been isolated from the reaction of the bis-thiolate complex Fe(STbt)2 (2) with elemental sulfur. This cluster 3 has been characterized by X-ray crystallography, zero-field 57 Fe Mössbauer spectroscopy, cyclic voltammetry, and other relevant physico-chemical methods. Based on all the data, the electronic ground state of the cluster has been assigned to be Stot =0.
Collapse
Affiliation(s)
- Golam Moula
- Research Center for Materials Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8602, Japan),
| | - Tsuyoshi Matsumoto
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601, Japan
| | - Matthias E Miehlich
- Department of Chemistry and Pharmacy, Inorganic Chemistry, Friedrich-Alexander-University Erlangen-Nürnberg (FAU), Egerlandstrasse 1, 91058, Erlangen, Bavaria, Germany
| | - Karsten Meyer
- Department of Chemistry and Pharmacy, Inorganic Chemistry, Friedrich-Alexander-University Erlangen-Nürnberg (FAU), Egerlandstrasse 1, 91058, Erlangen, Bavaria, Germany
| | - Kazuyuki Tatsumi
- Research Center for Materials Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8602, Japan),
| |
Collapse
|
19
|
Moula G, Matsumoto T, Miehlich ME, Meyer K, Tatsumi K. Synthesis of an All-Ferric Cuboidal Iron-Sulfur Cluster [FeIII
4
S4
(SAr)4
]. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201803679] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Golam Moula
- Research Center for Materials Science; Nagoya University; Furo-cho Chikusa-ku Nagoya 464-8602 Japan),
| | - Tsuyoshi Matsumoto
- Institute of Transformative Bio-Molecules (WPI-ITbM); Nagoya University; Furo-cho Chikusa-ku Nagoya 464-8601 Japan
| | - Matthias E. Miehlich
- Department of Chemistry and Pharmacy; Inorganic Chemistry; Friedrich-Alexander-University Erlangen-Nürnberg (FAU); Egerlandstrasse 1 91058 Erlangen Bavaria Germany
| | - Karsten Meyer
- Department of Chemistry and Pharmacy; Inorganic Chemistry; Friedrich-Alexander-University Erlangen-Nürnberg (FAU); Egerlandstrasse 1 91058 Erlangen Bavaria Germany
| | - Kazuyuki Tatsumi
- Research Center for Materials Science; Nagoya University; Furo-cho Chikusa-ku Nagoya 464-8602 Japan),
| |
Collapse
|
20
|
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.
Collapse
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.
| |
Collapse
|
21
|
Ohta S, Ohki Y. Impact of ligands and media on the structure and properties of biological and biomimetic iron-sulfur clusters. Coord Chem Rev 2017. [DOI: 10.1016/j.ccr.2017.02.018] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
|
22
|
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]
|
23
|
Schmid G, Auerbach H, Pierik AJ, Schünemann V, Boll M. ATP-Dependent Electron Activation Module of Benzoyl-Coenzyme A Reductase from the Hyperthermophilic Archaeon Ferroglobus placidus. Biochemistry 2016; 55:5578-5586. [PMID: 27597116 DOI: 10.1021/acs.biochem.6b00729] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The class I benzoyl-coenzyme A (BzCoA) reductases (BCRs) are key enzymes in the anaerobic degradation of aromatic compounds that catalyze the ATP-dependent dearomatization of their substrate to a cyclic dienoyl-CoA. The phylogenetically distinct Thauera- and Azoarcus-type BCR subclasses are iron-sulfur enzymes and consist of an ATP-hydrolyzing electron activation module and a BzCoA reduction module. More than 20 years after their initial identification, all biochemical information about class I BCRs derives from studies of the wild-type enzyme from the denitrifying bacterium Thauera aromatica (BCRTaro). Here, we describe the first heterologous production and purification of the ATP-hydrolyzing, electron-activating module of an Azoarcus-type BCR from the hyperthermophilic archaeon Ferroglobus placidus, BzdPQFpla. The Fe content, UV/vis spectroscopic, and Mössbauer spectroscopic properties of the 57Fe-enriched enzyme clearly identified a [4Fe-4S]+/2+ cluster with a redox potential (E°') of -376 mV as a cofactor. ATP hydrolysis is required to overcome a redox barrier of ∼250 mV for stoichiometric electron transfer from the [4Fe-4S]+ cluster to the substrate benzene ring (E°'BzCoA/dienoyl-CoA = -622 mV). BzdPQFpla exhibited ATPase activity (15 nmol min-1 mg-1; Km = 270 μM) at 75 °C, which was relatively stable in air in contrast to BCRTaro. The results obtained revealed high levels of functional and molecular similarity between Azoarcus-type BCRs and the homologous ATP-dependent activator components of 2-hydroxyacyl-CoA dehydratases involved in amino acid fermentations. Insights into the diversity and evolution of ATP-dependent electron-activating modules for catalytic or stoichiometric low-potential electron transfer processes are presented.
Collapse
Affiliation(s)
- Georg Schmid
- Fakultät für Biologie-Mikrobiologie, Institut für Biologie II, Albert-Ludwigs-Universität Freiburg , D-79104 Freiburg, Germany
| | - Hendrik Auerbach
- Fachbereich Physik, TU Kaiserslautern , 67663 Kaiserslautern, Germany
| | - Antonio J Pierik
- Fachbereich Chemie, TU Kaiserslautern , 67663 Kaiserslautern, Germany
| | - Volker Schünemann
- Fachbereich Physik, TU Kaiserslautern , 67663 Kaiserslautern, Germany
| | - Matthias Boll
- Fakultät für Biologie-Mikrobiologie, Institut für Biologie II, Albert-Ludwigs-Universität Freiburg , D-79104 Freiburg, Germany
| |
Collapse
|
24
|
Roncaroli F, Bill E, Friedrich B, Lenz O, Lubitz W, Pandelia ME. Cofactor composition and function of a H 2-sensing regulatory hydrogenase as revealed by Mössbauer and EPR spectroscopy. Chem Sci 2015; 6:4495-4507. [PMID: 29142700 PMCID: PMC5665086 DOI: 10.1039/c5sc01560j] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Accepted: 05/26/2015] [Indexed: 01/22/2023] Open
Abstract
The regulatory hydrogenase (RH) from Ralstonia eutropha H16 acts as a sensor for the detection of environmental H2 and regulates gene expression related to hydrogenase-mediated cellular metabolism. In marked contrast to prototypical energy-converting [NiFe] hydrogenases, the RH is apparently insensitive to inhibition by O2 and CO. While the physiological function of regulatory hydrogenases is well established, little is known about the redox cycling of the [NiFe] center and the nature of the iron-sulfur (FeS) clusters acting as electron relay. The absence of any FeS cluster signals in EPR had been attributed to their particular nature, whereas the observation of essentially only two active site redox states, namely Ni-SI and Ni-C, invoked a different operant mechanism. In the present work, we employ a combination of Mössbauer, FTIR and EPR spectroscopic techniques to study the RH, and the results are consistent with the presence of three [4Fe-4S] centers in the small subunit. In the as-isolated, oxidized RH all FeS clusters reside in the EPR-silent 2+ state. Incubation with H2 leads to reduction of two of the [4Fe-4S] clusters, whereas only strongly reducing agents lead to reduction of the third cluster, which is ascribed to be the [4Fe-4S] center in 'proximal' position to the [NiFe] center. In the two different active site redox states, the low-spin FeII exhibits distinct Mössbauer features attributed to changes in the electronic and geometric structure of the catalytic center. The results are discussed with regard to the spectral characteristics and physiological function of H2-sensing regulatory hydrogenases.
Collapse
Affiliation(s)
- Federico Roncaroli
- Max-Planck-Institut für Chemische Energiekonversion , Stiftstraße 34-36 , 45470 Mülheim an der Ruhr , Germany . ; .,Department of Condensed Matter Physics , Centro Atómico Constituyentes , Comisión Nacional de Energía Atómica (CNEA) , Argentina
| | - Eckhard Bill
- Max-Planck-Institut für Chemische Energiekonversion , Stiftstraße 34-36 , 45470 Mülheim an der Ruhr , Germany . ;
| | - Bärbel Friedrich
- Institut für Biologie/Mikrobiologie , Humboldt-Universität zu Berlin , Chausseestraße 117 , 10115 Berlin , Germany
| | - Oliver Lenz
- Institut für Biologie/Mikrobiologie , Humboldt-Universität zu Berlin , Chausseestraße 117 , 10115 Berlin , Germany.,Institut für Chemie , Technische Universität Berlin , Max-Volmer-Laboratorium , Straße des 17. Juni 135 , 10623 Berlin , Germany
| | - Wolfgang Lubitz
- Max-Planck-Institut für Chemische Energiekonversion , Stiftstraße 34-36 , 45470 Mülheim an der Ruhr , Germany . ;
| | - Maria-Eirini Pandelia
- The Pennsylvania State University , Department of Chemistry , State College , PA 16802 , USA . .,Max-Planck-Institut für Chemische Energiekonversion , Stiftstraße 34-36 , 45470 Mülheim an der Ruhr , Germany . ;
| |
Collapse
|
25
|
Mössbauer spectroscopy of Fe/S proteins. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2014; 1853:1395-405. [PMID: 25498248 DOI: 10.1016/j.bbamcr.2014.12.005] [Citation(s) in RCA: 85] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Revised: 11/17/2014] [Accepted: 12/03/2014] [Indexed: 01/02/2023]
Abstract
Iron-sulfur (Fe/S) clusters are structurally and functionally diverse cofactors that are found in all domains of life. (57)Fe Mössbauer spectroscopy is a technique that provides information about the chemical nature of all chemically distinct Fe species contained in a sample, such as Fe oxidation and spin state, nuclearity of a cluster with more than one metal ion, electron spin ground state of the cluster, and delocalization properties in mixed-valent clusters. Moreover, the technique allows for quantitation of all Fe species, when it is used in conjunction with electron paramagnetic resonance (EPR) spectroscopy and analytical methods. (57)Fe-Mössbauer spectroscopy played a pivotal role in unraveling the electronic structures of the "well-established" [2Fe-2S](2+/+), [3Fe-4S](1+/0), and [4Fe-4S](3+/2+/1+/0) clusters and -more-recently- was used to characterize novel Fe/S clustsers, including the [4Fe-3S] cluster of the O2-tolerant hydrogenase from Aquifex aeolicus and the 3Fe-cluster intermediate observed during the reaction of lipoyl synthase, a member of the radical SAM enzyme superfamily.
Collapse
|
26
|
Buckel W, Kung JW, Boll M. The benzoyl-coenzyme a reductase and 2-hydroxyacyl-coenzyme a dehydratase radical enzyme family. Chembiochem 2014; 15:2188-94. [PMID: 25204868 DOI: 10.1002/cbic.201402270] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Indexed: 11/10/2022]
Affiliation(s)
- Wolfgang Buckel
- Laboratorium für Mikrobiologie, Fachbereich Biologie, Philipps-Universität Marburg, Karl-von-Frisch-Strasse 8, 35043 Marburg (Germany)
| | | | | |
Collapse
|
27
|
Weber K, Erdem ÖF, Bill E, Weyhermüller T, Lubitz W. Modeling the Active Site of [NiFe] Hydrogenases and the [NiFeu] Subsite of the C-Cluster of Carbon Monoxide Dehydrogenases: Low-Spin Iron(II) Versus High-Spin Iron(II). Inorg Chem 2014; 53:6329-37. [DOI: 10.1021/ic500910z] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Katharina Weber
- Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, D-45470 Mülheim an der Ruhr, Germany
| | - Özlen F. Erdem
- Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, D-45470 Mülheim an der Ruhr, Germany
| | - Eckhard Bill
- Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, D-45470 Mülheim an der Ruhr, Germany
| | - Thomas Weyhermüller
- Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, D-45470 Mülheim an der Ruhr, Germany
| | - Wolfgang Lubitz
- Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, D-45470 Mülheim an der Ruhr, Germany
| |
Collapse
|
28
|
Lee SC, Lo W, Holm RH. Developments in the biomimetic chemistry of cubane-type and higher nuclearity iron-sulfur clusters. Chem Rev 2014; 114:3579-600. [PMID: 24410527 PMCID: PMC3982595 DOI: 10.1021/cr4004067] [Citation(s) in RCA: 159] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
| | - Wayne Lo
- Department of Chemistry, University of Waterloo, Waterloo, Ontario N2L 3G1 Canada and the Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138
| | - R. H. Holm
- Corresponding Authors: S. C. Lee: . R. H. Holm:
| |
Collapse
|
29
|
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
![]()
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.
Collapse
Affiliation(s)
- Kresimir Rupnik
- Department of Chemistry, Louisiana State University , Baton Rouge, Louisiana 70808, United States
| | | | | | | | | | | |
Collapse
|
30
|
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.
Collapse
Affiliation(s)
- Devrani Mitra
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois 60637, USA
| | | | | | | | | | | | | | | | | |
Collapse
|
31
|
Albers A, Demeshko S, Pröpper K, Dechert S, Bill E, Meyer F. A Super-Reduced Diferrous [2Fe–2S] Cluster. J Am Chem Soc 2013; 135:1704-7. [DOI: 10.1021/ja311563y] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Antonia Albers
- Institute of Inorganic Chemistry, Georg-August-University Göttingen, Tammannstrasse
4, D-37077 Göttingen, Germany
| | - Serhiy Demeshko
- Institute of Inorganic Chemistry, Georg-August-University Göttingen, Tammannstrasse
4, D-37077 Göttingen, Germany
| | - Kevin Pröpper
- Institute of Inorganic Chemistry, Georg-August-University Göttingen, Tammannstrasse
4, D-37077 Göttingen, Germany
| | - Sebastian Dechert
- Institute of Inorganic Chemistry, Georg-August-University Göttingen, Tammannstrasse
4, D-37077 Göttingen, Germany
| | - Eckhard Bill
- Max-Planck-Institute for Chemical Energy Conversion, Stiftstrasse 34 −
36, D-45470 Mülheim an der Ruhr, Germany
| | - Franc Meyer
- Institute of Inorganic Chemistry, Georg-August-University Göttingen, Tammannstrasse
4, D-37077 Göttingen, Germany
| |
Collapse
|
32
|
Knauer SH, Buckel W, Dobbek H. On the ATP-dependent activation of the radical enzyme (R)-2-hydroxyisocaproyl-CoA dehydratase. Biochemistry 2012; 51:6609-22. [PMID: 22827463 DOI: 10.1021/bi300571z] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Members of the 2-hydroxyacyl-CoA dehydratase enzyme family catalyze the β,α-dehydration of various CoA-esters in the fermentation of amino acids by clostridia. Abstraction of the nonacidic β-proton of the 2-hydroxyacyl-CoA compounds is achieved by the reductive generation of ketyl radicals on the substrate, which is initiated by the transfer of an electron at low redox potentials. The highly energetic electron needed on the dehydratase is donated by a [4Fe-4S] cluster containing ATPase, termed activator. We investigated the activator of the 2-hydroxyisocaproyl-CoA dehydratase from Clostridium difficile. The activator is a homodimeric protein structurally related to acetate and sugar kinases, Hsc70 and actin, and has a [4Fe-4S] cluster bound in the dimer interface. The crystal structures of the Mg-ADP, Mg-ADPNP, and nucleotide-free states of the reduced activator have been solved at 1.6-3.0 Å resolution, allowing us to define the position of Mg(2+) and water molecules in the vicinity of the nucleotides and the [4Fe-4S] cluster. The structures reveal redox- and nucleotide dependent changes agreeing with the modulation of the reduction potential of the [4Fe-4S] cluster by conformational changes. We also investigated the propensity of the activator to form a complex with its cognate dehydratase in the presence of Mg-ADP and Mg-ADPNP and together with the structural data present a refined mechanistic scheme for the ATP-dependent electron transfer between activator and dehydratase.
Collapse
Affiliation(s)
- Stefan H Knauer
- Institut für Biologie, Strukturbiologie/Biochemie, Humboldt-Universität zu Berlin, D-10099 Berlin, Germany
| | | | | |
Collapse
|
33
|
Enzyme catalyzed radical dehydrations of hydroxy acids. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2011; 1824:1278-90. [PMID: 22178228 DOI: 10.1016/j.bbapap.2011.11.009] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2011] [Accepted: 11/28/2011] [Indexed: 11/24/2022]
Abstract
BACKGROUND The steadily increasing field of radical biochemistry is dominated by the large family of S-adenosylmethionine dependent enzymes, the so-called radical SAM enzymes, of which several new members are discovered every year. Here we report on 2- and 4-hydroxyacyl-CoA dehydratases which apply a very different method of radical generation. In these enzymes ketyl radicals are formed by one-electron reduction or oxidation and are recycled after each turnover without further energy input. Earlier reviews on 2-hydroxyacyl-CoA dehydratases were published in 2004 [J. Kim, M. Hetzel, C.D. Boiangiu, W. Buckel, FEMS Microbiol. Rev. 28 (2004) 455-468. W. Buckel, M. Hetzel, J. Kim, Curr. Opin. Chem. Biol. 8 (2004) 462-467.] SCOPE OF REVIEW The review focuses on four types of 2-hydroxyacyl-CoA dehydratases that are involved in the fermentation of amino acids by anaerobic bacteria, especially clostridia. These enzymes require activation by one-electron transfer from an iron-sulfur protein driven by hydrolysis of ATP. The review further describes the proposed mechanism that is highlighted by the identification of the allylic ketyl radical intermediate and the elucidation of the crystal structure of 2-hydroxyisocapryloyl-CoA dehydratase. With 4-hydroxybutyryl-CoA dehydratase the crystal structure, the complete stereochemistry and the function of several conserved residues around the active site could be identified. Finally potential biotechnological applications of the radical dehydratases are presented. GENERAL SIGNIFICANCE The action of the activator as an 'Archerase' shooting electrons into difficultly reducible acceptors becomes an emerging principle in anaerobic metabolism. The dehydratases may provide useful tools in biotechnology. This article is part of a Special Issue entitled: Radical SAM enzymes and Radical Enzymology.
Collapse
|
34
|
|
35
|
Abstract
Nitrogenase is a globally important enzyme that catalyses the reduction of atmospheric dinitrogen into ammonia and is thus an important part of the nitrogen cycle. The nitrogenase enzyme is composed of a catalytic molybdenum-iron protein (MoFe protein) and a protein containing an [Fe4-S4] cluster (Fe protein) that functions as a dedicated ATP-dependent reductase. The current understanding of electron transfer between these two proteins is based on stopped-flow spectrophotometry, which has allowed the rates of complex formation and electron transfer to be accurately determined. Surprisingly, a total of four Fe protein molecules are required to saturate one MoFe protein molecule, despite there being only two well-characterized Fe-protein-binding sites. This has led to the conclusion that the purified Fe protein is only half-active with respect to electron transfer to the MoFe protein. Studies on the electron transfer between both proteins using rapid-quench EPR confirmed that, during pre-steady-state electron transfer, the Fe protein only becomes half-oxidized. However, stopped-flow spectrophotometry on MoFe protein that had only one active site occupied was saturated by approximately three Fe protein equivalents. These results imply that the Fe protein has a second interaction during the initial stages of mixing that is not involved in electron transfer.
Collapse
|
36
|
Chakrabarti M, Münck E, Bominaar EL. Density functional theory study of an all ferrous 4Fe-4S cluster. Inorg Chem 2011; 50:4322-6. [PMID: 21476577 DOI: 10.1021/ic102287j] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The all-ferrous, carbene-capped Fe(4)S(4) cluster, synthesized by Deng and Holm (DH complex), has been studied with density functional theory (DFT). The geometry of the complex was optimized for several electronic configurations. The lowest energy was obtained for the broken-symmetry (BS) configuration derived from the ferromagnetic state by reversing the spin projection of one of the high spin (S(i) = 2) irons. The optimized geometry of the latter configuration contains one unique and three equivalent iron sites, which are both structurally and electronically clearly distinguishable. For example, a distinctive feature of the unique iron site is the diagonal Fe···S distance, which is 0.3 Å longer than for the equivalent irons. The calculated (57)Fe hyperfine parameters show the same 1:3 pattern as observed in the Mössbauer spectra and are in good agreement with experiment. BS analysis of the exchange interactions in the optimized geometry for the 1:3, M(S) = 4, BS configuration confirms the prediction of an earlier study that the unique site is coupled to the three equivalent ones by strong antiferromagnetic exchange (J > 0 in J Σ(j<4)Ŝ(4)·Ŝ(j)) and that the latter are mutually coupled by ferromagnetic exchange (J' < 0 in J' Σ(i<j<4)Ŝ(i)·Ŝ(j)). In combination, these exchange couplings stabilize an S = 4 ground state in which the composite spin of the three equivalent sites (S(123) = 6) is antiparallel to the spin (S(4) = 2) of the unique site. Thus, DFT analysis supports the idea that the unprecedented high value of the spin of the DH complex and, by analogy, of the all-ferrous cluster of the Fe-protein of nitrogenase, results from a remarkably strong dependence of the exchange interactions on cluster core geometry. The structure dependence of the exchange-coupling constants in the Fe(II)-(μ(3)-S)(2)-Fe(II) moieties of the all-ferrous clusters is compared with the magneto-structural correlations observed in the data for dinuclear copper complexes. Finally, we discuss two all-ferric clusters in the light of the results for the all-ferrous cluster.
Collapse
Affiliation(s)
- Mrinmoy Chakrabarti
- Department of Chemistry, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, USA
| | | | | |
Collapse
|
37
|
Kung JW, Baumann S, von Bergen M, Müller M, Hagedoorn PL, Hagen WR, Boll M. Reversible biological Birch reduction at an extremely low redox potential. J Am Chem Soc 2010; 132:9850-6. [PMID: 20578740 DOI: 10.1021/ja103448u] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The Birch reduction of aromatic rings to cyclohexadiene compounds is widely used in chemical synthesis and requires solvated electrons, the most potent reductants known in organic chemistry. Benzoyl-coenzyme A (CoA) reductases (BCR) are key enzymes in the anaerobic bacterial degradation of aromatic compounds and catalyze an analogous reaction under physiological conditions. Class I BCRs are FeS enzymes and couple the reductive dearomatization of benzoyl-CoA to cyclohexa-1,5-diene-1-carboxyl-CoA (dienoyl-CoA) to a stoichiometric ATP hydrolysis. Here, we report on a tungsten-containing class II BCR from Geobacter metallireducens that catalyzed the fully reversible, ATP-independent dearomatization of benzoyl-CoA to dienoyl-CoA. BCR additionally catalyzed the disproportionation of dienoyl-CoA to benzoyl-CoA/monoenoyl-CoA and the four- and six-electron reduction of benzoyl-CoA in the presence of a reduced low-potential bridged 2,2'-bipyridyl redox dye. Reversible redox titration experiments in the presence of this redox dye revealed a midpoint potential of E(0)' = -622 mV for the benzoyl-CoA/dienoyl-CoA couple, which is far below the values of other known reversible substrate/product redox couples in enzymology. This work demonstrates the efficiency of reversible metalloenzyme catalysis, which in chemical synthesis can only be achieved under essentially irreversible conditions.
Collapse
Affiliation(s)
- Johannes W Kung
- Institute of Biochemistry, University of Leipzig, 04103 Leipzig, Germany
| | | | | | | | | | | | | |
Collapse
|
38
|
Deng L, Bill E, Wieghardt K, Holm RH. Cubane-type Co4S4 clusters: synthesis, redox series, and magnetic ground states. J Am Chem Soc 2009; 131:11213-21. [PMID: 19722678 PMCID: PMC3170832 DOI: 10.1021/ja903847a] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The recent demonstration that the carbene cluster [Fe(4)S(4)(Pr(i)(2)NHCMe(2))(4)] (9) is an accurate structural and electronic analogue of the fully reduced cluster of the iron protein of Azotobacter vinelandii nitrogenase, including a common S = 4 ground state, raises the issue of the existence and magnetism of other [M(4)S(4)L(4)](z) clusters, none of which are known with transition metals other than iron. The system CoCl(2)/Pr(i)(3)P/(Me(3)Si)(2)S/THF assembles [Co(4)S(4)(PPr(i)(3))(4)] (3), which is converted to [Co(4)S(4)(Pr(i)(2)NHCMe(2))(4)] (5) upon reaction with carbene. The clusters support the redox series [3](1-/0/1+) and [5](0/1+/2+); monocations (4, 6) have been isolated by chemical oxidation. Redox potentials and substitution reactions indicate that the carbene is the more effective electron donor to tetrahedral Fe(II) and Co(II) sites. Clusters 3-6 have the same overall cubane-type geometry as 9. Neutral clusters 3 and 5 have an S = 3 ground state. As with the S = 4 state of 9 with local spins S(Fe) = 2, the septet spin state can be described in terms of the coupling of three parallel and one antiparallel spins S(Co) = 3/2. The octanuclear clusters [Co(8)S(8)(PPr(i)(3))(6)](0,1+) were isolated as minor byproducts of the formation and chemical oxidation of 3. The clusters exhibit a rhomb-bridged noncubane (RBNC) structure, whereas clusters with the Fe(8)S(8) core possess edge-bridged double-cubane (EBDC) stereochemistry. There are two structural solutions for the M(8)S(8) core in the form of topological isomers whose stability may depend on valence electron count. A conceptual model for the RBNC <--> EBDC interconversion is presented. (Pr(i)(2)NHCMe(2) = C(11)H(20)N(2) = 1,3-diisopropyl-4,5-dimethylimidazol-2-ylidene).
Collapse
Affiliation(s)
- Liang Deng
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138
| | - Eckhard Bill
- Max-Planck-Institut für Bioanorganische Chemie, Mülheim an der Ruhr, Germany
| | - Karl Wieghardt
- Max-Planck-Institut für Bioanorganische Chemie, Mülheim an der Ruhr, Germany
| | - R. H. Holm
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138
| |
Collapse
|
39
|
Chakrabarti M, Deng L, Holm RH, Münck E, Bominaar EL. Mössbauer, electron paramagnetic resonance, and theoretical studies of a carbene-based all-ferrous Fe4S4 cluster: electronic origin and structural identification of the unique spectroscopic site. Inorg Chem 2009; 48:2735-47. [PMID: 19326927 DOI: 10.1021/ic802192w] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
It is well established that the cysteinate-coordinated [Fe(4)S(4)] cluster of the iron protein of nitrogenase from Azotobacter vinelandii (Av2) can attain the all-ferrous core oxidation state. Mössbauer and electron paramagnetic resonance (EPR) studies have shown that the all-ferrous cluster has a ground-state spin S = 4 and an effective 3:1 site symmetry in the spin structure and (57)Fe quadrupole interactions. Recently, Deng and Holm reported the synthesis of [Fe(4)S(4)(Pr(i)(2)NHCMe(2))(4)],(2) (1; Pr(i)(2)NHCMe(2) = 1,3-diisopropyl-4,5-dimethylimidazol-2-ylidene) and showed that the all-ferrous carbene-coordinated cluster is amenable to physicochemical studies. Mössbauer and EPR studies of 1, reported here, reveal that the electronic structure of this complex is strikingly similar to that of the protein-bound cluster, suggesting that the ground-state spin and the 3:1 site ratio are consequences of spontaneous distortions of the cluster core. To gain insight into the origin of the peculiar ground state of the all-ferrous clusters in 1 and Av2, we have studied a theoretical model that is based on a Heisenberg-Dirac-van Vleck Hamiltonian whose exchange-coupling constants are a function of the Fe-Fe distances. By combining the exchange energies with the elastic deformation energies in the harmonic approximation, we obtain for a T(2) distortion a minimum with spin S = 4 and a C(3v) core structure in which one iron is unique and three irons are equivalent. This minimum has all of the spectroscopic and structural characteristics of the all-ferrous clusters of 1 and Av2. Our analysis maps the unique spectroscopic iron site to a specific site in the X-ray structure of the [Fe(4)S(4)](0) core both in complex 1 and in Av2.
Collapse
Affiliation(s)
- Mrinmoy Chakrabarti
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA
| | | | | | | | | |
Collapse
|
40
|
Affiliation(s)
- Eckard Münck
- Department of Chemistry, Carnegie Mellon University, 4400 Fifth Street, Pittsburgh, PA 15213, USA
| | - Emile L. Bominaar
- Department of Chemistry, Carnegie Mellon University, 4400 Fifth Street, Pittsburgh, PA 15213, USA
| |
Collapse
|