Bioassembly of complex iron–sulfur enzymes: hydrogenases and nitrogenases
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ABSTRACT:
SUBMITTER: Britt R
PROVIDER: S-EPMC8023223 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:One S less: recent crystallographic studies have revealed a new, oxygen-tolerant kind of iron-sulfide cluster [4Fe-3S], which contains only three rather than four sulfur atoms in its cage (see picture; yellow=S, red=Fe, blue=N, green=cysteine). It is proposed that the cluster's ability to transfer multiple electrons increases the oxygen tolerance by enabling the enzyme to reduce O(2) rapidly, converting the dioxygen into harmless water before it can damage the protein.
| S-EPMC3465487 | biostudies-literature
Project description:In the absence of base, the reaction of [Fe(II)(TMCS)]PF6 (1, TMCS = 1-(2-mercaptoethyl)-4,8,11-trimethyl-1,4,8,11-tetraazacyclotetradecane) with peracid in methanol at -20 °C did not yield the oxoiron(IV) complex (2, [Fe(IV)(O)(TMCS)]PF6), as previously observed in the presence of strong base (KO(t)Bu). Instead, the addition of 1 equiv of peracid resulted in 50% consumption of 1. The addition of a second equivalent of peracid resulted in the complete consumption of 1 and the formation of a new species 3, as monitored by UV-vis, ESI-MS, and Mössbauer spectroscopies. ESI-MS showed 3 to be formulated as [Fe(II)(TMCS) + 2O](+), while EXAFS analysis suggested that 3 was an O-bound iron(II)-sulfinate complex (Fe-O = 1.95 Å, Fe-S = 3.26 Å). The addition of a third equivalent of peracid resulted in the formation of yet another compound, 4, which showed electronic absorption properties typical of an oxoiron(IV) species. Mössbauer spectroscopy confirmed 4 to be a novel iron(IV) compound, different from 2, and EXAFS (Fe?O = 1.64 Å) and resonance Raman (?(Fe?O) = 831 cm(-1)) showed that indeed an oxoiron(IV) unit had been generated in 4. Furthermore, both infrared and Raman spectroscopy gave indications that 4 contains a metal-bound sulfinate moiety (?(s)(SO2) ? 1000 cm (-1), ?(as)(SO2) ? 1150 cm (-1)). Investigations into the reactivity of 1 and 2 toward H(+) and oxygen atom transfer reagents have led to a mechanism for sulfur oxidation in which 2 could form even in the absence of base but is rapidly protonated to yield an oxoiron(IV) species with an uncoordinated thiol moiety that acts as both oxidant and substrate in the conversion of 2 to 3.
| S-EPMC3049993 | biostudies-literature
Project description:From the very first discovery of biological iron-sulfur clusters with EPR, the spectroscopy has been used to study not only purified proteins but also complex systems such as respiratory complexes, membrane particles and, later, whole cells. In recent times, the emphasis of iron-sulfur biochemistry has moved from characterization of individual proteins to the systems biology of iron-sulfur biosynthesis, regulation, degradation, and implications for human health. Although this move would suggest a blossoming of System-EPR as a specific, non-invasive monitor of Fe/S (dys)homeostasis in whole cells, a review of the literature reveals limited success possibly due to technical difficulties in adherence to EPR spectroscopic and biochemical standards. In an attempt to boost application of System-EPR the required boundary conditions and their practical applications are explicitly and comprehensively formulated.
| S-EPMC6006208 | biostudies-literature
Project description:Conserved Iron-Sulfur (Fe-S) clusters are found in a growing family of metalloproteins that are implicated in prokaryotic and eukaryotic DNA replication and repair. Among these are DNA helicase and helicase-nuclease enzymes that preserve chromosomal stability and are genetically linked to diseases characterized by DNA repair defects and/or a poor response to replication stress. Insight to the structural and functional importance of the conserved Fe-S domain in DNA helicases has been gleaned from structural studies of the purified proteins and characterization of Fe-S cluster site-directed mutants. In this review, we will provide a current perspective of what is known about the Fe-S cluster helicases, with an emphasis on how the conserved redox active domain may facilitate mechanistic aspects of helicase function. We will discuss testable models for how the conserved Fe-S cluster might operate in helicase and helicase-nuclease enzymes to conduct their specialized functions that help to preserve the integrity of the genome.
| S-EPMC3378879 | biostudies-literature
Project description:Frataxin, a mitochondrial protein that is directly involved in regulating cellular iron homeostasis, has been suggested to serve as an iron chaperone during cellular Fe-S cluster biosynthesis. In humans, decreased amounts or impaired function of frataxin causes the autosomal recessive neurodegenerative disorder Friedreich's ataxia. Cellular production of Fe-S clusters is accomplished by the Fe cofactor assembly platform enzymes Isu (eukaryotes) and IscU (prokaryotes). In this report, we have characterized the overall stability and iron binding properties of the Drosophila frataxin homologue (Dfh). Dfh is highly folded with secondary structural elements consistent with the structurally characterized frataxin orthologs. While the melting temperature ( T M approximately 59 degrees C) and chemical stability ([urea] 50% approximately 2.4 M) of Drosophila frataxin, measured using circular dichroism (CD) and fluorescence spectroscopy, closely match values determined for the human ortholog, pure Dfh is more stable against autodegradation than both the human and yeast proteins. The ferrous iron binding affinity ( K d approximately 6.0 microM) and optimal metal to protein stoichiometry (1:1) for Dfh have been measured using isothermal titration calorimetry (ITC). Under anaerobic conditions with salt present, holo-Dfh is a stable iron-loaded protein monomer. Frataxin prevents reactive oxygen species-induced oxidative damage to DNA when presented with both Fe(II) and H 2O 2. Ferrous iron bound to Dfh is high-spin and held in a partially symmetric Fe-(O/N) 6 coordination environment, as determined by X-ray absorption spectroscopy (XAS). Extended X-ray absorption fine structure (EXAFS) simulations indicate the average Fe-O/N bond length in Dfh is 2.13 A, consistent with a ligand geometry constructed by water and carboxylate oxygens most likely supplied in part by surface-exposed conserved acidic residues located on helix 1 and strand 1 in the structurally characterized frataxin orthologs. The iron-dependent binding affinity ( K d approximately 0.21 microM) and optimal holo-Dfh to Isu monomer stoichiometry (1:1) have also been determined using ITC. Finally, frataxin mediates the delivery of Fe(II) to Isu, promoting Fe-S cluster assembly in vitro. The Dfh-assisted assembly of Fe-S clusters occurs with an observed kinetic rate constant ( k obs) of 0.096 min (-1).
| S-EPMC2664653 | biostudies-literature
Project description:Plastids surrounded by four membranes harbor a special compartment between the outer and inner plastid membrane pair, the so-called periplastidal compartment (PPC). This cellular structure is usually presumed to be the reduced cytoplasm of a eukaryotic phototrophic endosymbiont, which was integrated into a host cell and streamlined into a plastid with a complex membrane structure. Up to date, no mitochondrion or mitochondrion-related organelle has been identified in the PPC of any representative. However, two prominent groups, the cryptophytes and the chlorarachniophytes, still harbor a reduced cell nucleus of symbiont origin, the nucleomorph, in their PPCs. Generally, many cytoplasmic and nucleus-located eukaryotic proteins need an iron-sulfur cofactor for their functionality. Beside some exceptions, their synthesis is depending on a so-called iron-sulfur complex (ISC) assembly machinery located in the mitochondrion. This machinery provides the cytoplasm with a still unknown sulfur component, which is then converted into iron-sulfur clusters via a cytosolic iron-sulfur protein assembly (CIA) machinery. Here, we investigated if a CIA machinery is present in mitochondrion-lacking PPCs. By using bioinformatic screens and in vivo-localizations of candidate proteins, we show that the presence of a PPC-specific CIA machinery correlates with the presence of a nucleomorph. Phylogenetic analyses of PPC- and host specific CIA components additionally indicate a complex evolution of the CIA machineries in organisms having plastids surrounded by four membranes.
| S-EPMC6105332 | biostudies-literature
Project description:We report the synthesis and characterization of the first terminal imido complex of an Fe-S cluster, (IMes)3 Fe4 S4 =NDipp (2; IMes=1,3-dimesitylimidazol-2-ylidene, Dipp=2,6-diisopropylphenyl), which is generated by oxidative group transfer from DippN3 to the all-ferrous cluster (IMes)3 Fe4 S4 (PPh3 ). This two-electron process is achieved by formal one-electron oxidation of the imido-bound Fe site and one-electron oxidation of two IMes-bound Fe sites. Structural, spectroscopic, and computational studies establish that the Fe-imido site is best described as a high-spin Fe3+ center, which is manifested in its long Fe-N(imido) distance of 1.763(2) Å. Cluster 2 abstracts hydrogen atoms from 1,4-cyclohexadiene to yield the corresponding anilido complex, demonstrating competency for C-H activation.
| S-EPMC8294340 | biostudies-literature
Project description:In plants, the cysteine desulfurase (AtNFS1) and frataxin (AtFH) are involved in the formation of Fe-S groups in mitochondria, specifically, in Fe and sulfur loading onto scaffold proteins, and the subsequent formation of the mature Fe-S cluster. We found that the small mitochondrial chaperone, AtISD11, and AtFH are positive regulators for AtNFS1 activity in Arabidopsis. Moreover, when the three proteins were incubated together, a stronger attenuation of the Fenton reaction was observed compared to that observed with AtFH alone. Using pull-down assays, we found that these three proteins physically interact, and sequence alignment and docking studies showed that several amino acid residues reported as critical for the interaction of their human homologous are conserved. Our results suggest that AtFH, AtNFS1 and AtISD11 form a multiprotein complex that could be involved in different stages of the iron-sulfur cluster (ISC) pathway in plant mitochondria.
| S-EPMC7570111 | biostudies-literature
Project description:Described herein are preparations of synthetic models for the deactivated Ni(II)Fe(II) states of the [NiFe]-hydrogenases. Iodination of the S = ½ species [(dppe)Ni(pdt)Fe(CO)(3)](+) afforded the diamagnetic iodo complex [(dppe)Ni(pdt)IFe(CO)(3)](+). Crystallographic analysis of this species confirmed the presence of square-pyramidal Ni linked to an octahedral Fe centre. The NiFe separation of 3.018 Å indicated the absence of metal-metal bonding. This complex could be reduced to give (dppe)Ni(pdt)Fe(CO)(3) and, in the presence of iodide, decarbonylated to afford (dppe)Ni(pdt)FeI(2). Derivatives of the type [(diphosphine)Ni(dithiolate)XFe(CO)(2)L](+) (X = Cl, Br, I) were prepared by halogenation of mixed-valence precursors [(diphosphine)Ni(dithiolate)Fe(CO)(2)L](+) (diphosphine = dppe, dcpe; L = tertiary phosphine or CO). The Fe(CO)(2)(PR(3))-containing derivatives are more robust than the related tricarbonyl derivatives. Exploiting this greater stability, we characterised examples of chloride and bromide derivatives. Related fluorides could be prepared by F(-) abstraction from BF(4)(-). Spectroscopic evidence is presented for the hydroperoxide [(dppe)Ni(pdt)(OOH)Fe(CO)(2)L](+), which represents a model for the Ni-SU state.
| S-EPMC3489918 | biostudies-literature
Project description:Modern day aerobic respiration in mitochondria involving complex I converts redox energy into chemical energy and likely evolved from a simple anaerobic system now represented by hydrogen gas-evolving hydrogenase (MBH) where protons are the terminal electron acceptor. Here we present the cryo-EM structure of an early ancestor in the evolution of complex I, the elemental sulfur (S0)-reducing reductase MBS. Three highly conserved protein loops linking cytoplasmic and membrane domains enable scalable energy conversion in all three complexes. MBS contains two proton pumps compared to one in MBH and likely conserves twice the energy. The structure also reveals evolutionary adaptations of MBH that enabled S0 reduction by MBS catalyzed by a site-differentiated iron-sulfur cluster without participation of protons or amino acid residues. This is the simplest mechanism proposed for reduction of inorganic or organic disulfides. It is of fundamental significance in the iron and sulfur-rich volcanic environments of early earth and possibly the origin of life. MBS provides a new perspective on the evolution of modern-day respiratory complexes and of catalysis by biological iron-sulfur clusters.
| S-EPMC7684303 | biostudies-literature