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Abstract
Reactive oxygen species (ROS) play an important role in the biochemistry of the cell and occur in degenerative processes as well as in signal transduction. Iron-sulfur proteins are particularly oxygen-sensitive and their inorganic cofactors frequently undergo ROS-induced decomposition reactions. As experimental knowledge about these processes is still incomplete we present here a quantum chemical study of the relative energetics for the binding of the most relevant ROS to [Fe4S4] clusters. We find that cubane clusters with one uncoordinated Fe atom (as found, for instance, in aconitase) bind all oxygen derivatives considered, whereas activation of triplet O2 to singlet O2 is required for binding to valence-saturated iron centers in these clusters. The radicals NO and OH feature the most exothermic binding energies to Fe atoms. Direct sulfoxidation of coordinating cysteine residues is only possible by OH or H2O2 as attacking agents. The thermodynamic picture of ROS binding to iron-sulfur clusters established here can serve as a starting point for studying reactivity-modulating effects of the cluster-embedding protein environment on ROS-induced decomposition of iron-sulfur proteins.
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Affiliation(s)
- Marta K Bruska
- ETH Zürich, Laboratorium für Physikalische Chemie, Vladimir-Prelog-Weg 2, 8093 Zürich (Switzerland)
| | - Martin T Stiebritz
- ETH Zürich, Laboratorium für Physikalische Chemie, Vladimir-Prelog-Weg 2, 8093 Zürich (Switzerland)
| | - Markus Reiher
- ETH Zürich, Laboratorium für Physikalische Chemie, Vladimir-Prelog-Weg 2, 8093 Zürich (Switzerland).
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2
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Abstract
Iron-sulfur clusters [Fe-S] are small, ubiquitous inorganic cofactors representing one of the earliest catalysts during biomolecule evolution and are involved in fundamental biological reactions, including regulation of enzyme activity, mitochondrial respiration, ribosome biogenesis, cofactor biogenesis, gene expression regulation, and nucleotide metabolism. Although simple in structure, [Fe-S] biogenesis requires complex protein machineries and pathways for assembly. [Fe-S] are assembled from cysteine-derived sulfur and iron onto scaffold proteins followed by transfer to recipient apoproteins. Several predominant iron-sulfur biogenesis systems have been identified, including nitrogen fixation (NIF), sulfur utilization factor (SUF), iron-sulfur cluster (ISC), and cytosolic iron-sulfur protein assembly (CIA), and many protein components have been identified and characterized. In eukaryotes ISC is mainly localized to mitochondria, cytosolic iron-sulfur protein assembly to the cytosol, whereas plant sulfur utilization factor is localized mainly to plastids. Because of this spatial separation, evidence suggests cross-talk mediated by organelle export machineries and dual targeting mechanisms. Although research efforts in understanding iron-sulfur biogenesis has been centered on bacteria, yeast, and plants, recent efforts have implicated inappropriate [Fe-S] biogenesis to underlie many human diseases. In this review we detail our current understanding of [Fe-S] biogenesis across species boundaries highlighting evolutionary conservation and divergence and assembling our knowledge into a cellular context.
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Affiliation(s)
- Xiang Ming Xu
- Centre for Organelle Research CORE, University of Stavanger, Norway
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3
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Abstract
The cleavage of [4Fe-4S]-type clusters is thought to be important in proteins such as Fe-S scaffold proteins and nitrogenase. However, most [4Fe-4S](2+) clusters in proteins have two antiferromagnetically coupled high-spin layers in which a minority spin is delocalized in each layer, thus forming a symmetric Fe(2.5+)-Fe(2.5+) pair, and how cleavage occurs between the irons is puzzling because of the shared electron. Previously, we proposed a novel mechanism for the fission of a [4Fe-4S] core into two [2Fe-2S] cores in which the minority spin localizes on one iron, thus breaking the symmetry and creating a transition state with two Fe(3+)-Fe(2+) pairs. Cleavage first through the weak Fe(2+)-S bonds lowers the activation energy. Here, we propose a test of this mechanism: break the symmetry of the cluster by changing the ligands to promote spin localization, which should enhance reactivity. The cleavage reactions for the homoligand [Fe(4)S(4)L(4)](2-) (L = SCH(3), Cl, H) and heteroligand [Fe(4)S(4)(SCH(3))(2)L(2)](2-) (L = Cl, H) clusters in the gas phase were examined via broken-symmetry density functional theory calculations. In the heteroligand clusters, the minority spin localized on the iron coordinated by the weaker electron-donor ligand, and the reaction energy and activation barrier of the cleavage were lowered, which is in accord with our proposed mechanism and consistent with photoelectron spectroscopy and collision-induced dissociation experiments. These studies suggest that proteins requiring facile fission of their [4Fe-4S] cluster in their biological function might have spin-localized [4Fe-4S] clusters.
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Affiliation(s)
- Shuqiang Niu
- Department of Chemistry, Georgetown University, Washington, D.C. 20057-1227, USA
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4
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Hasan MN, Kwakernaak C, Sloof WG, Hagen WR, Heering HA. Pyrococcus furiosus 4Fe-ferredoxin, chemisorbed on gold, exhibits gated reduction and ionic strength dependent dimerization. J Biol Inorg Chem 2006; 11:651-62. [PMID: 16791647 DOI: 10.1007/s00775-006-0117-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2006] [Accepted: 05/05/2006] [Indexed: 10/24/2022]
Abstract
Pyrococcus furiosus ferredoxin is a small metalloprotein that shuttles electrons between redox enzymes. In its native 4Fe-4S form the protein is highly thermostable. In addition to three cluster-ligating cysteines, two surface cysteine residues (C21 and C48) are present. We used the reactivity of these surface thiols to directly immobilize ferredoxin on a bare gold electrode, with an orientation in which the cluster is exposed to solution. Voltammetry, X-ray photoelectron spectroscopy (XPS), and atomic force microscopy (AFM) studies established the immobilization of the 4Fe form. Native and recombinant wild-type ferredoxins were compared with the C48S, C21S, and C21S/C48S mutants. The variants with one and two surface cysteines can be directly chemisorbed on bare gold. Cyclic voltammetry demonstrated that the reduction potentials are similar to those in solution. The interfacial electron transfer kinetics revealed that the reduction is gated by the interconversion between two oxidized species. AFM images showed that dimers are chemisorbed at low ionic strength, while monomers are present at high ionic strength. XPS spectra revealed the presence of S, Fe, C, N, and O at the surface, which are assigned to the corresponding atoms in the peptide and the cofactor. Analysis of the sulfur spectrum corroborates that both C21 and C48 form gold-thiolate bonds. Moreover, two inorganic sulfide and two iron species were identified, suggesting an inhomogeneous charge distribution in the 4Fe-4S cluster. In conclusion, P. furiosus ferredoxin can be directly and vectorially chemisorbed on gold with retention of its properties. This may provide a biocompatible electrode surface with docking sites for redox enzymes.
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Affiliation(s)
- M Nahid Hasan
- Department of Biotechnology, Faculty of Applied Sciences, Delft University of Technology, Julianalaan 67, 2628 BC, Delft, The Netherlands
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5
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Takagi T, Habe H, Yoshida T, Yamane H, Omori T, Nojiri H. Characterization of [3Fe-4S] ferredoxin DbfA3, which functions in the angular dioxygenase system of Terrabacter sp. strain DBF63. Appl Microbiol Biotechnol 2005; 68:336-45. [PMID: 15717172 DOI: 10.1007/s00253-005-1928-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2004] [Revised: 12/26/2004] [Accepted: 01/21/2005] [Indexed: 10/25/2022]
Abstract
Dibenzofuran 4,4a-dioxygenase (DFDO) from Terrabacter sp. strain DBF63 is comprised of three components, i.e., terminal oxygenase (DbfA1, DbfA2), putative [3Fe-4S] ferredoxin (ORF16b product), and unidentified ferredoxin reductase. We produced DbfA1 and DbfA2 using recombinant Escherichia coli BL21(DE3) cells as a native form and purified the complex to apparent homogeneity. We also produced and purified a putative [3Fe-4S] ferredoxin encoded by ORF16b, which is located 2.5 kb downstream of the dbfA1A2 genes, with E. coli as a histidine (His)-tagged form. The reconstructed DFDO system with three purified components, i.e., DbfA1A2, His-tagged ORF16b product, and His-tagged PhtA4 (which is a tentative reductase derived from the phthalate dioxygenase system of strain DBF63) could convert fluorene to 9-fluorenol (specific activity: 14.4 nmol min(-1) mg(-1)) and convert dibenzofuran to 2,2',3-trihydroxybiphenyl. This indicates that the ORF16b product can transport electrons to the DbfA1A2 complex; and therefore it was designated DbfA3. Based on spectroscopic UV-visible absorption characteristics and electron paramagnetic resonance spectra, DbfA3 was elucidated to contain a [3Fe-4S] cluster. Ferredoxin interchangeability analysis using several types of ferredoxins suggested that the redox partner of the DbfA1A2 complex may be rather specific to DbfA3.
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Affiliation(s)
- Terufumi Takagi
- Biotechnology Research Center, The University of Tokyo, Bunkyo-ku, Japan
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6
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Affiliation(s)
- C Kim
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602, USA
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7
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Affiliation(s)
- G N La Mar
- Department of Chemistry, University of California, Davis, California 95616, USA
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8
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Jung YS, Bonagura CA, Tilley GJ, Gao-Sheridan HS, Armstrong FA, Stout CD, Burgess BK. Structure of C42D Azotobacter vinelandii FdI. A Cys-X-X-Asp-X-X-Cys motif ligates an air-stable [4Fe-4S]2+/+ cluster. J Biol Chem 2000; 275:36974-83. [PMID: 10961993 DOI: 10.1074/jbc.m004947200] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
All naturally occurring ferredoxins that have Cys-X-X-Asp-X-X-Cys motifs contain [4Fe-4S](2+/+) clusters that can be easily and reversibly converted to [3Fe-4S](+/0) clusters. In contrast, ferredoxins with unmodified Cys-X-X-Cys-X-X-Cys motifs assemble [4Fe-4S](2+/+) clusters that cannot be easily interconverted with [3Fe-4S](+/0) clusters. In this study we changed the central cysteine of the Cys(39)-X-X-Cys(42)-X-X-Cys(45) of Azotobacter vinelandii FdI, which coordinates its [4Fe-4S](2+/+) cluster, into an aspartate. UV-visible, EPR, and CD spectroscopies, metal analysis, and x-ray crystallography show that, like native FdI, aerobically purified C42D FdI is a seven-iron protein retaining its [4Fe-4S](2+/+) cluster with monodentate aspartate ligation to one iron. Unlike known clusters of this type the reduced [4Fe-4S](+) cluster of C42D FdI exhibits only an S = 1/2 EPR with no higher spin signals detected. The cluster shows only a minor change in reduction potential relative to the native protein. All attempts to convert the cluster to a 3Fe cluster using conventional methods of oxygen or ferricyanide oxidation or thiol exchange were not successful. The cluster conversion was ultimately accomplished using a new electrochemical method. Hydrophobic and electrostatic interaction and the lack of Gly residues adjacent to the Asp ligand explain the remarkable stability of this cluster.
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Affiliation(s)
- Y S Jung
- Department of Molecular Biology and Biochemistry, University of California, Irvine, California 92697, USA
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9
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10
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Affiliation(s)
- D Bentrop
- Magnetic Resonance Center University of Florence Via L. Sacconi 6, 50019 Sesto Fiorentino (Italy)
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11
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Iwasaki T, Watanabe E, Ohmori D, Imai T, Urushiyama A, Akiyama M, Hayashi-Iwasaki Y, Cosper NJ, Scott RA. Spectroscopic investigation of selective cluster conversion of archaeal zinc-containing ferredoxin from Sulfolobus sp. strain 7. J Biol Chem 2000; 275:25391-401. [PMID: 10827091 DOI: 10.1074/jbc.m909243199] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Archaeal zinc-containing ferredoxin from Sulfolobus sp. strain 7 contains one [3Fe-4S] cluster (cluster I), one [4Fe-4S] cluster (cluster II), and one isolated zinc center. Oxidative degradation of this ferredoxin led to the formation of a stable intermediate with 1 zinc and approximately 6 iron atoms. The metal centers of this intermediate were analyzed by electron paramagnetic resonance (EPR), low temperature resonance Raman, x-ray absorption, and (1)H NMR spectroscopies. The spectroscopic data suggest that (i) cluster II was selectively converted to a cubane [3Fe-4S](1+) cluster in the intermediate, without forming a stable radical species, and that (ii) the local metric environments of cluster I and the isolated zinc site did not change significantly in the intermediate. It is concluded that the initial step of oxidative degradation of the archaeal zinc-containing ferredoxin is selective conversion of cluster II, generating a novel intermediate containing two [3Fe-4S] clusters and an isolated zinc center. At this stage, significant structural rearrangement of the protein does not occur. We propose a new scheme for oxidative degradation of dicluster ferredoxins in which each cluster converts in a stepwise manner, prior to apoprotein formation, and discuss its structural and evolutionary implications.
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Affiliation(s)
- T Iwasaki
- Department of Biochemistry and Molecular Biology, Nippon Medical School, Sendagi, Tokyo, Japan. iwasaki/
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12
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Abstract
We have studied four proteins containing oxidized 3Fe clusters ([Fe3S4]+, S=1/2, composed of three, antiferromagnetically coupled high-spin ferric ions) by continuous wave (CW) and pulsed EPR techniques: Azotobacter vinelandii ferredoxin I, Desulfovibrio gigas ferredoxin II, and the 3Fe forms of Pyrococcus furiosus ferredoxin and aconitase. The 35 GHz (Q-band) CW EPR signals are simulated to yield experimental g tensors, which either had not been reported, or had been reported only at X-band microwave frequency. Pulsed X- and Q-band EPR techniques are used to determine electron spin-lattice (T1, longitudinal) relaxation times at several positions on the samples' EPR envelope over the temperature range 2-4.2 K. The T1, values vary sharply across the EPR envelope, a reflection of the fact that the envelope results from a distribution in cluster properties, as seen earlier as a distribution in g3 values and in 57 Fe hyperfine interactions, as detected by electron nuclear double resonance spectroscopy. The temperature dependence of 1/T1 is analyzed in terms of the Orbach mechanism, with relaxation dominated by resonant two-phonon transitions to a doublet excited state at approximately 20 cm(-1) above the doublet ground state for all four of these 3Fe proteins. The experimental EPR data are combined with previously reported 57Fe hyperfine data to determine electronic spin exchange-coupling within the clusters, following the model of Kent et al. Their model defines the coupling parameters as follows: J13=J, J12=J(1+epsilon'), J23=J(1+epsilon), where Jij is the isotropic exchange coupling between ferric ions i and j, and epsilon' and epsilon' are measures of coupling inequivalence. We have extended their theory to include the effects of epsilon' not equal to 0 and thus derived an exact expression for the energy of the doublet excited state for any epsilon, epsilon'. This excited state energy corresponds roughly to epsilonJ and is in the range 5-10 cm(-1) for each of these four 3Fe proteins. This magnitude of the product epsilonJ, determined by our time-domain relaxation studies in the temperature range 2-4 K, is the same as that obtained from three other distinct types of study: CW EPR studies of spin relaxation in the range 5.5-50 K, NMR studies in the range 293-303 K, and static susceptibility measurements in the range 1.8-200 K. We suggest that an apparent disagreement as to the individual values of J and epsilon be resolved in favor of the values obtained by susceptibility and NMR (J > or approximately 200 cm(-1) and epsilon> or =0.02 cm(-1)). as opposed to a smaller J and larger r as suggested in CW EPR studies. However, we note that this resolution casts doubt on the accepted theoretical model for describing the distribution in magnetic properties of 3Fe clusters.
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Affiliation(s)
- J Telser
- Department of Chemistry, Northwestern University, Evanston, IL 60208-3113, USA
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13
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Johnson MK, Duderstadt RE, Duin EC. Biological and Synthetic [Fe3S4] Clusters. ADVANCES IN INORGANIC CHEMISTRY 1999. [DOI: 10.1016/s0898-8838(08)60076-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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14
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Gao-Sheridan HS, Kemper MA, Khayat R, Tilley GJ, Armstrong FA, Sridhar V, Prasad GS, Stout CD, Burgess BK. A T14C variant of Azotobacter vinelandii ferredoxin I undergoes facile [3Fe-4S]0 to [4Fe-4S]2+ conversion in vitro but not in vivo. J Biol Chem 1998; 273:33692-701. [PMID: 9837955 DOI: 10.1074/jbc.273.50.33692] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
[4Fe-4S]2+/+ clusters that are ligated by Cys-X-X-Cys-X-X-Cys sequence motifs share the general feature of being hard to convert to [3Fe-4S]+/0 clusters, whereas those that contain a Cys-X-X-Asp-X-X-Cys motif undergo facile and reversible cluster interconversion. Little is known about the factors that control the in vivo assembly and conversion of these clusters. In this study we have designed and constructed a 3Fe to 4Fe cluster conversion variant of Azotobacter vinelandii ferredoxin I (FdI) in which the sequence that ligates the [3Fe-4S] cluster in native FdI was altered by converting a nearby residue, Thr-14, to Cys. Spectroscopic and electrochemical characterization shows that when purified in the presence of dithionite, T14C FdI is an O2-sensitive 8Fe protein. Both the new and the indigenous clusters have reduction potentials that are significantly shifted compared with those in native FdI, strongly suggesting a significantly altered environment around the clusters. Interestingly, whole cell EPR have revealed that T14C FdI exists as a 7Fe protein in vivo. This 7Fe form of T14C FdI is extremely similar to native FdI in its spectroscopic, electrochemical, and structural features. However, unlike native FdI which does not undergo facile cluster conversion, the 7Fe form T14C FdI quickly converts to the 8Fe form with a high efficiency under reducing conditions.
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Affiliation(s)
- H S Gao-Sheridan
- Department of Molecular Biology and Biochemistry, University of California, Irvine, California 92697-3900, USA
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15
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Abstract
Ferredoxins are a group of iron-sulfur proteins for which a wealth of structural and mutational data have recently become available. Previously unknown structures of ferredoxins which are adapted to halophilic, acidophilic or hyperthermophilic environments and new cysteine patterns for cluster ligation and non-cysteine cluster ligation have been described. Site-directed mutagenesis experiments have given insight into factors that influence the geometry, stability, redox potential, electronic properties and electron-transfer reactivity of iron-sulfur clusters.
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Affiliation(s)
- H Sticht
- Lehrstuhl für Struktur und Chemie der Biopolymere, Universität Bayreuth, Germany.
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16
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Fawcett SE, Davis D, Breton JL, Thomson AJ, Armstrong FA. Voltammetric studies of the reactions of iron-sulphur clusters ([3Fe-4S] or [M3Fe-4S]) formed in Pyrococcus furiosus ferredoxin. Biochem J 1998; 335 ( Pt 2):357-68. [PMID: 9761735 PMCID: PMC1219790 DOI: 10.1042/bj3350357] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Reactions of the [3Fe-4S] cluster and various metallated [M3Fe-4S] adducts co-ordinated in the ferredoxin from the hyperthermophile Pyrococcus furiosus have been studied by protein-film voltammetry, bulk-solution voltammetry, solution kinetics and magnetic CD (MCD). The [3Fe-4S] cluster exhibits two couples, [3Fe-4S]+/0 and [3Fe-4S]0/2-. Film voltammetry is possible over a wide pH range (2-8), revealing that the [3Fe-4S]+/0 couple shows a complex pH dependence with pKred1=2.8, pKox=4.9 and pKred2=6.7. From MCD, pKred1 corresponds with protonation of [3Fe-4S]0 to give a spectroscopically distinct species, as reported for ferredoxins from Azotobacter and Sulfolobus. The status of the disulphide/disulphydryl entity makes no significant difference to the data (given for the -S-S- form). Formation of the hyper-reduced [3Fe-4S]2- state is observed, requiring 3H+ for the overall 3e- reduction of [3Fe-4S]+, the change therefore being electroneutral. By comparison with the ferredoxin from Desulfovibrio africanus, uptake of Fe(II) and other M(II) by [3Fe-4S]0 to give [M3Fe-4S] clusters is slow (t1/2>10 min at room temperature, slower still if the protein is adsorbed on the electrode), whereas reaction with Tl(I) to produce [Tl3Fe-4S] is very rapid (t1/2<<1 s), suggesting that co-ordination of Tl does not require reorganization of the protein structure. Rates of formation of [3Fe-4S] from [M3Fe-4S] adducts increase sharply at high potentials, showing that metal release involves a labile 'super-oxidized' [M3Fe-4S]3+ state.
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Affiliation(s)
- S E Fawcett
- Department of Chemistry, University of Oxford, South Parks Road, Oxford, OX1 3QR, UK
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17
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Davy SL, Osborne MJ, Moore GR. Determination of the structure of oxidised Desulfovibrio africanus ferredoxin I by 1H NMR spectroscopy and comparison of its solution structure with its crystal structure. J Mol Biol 1998; 277:683-706. [PMID: 9533888 DOI: 10.1006/jmbi.1998.1631] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The solution structure of the 64 amino acid Fe4S4 ferredoxin I from Desulfovibrio africanus has been determined using two-dimensional 1H NMR spectroscopy. Sequence-specific assignments were obtained for 59 amino acid residues and the structure determined with the program DIANA on the basis of 549 nuclear Overhauser enhancement (NOE) upper distance limits, and four dihedral angle and 52 distance constraints for the Fe4S4 cluster. The NMR structure was refined using the simulated annealing and energy minimisation protocols of the program X-PLOR to yield a final family of 19 structures selected on the basis of good covalent geometry and minimal restraint violations. The r.m.s.d. values to the average structure for this family are 0.49(+/-0.07) A and 0.94(+/-0.09) A for the backbone and heavy-atoms of residues 3 to 62, respectively. The NMR structure has been compared to the previously reported X-ray structures for the two molecules within the asymmetric unit of the crystal, which have a network of seven hydrogen bonds between them. This intermolecular interface, involving residues 38, 40 to 43 and 46, has the same conformation in the solution structures showing that the crystal packing does not perturb the structure. There are three regions in which the NMR and X-ray structures differ: around the cluster, a turn involving residues 8 to 10, and a loop involving residues 29 to 32. In the family of solution structures the backbone of the loop region incorporating residues 29 to 32 is well-defined whilst in both of the X-ray molecules it is ill-defined. The small differences between the X-ray and NMR structures for the cluster environment and the turn between residues 8 to 10 probably reflects a lack of NMR constraints. The observation of relatively rapid amide NH hydrogen exchange of NH groups close to the cluster, together with rapid flipping for Phe25, which is also close to the cluster, indicates that the cluster environment is more dynamic than the corresponding regions of related Fe/S proteins.
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Affiliation(s)
- S L Davy
- School of Chemical Sciences, University of East Anglia, Norwich, NR4 7TJ, U.K
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18
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19
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Sticht H, Wildegger G, Bentrop D, Darimont B, Sterner R, Rösch P. An NMR-derived model for the solution structure of oxidized Thermotoga maritima 1[Fe4-S4] ferredoxin. Eur J Biochem 1996; 237:726-35. [PMID: 8647119 DOI: 10.1111/j.1432-1033.1996.0726p.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The solution structure of the 60-residue 1[Fe4-S4] ferredoxin from the hyperthermophilic bacterium Thermotoga maritima was determined based on 683 distance and 35 dihedral angle restraints that were obtained from NMR data. In addition, data known from crystallographic studies of ferredoxins was used for modeling of the iron-sulfur cluster and its environment. The protein shows a globular fold very similar to the fold of the related 1[Fe4-S4] ferredoxins from Desulfovibrio gigas and Desulfovibrio africanus, and elements of regular secondary structure similar to those in other ferredoxins were found in the T. maritima protein. In particular, the T. maritima protein displayed a beta-sheet structure made up of strands located at the very NH(2) and COOH termini of the protein, and an internal alpha-helix. The internal beta-sheet observed in the D. gigas and D. africanus ferredoxins could not be confirmed in T. maritima ferredoxin and is thus suggested to be only weakly present or even absent in this protein. This result suggests that thermostability in ferredoxins is not necessarily correlated with the content of stable elements of regular secondary structure.
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Affiliation(s)
- H Sticht
- Lehrstuhl für Biopolymere, Universität Bayreuth, Germany
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20
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Bentrop D, Bertini I, Luchinat C, Mendes J, Piccioli M, Teixeira M. Paramagnetic NMR analysis of the seven-iron ferredoxin from the hyperthermoacidophilic archaeon Desulfurolobus ambivalens reveals structural similarity to other dicluster ferredoxins. Eur J Biochem 1996; 236:92-9. [PMID: 8617291 DOI: 10.1111/j.1432-1033.1996.00092.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The seven-iron ferredoxin from the hyperthermophilic archaeon Desulfurolobus ambivalens has been investigated by one-dimensional and two-dimensional 1H-NMR in its oxidized and dithionite-reduced states. All iron atoms of both the three-iron and the four-iron cluster are bound to cysteine residues whose hyperfine-shifted resonances were characterized. The pattern of these resonances is similar to those from three-iron, four-iron and eight-iron ferredoxins previously described in the literature, but the four-iron cluster has a shift pattern different from that in other seven-iron proteins. A second set of hyperfine-shifted resonances clearly indicates sample heterogeneity, which possibly involves the four-iron cluster. The observation of interresidue NOEs between two different cysteine residues proves the existence of close spatial proximity of the two clusters in D. ambivalens ferredoxin and therefore indicates structural homology to other dicluster ferredoxins. Moreover, this feature is crucial for the sequence-specific assignment of the hyperfine-shifted resonances. The C alpha-C beta-S-Fe dihedral angles of the cysteine residues coordinating the four-iron cluster could be estimated, and the electronic structure of the three-iron cluster is discussed.
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Affiliation(s)
- D Bentrop
- Department of Chemistry, University of Florence, Italy
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Adams MW, Kletzin A. Oxidoreductase-type enzymes and redox proteins involved in fermentative metabolisms of hyperthermophilic Archaea. Adv Protein Chem 1996; 48:101-80. [PMID: 8791625 DOI: 10.1016/s0065-3233(08)60362-9] [Citation(s) in RCA: 60] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- M W Adams
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens 30602, USA
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Bertini I, Donaire A, Feinberg BA, Luchinat C, Piccioli M, Yuan H. Solution structure of the oxidized 2[4Fe-4S] ferredoxin from Clostridium pasteurianum. Eur J Biochem 1995; 232:192-205. [PMID: 7556151 DOI: 10.1111/j.1432-1033.1995.tb20799.x] [Citation(s) in RCA: 79] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Following the recently developed approach to the solution structure of paramagnetic high-potential iron-sulfur proteins, the three-dimensional structure in solution of the oxidized Clostridium pasteurianum ferredoxin has been solved by 1H-NMR. The X-ray structure is not available. The protein contains 55 amino acids and two [4Fe-4S] clusters. In the oxidized state, the clusters have S = 0 ground states, but are paramagnetic because of thermal population of excited states. Due to the somewhat small size of the protein and to the presence of two clusters, approximately 55% of the residues have at least one proton with a non-selective T1 smaller than 25 ms. The protein has thus been used as a test system to challenge the present paramagnetic NMR methodology both in achieving an extended assignment and in obtaining a suitable number of constraints. 79% of protein protons have been assigned. Analogy with other ferredoxins of known structure has been of help to speed up the final stages of the assignment, although we have shown that this independent information is not necessary. In addition to dipolar connectivities, partially detected through tailored experiments, 3JHN-H alpha, H-bond constraints and dihedral angle constraints on the Cys chi 2 angles have been generated by using a recently derived Karplus-type relationship for the hyperfine shifts of cysteine beta CH2 protons. In total, 456 constraints have been used in distance geometry calculations. The final quality of the structures is satisfactory, with root-mean-square deviation values of 66 pm and 108 pm for backbone and heavy atoms, respectively. The resulting structure is compared with that of Clostridium acidi urici ferredoxin [Duée, E. D., Fanchon, E., Vicat, J., Sieker, L. C., Meyer, J. & Moulis, J.-M. (1994) J. Mol. Biol. 243, 683-695]. The two proteins are very similar in the overall folding, secondary structure elements and side-chain orientations. The C alpha root-mean-square deviation values between the X-ray-determined C. acidi urici ferredoxin structure and the conformer with lowest energy of the C. pasteurianum ferredoxin family is 78 pm (residues 3-53). Discrepancies in residues 26-28 may arise from the disorder observed in the X-ray structure in that region.
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Affiliation(s)
- I Bertini
- Department of Chemistry, University of Florence, Italy
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