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Prioretti L, D’Ermo G, Infossi P, Kpebe A, Lebrun R, Bauzan M, Lojou E, Guigliarelli B, Giudici-Orticoni MT, Guiral M. Carbon Fixation in the Chemolithoautotrophic Bacterium Aquifex aeolicus Involves Two Low-Potential Ferredoxins as Partners of the PFOR and OGOR Enzymes. Life (Basel) 2023; 13:life13030627. [PMID: 36983784 PMCID: PMC10052474 DOI: 10.3390/life13030627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 02/21/2023] [Accepted: 02/22/2023] [Indexed: 02/27/2023] Open
Abstract
Aquifex aeolicus is a microaerophilic hydrogen- and sulfur -oxidizing bacterium that assimilates CO2 via the reverse tricarboxylic acid cycle (rTCA). Key enzymes of this pathway are pyruvate:ferredoxin oxidoreductase (PFOR) and 2-oxoglutarate:ferredoxin oxidoreductase (OGOR), which are responsible, respectively, for the reductive carboxylation of acetyl-CoA to pyruvate and of succinyl-CoA to 2-oxoglutarate, two energetically unfavorable reactions that require a strong reduction potential. We have confirmed, by biochemistry and proteomics, that A. aeolicus possesses a pentameric version of these enzyme complexes ((αβγδε)2) and that they are highly abundant in the cell. In addition, we have purified and characterized, from the soluble fraction of A. aeolicus, two low redox potential and oxygen-stable [4Fe-4S] ferredoxins (Fd6 and Fd7, E0 = −440 and −460 mV, respectively) and shown that they can physically interact and exchange electrons with both PFOR and OGOR, suggesting that they could be the physiological electron donors of the system in vivo. Shotgun proteomics indicated that all the enzymes assumed to be involved in the rTCA cycle are produced in the A. aeolicus cells. A number of additional enzymes, previously suggested to be part of a putative partial Wood-Ljungdahl pathway used for the synthesis of serine and glycine from CO2 were identified by mass spectrometry, but their abundance in the cell seems to be much lower than that of the rTCA cycle. Their possible involvement in carbon assimilation is discussed.
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Affiliation(s)
- Laura Prioretti
- CNRS, Bioénergétique et Ingénierie des Protéines, Aix Marseille Université, IMM, 13009 Marseille, France
| | - Giulia D’Ermo
- CNRS, Bioénergétique et Ingénierie des Protéines, Aix Marseille Université, IMM, 13009 Marseille, France
| | - Pascale Infossi
- CNRS, Bioénergétique et Ingénierie des Protéines, Aix Marseille Université, IMM, 13009 Marseille, France
| | - Arlette Kpebe
- CNRS, Bioénergétique et Ingénierie des Protéines, Aix Marseille Université, IMM, 13009 Marseille, France
| | - Régine Lebrun
- CNRS, Aix Marseille Université, IMM, 13009 Marseille, France
| | - Marielle Bauzan
- CNRS, Aix Marseille Université, IMM, 13009 Marseille, France
| | - Elisabeth Lojou
- CNRS, Bioénergétique et Ingénierie des Protéines, Aix Marseille Université, IMM, 13009 Marseille, France
| | - Bruno Guigliarelli
- CNRS, Bioénergétique et Ingénierie des Protéines, Aix Marseille Université, IMM, 13009 Marseille, France
| | | | - Marianne Guiral
- CNRS, Bioénergétique et Ingénierie des Protéines, Aix Marseille Université, IMM, 13009 Marseille, France
- Correspondence:
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2
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Brown AC, Suess DLM. An Open-Cuboidal [Fe 3S 4] Cluster Characterized in Both Biologically Relevant Redox States. J Am Chem Soc 2023; 145:2075-2080. [PMID: 36688844 DOI: 10.1021/jacs.2c13126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Synthetic analogues of the three common types of Fe-S clusters found in biology─diamond-core [Fe2S2] clusters, open-cuboidal [Fe3S4] clusters, and cuboidal [Fe4S4] clusters─have been reported in each biologically relevant redox state with one exception: the open-cuboidal [Fe3S4]+ cluster. Here, we describe the synthesis and characterization of an open-cuboidal [Fe3S4] cluster in both biologically relevant redox states: [Fe3S4]+ and [Fe3S4]0. Like their biological counterparts, the oxidized cluster has a spin-canted, S = 1/2 ground state, and the reduced cluster has an S = 2 ground state. Structural analysis reveals that the [Fe3S4] core undergoes substantial contraction upon oxidation, in contrast to the minimal structural changes observed for the only [Fe3S4] protein for which high-resolution structures are available in both redox states (Azotobacter vinelandii ferredoxin I; Av FdI). This difference between the synthetic models and Av FdI is discussed in the context of electron transfer by [Fe3S4] proteins.
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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
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3
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Paramagnetic NMR Spectroscopy Is a Tool to Address Reactivity, Structure, and Protein–Protein Interactions of Metalloproteins: The Case of Iron–Sulfur Proteins. MAGNETOCHEMISTRY 2020. [DOI: 10.3390/magnetochemistry6040046] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The study of cellular machineries responsible for the iron–sulfur (Fe–S) cluster biogenesis has led to the identification of a large number of proteins, whose importance for life is documented by an increasing number of diseases linked to them. The labile nature of Fe–S clusters and the transient protein–protein interactions, occurring during the various steps of the maturation process, make their structural characterization in solution particularly difficult. Paramagnetic nuclear magnetic resonance (NMR) has been used for decades to characterize chemical composition, magnetic coupling, and the electronic structure of Fe–S clusters in proteins; it represents, therefore, a powerful tool to study the protein–protein interaction networks of proteins involving into iron–sulfur cluster biogenesis. The optimization of the various NMR experiments with respect to the hyperfine interaction will be summarized here in the form of a protocol; recently developed experiments for measuring longitudinal and transverse nuclear relaxation rates in highly paramagnetic systems will be also reviewed. Finally, we will address the use of extrinsic paramagnetic centers covalently bound to diamagnetic proteins, which contributed over the last twenty years to promote the applications of paramagnetic NMR well beyond the structural biology of metalloproteins.
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4
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Lee Y, Jeon IR, Abboud KA, García-Serres R, Shearer J, Murray LJ. A [3Fe–3S]3+ cluster with exclusively μ-sulfide donors. Chem Commun (Camb) 2016; 52:1174-7. [DOI: 10.1039/c5cc07813j] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
A [3Fe–3(μ-S)]3+ cluster is reported in which each ferric center has a distorted trigonal pyramidal geometry, with an S = 1/2 ground state for the cluster and unusually anisotropic hyperfine coupling constants as determined by variable temperature magnetometry and Mössbauer spectroscopy.
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Affiliation(s)
- Yousoon Lee
- Department of Chemistry
- Center for Catalysis
- University of Florida
- Gainesville
- USA
| | - Ie-Rang Jeon
- Department of Chemistry
- Northwestern University
- Evanston
- USA
| | - Khalil A. Abboud
- Department of Chemistry
- Center for Catalysis
- University of Florida
- Gainesville
- USA
| | | | - Jason Shearer
- Department of Chemistry
- University of Nevada
- Reno
- Reno
- USA
| | - Leslie J. Murray
- Department of Chemistry
- Center for Catalysis
- University of Florida
- Gainesville
- USA
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5
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Couture MMJ, Martin VJJ, Mohn WW, Eltis LD. Characterization of DitA3, the [Fe3S4] ferredoxin of an aromatic ring-hydroxylating dioxygenase from a diterpenoid-degrading microorganism. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2006; 1764:1462-9. [PMID: 16952485 DOI: 10.1016/j.bbapap.2006.06.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2006] [Revised: 06/23/2006] [Accepted: 06/26/2006] [Indexed: 10/24/2022]
Abstract
DitA3, a small soluble ferredoxin, is a component of a ring-hydroxylating dioxygenase involved in the microbial degradation of the diterpenoid, dehydroabietic acid. The anaerobic purification of a heterologously expressed his-tagged DitA3 yielded 20 mg of apparently homogeneous recombinant protein, rcDitA3, per liter of cell culture. Each mole of purified rcDitA3 contained 2.9 equivalents of iron and 4.2 equivalents of sulfur, indicating the presence of a single [Fe(3)S(4)] cluster. This conclusion was corroborated by UV-Visible absorption (epsilon(412)=13.4 mM(-1) cm(-1)) and EPR (g(x,y)=2.00 and g(z)=2.02) spectroscopies. The reduction potential of rcDitA3, determined using a highly oriented parallel graphite (HOPG) electrode, was -177.0+/-0.5 mV vs. the standard hydrogen electrode (SHE) (20 mM MOPS, 80 mM KCl, pH 7.0, 22 degrees C). This potential is similar to those of small, soluble Rieske-type ferredoxin components of aromatic-ring dihydroxylating dioxygenases. In contrast to these Rieske-type ferredoxins, DitA3 appears to exist as a dimer in solution. The dimeric ferredoxin may be more stable or may increase the catalytic efficiency of the dioxygenase by delivering the two reducing equivalents required for turnover of the oxygenase.
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Affiliation(s)
- Manon M-J Couture
- Department of Biochemistry, Université Laval, Ste-Foy, Québec, Canada G1K 7P4.
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6
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Rodrigues PM, Macedo AL, Goodfellow BJ, Moura I, Moura JJG. Desulfovibrio gigas ferredoxin II: redox structural modulation of the [3Fe-4S] cluster. J Biol Inorg Chem 2006; 11:307-15. [PMID: 16453120 DOI: 10.1007/s00775-005-0077-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2005] [Accepted: 12/22/2005] [Indexed: 11/25/2022]
Abstract
Desulfovibrio gigas ferredoxin II (DgFdII) is a small protein with a polypeptide chain composed of 58 amino acids, containing one Fe3S4 cluster per monomer. Upon studying the redox cycle of this protein, we detected a stable intermediate (FdIIint) with four 1H resonances at 24.1, 20.5, 20.8 and 13.7 ppm. The differences between FdIIox and FdIIint were attributed to conformational changes resulting from the breaking/formation of an internal disulfide bridge. The same 1H NMR methodology used to fully assign the three cysteinyl ligands of the [3Fe-4S] core in the oxidized state (DgFdIIox) was used here for the assignment of the same three ligands in the intermediate state (DgFdIIint). The spin-coupling model used for the oxidized form of DgFdII where magnetic exchange coupling constants of around 300 cm-1 and hyperfine coupling constants equal to 1 MHz for all the three iron centres were found, does not explain the isotropic shift temperature dependence for the three cysteinyl cluster ligands in DgFdIIint. This study, together with the spin delocalization mechanism proposed here for DgFdIIint, allows the detection of structural modifications at the [3Fe-4S] cluster in DgFdIIox and DgFdIIint.
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Affiliation(s)
- Pedro M Rodrigues
- FCMA, CCMAR, Universidade do Algarve, Campus de Gambelas, 8005-139, Faro, Portugal
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7
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Dey A, Glaser T, Moura JJG, Holm RH, Hedman B, Hodgson KO, Solomon EI. Ligand K-edge X-ray Absorption Spectroscopy and DFT Calculations on [Fe3S4]0,+ Clusters: Delocalization, Redox, and Effect of the Protein Environment. J Am Chem Soc 2004; 126:16868-78. [PMID: 15612726 DOI: 10.1021/ja0466208] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Ligand K-edge XAS of an [Fe3S4]0 model complex is reported. The pre-edge can be resolved into contributions from the mu(2)S(sulfide), mu(3)S(sulfide), and S(thiolate) ligands. The average ligand-metal bond covalencies obtained from these pre-edges are further distributed between Fe(3+) and Fe(2.5+) components using DFT calculations. The bridging ligand covalency in the [Fe2S2]+ subsite of the [Fe3S4]0 cluster is found to be significantly lower than its value in a reduced [Fe2S2] cluster (38% vs 61%, respectively). This lowered bridging ligand covalency reduces the superexchange coupling parameter J relative to its value in a reduced [Fe2S2]+ site (-146 cm(-1) vs -360 cm(-1), respectively). This decrease in J, along with estimates of the double exchange parameter B and vibronic coupling parameter lambda2/k(-), leads to an S = 2 delocalized ground state in the [Fe3S4]0 cluster. The S K-edge XAS of the protein ferredoxin II (Fd II) from the D. gigas active site shows a decrease in covalency compared to the model complex, in the same oxidation state, which correlates with the number of H-bonding interactions to specific sulfur ligands present in the active site. The changes in ligand-metal bond covalencies upon redox compared with DFT calculations indicate that the redox reaction involves a two-electron change (one-electron ionization plus a spin change of a second electron) with significant electronic relaxation. The presence of the redox inactive Fe(3+) center is found to decrease the barrier of the redox process in the [Fe3S4] cluster due to its strong antiferromagnetic coupling with the redox active Fe2S2 subsite.
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Affiliation(s)
- Abhishek Dey
- Department of Chemistry and Stanford Synchrotron Radiation Laboratory, Stanford University, Stanford, CA 94305, USA
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8
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Meyer J, Clay MD, Johnson MK, Stubna A, Münck E, Higgins C, Wittung-Stafshede P. A hyperthermophilic plant-type [2Fe-2S] ferredoxin from Aquifex aeolicus is stabilized by a disulfide bond. Biochemistry 2002; 41:3096-108. [PMID: 11863449 DOI: 10.1021/bi015981m] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A [2Fe-2S] ferredoxin (Fd1) from the hyperthermophilic bacterium Aquifex aeolicus has been obtained by heterologous expression of the encoding gene in Escherichia coli. Sequence comparisons show that this protein belongs to the extended family of plant- and mammalian-type [2Fe-2S] ferredoxins but also indicate that it is not closely similar to either the plant-type or mammalian-type subfamilies. Instead, it appears to bear some similarity to novel members of this family, in particular the Isc-type ferredoxins involved in the assembly of iron-sulfur clusters in vivo. The two redox levels of the [2Fe-2S](2+/+) metal site of A. aeolicus ferredoxin have been studied by UV-visible, resonance Raman, EPR, variable temperature magnetic circular dichroism, and Mössbauer spectroscopies. A full-spin Hamiltonian analysis is given for the Mössbauer spectra. In aggregate, the spectroscopic data reveal differences with both the plant-type and mammalian-type ferredoxins, in keeping with the sequence comparisons. The midpoint potential of the [2Fe-2S](2+/+) couple, at -375 mV versus the normal hydrogen electrode, is more negative than those of mammalian-type ferredoxins and at the upper end of the range covered by plant-type ferredoxins. A. aeolicus ferredoxin contains two cysteines in addition to the four that are committed as ligands of the [2Fe-2S] cluster. These two residues have been shown by chemical modification and site-directed mutagenesis to form a disulfide bridge in the native protein. While that cystine unit plays a significant role in the exceptional thermostability of A. aeolicus ferredoxin (T(m) = 121 degrees C at pH 7 versus T(m) = 113 degrees C in a molecular variant where the disulfide bridge has been removed), it does not bear on the properties of the [2Fe-2S](2+/+) chromophore. This observation is consistent with the large distance (ca. 20 A) that is predicted to separate the iron-sulfur chromophore from the disulfide bridge.
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Affiliation(s)
- Jacques Meyer
- Département de Biologie Moléculaire et Structurale, CEA-Grenoble, 38054 Grenoble, France.
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9
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Affiliation(s)
- G N La Mar
- Department of Chemistry, University of California, Davis, California 95616, USA
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10
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Sanakis Y, Macedo AL, Moura I, Moura JJG, Papaefthymiou V, Münck E. Evidence for Antisymmetric Exchange in Cuboidal [3Fe−4S]+ Clusters. J Am Chem Soc 2000. [DOI: 10.1021/ja002658i] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yiannis Sanakis
- Contribution from the Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, Institute of Materials Science, NCSR “Demokritos”, 15310 Ag. Paraskevi, Attiki, Greece, Departamento de Química, C.Q.F.B., Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Quinta da Torre, 2825-114 Caparica, Portugal, and Department of Physics, University of Ioannina, Ioannina, Greece
| | - Anjos L. Macedo
- Contribution from the Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, Institute of Materials Science, NCSR “Demokritos”, 15310 Ag. Paraskevi, Attiki, Greece, Departamento de Química, C.Q.F.B., Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Quinta da Torre, 2825-114 Caparica, Portugal, and Department of Physics, University of Ioannina, Ioannina, Greece
| | - Isabel Moura
- Contribution from the Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, Institute of Materials Science, NCSR “Demokritos”, 15310 Ag. Paraskevi, Attiki, Greece, Departamento de Química, C.Q.F.B., Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Quinta da Torre, 2825-114 Caparica, Portugal, and Department of Physics, University of Ioannina, Ioannina, Greece
| | - Jose J. G. Moura
- Contribution from the Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, Institute of Materials Science, NCSR “Demokritos”, 15310 Ag. Paraskevi, Attiki, Greece, Departamento de Química, C.Q.F.B., Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Quinta da Torre, 2825-114 Caparica, Portugal, and Department of Physics, University of Ioannina, Ioannina, Greece
| | - Vasilios Papaefthymiou
- Contribution from the Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, Institute of Materials Science, NCSR “Demokritos”, 15310 Ag. Paraskevi, Attiki, Greece, Departamento de Química, C.Q.F.B., Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Quinta da Torre, 2825-114 Caparica, Portugal, and Department of Physics, University of Ioannina, Ioannina, Greece
| | - Eckard Münck
- Contribution from the Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, Institute of Materials Science, NCSR “Demokritos”, 15310 Ag. Paraskevi, Attiki, Greece, Departamento de Química, C.Q.F.B., Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Quinta da Torre, 2825-114 Caparica, Portugal, and Department of Physics, University of Ioannina, Ioannina, Greece
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Telser J, Lee HI, Hoffman BM. Investigation of exchange couplings in [Fe3S4]+ clusters by electron spin-lattice relaxation. J Biol Inorg Chem 2000; 5:369-80. [PMID: 10907748 DOI: 10.1007/pl00010666] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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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12
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The 3Fe containing ferredoxin from Desulfovibrio gigas: an NMR characterization of the oxidised and intermediate states. Coord Chem Rev 1999. [DOI: 10.1016/s0010-8545(99)00126-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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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] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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14
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Sticht H, Rösch P. The structure of iron-sulfur proteins. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 1998; 70:95-136. [PMID: 9785959 DOI: 10.1016/s0079-6107(98)00027-3] [Citation(s) in RCA: 114] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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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15
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Butt JN, Fawcett SEJ, Breton J, Thomson AJ, Armstrong FA. Electrochemical Potential and pH Dependences of [3Fe-4S] ↔ [M3Fe-4S] Cluster Transformations (M = Fe, Zn, Co, and Cd) in Ferredoxin III from Desulfovibrio africanus and Detection of a Cluster with M = Pb. J Am Chem Soc 1997. [DOI: 10.1021/ja971403a] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Julea N. Butt
- Contribution from the Inorganic Chemistry Laboratory, South Parks Road, Oxford OX1 3QR, England, and School of Chemical Sciences, University of East Anglia, Norwich NR4 7TJ, England
| | - Sarah E. J. Fawcett
- Contribution from the Inorganic Chemistry Laboratory, South Parks Road, Oxford OX1 3QR, England, and School of Chemical Sciences, University of East Anglia, Norwich NR4 7TJ, England
| | - Jacques Breton
- Contribution from the Inorganic Chemistry Laboratory, South Parks Road, Oxford OX1 3QR, England, and School of Chemical Sciences, University of East Anglia, Norwich NR4 7TJ, England
| | - Andrew J. Thomson
- Contribution from the Inorganic Chemistry Laboratory, South Parks Road, Oxford OX1 3QR, England, and School of Chemical Sciences, University of East Anglia, Norwich NR4 7TJ, England
| | - Fraser A. Armstrong
- Contribution from the Inorganic Chemistry Laboratory, South Parks Road, Oxford OX1 3QR, England, and School of Chemical Sciences, University of East Anglia, Norwich NR4 7TJ, England
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16
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Macedo-Ribeiro S, Darimont B, Sterner R, Huber R. Small structural changes account for the high thermostability of 1[4Fe-4S] ferredoxin from the hyperthermophilic bacterium Thermotoga maritima. Structure 1996; 4:1291-301. [PMID: 8939753 DOI: 10.1016/s0969-2126(96)00137-2] [Citation(s) in RCA: 89] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
BACKGROUND The characterization of the structural features that account for the high thermostability of some proteins is of great scientific and biotechnological interest. Proteins from hyperthermophilic organisms with optimum growth temperatures of 80 degrees C and higher generally show high intrinsic stabilities. The comparison of high resolution X-ray structures of these proteins with their counterparts from mesophilic organisms has therefore helped to identify potentially stabilizing forces in a number of cases. Small monomeric proteins which comprise only a single domain, such as ferredoxins, are especially suitable for such comparisons since the search for determinants of protein stability is considerably simplified. RESULTS The 1.75 A crystal structure of the extremely thermostable 1[4Fe-4S] ferredoxin from Thermotoga maritima (FdTm) was determined and compared with other monocluster-containing ferredoxins with different degrees of thermostability. CONCLUSIONS A comparison of the three-dimensional structure of FdTm with that of ferredoxins from mesophilic organisms suggests that the very high thermostability of FdTm is unexpectedly achieved without large changes of the overall protein structure. Instead, an increased number of potentially stabilizing features is observed in FdTm, compared with mesophilic ferredoxins. These include stabilization of alpha helices, replacement of residues in strained conformation by glycines, strong docking of the N-terminal methionine and an overall increase in the number of hydrogen bonds. Most of these features stabilize several secondary structure elements and improve the overall rigidity of the polypeptide backbone. The decreased flexibility will certainly play a relevant role in shielding the iron-sulfur cluster against physiologically high temperatures and further improve the functional integrity of FdTm.
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Affiliation(s)
- S Macedo-Ribeiro
- Max-Planck Institut für Biochemie, D-82152 Martinsried, Germany.
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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. EUROPEAN JOURNAL OF BIOCHEMISTRY 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] [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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Adams MW, Kletzin A. Oxidoreductase-type enzymes and redox proteins involved in fermentative metabolisms of hyperthermophilic Archaea. ADVANCES IN PROTEIN CHEMISTRY 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] [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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Chen B, Menon NK, Dervertarnian L, Moura JJ, Przybyla AE. Cloning, sequencing and overexpression of the Desulfovibrio gigas ferredoxin gene in E. coli. FEBS Lett 1994; 351:401-4. [PMID: 8082803 DOI: 10.1016/0014-5793(94)00891-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
We have cloned the gene encoding Desulfovibrio gigas ferredoxin using a photodigoxigenin-labelled probe synthesized with the polymerase chain reaction. The DNA sequence of the gene predicts a polypeptide of 58 residues after removal of the initial formyl methionine (polypeptide M(r) = 6,276). The ferredoxin gene was expressed in aerobically grown E. coli behind the lac promoter of pUC18 resulting in a high level of ferredoxin expression which comprises about 10% of the total cell protein. EPR analysis of recombinant ferredoxin revealed the presence of a [3Fe-4S] cluster which is characteristic of native D. gigas ferredoxin II.
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Affiliation(s)
- B Chen
- Department of Biochemistry, University of Georgia, Athens 30602
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