Electron spin echo envelope modulation spectroscopy supports the suggested coordination of two histidine ligands to the Rieske iron-sulfur centers of the cytochrome b6f complex on spinach and the cytochrome bc1 complexes of Rhodospirillum rubrum, Rhodobacter sphaeroides R-26, and bovine heart mitochondria

Britt, R. David; Sauer, Kenneth; Klein, Melvin P.; Knaff, David B.; Kriauciunas, Aidas; Yu, Linda; Malkin, Richard

doi:10.1021/bi00221a023

Cited by 122 publications

(111 citation statements)

References 51 publications

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“…1 shows the superimposed plots of three-pulse ESEEM spectra (frequencies Ͻ10 MHz) of ISP red for three bc 1 complex samples. The spectra contain a set of lines in the region 0 -8 MHz attributable to local interaction with 14 N nitrogens (19, 20,28). The data in Fig.…”

Section: Resultsmentioning

confidence: 99%

“…Although none of the crystallographic structures shows any occupancy of the site by the substrate ubihydroquinone (quinol, QH 2 ), or the product ubiquinone (quinone, Q), much biophysical evidence had suggested that both these native occupants interact with the ISP through a similar configuration (2, 13-18). Previous applications in the g y region found minor effects of inhibitors on the ESEEM spectra of UHDBTtreated mitochondrial bc 1 complex (19), and DBMIB-treated b 6 f complex isolated from spinach chloroplasts (20). No conclusions * This work was supported by National Institutes of Health Grant GM35438 (to A. R. C.); NATO Grant 977132 (to A. R. C. and R. S.); National Science Foundation Grant DBI-9602240 (to D. K.); National Science Foundation Grant INT-9910113 (to S. A. D.); Ministry of Education, Science, Sport and Culture of Japan Grant-in-aid 1169237, and Japan-United States Cooperative Science Program Grant from JSPS BSAR-507 (to T.…”

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confidence: 98%

“…Although none of the crystallographic structures shows any occupancy of the site by the substrate ubihydroquinone (quinol, QH 2 ), or the product ubiquinone (quinone, Q), much biophysical evidence had suggested that both these native occupants interact with the ISP through a similar configuration (2,(13)(14)(15)(16)(17)(18). Previous applications in the g y region found minor effects of inhibitors on the ESEEM spectra of UHDBTtreated mitochondrial bc 1 complex (19), and DBMIB-treated b 6 f complex isolated from spinach chloroplasts (20). No conclusions were drawn about possible interactions of the inhibitors with the cluster or changes in geometry of ligands.…”

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confidence: 99%

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The Interaction of the Rieske Iron-Sulfur Protein with Occupants of the Qo-site of the bc 1 Complex, Probed by Electron Spin Echo Envelope Modulation

Samoilova¹,

Kolling²,

Uzawa³

et al. 2002

Journal of Biological Chemistry

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The bifurcated reaction at the Q o -site of the bc 1 complex provides the mechanistic basis of the proton pumping activity through which the complex conserves redox energy in the proton gradient. Structural information about the binding of quinone at the site is lacking, because the site is vacant in crystals of the native complexes. We now report the first structural characterization of the interaction of the native quinone occupant with the Rieske iron-sulfur protein in the bc 1 complex of Rhodobacter sphaeroides, using high resolution EPR. We have compared the binding configuration in the presence of quinone with the known structures for the complex with stigmatellin and myxothiazol. We have shown by using EPR and orientation-selective electron spin echo envelope modulation (ESEEM) measurements of the iron-sulfur protein that when quinone is present in the site, the isotropic hyperfine constant of one of the N ␦ atoms of a liganding histidine of the [2Fe-2S] cluster is similar to that observed when stigmatellin is present and different from the configuration in the presence of myxothiazol. The spectra also show complementary differences in nitrogen quadrupole splittings in some orientations. We suggest that the EPR characteristics, the ESEEM spectra, and the hyperfine couplings reflect a similar interaction between the iron-sulfur protein and the quinone or stigmatellin and that the N ␦ involved is that of a histidine (equivalent to His-161 in the chicken mitochondrial complex) that forms both a ligand to the cluster and a hydrogen bond with a carbonyl oxygen atom of the Q o -site occupant.The cytochrome (cyt) 1 bc 1 complex family plays an essential role in the energy metabolism of the biosphere (1, 2), providing the central enzymes in the electron transfer chains of all the major pathways. In bacteria, and their mitochondrial and chloroplasts descendants, the complex catalyzes oxidation of quinol and reduction of a diffusible small protein (cyt c or c 2 in ␣-proteobacteria) through a modified Q-cycle (3-6).Interest in the bc 1 complex has been heightened by the recent availability of structures and the new insights into functional aspects that these have encouraged (2, 7-12). However, with the structures has come the realization that the static models do not provide all the information needed to understand mechanism at a deeper level. The reactions of greatest interest are the proton-coupled electron transfers at the quinone-processing sites. In particular, oxidation of ubiquinol at the Q o -site of the complex is the key reaction of the Q-cycle, providing the bifurcation of electron transfer between two different acceptor chains that allows coupling to proton transfer. The Q o -site of the mitochondrial complex, and its mechanism, are also of central importance to the physiology of cellular damage and aging, because it is a major site for generation of reactive oxygen species.To understand the mechanism, we need detailed information about the local reaction environment, including protein structure, hydroge...

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Section: Resultsmentioning

confidence: 99%

mentioning

confidence: 98%

“…Although none of the crystallographic structures shows any occupancy of the site by the substrate ubihydroquinone (quinol, QH 2 ), or the product ubiquinone (quinone, Q), much biophysical evidence had suggested that both these native occupants interact with the ISP through a similar configuration (2,(13)(14)(15)(16)(17)(18). Previous applications in the g y region found minor effects of inhibitors on the ESEEM spectra of UHDBTtreated mitochondrial bc 1 complex (19), and DBMIB-treated b 6 f complex isolated from spinach chloroplasts (20). No conclusions were drawn about possible interactions of the inhibitors with the cluster or changes in geometry of ligands.…”

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confidence: 99%

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The Interaction of the Rieske Iron-Sulfur Protein with Occupants of the Qo-site of the bc 1 Complex, Probed by Electron Spin Echo Envelope Modulation

Samoilova¹,

Kolling²,

Uzawa³

et al. 2002

Journal of Biological Chemistry

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“…Histidine and aspartate replace the second cysteine in the motif of De3 and Xf, suggesting that these residues are ligands for the ironsulfur cluster in these homologs. A role for histidine and aspartate in ligation of iron-sulfur centers is uncommon but not without precedent (3,5,8,9,24,26). Following the previously described Isf homologs, the BLASTP alignments with the next lowest E values were the alignments with several FMN-binding tryptophan repressor binding proteins that do not contain iron -FIG.…”

Section: Discussionmentioning

confidence: 99%

Iron-Sulfur Flavoprotein (Isf) from Methanosarcina thermophila Is the Prototype of a Widely Distributed Family

2001

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A total of 35 homologs of the iron-sulfur flavoprotein (Isf) from Methanosarcina thermophila were identified in databases. All three domains were represented, and multiple homologs were present in several species. An unusually compact cysteine motif ligating the 4Fe-4S cluster in Isf is conserved in all of the homologs except two, in which either an aspartate or a histidine has replaced the second cysteine in the motif. A phylogenetic analysis of Isf homologs identified four subgroups, two of which were supported by bootstrap data. Three homologs from metabolically and phylogenetically diverse species in the Bacteria and Archaea domains (Af3 from Archaeoglobus fulgidus, Cd1 from Clostridium difficile, and Mj2 from Methanococcus jannaschii) were overproduced in Escherichia coli. Each homolog purified as a homodimer, and the UV-visible absorption spectra were nearly identical to that of Isf. After reconstitution with iron, sulfide, and flavin mononucleotide (FMN) the homologs contained six to eight nonheme iron atoms and 1.6 to 1.7 FMN molecules per dimer, suggesting that two 4Fe-4S or 3Fe-4S clusters and two FMN cofactors were bound to each dimer, which is consistent with Isf data. Homologs Af3 and Mj2 were reduced by CO in reactions catalyzed by cell extract of acetate-grown M. thermophila, but Cd1 was not. Homologs Af3 and Mj2 were reduced by CO in reactions catalyzed by A. fulgidus and M. jannaschii cell extracts. Cell extract of Clostridium thermoaceticum catalyzed CO reduction of Cd1. Our database sequence analyses and biochemical characterizations indicate that Isf is the prototype of a family of iron-sulfur flavoproteins that occur in members of all three domains.Methane produced by the acetate fermentation pathway accounts for two-thirds of all biologically produced methane. In Methanosarcina thermophila, acetate is cleaved into carbonyl and methyl groups by the CO dehydrogenase (CODH)-acetyl coenzyme A (acetyl-CoA) synthase (ACS) enzyme complex. The methyl group is subsequently reduced to methane by electrons derived from oxidation of the carbonyl group to CO 2 by the CODH-ACS complex (7). An iron-sulfur flavoprotein (Isf) from M. thermophila has been overproduced in Escherichia coli, purified, and characterized. Isf is purified as a homodimer which binds two 4Fe-4S clusters and two flavin mononucleotide (FMN) cofactors (2, 14). Ferredoxin, the electron acceptor of the CODH-ACS complex, is the physiological electron donor for Isf. Additional results support the hypothesis that Isf plays a role in electron transport during fermentation of acetate to methane (14). The deduced amino acid sequence of Isf contains an unusually compact cysteine motif (CX 2 CX 2 CX 5 C) that has been shown, on the basis of site-directed mutagenesis and electron paramagnetic resonance studies, to ligate the 4Fe-4S cluster (15). The midpoint potential values are -394 mV for the 4Fe-4S cluster and -277 mV for the FMN in Isf, suggesting that electrons derived from oxidation of the carbonyl group of acetate flow from ferredoxin to t...

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“…Indeed, the coordination of the Rieske cluster by histidyl ligands was initially established by electron nuclear double resonance spectroscopy (14 -16) and confirmed by ESEEM (17,18) before being demonstrated through crystallography (19). Further studies of the Rieske cluster by X-band oneand two-dimensional ESEEM (20 -22) have shown that the major contribution in these spectra comes from the coordinating N ␦ of histidines.…”

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confidence: 98%

Identification of Hydrogen Bonds to the Rieske Cluster through the Weakly Coupled Nitrogens Detected by Electron Spin Echo Envelope Modulation Spectroscopy

Dikanov

Kolling

Endeward

et al. 2006

Journal of Biological Chemistry

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Proteins containing Rieske-type [2Fe-2S] clusters with two histidyl and two cysteinyl ligands play important roles in many biological electron transfer reactions such as aerobic respiration, photosynthesis, and biodegradation of various alkene and aromatic compounds. The distinct biological functions of this protein family are in part associated with the cluster redox potential and the pK of the oxidized form, which are roughly correlated with the number of hydrogen bonds from protein side chains and the peptide backbone to the cluster and its immediate ligands (1-6).In the cytochrome bc 1 /b 6f family, a Rieske iron-sulfur protein (ISP) 4 is a constituent of the high potential electron transfer chain that accepts the first electron in the bifurcated reaction at the ubihydroquinone (quinol, QH 2 ) oxidizing Q o site. In the catalytic mechanism at the Q o site, the redox reaction involves extraction of both an electron and a proton from the bound quinol and their transfer to the ISP through a short pathway that includes the ISP His-161 ring and the H-bond between N ⑀ and the -OH of the quinol substrate (7). It has been proposed that the electron transfer is gated by the low probability of finding the H-atom of the H-bond in the kinetically favorable position, determined by the pK difference between the quinol and the oxidized ISP (ISP ox ) (reviewed in Refs. 5 and 6). The pK on ISP ox is contributed by one of the cluster ligands, His-161 in bovine numbering, and is associated with H ϩ dissociation from the N ⑀ involved in the H-bond. The gating accounts for the fact that this first electron transfer is slower by more than 3 orders of magnitude than would be expected from the short distance (ϳ7 Å) involved (6, 7). The first electron transfer is the ratedetermining step in quinol oxidation under conditions of substrate saturation. Rate determination at this reaction is demonstrated by the fact that the overall rate depends on its driving force in a classical Marcus fashion, as shown through use of mutants of the ISP with modified redox potential (6 -13). Briefly, the driving force, ⌬G o , for the first electron transfer is determined by the redox potential difference between the donor (SQ/QH 2 ) and acceptor (ISP ox /ISPH) couples. Assuming that mutations in the ISP do not change E m (SQ/QH 2 ), a change in * This work was supported by National Institutes of Health Grants GM 35438 (to A. R. C.) and GM 62954 (to S. A. D.), Fogarty Grant PHS 1 RO3 TW 01495 (to A. R. C. and R. I. S.), and National Institutes of Health/National Center for Research Resources Grant S10-RR15878 for instrumentation. The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked "advertisement" in accordance with 18 U.S.C. Section 1734 solely to indicate this fact. 1 To whom correspondence may be addressed. E-mail: dikanov@uiuc.edu. 2 Present address: Dept. of Chemistry, Princeton University, Princeton, NJ 08540. 3 To whom correspondence may be addressed. E-mail:...

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Cited by 122 publications

References 51 publications

The Interaction of the Rieske Iron-Sulfur Protein with Occupants of the Qo-site of the bc 1 Complex, Probed by Electron Spin Echo Envelope Modulation

The Interaction of the Rieske Iron-Sulfur Protein with Occupants of the Qo-site of the bc 1 Complex, Probed by Electron Spin Echo Envelope Modulation

Iron-Sulfur Flavoprotein (Isf) from Methanosarcina thermophila Is the Prototype of a Widely Distributed Family

Identification of Hydrogen Bonds to the Rieske Cluster through the Weakly Coupled Nitrogens Detected by Electron Spin Echo Envelope Modulation Spectroscopy

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