Formation and properties of an iron-nickel sulfide (NiFe3S4) cluster in Pyrococcus furiosus ferredoxin

Conover, Richard C.; Park, Jae Bum; Adams, Michael W. W.; Johnson, Michael K.

doi:10.1021/ja00167a074

Cited by 75 publications

(50 citation statements)

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“…DgFdII can be converted to FdI following incubation with excess Fe 2+ in the presence of dithiothreitol [47], showing that the polypeptide chain of DgFd can accommodate both [3Fe-4S] and [4Fe-4S] clusters. This cluster interconversion leads to the incorporation of other transition metals into the [3Fe-4S] cluster, with the [Co, 3Fe-4S] heterometal centre in DgFdII being the first reported [48], and similar results were subsequently found for D. africanus FdIII [49] and Pyrococcus furiosus Fd [50]. Other [Zn, 3Fe-4S] and [Ni, 3Fe-4S] centres were also produced from this protein [51,52].…”

Section: Introductionsupporting

confidence: 58%

Desulfovibrio gigas ferredoxin II: redox structural modulation of the [3Fe–4S] cluster

et al. 2006

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Desulfovibrio gigas ferredoxin II (DgFdII) is a small protein with a polypeptide chain composed of 58 amino acids, containing one Fe 3 S 4 cluster per monomer. Upon studying the redox cycle of this protein, we detected a stable intermediate (FdII int ) with four 1 H resonances at 24.1, 20.5, 20.8 and 13.7 ppm. The differences between FdII ox and FdII int were attributed to conformational changes resulting from the breaking/formation of an internal disulfide bridge. The same 1 H NMR methodology used to fully assign the three cysteinyl ligands of the [3Fe-4S] core in the oxidized state (DgFdII ox ) was used here for the assignment of the same three ligands in the intermediate state (DgFdII int ). The spin-coupling model used for the oxidized form of DgFdII where magnetic exchange coupling constants of around 300 cm À1 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 DgFdII int . This study, together with the spin delocalization mechanism proposed here for DgFdII int , allows the detection of structural modifications at the [3Fe-4S] cluster in DgFdII ox and DgFdII int .

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Section: Introductionsupporting

confidence: 58%

Desulfovibrio gigas ferredoxin II: redox structural modulation of the [3Fe–4S] cluster

et al. 2006

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“…44 Based on extensive spectroscopic studies on biological and synthetic [Fe 4 S 4 ] clusters, the frequency of the totally symmetric Fe and bridging S breathing mode can be used to indicate cluster ligation, 333–339 cm −1 for a [Fe 4 S 4 ] cluster with complete cysteinyl ligation, and 340–343 cm −1 for a [Fe 4 S 4 ] cluster with a unique Fe site with OH − , serinate or aspartate ligation. 45,46 Thus the frequency of the totally symmetric breathing mode at 338 cm −1 observed for the [Fe 4 S 4 ] 2+ cluster in Sc Grx5 suggests complete cysteinyl ligation for the [Fe 4 S 4 ] 2+ cluster. The Raman band at 352 cm −1 is assigned to an asymmetric Fe-S(Cys) stretching mode, however the intensity of this band in [Fe 4 S 4 ]-Grx5 is anomalously high compared to that of other biological [Fe 4 S 4 ] 2+ clusters.…”

Section: Resultsmentioning

confidence: 91%

Monothiol Glutaredoxins Can Bind Linear [Fe₃S₄]⁺ and [Fe₄S₄]²⁺ Clusters in Addition to [Fe₂S₂]²⁺ Clusters: Spectroscopic Characterization and Functional Implications

et al. 2013

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Saccharomyces cerevisiae mitochondrial glutaredoxin 5 (Grx5) is the archetypical member of a ubiquitous class of monothiol glutaredoxins with a strictly conserved CGFS active-site sequence that has been shown to function in biological [Fe2S2]2+ cluster trafficking. In this work, we show that recombinant S. cerevisiae Grx5 purified aerobically after prolonged exposure of the cell-free extract to air or after anaerobic reconstitution in the presence of glutathione, predominantly contains a linear [Fe3S4]+ cluster. The excited state electronic properties and ground state electronic and vibrational properties of the linear [Fe3S4]+ cluster have been characterized using UV-visible absorption/CD/MCD, EPR, Mössbauer and resonance Raman spectroscopies. The results reveal a rhombic S = 5/2 linear [Fe3S4]+ cluster with properties similar to those reported for synthetic linear [Fe3S4]+ clusters and the linear [Fe3S4]+ clusters in purple aconitase. Moreover, the results indicate that the Fe-S cluster content previously reported for many monothiol Grxs has been misinterpreted exclusively in terms of [Fe2S2]2+ clusters, rather than linear [Fe3S4]+ clusters or mixtures of linear [Fe3S4]+ and [Fe2S2]2+ clusters. In the absence of GSH, anaerobic reconstitution of Grx5 yields a dimeric form containing one [Fe4S4]2+ cluster that competent for in vitro activation of apo-aconitase, via intact cluster transfer. The ligation of the linear [Fe3S4]+ and [Fe4S4]2+ clusters in Grx5 has been assessed by spectroscopic, mutational and analytical studies. Potential roles for monothiol Grx5 in scavenging and recycling linear [Fe3S4]+ clusters released during protein unfolding under oxidative stress conditions and in maturation of [Fe4S4]2+ cluster-containing proteins are discussed in light of these results.

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“…This structure of R. rubrum CODH provides a three-dimensional view of an Ni-Fe-S cluster capable of catalyzing the biological oxidation of CO. (33), such a cluster in CODH would represent the first example of a naturally occurring Ni-Fe-S cubane. This assembly of Ni, Fe, and S may be a relic of a time when CO and CO 2 were predominant in the environment, and organisms needed to find ways to derive energy from these carbon sources to survive.…”

Section: Resultsmentioning

confidence: 99%

Life on carbon monoxide: X-ray structure of Rhodospirillum rubrum Ni-Fe-S carbon monoxide dehydrogenase

Drennan

Heo

Sintchak

et al. 2001

Proc. Natl. Acad. Sci. U.S.A.

290

274

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A crystal structure of the anaerobic Ni-Fe-S carbon monoxide dehydrogenase (CODH) from Rhodospirillum rubrum has been determined to 2.8-Å resolution. The CODH family, for which the R. rubrum enzyme is the prototype, catalyzes the biological oxidation of CO at an unusual Ni-Fe-S cluster called the C-cluster. The Ni-Fe-S C-cluster contains a mononuclear site and a four-metal cubane. Surprisingly, anomalous dispersion data suggest that the mononuclear site contains Fe and not Ni, and the four-metal cubane has the form [NiFe3S4] and not [Fe4S4]. The mononuclear site and the four-metal cluster are bridged by means of Cys 531 and one of the sulfides of the cube. CODH is organized as a dimer with a previously unidentified [Fe4S4] cluster bridging the two subunits. Each monomer is comprised of three domains: a helical domain at the N terminus, an ␣͞␤ (Rossmann-like) domain in the middle, and an ␣͞␤ (Rossmann-like) domain at the C terminus. The helical domain contributes ligands to the bridging [Fe4S4] cluster and another [Fe4S4] cluster, the B-cluster, which is involved in electron transfer. The two Rossmann domains contribute ligands to the active site C-cluster. This x-ray structure provides insight into the mechanism of biological CO oxidation and has broader significance for the roles of Ni and Fe in biological systems. P hototrophic anaerobes such as Rhodospirillum rubrum have the ability to use CO as a sole carbon and energy source (1). This ability derives from the oxidation of CO to CO 2 catalyzed by carbon monoxide dehydrogenases (CODHs). Some CODH enzymes also participate in the synthesis or degradation of acetyl-CoA and are referred to as CODH͞acetyl CoA synthases (CODH͞ACS). The dual role of these CODH͞ACSs is found in CO 2 fixation to acetyl-CoA by acetogens via the well studied Wood͞Ljungdahl pathway (reviewed in ref.2). Methanogens also use CODH͞ACSs in the conversion of acetyl-CoA to methane. As a consequence of these activities, CODHs are essential for the proper regulation of environmental carbon monoxide. Each year, up to 10 8 tons of CO are oxidized to CO 2 by aerobic and anaerobic bacteria containing CODH enzymes (3). Prehistoric environments rich in CO and CO 2 and deficient in oxygen (4) prompt speculation that early life forms relied on CO͞CO 2 as prime sources of both carbon and energy. In an effort to understand the detailed biochemical workings of early and current life on CO, we present the three-dimensional structure of an anaerobic Ni-Fe-S CODH enzyme.CODHs catalyze the oxidation of carbon monoxide in the two-electron process.The mechanism of CO oxidation is thought to involve binding and deprotonation of an H 2 O molecule to form hydroxide at a unique Ni-Fe-S center called the C-cluster (5). CO is believed to bind to a site on the C-cluster adjacent to the hydroxide. Thus, a metal-bound hydroxide may attack the CO carbon. Then the resulting metal-COOH intermediate is deprotonated and CO 2 is lost to yield a two-electron-reduced C-cluster (reviewed in ref.2). In R. rubrum, electrons are pas...

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Formation and properties of an iron-nickel sulfide (NiFe3S4) cluster in Pyrococcus furiosus ferredoxin

Cited by 75 publications

References 0 publications

Desulfovibrio gigas ferredoxin II: redox structural modulation of the [3Fe–4S] cluster

Desulfovibrio gigas ferredoxin II: redox structural modulation of the [3Fe–4S] cluster

Monothiol Glutaredoxins Can Bind Linear [Fe₃S₄]⁺ and [Fe₄S₄]²⁺ Clusters in Addition to [Fe₂S₂]²⁺ Clusters: Spectroscopic Characterization and Functional Implications

Life on carbon monoxide: X-ray structure of Rhodospirillum rubrum Ni-Fe-S carbon monoxide dehydrogenase

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Formation and properties of an iron-nickel sulfide (NiFe3S4) cluster in Pyrococcus furiosus ferredoxin

Cited by 75 publications

References 0 publications

Desulfovibrio gigas ferredoxin II: redox structural modulation of the [3Fe–4S] cluster

Desulfovibrio gigas ferredoxin II: redox structural modulation of the [3Fe–4S] cluster

Monothiol Glutaredoxins Can Bind Linear [Fe3S4]+ and [Fe4S4]2+ Clusters in Addition to [Fe2S2]2+ Clusters: Spectroscopic Characterization and Functional Implications

Life on carbon monoxide: X-ray structure of Rhodospirillum rubrum Ni-Fe-S carbon monoxide dehydrogenase

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Monothiol Glutaredoxins Can Bind Linear [Fe₃S₄]⁺ and [Fe₄S₄]²⁺ Clusters in Addition to [Fe₂S₂]²⁺ Clusters: Spectroscopic Characterization and Functional Implications