Structure and electrochemistry of proteins harboring iron-sulfur clusters of different nuclearities. Part II. [4Fe-4S] and [3Fe-4S] iron-sulfur proteins

Zanello, Piero

doi:10.1016/j.jsb.2018.01.010

Cited by 12 publications

(4 citation statements)

References 167 publications

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“…This is in contrast to other characterized hydrogenases, including O 2 -tolerant variants, that possess one or more [4Fe-4S] clusters 21,35 . [3Fe-4S] clusters generally undergo their +/0 redox transition at approximately +250 mV higher potential than [4Fe-4S] 2+/+ clusters 36 . As the potential of the electron transfer chain has previously been shown to dictate catalytic bias in other hydrogenases, the presence of exclusively [3Fe-4S] clusters in Huc probably has a major role in tuning the overpotential of the enzyme 37 .…”

Section: Huc Oligomerizes Around a Central Stalkmentioning

confidence: 99%

Structural basis for bacterial energy extraction from atmospheric hydrogen

Grinter

Kropp

Venugopal

et al. 2023

Nature

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Diverse aerobic bacteria use atmospheric H2 as an energy source for growth and survival1. This globally significant process regulates the composition of the atmosphere, enhances soil biodiversity and drives primary production in extreme environments2,3. Atmospheric H2 oxidation is attributed to uncharacterized members of the [NiFe] hydrogenase superfamily4,5. However, it remains unresolved how these enzymes overcome the extraordinary catalytic challenge of oxidizing picomolar levels of H2 amid ambient levels of the catalytic poison O2 and how the derived electrons are transferred to the respiratory chain1. Here we determined the cryo-electron microscopy structure of the Mycobacterium smegmatis hydrogenase Huc and investigated its mechanism. Huc is a highly efficient oxygen-insensitive enzyme that couples oxidation of atmospheric H2 to the hydrogenation of the respiratory electron carrier menaquinone. Huc uses narrow hydrophobic gas channels to selectively bind atmospheric H2 at the expense of O2, and 3 [3Fe–4S] clusters modulate the properties of the enzyme so that atmospheric H2 oxidation is energetically feasible. The Huc catalytic subunits form an octameric 833 kDa complex around a membrane-associated stalk, which transports and reduces menaquinone 94 Å from the membrane. These findings provide a mechanistic basis for the biogeochemically and ecologically important process of atmospheric H2 oxidation, uncover a mode of energy coupling dependent on long-range quinone transport, and pave the way for the development of catalysts that oxidize H2 in ambient air.

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Section: Huc Oligomerizes Around a Central Stalkmentioning

confidence: 99%

Structural basis for bacterial energy extraction from atmospheric hydrogen

Grinter

Kropp

Venugopal

et al. 2023

Nature

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“…For example, both FeS and FeS 2 could accelerate electron transport on the surface of nanoscale zero-valent iron (Xu et al, 2020). Multiple kinds of iron-sulfur clusters, such as [4Fe-4S] and [3Fe-4S], are also responsible for transferring electrons to metalloproteins (Zanello, 2018).…”

Section: Figure 4 |mentioning

confidence: 99%

Iron Sulfide Enhanced the Dechlorination of Trichloroethene by Dehalococcoides mccartyi Strain 195

Zhao

Zhu

2021

Front. Microbiol.

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Iron sulfide (FeS) nanoparticles have great potential in environmental remediation. Using the representative species Dehalococcoides mccartyi strain 195 (Dhc 195), the effect of FeS on trichloroethene (TCE) dechlorination was studied with hydrogen and acetate as the electron donor and carbon source, respectively. With the addition of 0.2 mM Fe2+ and S2–, the dechlorination rate of TCE was enhanced from 25.46 ± 1.15 to 37.84 ± 1.89 μmol⋅L–1⋅day–1 by the in situ formed FeS nanoparticles, as revealed through X-ray diffraction. Comparing the tceA gene copy numbers between with FeS and without FeS, real-time polymerase chain reaction (PCR) indicated that the abundance of the tceA gene increased from (2.83 ± 0.13) × 107 to (4.27 ± 0.21) × 108 copies/ml on day 12. The transcriptional activity of key genes involved in the electron transport chain was upregulated after the addition of FeS, including those responsible for the iron–sulfur cluster assembly protein gene (DET1632) and transmembrane transport of iron (DET1503, DET0685), cobalamin (DET0685, DET1139), and molybdenum (DET1161) genes. Meanwhile, the reverse transcription of tceA was increased approximately five times on the 12th day. These upregulations together suggested that the electron transport of D. mccartyi strain 195 was enhanced by FeS for apparent TCE dechlorination. Overall, the present study provided an eco-friendly and effective method to achieve high remediation efficiency for organohalide-polluted groundwater and soil.

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“…4A, panel ii) (27). To discern the charge state of the 4Fe-4S cluster, we treated DndCDE-FeS with either dithiothreitol or dithionite (28,29). Dithiothreitol can reduce [4Fe-4S] 3ϩ to [4Fe-4Fe] 2ϩ , whereas dithionite reduces [4Fe-4Fe] 2ϩ to [4Fe-4Fe] ϩ (29) We observed that when the protein was treated with dithiothreitol, the peak characteristic of [4Fe-4S] 3ϩ was abolished, and only residual resonances, with g values of 2.035 and 2.001, remained (Fig.…”

Section: Dndcde-fes Actively Decomposes H 2 Omentioning

confidence: 99%

Phosphorothioated DNA Is Shielded from Oxidative Damage

Mei

et al. 2019

Appl Environ Microbiol

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DNA is the carrier of genetic information. DNA modifications play a central role in essential physiological processes. Phosphorothioation (PT) modification involves the replacement of an oxygen atom on the DNA backbone with a sulfur atom. PT modification can cause genomic instability inSalmonella entericaunder hypochlorous acid stress. This modification restores hydrogen peroxide (H2O2) resistance in the catalase-deficientEscherichia coliHpx−strain. Here, we report biochemical characterization results for a purified PT modification protein complex (DndCDE) fromS. enterica. We observed multiplex oligomeric states of DndCDE by using native PAGE. This protein complex bound avidly to PT-modified DNA. DndCDE with an intact iron-sulfur cluster (DndCDE-FeS) possessed H2O2decomposition activity, with aVmaxof 10.58 ± 0.90 mM min−1and a half-saturation constant,K0.5S, of 31.03 mM. The Hill coefficient was 2.419 ± 0.59 for this activity. The protein’s activity toward H2O2was observed to be dependent on the intact DndCDE and on the formation of an iron-sulfur (Fe-S) cluster on the DndC subunit. In addition to cysteine residues that mediate the formation of this Fe-S cluster, other cysteine residues play a catalytic role. Finally, catalase activity was also detected in DndCDE fromPseudomonas fluorescensPf0-1. The data and conclusions presented suggest that DndCDE-FeS is a short-lived catalase. Our experiments also indicate that the complex binds to PT sites, shielding PT DNA from H2O2damage. This catalase shield might be able to extend from PT sites to the entire bacterial genome.IMPORTANCEDNA phosphorothioation has been reported in many bacteria. These PT-hosting bacteria live in very different environments, such as the human body, soil, or hot springs. The physiological function of DNA PT modification is still elusive. A remarkable property of PT modification is that purified genomic PT DNA is susceptible to oxidative cleavage. Among the oxidants, hypochlorous acid and H2O2are of physiological relevance for human pathogens since they are generated during the human inflammation response to bacterial infection. However, expression of PT genes in the catalase-deficientE. coliHpx−strain restores H2O2resistance. Here, we seek to solve this obvious paradox. We demonstrate that DndCDE-FeS is a short-lived catalase that binds tightly to PT DNA. It is thus possible that by docking to PT sites the catalase activity protects the bacterial genome against H2O2damage.

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Structure and electrochemistry of proteins harboring iron-sulfur clusters of different nuclearities. Part II. [4Fe-4S] and [3Fe-4S] iron-sulfur proteins

Cited by 12 publications

References 167 publications

Structural basis for bacterial energy extraction from atmospheric hydrogen

Structural basis for bacterial energy extraction from atmospheric hydrogen

Iron Sulfide Enhanced the Dechlorination of Trichloroethene by Dehalococcoides mccartyi Strain 195

Phosphorothioated DNA Is Shielded from Oxidative Damage

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