De Novo Design of Iron–Sulfur Proteins

Dizicheh, Zahra Bahrami; Halloran, Nicholas; Asma, William; Ghirlanda, Giovanna

doi:10.1016/bs.mie.2017.07.014

Cited by 6 publications

(5 citation statements)

References 56 publications

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“…Top five obtained models of TCR structure showed that two triplet cysteine motifs positioned in two distinct helices (Figure S2B), which is consistent with the data obtained by Phyre2 (Figure S2A), and a disulfide bond was formed between the two helices of the first obtained model of TCR structure (Figure S2B). The remaining four cysteine residues of this predicted model (Figure S2B) seemed to coordinate an iron-sulfur cluster, as shown in several iron-sulfur proteins designed de novo (Dizicheh et al, 2017;Nanda et al, 2016); however, in most cases, the iron-sulfur cluster(s) is bound in loop region(s) in natural proteins. These unique characteristics of TCR prompted us to proceed with the characterization of TCR function in relation to photosynthetic regulation.…”

Section: Identification Of Tcrmentioning

confidence: 62%

The evolutionary conserved iron-sulfur protein TCR controls P700 oxidation in photosystem I

et al. 2021

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Summary In natural habitats, plants have developed sophisticated regulatory mechanisms to optimize the photosynthetic electron transfer rate at the maximum efficiency and cope with the changing environments. Maintaining proper P700 oxidation at photosystem I (PSI) is the common denominator for most regulatory processes of photosynthetic electron transfers. However, the molecular complexes and cofactors involved in these processes and their function(s) have not been fully clarified. Here, we identified a redox-active chloroplast protein, the triplet-cysteine repeat protein (TCR). TCR shared similar expression profiles with known photosynthetic regulators and contained two triplet-cysteine motifs (CxxxCxxxC). Biochemical analysis indicated that TCR localizes in chloroplasts and has a [3Fe-4S] cluster. Loss of TCR limited the electron sink downstream of PSI during dark-to-light transition. Arabidopsis pgr5-tcr double mutant reduced growth significantly and showed unusual oxidation and reduction of plastoquinone pool. These results indicated that TCR is involved in electron flow(s) downstream of PSI, contributing to P700 oxidation.

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Section: Identification Of Tcrmentioning

confidence: 62%

The evolutionary conserved iron-sulfur protein TCR controls P700 oxidation in photosystem I

et al. 2021

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“…Both KshB and TDO contain FAD- and NADH-binding domains in the N-terminal region and iron–sulfur clusters at the C-terminus (Figures A, B, and C). Iron–sulfur clusters are crucial in mediating the electron-transfer processes. , TDO contains a Rieske cluster [2Fe–2S] (Fe 2 S 2 Cys 2 His 2 ), with protein ligands H44, H64, C42, and C61 (Figure A), in which each iron atom is coordinated by two sulfur atoms and two Cys thiolates or His residues. Meanwhile, KshB contains a plant-type ferredoxin [2Fe–2S] (Fe 2 S 2 Cys 4 ) with protein ligands C306, C310, C314, and C344 (Figure B).…”

Section: Resultsmentioning

confidence: 99%

Development of Engineered Ferredoxin Reductase Systems for the Efficient Hydroxylation of Steroidal Substrates

Zhu

Gao

Song

et al. 2020

ACS Sustainable Chem. Eng.

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9α-Hydroxy-4-androstene-3,17-dione (9OHAD), formed by the 9α-hydroxylation reaction catalyzed by 3-ketosteroid-9-hydroxylase (KSH), is an important precursor for the synthesis of adrenocortical hormones. KSH, a key enzyme complex in microbial steroid catabolism, contains a Rieske oxygenase (KshA) and a ferredoxin reductase (KshB). In this study, first we determined that the activity of KshB was rate-limiting in 9OHAD production. Thus, several potential alternative reductases were screened; a toluene 2,3-dioxygenase (TDO) reductase showed the highest activity toward NADH. In pathway optimization, the addition of a Rieske [2Fe−2S] cluster to KshB or TDO resulted in improved 9OHAD yields, which implies an improved efficiency of electron transfer. A sufficient supply system of NADH was ensured by introducing formate dehydrogenase (FDH) to construct an NADH regeneration system. The biosynthesis of 9OHAD was then optimized in a whole Escherichia coli cell catalysis system expressing FDH, KshA, and a variant of TDO reductase containing five point mutations and an added Rieske [2Fe−2S] cluster, which resulted in the final production of 5.24 g/L 9OHAD from 4androstene-3,17-dione with 99.3% yield. This research provides detailed insight into the electron-transfer system for steroid hydroxylation reactions.

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“…Phosphorus and iron are closely coupled to the activity of SRB [48]. Iron plays an important role for most organisms in electron-transfer reactions and prosthetic groups, such as hemes or ironsulfur clusters [49]. The zerovalent iron (Fe 0 ) contributes to the formation of an anaerobic environment, and the iron sulfide precipitation could relieve the inhibition of sulfide to improve sulfate-reduction capacity, which is beneficial to SRB [50][51][52].…”

Section: Major Environmental Factors Affecting the Sulfate Reductionmentioning

confidence: 99%

L-Cysteine Synthase Enhanced Sulfide Biotransformation in Subtropical Marine Mangrove Sediments as Revealed by Metagenomics Analysis

et al. 2021

Water

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High sulfides concentrations can be poisonous to environment because of anthropogenic waste production or natural occurrences. How to elucidate the biological transformation mechanisms of sulfide pollutants in the subtropical marine mangrove ecosystem has gained increased interest. Thus, in the present study, the sulfide biotransformation in subtropical mangroves ecosystem was accurately evaluated using metagenomic sequencing and quantitative polymerase chain reaction analysis. Most abundant genes were related to the organic sulfur transformation. Furthermore, an ecological model of sulfide conversion was constructed. Total phosphorus was the dominant environmental factor that drove the sulfur cycle and microbial communities. We compared mangrove and non-mangrove soils and found that the former enhanced metabolism that was related to sulfate reduction when compared to the latter. Total organic carbon, total organic nitrogen, iron, and available sulfur were the key environmental factors that effectively influenced the dissimilatory sulfate reduction. The taxonomic assignment of dissimilatory sulfate-reducing genes revealed that Desulfobacterales and Chromatiales were mainly responsible for sulfate reduction. Chromatiales were most sensitive to environmental factors. The high abundance of cysE and cysK could contribute to the coping of the microbial community with the toxic sulfide produced by Desulfobacterales. Collectively, these findings provided a theoretical basis for the mechanism of the sulfur cycle in subtropical mangrove ecosystems.

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De Novo Design of Iron–Sulfur Proteins

Cited by 6 publications

References 56 publications

The evolutionary conserved iron-sulfur protein TCR controls P700 oxidation in photosystem I

The evolutionary conserved iron-sulfur protein TCR controls P700 oxidation in photosystem I

Development of Engineered Ferredoxin Reductase Systems for the Efficient Hydroxylation of Steroidal Substrates

L-Cysteine Synthase Enhanced Sulfide Biotransformation in Subtropical Marine Mangrove Sediments as Revealed by Metagenomics Analysis

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