Asymmetric Dimeric Structure of Ferredoxin-NAD(P)+ Oxidoreductase from the Green Sulfur Bacterium Chlorobaculum tepidum: Implications for Binding Ferredoxin and NADP+

Muraki, Norifumi; Seo, Daisuke; Shiba, T.; Sakurai, Takeshi; Kurisu, Genji

doi:10.1016/j.jmb.2010.06.024

Cited by 26 publications

(43 citation statements)

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“…FNRs are structurally and phylogenetically classified into two unrelated families including five subgroups (Aliverti et al 2008;Dym and Eisenberg 2001;Correll et al 1993;Karplus and Faber 2004;Seo et al 2004;Muraki et al 2010). Phylogenetic analyses of the deduced amino acid sequences (Seo et al 2004) and crystal structures of FNRs from the green sulfur bacterium Chlorobaculum tepidum (Muraki et al 2010), the low GC gram positive bacterium Bacillus subtilis (BsFNR, Komori et al 2010) and thermophile Thermus thermophiles (PDB code; 2ZBW) have revealed that these FNRs are homologous to the NADPH-dependent bacterial thioredoxin reductase (TrxR) from Escherichia coli (EcTrxR) (Waksman et al 1994), referred as a TrxR-type FNR.…”

Section: Introductionmentioning

confidence: 99%

“…Phylogenetic analyses of the deduced amino acid sequences (Seo et al 2004) and crystal structures of FNRs from the green sulfur bacterium Chlorobaculum tepidum (Muraki et al 2010), the low GC gram positive bacterium Bacillus subtilis (BsFNR, Komori et al 2010) and thermophile Thermus thermophiles (PDB code; 2ZBW) have revealed that these FNRs are homologous to the NADPH-dependent bacterial thioredoxin reductase (TrxR) from Escherichia coli (EcTrxR) (Waksman et al 1994), referred as a TrxR-type FNR. The deduced genes of TrxR-type FNR are distributed among most of Firmicutes except for clostridia and heliobacteria, several alphaproteobacteria including purple non-sulfur bacteria, green sulfur bacteria, and several archaea.…”

Section: Introductionmentioning

confidence: 99%

“…Replacement of the re-face His324 in BsFNR (Komori et al 2010) and CtFNR (Muraki et al 2010) did not significantly affect the reactivity and selectivity toward NAD(P)H. These results are in contrast to the reports on the role of the corresponding residues on the re-face of the isoalloxazine ring moiety in the plant-type FNR super families (Piubelli et al 2000;Nogues et al 2004;Tejero et al 2005;Neeli et al 2005;Baroni et al 2012). Herein, we report the replacement of the si-face Tyr50 residue in TrxR-type BsFNR to Trp, Ser and Gly, and the resulting effects on the spectroscopic and enzymatic properties by steady-state reaction analyses.…”

Section: Introductionmentioning

confidence: 99%

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Replacement of Tyr50 stacked on the si-face of the isoalloxazine ring of the flavin adenine dinucleotide prosthetic group modulates Bacillus subtilis ferredoxin-NADP+ oxidoreductase activity toward NADPH

et al. 2015

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Replacement of Tyr50 stacked on the si-face of the isoalloxazine ring of the flavin adenine dinucleotide prosthetic group modulates Bacillus subtilis ferredoxin-NADP+ oxidoreductase activity toward NADPH

et al. 2015

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“…The plant-type Fdx functions primarily as the electron acceptor of photosystem I, and upon reduction Fdx functions as an electron donor in a myriad of key metabolic pathways (e.g., NADP þ reduction, carbon assimilation, nitrite and sulfite reduction, glutamate synthesis, and thioredoxin reduction, etc.) (22,23,(31)(32)(33)(34)(35).…”

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confidence: 99%

Allostery in the ferredoxin protein motif does not involve a conformational switch

Nechushtai

Lammert²,

Michaeli³

et al. 2011

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

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Regulation of protein function via cracking, or local unfolding and refolding of substructures, is becoming a widely recognized mechanism of functional control. Oftentimes, cracking events are localized to secondary and tertiary structure interactions between domains that control the optimal position for catalysis and/or the formation of protein complexes. Small changes in free energy associated with ligand binding, phosphorylation, etc., can tip the balance and provide a regulatory functional switch. However, understanding the factors controlling function in single-domain proteins is still a significant challenge to structural biologists. We investigated the functional landscape of a single-domain planttype ferredoxin protein and the effect of a distal loop on the electron-transfer center. We find the global stability and structure are minimally perturbed with mutation, whereas the functional properties are altered. Specifically, truncating the L1,2 loop does not lead to large-scale changes in the structure, determined via X-ray crystallography. Further, the overall thermal stability of the protein is only marginally perturbed by the mutation. However, even though the mutation is distal to the iron-sulfur cluster (∼20 Å), it leads to a significant change in the redox potential of the ironsulfur cluster (57 mV). Structure-based all-atom simulations indicate correlated dynamical changes between the surface-exposed loop and the iron-sulfur cluster-binding region. Our results suggest intrinsic communication channels within the ferredoxin fold, composed of many short-range interactions, lead to the propagation of long-range signals. Accordingly, protein interface interactions that involve L1,2 could potentially signal functional changes in distal regions, similar to what is observed in other allosteric systems.electron transfer | functional energy landscape | iron-sulfur proteins | protein folding O ver the last several decades, our understanding of protein function has evolved from a rather static perspective, where signaling and function have been understood through surface complementarity arguments, such as the "lock and key" paradigm (1, 2), to a more dynamic view where protein conformational fluctuations are inextricably linked to function (3). As our understanding of protein dynamics expands, we are revealing many mechanisms by which proteins exploit conformational fluctuations to perform cellular function. In multidomain proteins, relative repositioning of domains is often linked to their levels of activity. For example, large-scale domain rearrangements in the four-domain Src kinase (4) and C-terminal Src kinase (5, 6) lead to these proteins being in so-called "on" or "off" states, and functional regulation may be obtained by adjusting the balance between these conformations (7). In proteins such as adenylate kinase, domain rearrangements can be rate limiting during each round of catalysis (8), where the enzyme cycles between ligandcompetent and ligand-release conformations. Because the kinetics of these tra...

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“…1, equation a) (8-11). Recently, the thioredoxin reductase-like (TrxR-type) FNORs were found, and they are widely distributed among the bacteria and archaea (12)(13)(14). Even these types of FNORs are more homologous to bacterial NADPH-TrxRs, but they have catalytic properties similar to those of FNOR (14).…”

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confidence: 99%

Ferredoxin:NAD ⁺ Oxidoreductase of Thermoanaerobacterium saccharolyticum and Its Role in Ethanol Formation

Tian

Shao

et al. 2016

Appl Environ Microbiol

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Ferredoxin:NAD؉ oxidoreductase (NADH-FNOR) catalyzes the transfer of electrons from reduced ferredoxin to NAD ؉ . This enzyme has been hypothesized to be the main enzyme responsible for ferredoxin oxidization in the NADH-based ethanol pathway in Thermoanaerobacterium saccharolyticum; however, the corresponding gene has not yet been identified. Here, we identified the Tsac_1705 protein as a candidate FNOR based on the homology of its functional domains. We then confirmed its activity in vitro with a ferredoxin-based FNOR assay. To determine its role in metabolism, the tsac_1705 gene was deleted in different strains of T. saccharolyticum. In wild-type T. saccharolyticum, deletion of tsac_1705 resulted in a 75% loss of NADH-FNOR activity, which indicated that Tsac_1705 is the main NADH-FNOR in T. saccharolyticum. When both NADH-and NADPH-linked FNOR genes were deleted, the ethanol titer decreased and the ratio of ethanol to acetate approached unity, indicative of the absence of FNOR activity. Finally, we tested the effect of heterologous expression of Tsac_1705 in Clostridium thermocellum and found improvements in both the titer and the yield of ethanol. IMPORTANCERedox balance plays a crucial role in many metabolic engineering strategies. Ferredoxins are widely used as electron carriers for anaerobic microorganism and plants. This study identified the gene responsible for electron transfer from ferredoxin to NAD ؉ , a key reaction in the ethanol production pathway of this organism and many other metabolic pathways. Identification of this gene is an important step in transferring the ethanol production ability of this organism to other organisms. Ferredoxins are iron-sulfur proteins found in many anaerobic bacteria and archaea and mediate electron transfer in various metabolic processes, including photosynthesis (1, 2), alcohol production (3, 4), nitrogen fixation (5, 6), and hydrogen production (7). Lack of knowledge about these ferredoxin-dependent pathways currently limits our ability to incorporate them into metabolic engineering strategies. The ferredoxin:NAD ϩ /NADP ϩ oxidoreductase (FNOR) enzyme (EC 1.18.1.2/EC 1.18.1.3) forms a key bridge in metabolism between the nicotinamide cofactor (i.e., NAD ϩ , NADH, NADP ϩ , and NADPH)-dependent pathways and ferredoxin-dependent pathways (Fig. 1, equation a) (8-11). Recently, the thioredoxin reductase-like (TrxR-type) FNORs were found, and they are widely distributed among the bacteria and archaea (12)(13)(14). Even these types of FNORs are more homologous to bacterial NADPH-TrxRs, but they have catalytic properties similar to those of FNOR (14). FNOR enzymes are widely believed to be of central importance for the bioenergetics of anaerobic bacteria due to their ability to couple electron transport with ion or Na ϩ gradient generation (15) or transhydrogenation. Furthermore, they are the key enzymes for many biochemical and biofuel pathways, including isopropanol, ethanol, and n-butanol (3,4,16). Since ferredoxin has a lower standard reduction potential than...

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Asymmetric Dimeric Structure of Ferredoxin-NAD(P)+ Oxidoreductase from the Green Sulfur Bacterium Chlorobaculum tepidum: Implications for Binding Ferredoxin and NADP+

Cited by 26 publications

References 43 publications

Replacement of Tyr50 stacked on the si-face of the isoalloxazine ring of the flavin adenine dinucleotide prosthetic group modulates Bacillus subtilis ferredoxin-NADP+ oxidoreductase activity toward NADPH

Replacement of Tyr50 stacked on the si-face of the isoalloxazine ring of the flavin adenine dinucleotide prosthetic group modulates Bacillus subtilis ferredoxin-NADP+ oxidoreductase activity toward NADPH

Allostery in the ferredoxin protein motif does not involve a conformational switch

Ferredoxin:NAD ⁺ Oxidoreductase of Thermoanaerobacterium saccharolyticum and Its Role in Ethanol Formation

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Asymmetric Dimeric Structure of Ferredoxin-NAD(P)+ Oxidoreductase from the Green Sulfur Bacterium Chlorobaculum tepidum: Implications for Binding Ferredoxin and NADP+

Cited by 26 publications

References 43 publications

Replacement of Tyr50 stacked on the si-face of the isoalloxazine ring of the flavin adenine dinucleotide prosthetic group modulates Bacillus subtilis ferredoxin-NADP+ oxidoreductase activity toward NADPH

Replacement of Tyr50 stacked on the si-face of the isoalloxazine ring of the flavin adenine dinucleotide prosthetic group modulates Bacillus subtilis ferredoxin-NADP+ oxidoreductase activity toward NADPH

Allostery in the ferredoxin protein motif does not involve a conformational switch

Ferredoxin:NAD + Oxidoreductase of Thermoanaerobacterium saccharolyticum and Its Role in Ethanol Formation

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Ferredoxin:NAD ⁺ Oxidoreductase of Thermoanaerobacterium saccharolyticum and Its Role in Ethanol Formation