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Lesanavičius M, Seo D, Maurutytė G, Čėnas N. Redox Properties of Bacillus subtilis Ferredoxin:NADP + Oxidoreductase: Potentiometric Characteristics and Reactions with Pro-Oxidant Xenobiotics. Int J Mol Sci 2024; 25:5373. [PMID: 38791410 PMCID: PMC11121358 DOI: 10.3390/ijms25105373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 05/03/2024] [Accepted: 05/10/2024] [Indexed: 05/26/2024] Open
Abstract
Bacillus subtilis ferredoxin:NADP+ oxidoreductase (BsFNR) is a thioredoxin reductase-type FNR whose redox properties and reactivity with nonphysiological electron acceptors have been scarcely characterized. On the basis of redox reactions with 3-acetylpyridine adenine dinucleotide phosphate, the two-electron reduction midpoint potential of the flavin adenine dinucleotide (FAD) cofactor was estimated to be -0.240 V. Photoreduction using 5-deazaflavin mononucleotide (5-deazaFMN) as a photosensitizer revealed that the difference in the redox potentials between the first and second single-electron transfer steps was 0.024 V. We examined the mechanisms of the reduction of several different groups of non-physiological electron acceptors catalyzed by BsFNR. The reactivity of quinones and aromatic N-oxides toward BsFNR increased when increasing their single-electron reduction midpoint redox potentials. The reactivity of nitroaromatic compounds was lower due to their lower electron self-exchange rate, but it exhibited the same trend. A mixed single- and two-electron reduction reaction was characteristic of quinones, whereas reactions involving nitroaromatics proceeded exclusively via the one-electron reduction reaction. The oxidation of FADH• to FAD is the rate-limiting step during the oxidation of fully reduced FAD. The calculated electron transfer distances in the reaction with nitroaromatics were close to those of other FNRs including the plant-type enzymes, thus demonstrating their similar active site accessibility to low-molecular-weight oxidants despite the fundamental differences in their structures.
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Affiliation(s)
- Mindaugas Lesanavičius
- Department of Xenobiotics Biochemistry, Institute of Biochemistry, Life Sciences Center, Vilnius University, Saulėtekio Av. 7, LT-10257 Vilnius, Lithuania; (M.L.); (G.M.)
| | - Daisuke Seo
- Division of Material Sciences, Graduate School of Natural Science and Technology, Kanazawa University, Kakuma, Kanazawa 920-1192, Japan;
| | - Gintarė Maurutytė
- Department of Xenobiotics Biochemistry, Institute of Biochemistry, Life Sciences Center, Vilnius University, Saulėtekio Av. 7, LT-10257 Vilnius, Lithuania; (M.L.); (G.M.)
| | - Narimantas Čėnas
- Department of Xenobiotics Biochemistry, Institute of Biochemistry, Life Sciences Center, Vilnius University, Saulėtekio Av. 7, LT-10257 Vilnius, Lithuania; (M.L.); (G.M.)
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Thioredoxin Reductase-Type Ferredoxin: NADP+ Oxidoreductase of Rhodopseudomonas palustris: Potentiometric Characteristics and Reactions with Nonphysiological Oxidants. Antioxidants (Basel) 2022; 11:antiox11051000. [PMID: 35624864 PMCID: PMC9137726 DOI: 10.3390/antiox11051000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 05/15/2022] [Accepted: 05/17/2022] [Indexed: 11/17/2022] Open
Abstract
Rhodopseudomonas palustris ferredoxin:NADP+ oxidoreductase (RpFNR) belongs to a novel group of thioredoxin reductase-type FNRs with partly characterized redox properties. Based on the reactions of RpFNR with the 3-acetylpyridine adenine dinucleotide phosphate redox couple, we estimated the two-electron reduction midpoint potential of the FAD cofactor to be −0.285 V. 5-Deaza-FMN-sensitized photoreduction revealed −0.017 V separation of the redox potentials between the first and second electron transfer events. We examined the mechanism of oxidation of RpFNR by several different groups of nonphysiological electron acceptors. The kcat/Km values of quinones and aromatic N-oxides toward RpFNR increase with their single-electron reduction midpoint potential. The lower reactivity, mirroring their lower electron self-exchange rate, is also seen to have a similar trend for nitroaromatic compounds. A mixed single- and two-electron reduction was characteristic of quinones, with single-electron reduction accounting for 54% of the electron flux, whereas nitroaromatics were reduced exclusively via single-electron reduction. It is highly possible that the FADH· to FAD oxidation reaction is the rate-limiting step during the reoxidation of reduced FAD. The calculated electron transfer distances in the reaction with quinones and nitroaromatics were close to those of Anabaena and Plasmodium falciparum FNRs, thus demonstrating their similar “intrinsic” reactivity.
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Overview of structurally homologous flavoprotein oxidoreductases containing the low M r thioredoxin reductase-like fold - A functionally diverse group. Arch Biochem Biophys 2021; 702:108826. [PMID: 33684359 DOI: 10.1016/j.abb.2021.108826] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 02/23/2021] [Accepted: 02/27/2021] [Indexed: 01/12/2023]
Abstract
Structural studies show that enzymes have a limited number of unique folds, although structurally related enzymes have evolved to perform a large variety of functions. In this review, we have focused on enzymes containing the low molecular weight thioredoxin reductase (low Mr TrxR) fold. This fold consists of two domains, both containing a three-layer ββα sandwich Rossmann-like fold, serving as flavin adenine dinucleotide (FAD) and, in most cases, pyridine nucleotide (NAD(P)H) binding-domains. Based on a search of the Protein Data Bank for all published structures containing the low Mr TrxR-like fold, we here present a comprehensive overview of enzymes with this structural architecture. These range from TrxR-like ferredoxin/flavodoxin NAD(P)+ oxidoreductases, through glutathione reductase, to NADH peroxidase. Some enzymes are solely composed of the low Mr TrxR-like fold, while others contain one or two additional domains. In this review, we give a detailed description of selected enzymes containing only the low Mr TrxR-like fold, however, catalyzing a diversity of chemical reactions. Our overview of this structurally similar, yet functionally distinct group of flavoprotein oxidoreductases highlights the fascinating and increasing number of studies describing the diversity among these enzymes, especially during the last decade(s).
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Rubredoxin from the green sulfur bacterium Chlorobaculum tepidum donates a redox equivalent to the flavodiiron protein in an NAD(P)H dependent manner via ferredoxin-NAD(P) + oxidoreductase. Arch Microbiol 2020; 203:799-808. [PMID: 33051772 DOI: 10.1007/s00203-020-02079-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Revised: 09/24/2020] [Accepted: 10/01/2020] [Indexed: 10/23/2022]
Abstract
The green sulfur bacterium, Chlorobaculum tepidum, is an anaerobic photoautotroph that performs anoxygenic photosynthesis. Although genes encoding rubredoxin (Rd) and a putative flavodiiron protein (FDP) were reported in the genome, a gene encoding putative NADH-Rd oxidoreductase is not identified. In this work, we expressed and purified the recombinant Rd and FDP and confirmed dioxygen reductase activity in the presence of ferredoxin-NAD(P)+ oxidoreductase (FNR). FNR from C. tepidum and Bacillus subtilis catalyzed the reduction of Rd at rates comparable to those reported for NADH-Rd oxidoreductases. Also, we observed substrate inhibition at high concentrations of NADPH similar to that observed with ferredoxins. In the presence of NADPH, B. subtilis FNR and Rd, FDP promoted dioxygen reduction at rates comparable to those reported for other bacterial FDPs. Taken together, our results suggest that Rd and FDP participate in the reduction of dioxygen in C. tepidum and that FNR can promote the reduction of Rd in this bacterium.
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Seo D, Muraki N, Kurisu G. Kinetic and structural insight into a role of the re-face Tyr328 residue of the homodimer type ferredoxin-NADP + oxidoreductase from Rhodopseudomonas palustris in the reaction with NADP +/NADPH. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2019; 1861:148140. [PMID: 31838096 DOI: 10.1016/j.bbabio.2019.148140] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 08/10/2019] [Revised: 11/08/2019] [Accepted: 12/05/2019] [Indexed: 11/28/2022]
Abstract
Among the thioredoxin reductase-type ferredoxin-NAD(P)+ oxidoreductase (FNR) family, FNR from photosynthetic purple non‑sulfur bacterium Rhodopseudomonas palustris (RpFNR) is distinctive because the predicted residue on the re-face of the isoalloxazine ring portion of the FAD prosthetic group is a tyrosine. Here, we report the crystal structure of wild type RpFNR and kinetic analyses of the reaction of wild type, and Y328F, Y328H and Y328S mutants with NADP+/NADPH using steady state and pre-steady state kinetic approaches. The obtained crystal structure of wild type RpFNR confirmed the presence of Tyr328 on the re-face of the isoalloxazine ring of the FAD prosthetic group through the unique hydrogen bonding of its hydroxyl group. In the steady state assays, the substitution results in the decrease of Kd for NADP+ and KM for NADPH in the diaphorase assay; however, the kcat values also decreased significantly. In the stopped-flow spectrophotometry, mixing oxidized RpFNRs with NADPH and reduced RpFNRs with NADP+ resulted in rapid charge transfer complex formation followed by hydride transfer. The observed rate constants for the hydride transfer in both directions were comparable (>400 s-1). The substitution did not drastically affect the rate of hydride transfer, but substantially slowed down the subsequent release and re-association of NADP+/NADPH in both directions. The obtained results suggest that Tyr328 stabilizes the stacking of C-terminal residues on the isoalloxazine ring portion of the FAD prosthetic group, which impedes the access of NADP+/NADPH on the isoalloxazine ring portions, in turn, enhancing the release of the NADP+/NADPH and/or reaction with electron transfer proteins.
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Affiliation(s)
- Daisuke Seo
- Division of Material Science, Graduate School of Natural Science and Technology, Kanazawa University, Kakuma, Kanazawa, Ishikawa 920-1192, Japan.
| | - Norifumi Muraki
- Institute for Molecular Science, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki 444-8787, Japan; Department of Life Sciences, University of Tokyo, Komaba, Meguro-ku, Tokyo 153-8902, Japan; Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan
| | - Genji Kurisu
- Department of Life Sciences, University of Tokyo, Komaba, Meguro-ku, Tokyo 153-8902, Japan; Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan.
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Trisolini L, Gambacorta N, Gorgoglione R, Montaruli M, Laera L, Colella F, Volpicella M, De Grassi A, Pierri CL. FAD/NADH Dependent Oxidoreductases: From Different Amino Acid Sequences to Similar Protein Shapes for Playing an Ancient Function. J Clin Med 2019; 8:jcm8122117. [PMID: 31810296 PMCID: PMC6947548 DOI: 10.3390/jcm8122117] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 11/11/2019] [Accepted: 11/18/2019] [Indexed: 12/29/2022] Open
Abstract
Flavoprotein oxidoreductases are members of a large protein family of specialized dehydrogenases, which include type II NADH dehydrogenase, pyridine nucleotide-disulphide oxidoreductases, ferredoxin-NAD+ reductases, NADH oxidases, and NADH peroxidases, playing a crucial role in the metabolism of several prokaryotes and eukaryotes. Although several studies have been performed on single members or protein subgroups of flavoprotein oxidoreductases, a comprehensive analysis on structure-function relationships among the different members and subgroups of this great dehydrogenase family is still missing. Here, we present a structural comparative analysis showing that the investigated flavoprotein oxidoreductases have a highly similar overall structure, although the investigated dehydrogenases are quite different in functional annotations and global amino acid composition. The different functional annotation is ascribed to their participation in species-specific metabolic pathways based on the same biochemical reaction, i.e., the oxidation of specific cofactors, like NADH and FADH2. Notably, the performed comparative analysis sheds light on conserved sequence features that reflect very similar oxidation mechanisms, conserved among flavoprotein oxidoreductases belonging to phylogenetically distant species, as the bacterial type II NADH dehydrogenases and the mammalian apoptosis-inducing factor protein, until now retained as unique protein entities in Bacteria/Fungi or Animals, respectively. Furthermore, the presented computational analyses will allow consideration of FAD/NADH oxidoreductases as a possible target of new small molecules to be used as modulators of mitochondrial respiration for patients affected by rare diseases or cancer showing mitochondrial dysfunction, or antibiotics for treating bacterial/fungal/protista infections.
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Affiliation(s)
| | | | | | | | | | | | | | - Anna De Grassi
- Correspondence: (A.D.G.); or (C.L.P.); Tel.: +39-080-544-3614 (A.D.G. & C.L.P.); Fax: +39-080-544-2770 (A.D.G. & C.L.P.)
| | - Ciro Leonardo Pierri
- Correspondence: (A.D.G.); or (C.L.P.); Tel.: +39-080-544-3614 (A.D.G. & C.L.P.); Fax: +39-080-544-2770 (A.D.G. & C.L.P.)
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7
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Seo D, Kitashima M, Sakurai T, Inoue K. Kinetics of NADP +/NADPH reduction-oxidation catalyzed by the ferredoxin-NAD(P) + reductase from the green sulfur bacterium Chlorobaculum tepidum. PHOTOSYNTHESIS RESEARCH 2016; 130:479-489. [PMID: 27341807 DOI: 10.1007/s11120-016-0285-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Accepted: 06/13/2016] [Indexed: 06/06/2023]
Abstract
Ferredoxin-NAD(P)+ oxidoreductase (FNR, [EC 1.18.1.2], [EC 1.18.1.3]) from the green sulfur bacterium Chlorobaculum tepidum (CtFNR) is a homodimeric flavoprotein with significant structural homology to bacterial NADPH-thioredoxin reductases. CtFNR homologs have been found in many bacteria, but only in green sulfur bacteria among photoautotrophs. In this work, we examined the reactions of CtFNR with NADP+, NADPH, and (4S-2H)-NADPD by stopped-flow spectrophotometry. Mixing CtFNRox with NADPH yielded a rapid decrease of the absorbance in flavin band I centered at 460 nm within 1 ms, and then the absorbance further decreased gradually. The magnitude of the decrease increased with increasing NADPH concentration, but even with ~50-fold molar excess NADPH, the absorbance change was only ~45 % of that expected for fully reduced protein. The absorbance in the charge transfer (CT) band centered around 600 nm increased rapidly within 1 ms, then slowly decreased to about 70 % of the maximum. When CtFNRred was mixed with excess NADP+, the absorbance in the flavin band I increased to about 70 % of that of CtFNRox with an apparent rate of ~4 s-1, whereas almost no absorption changes were observed in the CT band. Obtained data suggest that the reaction between CtFNR and NADP+/NADPH is reversible, in accordance with its physiological function.
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Affiliation(s)
- Daisuke Seo
- Division of Material Science, Graduate School of Natural Science and Technology, Kanazawa University, Kakuma, Kanazawa, Ishikawa, 920-1192, Japan.
| | - Masaharu Kitashima
- Department of Biological Sciences, Kanagawa University, Tsuchiya, Hiratsuka, Kanagawa, 259-1293, Japan
- Research Institute for Integrated Science, Kanagawa University, Tsuchiya, Hiratsuka, Kanagawa, 259-1293, Japan
| | - Takeshi Sakurai
- Division of Material Science, Graduate School of Natural Science and Technology, Kanazawa University, Kakuma, Kanazawa, Ishikawa, 920-1192, Japan
| | - Kazuhito Inoue
- Department of Biological Sciences, Kanagawa University, Tsuchiya, Hiratsuka, Kanagawa, 259-1293, Japan
- Research Institute for Integrated Science, Kanagawa University, Tsuchiya, Hiratsuka, Kanagawa, 259-1293, Japan
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8
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Lofstad M, Gudim I, Hammerstad M, Røhr ÅK, Hersleth HP. Activation of the Class Ib Ribonucleotide Reductase by a Flavodoxin Reductase in Bacillus cereus. Biochemistry 2016; 55:4998-5001. [DOI: 10.1021/acs.biochem.6b00699] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Marie Lofstad
- Section
for Biochemistry and Molecular Biology, Department of Biosciences, University of Oslo, P.O.
Box 1066, Blindern, NO-0316 Oslo, Norway
| | - Ingvild Gudim
- Section
for Biochemistry and Molecular Biology, Department of Biosciences, University of Oslo, P.O.
Box 1066, Blindern, NO-0316 Oslo, Norway
| | - Marta Hammerstad
- Section
for Biochemistry and Molecular Biology, Department of Biosciences, University of Oslo, P.O.
Box 1066, Blindern, NO-0316 Oslo, Norway
| | - Åsmund Kjendseth Røhr
- Department
of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, P.O. Box 5003, NO-1432 Ås, Norway
| | - Hans-Petter Hersleth
- Section
for Biochemistry and Molecular Biology, Department of Biosciences, University of Oslo, P.O.
Box 1066, Blindern, NO-0316 Oslo, Norway
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Abstract
After a brief discussion of my graduate work at Duke University, I describe a series of investigations on redox proteins at the University of California, Berkeley. Starting with ferredoxin from fermentative bacteria, the Berkeley research fostered experiments that uncovered a pathway for fixing CO2 in bacterial photosynthesis. The carbon work, in turn, opened new vistas, including the discovery that thioredoxin functions universally in regulating the Calvin-Benson cycle in oxygenic photosynthesis. These experiments, which took place over a 50-year period, led to the formulation of a set of biological principles and set the stage for research demonstrating a role for redox in the regulation of previously unrecognized processes extending far beyond photosynthesis.
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Affiliation(s)
- Bob B Buchanan
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720;
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Seo D, Soeta T, Sakurai H, Sétif P, Sakurai T. Pre-steady-state kinetic studies of redox reactions catalysed by Bacillus subtilis ferredoxin-NADP(+) oxidoreductase with NADP(+)/NADPH and ferredoxin. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2016; 1857:678-87. [PMID: 26965753 DOI: 10.1016/j.bbabio.2016.03.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Revised: 02/12/2016] [Accepted: 03/01/2016] [Indexed: 11/30/2022]
Abstract
Ferredoxin-NADP(+) oxidoreductase ([EC1.18.1.2], FNR) from Bacillus subtilis (BsFNR) is a homodimeric flavoprotein sharing structural homology with bacterial NADPH-thioredoxin reductase. Pre-steady-state kinetics of the reactions of BsFNR with NADP(+), NADPH, NADPD (deuterated form) and B. subtilis ferredoxin (BsFd) using stopped-flow spectrophotometry were studied. Mixing BsFNR with NADP(+) and NADPH yielded two types of charge-transfer (CT) complexes, oxidized FNR (FNR(ox))-NADPH and reduced FNR (FNR(red))-NADP(+), both having CT absorption bands centered at approximately 600n m. After mixing BsFNR(ox) with about a 10-fold molar excess of NADPH (forward reaction), BsFNR was almost completely reduced at equilibrium. When BsFNR(red) was mixed with NADP(+), the amount of BsFNR(ox) increased with increasing NADP(+) concentration, but BsFNR(red) remained as the major species at equilibrium even with about 50-fold molar excess NADP(+). In both directions, the hydride-transfer was the rate-determining step, where the forward direction rate constant (~500 s(-1)) was much higher than the reverse one (<10 s(-1)). Mixing BsFd(red) with BsFNR(ox) induced rapid formation of a neutral semiquinone form. This process was almost completed within 1 ms. Subsequently the neutral semiquinone form was reduced to the hydroquinone form with an apparent rate constant of 50 to 70 s(-1) at 10°C, which increased as BsFd(red) increased from 40 to 120 μM. The reduction rate of BsFNR(ox) by BsFd(red) was markedly decreased by premixing BsFNR(ox) with BsFd(ox), indicating that the dissociation of BsFd(ox) from BsFNR(sq) is rate-limiting in the reaction. The characteristics of the BsFNR reactions with NADP(+)/NADPH were compared with those of other types of FNRs.
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Affiliation(s)
- Daisuke Seo
- Division of Material Science, Graduate School of Natural Science and Technology, Kanazawa University, Kakuma, Kanazawa, Ishikawa 920-1192, Japan.
| | - Takahiro Soeta
- Division of Material Science, Graduate School of Natural Science and Technology, Kanazawa University, Kakuma, Kanazawa, Ishikawa 920-1192, Japan
| | - Hidehiro Sakurai
- Research Institute for Photobiological Hydrogen Production, Kanagawa University, Tsuchiya, Hiratsuka, Kanagawa 259-1293, Japan
| | - Pierre Sétif
- CEA, iBiTecS, 91191 Gif sur Yvette, France; CNRS/Université Paris-Sud/CEA, I2BC, 91190 Gif sur Yvette, France
| | - Takeshi Sakurai
- Division of Material Science, Graduate School of Natural Science and Technology, Kanazawa University, Kakuma, Kanazawa, Ishikawa 920-1192, Japan
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Seo D, Naito H, Nishimura E, Sakurai T. 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. PHOTOSYNTHESIS RESEARCH 2015; 125:321-328. [PMID: 25698107 DOI: 10.1007/s11120-015-0099-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Accepted: 02/11/2015] [Indexed: 06/04/2023]
Abstract
Ferredoxin-NAD(P)(+) oxidoreductases ([EC 1.18.1.2], [EC 1.18.1.3], FNRs) from green sulfur bacteria, purple non-sulfur bacteria and most of Firmicutes, such as Bacillus subtilis (BsFNR) are homo-dimeric flavoproteins homologous to bacterial NADPH-thioredoxin reductase. These FNRs contain two unique aromatic residues stacked on the si- and re-face of the isoalloxazine ring moiety of the FAD prosthetic group whose configurations are often found among other types of flavoproteins including plant-type FNR and flavodoxin, but not in bacterial NADPH-thioredoxin reductase. To investigate the role of the si-face Tyr50 residue in BsFNR, we replaced Tyr50 with Gly, Ser, and Trp and examined its spectroscopic properties and enzymatic activities in the presence of NADPH and ferredoxin (Fd) from B. subtilis (BsFd). The replacement of Tyr50 to Gly (Y50G), Ser (Y50S), and Trp (Y50W) in BsFNR resulted in a blue shift of the FAD transition bands. The Y50G and Y50S mutations enhanced the FAD fluorescence emission, whereas those of the wild type and Y50W mutant were quenched. All three mutants decreased thermal stabilities compared to wild type. Using a diaphorase assay, the k cat values for the Y50G and Y50S mutants in the presence of NADPH and ferricyanide were decreased to less than 5 % of the wild type activity. The Y50W mutant retained approximately 20 % reactivity in the diaphorase assay and BsFd-dependent cytochrome c reduction assay relative to wild type. The present results suggest that Tyr50 modulates the electronic properties and positioning of the prosthetic group.
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Affiliation(s)
- Daisuke Seo
- Division of Material Science, Graduate School of Natural Science and Technology, Kanazawa University, Kakuma, Kanazawa, Ishikawa, 920-1192, Japan,
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12
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Holden JK, Lim N, Poulos TL. Identification of redox partners and development of a novel chimeric bacterial nitric oxide synthase for structure activity analyses. J Biol Chem 2014; 289:29437-45. [PMID: 25194416 DOI: 10.1074/jbc.m114.595165] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Production of nitric oxide (NO) by nitric oxide synthase (NOS) requires electrons to reduce the heme iron for substrate oxidation. Both FAD and FMN flavin groups mediate the transfer of NADPH derived electrons to NOS. Unlike mammalian NOS that contain both FAD and FMN binding domains within a single polypeptide chain, bacterial NOS is only composed of an oxygenase domain and must rely on separate redox partners for electron transfer and subsequent activity. Here, we report on the native redox partners for Bacillus subtilis NOS (bsNOS) and a novel chimera that promotes bsNOS activity. By identifying and characterizing native redox partners, we were also able to establish a robust enzyme assay for measuring bsNOS activity and inhibition. This assay was used to evaluate a series of established NOS inhibitors. Using the new assay for screening small molecules led to the identification of several potent inhibitors for which bsNOS-inhibitor crystal structures were determined. In addition to characterizing potent bsNOS inhibitors, substrate binding was also analyzed using isothermal titration calorimetry giving the first detailed thermodynamic analysis of substrate binding to NOS.
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Affiliation(s)
| | | | - Thomas L Poulos
- From the Departments of Molecular Biology and Biochemistry, Pharmaceutical Sciences, and Chemistry, University of California, Irvine, California 92697-3900
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13
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Seo D, Asano T, Komori H, Sakurai T. Role of the C-terminal extension stacked on the re-face of the isoalloxazine ring moiety of the flavin adenine dinucleotide prosthetic group in ferredoxin-NADP(+) oxidoreductase from Bacillus subtilis. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2014; 81:143-148. [PMID: 24529496 DOI: 10.1016/j.plaphy.2014.01.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2013] [Accepted: 01/20/2014] [Indexed: 06/03/2023]
Abstract
Ferredoxin-NADP(+) oxidoreductase [EC 1.18.1.2] from Bacillus subtilis (BsFNR) is homologous to the bacterial NADPH-thioredoxin reductase, but possesses a unique C-terminal extension that covers the re-face of the isoalloxazine ring moiety of the flavin adenine dinucleotide (FAD) prosthetic group. In this report, we utilize BsFNR mutants depleted of their C-terminal residues to examine the importance of the C-terminal extension in reactions with NADPH and ferredoxin (Fd) from B. subtilis by spectroscopic and steady-state reaction analyses. The depletions of residues Y313 to K332 (whole C-terminal extension region) and S325 to K332 (His324 intact) resulted in significant increases in the catalytic efficiency with NADPH in diaphorase assay with ferricyanide, whereas Km values for ferricyanide were increased. In the cytochrome c reduction assay in the presence of B. subtilis ferredoxin, the S325-K332 depleted mutant displayed a significant decrease in the turnover rate with an Fd concentration range of 1-10 μM. The Y313-K332 depleted mutant demonstrated an increase in the rate of the direct reduction of horse heart cytochrome c in the absence of Fd. These data indicated that depletion of the C-terminal extension plays an important role in the reaction of BsFNR with ferredoxin.
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Affiliation(s)
- Daisuke Seo
- Division of Material Science, Graduate School of Natural Science and Technology, Kanazawa University, Kakuma, Kanazawa, Ishikawa 920-1192, Japan.
| | - Tomoya Asano
- Division of Functional Genomics, Advanced Science Research Center, Kanazawa University, Takaramachi 13-1, Kanazawa, Ishikawa 920-0934, Japan
| | - Hirofumi Komori
- Faculty of Education, Kagawa University, 1-1 Saiwai, Takamatsu, Kagawa 760-8522, Japan
| | - Takeshi Sakurai
- Division of Material Science, Graduate School of Natural Science and Technology, Kanazawa University, Kakuma, Kanazawa, Ishikawa 920-1192, Japan
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Skråmo S, Hersleth HP, Hammerstad M, Andersson KK, Røhr ÅK. Cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of a ferredoxin/flavodoxin-NADP(H) oxidoreductase (Bc0385) from Bacillus cereus. ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS 2014; 70:777-80. [PMID: 24915092 DOI: 10.1107/s2053230x14008334] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Accepted: 04/13/2014] [Indexed: 11/10/2022]
Abstract
Ferredoxin/flavodoxin-NADP(H) oxidoreductases (FNRs) are key enzymes involved in catalysing electron transfer between ferredoxins/flavodoxins and NAD(P)H/NAD(P)+. In Bacillus cereus there are three genes that may encode FNRs, and the Bc0385 FNR has been cloned, overexpressed, purified and successfully crystallized in its NADPH/NADP+-free form. Diffraction data have been collected to 2.5 Å resolution from crystals belonging to the orthorhombic space group P2₁2₁2, with unit-cell parameters a=57.2, b=164.3, c=95.0 Å, containing two FNR molecules in the asymmetric unit. The structure of the Bc0385 FNR has been solved by molecular replacement, and is a member of the homodimeric thioredoxin reductase-like class of FNRs.
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Affiliation(s)
- Silje Skråmo
- Department of Biosciences, Section for Biochemistry and Molecular Biology, University of Oslo, PO Box 1066, Blindern, NO-0316 Oslo, Norway
| | - Hans Petter Hersleth
- Department of Biosciences, Section for Biochemistry and Molecular Biology, University of Oslo, PO Box 1066, Blindern, NO-0316 Oslo, Norway
| | - Marta Hammerstad
- Department of Biosciences, Section for Biochemistry and Molecular Biology, University of Oslo, PO Box 1066, Blindern, NO-0316 Oslo, Norway
| | - K Kristoffer Andersson
- Department of Biosciences, Section for Biochemistry and Molecular Biology, University of Oslo, PO Box 1066, Blindern, NO-0316 Oslo, Norway
| | - Åsmund K Røhr
- Department of Biosciences, Section for Biochemistry and Molecular Biology, University of Oslo, PO Box 1066, Blindern, NO-0316 Oslo, Norway
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Yan Z, Nam YW, Fushinobu S, Wakagi T. Sulfolobus tokodaii ST2133 is characterized as a thioredoxin reductase-like ferredoxin:NADP+ oxidoreductase. Extremophiles 2013; 18:99-110. [DOI: 10.1007/s00792-013-0601-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2013] [Accepted: 11/14/2013] [Indexed: 10/26/2022]
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Komori H, Seo D, Sakurai T, Higuchi Y. Crystal structure analysis of Bacillus subtilis ferredoxin-NADP(+) oxidoreductase and the structural basis for its substrate selectivity. Protein Sci 2010; 19:2279-90. [PMID: 20878669 DOI: 10.1002/pro.508] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2010] [Revised: 09/15/2010] [Accepted: 09/15/2010] [Indexed: 11/07/2022]
Abstract
Bacillus subtilis yumC encodes a novel type of ferredoxin-NADP+ oxidoreductase (FNR) with a primary sequence and oligomeric conformation distinct from those of previously known FNRs. In this study, the crystal structure of B. subtilis FNR (BsFNR) complexed with NADP+ has been determined. BsFNR features two distinct binding domains for FAD and NADPH in accordance with its structural similarity to Escherichia coli NADPH-thioredoxin reductase (TdR) and TdR-like protein from Thermus thermophilus HB8 (PDB code: 2ZBW). The deduced mode of NADP+ binding to the BsFNR molecule is nonproductive in that the nicotinamide and isoalloxazine rings are over 15 Å apart. A unique C-terminal extension, not found in E. coli TdR but in TdR-like protein from T. thermophilus HB8, covers the re-face of the isoalloxazine moiety of FAD. In particular, Tyr50 in the FAD-binding region and His324 in the C-terminal extension stack on the si- and re-faces of the isoalloxazine ring of FAD, respectively. Aromatic residues corresponding to Tyr50 and His324 are also found in the plastid-type FNR superfamily of enzymes, and the residue corresponding to His324 has been reported to be responsible for nucleotide specificity. In contrast to the plastid-type FNRs, replacement of His324 with Phe or Ser had little effect on the specificity or reactivity of BsFNR with NAD(P)H, whereas replacement of Arg190, which interacts with the 2'-phosphate of NADP+, drastically decreased its affinity toward NADPH. This implies that BsFNR adopts the same nucleotide binding mode as the TdR enzyme family and that aromatic residue on the re-face of FAD is hardly relevant to the nucleotide selectivity.
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Affiliation(s)
- Hirofumi Komori
- Department of Life Science, Graduate School of Life Science, University of Hyogo, Ako-gun, Hyogo 678-1297, Japan
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17
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Muraki N, Seo D, Shiba T, Sakurai T, Kurisu G. Asymmetric dimeric structure of ferredoxin-NAD(P)+ oxidoreductase from the green sulfur bacterium Chlorobaculum tepidum: implications for binding ferredoxin and NADP+. J Mol Biol 2010; 401:403-14. [PMID: 20600130 DOI: 10.1016/j.jmb.2010.06.024] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2009] [Revised: 06/09/2010] [Accepted: 06/11/2010] [Indexed: 10/19/2022]
Abstract
Ferredoxin-NAD(P)(+) oxidoreductase (FNR) catalyzes the reduction of NAD(P)(+) to NAD(P)H with the reduced ferredoxin (Fd) during the final step of the photosynthetic electron transport chain. FNR from the green sulfur bacterium Chlorobaculum tepidum is functionally analogous to plant-type FNR but shares a structural homology to NADPH-dependent thioredoxin reductase (TrxR). Here, we report the crystal structure of C. tepidum FNR to 2.4 A resolution, which reveals a unique structure-function relationship. C. tepidum FNR consists of two functional domains for binding FAD and NAD(P)H that form a homodimer in which the domains are arranged asymmetrically. One NAD(P)H domain is present as the open form, the other with the equivalent NAD(P)H domain as the relatively closed form. We used site-directed mutagenesis on the hinge region connecting the two domains in order to investigate the importance of the flexible hinge. The asymmetry of the NAD(P)H domain and the comparison with TrxR suggested that the hinge motion might be involved in pyridine nucleotide binding and binding of Fd. Surprisingly, the crystal structure revealed an additional C-terminal sub-domain that tethers one protomer and interacts with the other protomer by pi-pi stacking of Phe337 and the isoalloxazine ring of FAD. The position of this stacking Phe337 is almost identical with both of the conserved C-terminal Tyr residues of plant-type FNR and the active site dithiol of TrxR, implying a unique structural basis for enzymatic reaction of C. tepidum FNR.
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Affiliation(s)
- Norifumi Muraki
- Department of Life Sciences, University of Tokyo, Komaba, Meguro-ku, Tokyo 153-8902, Japan
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18
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Komori H, Seo D, Sakurai T, Higuchi Y. Crystallization and preliminary X-ray studies of ferredoxin-NADP+ oxidoreductase encoded by Bacillus subtilis yumC. Acta Crystallogr Sect F Struct Biol Cryst Commun 2010; 66:301-3. [PMID: 20208166 PMCID: PMC2833042 DOI: 10.1107/s1744309110000151] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2009] [Accepted: 01/04/2010] [Indexed: 11/11/2022]
Abstract
Ferredoxin-NADP(+) oxidoreductase encoded by Bacillus subtilis yumC has been purified and successfully crystallized in complex with NADP(+) in two forms. Diffraction data from crystals of these two forms were collected at resolutions of 1.8 and 1.9 A. The former belonged to space group P2(1)2(1)2, with unit-cell parameters a = 63.90, b = 135.72, c = 39.19 A, and the latter to space group C2, with unit-cell parameters a = 207.47, b = 64.85, c = 61.12 A, beta = 105.82 degrees. The initial structure was determined by the molecular-replacement method using a thioredoxin reductase-like protein as a search model.
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Affiliation(s)
- Hirofumi Komori
- Department of Life Science, Graduate School of Life Science, University of Hyogo, 3-2-1 Koto, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan
- RIKEN SPring-8 Center, 1-1-1 Koto, Mikazuki-cho, Sayo-gun, Hyogo 679-5248, Japan
| | - Daisuke Seo
- Division of Material Sciences, Graduate School of Natural Science and Technology, Kanazawa University, Kakuma, Kanazawa 920-1192, Japan
| | - Takeshi Sakurai
- Division of Material Sciences, Graduate School of Natural Science and Technology, Kanazawa University, Kakuma, Kanazawa 920-1192, Japan
| | - Yoshiki Higuchi
- Department of Life Science, Graduate School of Life Science, University of Hyogo, 3-2-1 Koto, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan
- RIKEN SPring-8 Center, 1-1-1 Koto, Mikazuki-cho, Sayo-gun, Hyogo 679-5248, Japan
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Protein recognition in ferredoxin–P450 electron transfer in the class I CYP199A2 system from Rhodopseudomonas palustris. J Biol Inorg Chem 2009; 15:315-28. [DOI: 10.1007/s00775-009-0604-7] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2009] [Accepted: 10/15/2009] [Indexed: 10/20/2022]
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