| 1. |
Nguyen HK, Minato T, Teramoto T, Ogo S, Kakuta Y, Yoon KS, Disassembly and reassembly of the non-conventional thermophilic C-phycocyanin, 2024.03. |
| 2. |
Besisa NHA, Yoon KS and Yamauchi M, In situ electrochemical regeneration of active 1,4-NADH for enzymatic lactic acid formation via concerted functions on Pt-modified TiO2/Ti, 2024.01. |
| 3. |
Moniruzzaman M, Khac Nguyen H, Kiyasu Y, Hirose T, Handa Y, Koide T, Ogo S, Yoon KS, H2-driven reduction of CO2 to formate using bacterial plasma membranes, 2023.12. |
| 4. |
Shimauchi D, Yatabe T, Ikesue Y, Kajiwara Y, Koide T, Ando T, Yoon KS, Nakai H, Ogo S, Storing electrons from H2 for transfer to CO2, all at room temperature, 2023.09. |
| 5. |
Hung Khac Nguyena, Takuo Minatoa, Mohammad Moniruzzaman, Yu Kiyasu, Seiji Ogoa, and Ki-Seok Yoon*, Selective formate production from H2 and CO2 using encapsulated whole-cells under mild reaction conditions, J. Biosci. Bioeng., 10.1016/j.jbiosc.2023.06.002. Epub 2023 Jul 1., 136, 3, 182-189, 136(30):182-189, 2023.07. |
| 6. |
Kaho Yamada, Takeshi Yatabe, Ki-Seok Yoon, Seiji Ogo,, Cp*Ir Complex with Mesobiliverdin Ligand Isolated from Thermoleptolyngbya sp. O-77., J. Organomet. Chem., 964, 122302, 2022.06. |
| 7. |
A. Chapman, E. Ertekin, M. Kubota, A.Nagao, K. Bertsch, A. Macadre, T. Tsuchiyama, T. Masamura, S. Takaki, R, Komoda, M.Dadfarnia, B. Somerday, A. Staykov, J. Sugimura, Y. Sawae, T. Morita, H. Tanaka, K. Yagi, V. Niste, P. Saravanan, S. Onitsuka, K-S. Yoon, S. Ogo, T.Matsushima, G. Tumen-Ulziil, D. Klotz, D. H. Nguyen, G. Harrington, C. Adachi, H. Matsumoto, L.Kwati, Y. Takahashi, N.Kosem, T. Ishihara, M. Yamauchi, B. B. Saha, M. A. Islam, J. Miyawaki, H. Sivasavkaran, M. Kohno, S. Fujikawa, R. Selyanchyn, T. Tsuji, Y. Higashi, R. Kirchheim, P. Sofronis, Achieving a Carbon Neutral Future through Advanced Functional Materials and Technologies, Bull. Chem. Soc. Jpn., 95, 1, 73-103, 2022.04. |
| 8. |
Takuo Minato, Takamasa Teramoto, Naruhiko Adachi, Nguyen Khac Hung, Kaho Yamada, Masato Kawasaki, Masato Akutsu, Toshio Moriya, Toshiya Senda, Seiji Ogo, Yoshimitsu Kakuta, Ki-Seok Yoon, Non-conventional Octameric Structure of C-phycocyanin, Communications Biology, 2021.11, C-phycocyanin (CPC), a blue pigment protein, is an indispensable component of giant phycobilisomes, which are light-harvesting antenna complexes in cyanobacteria that transfer energy efficiently to photosystems I and II. X-ray crystallographic and electron microscopy (EM) analyses have revealed the structure of CPC to be a closed toroidal hexamer by assembling two trimers. In this study, the structural characterization of non-conventional octameric CPC is reported for the first time. Analyses of the crystal and cryogenic EM structures of the native CPC from filamentous thermophilic cyanobacterium Thermoleptolyngbya sp. O-77 unexpectedly illustrated the coexistence of conventional hexamer and novel octamer. In addition, an unusual dimeric state, observed via analytical ultracentrifugation, was postulated to be a key intermediate structure in the assemble of the previously unobserved octamer. These observations provide new insights into the assembly processes of CPCs and the mechanism of energy transfer in the light-harvesting complexes.. |
| 9. |
Takeshi Yatabe, Kazuki Kamitakahara, Kaede Higashijima, Tatsuya Ando, Takahiro Matsumoto, Ki-Seok Yoon, Takao Enomoto, Seiji Ogo, Synthesis of acetic acid from CO2, CH3I and H2 using a Water-Soluble Electron Storage Catalyst, Chem. Commun., 57, 39, 4772-4774, 2021.10. |
| 10. |
Yatabe, Takeshi; Kamitakahara, Kazuki; Higashijima, Kaede; Ando, Tatsuya; Matsumoto, Takahiro; Yoon, Ki-Seok; Enomoto, Takao; Ogo, Seiji, Synthesis of acetic acid from CO2, CH3I and H2 using a Water-Soluble Electron Storage Catalyst, Chem. Commun., 57, 39, 4772-4774, 2021.05. |
| 11. |
Ogo, Seiji; Ando, Tatsuya; Thi Minh, Le Tu; Mori, Yuki; Matsumoto, Takahiro; Yatabe, Takeshi; Yoon, Ki-Seok; Sato, Yukio; Hibino, Takashi; Kaneko, Kenji, A NiRhS Fuel Cell Catalyst – Lessons from Hydrogenase, Chem. Commun., 56, 79, 11787-11790, 2021.03. |
| 12. |
Ogo, Seiji; Kishima, Takahiro; Yatabe, Takeshi; Miyazawa, Keishi; Yamasaki, Ryunosuke; Matsumoto, Takahiro; Ando, Tatsuya; Kikkawa, Mitsuhiro; Isegawa, Miho; Yoon, Ki-Seok; Hayami, Shinya, [NiFe], [FeFe], and [Fe] Hydrogenase Models from Isomers, Sci. Adv., 6, eaaz8181, 2020.06, The study of hydrogenase enzymes (H2ases) is necessary because of their importance to a future hydrogen energy
economy. These enzymes come in three distinct classes: [NiFe] H2ases, which have a propensity toward H2 oxidation;
[FeFe] H2ases, which have a propensity toward H2 evolution; and [Fe] H2ases, which catalyze H− transfer. Modeling
these enzymes has so far treated them as different species, which is understandable given the different cores and
ligand sets of the natural molecules. Here, we demonstrate, using x-ray analysis and nuclear magnetic resonance,
infrared, Mössbauer spectroscopies, and electrochemical measurement, that the catalytic properties of all three
enzymes can be mimicked with only three isomers of the same NiFe complex.. |
| 13. |
Takuo Minato, Takamasa Teramoto, Yoshimitsu Kakuta, Seiji Ogo, Ki-Seok Yoon, Biochemical and structural characterization of a thermostable Dps protein with His-type ferroxidase centers and outer metal-binding sites, FEBS openbio, 10.1002/2211-5463.12837, 2020.04, The DNA-binding protein from starved cells (Dps) is found in a wide range of microorganisms, and it has been well characterized. However, little is known about Dps proteins from non-heterocystous filamentous cyanobacteria. In this study, a Dps protein from the thermophilic non-heterocystous filamentous cyanobacterium Thermoleptolyngbya sp. O-77 (TlDps1) was purified and characterized. PAGE and CD analyses of TlDps1 illustrated that it had higher thermostability than previously reported Dps proteins. X-ray crystallographic analysis revealed that TlDps1 possessed His-type ferroxidase centers within the cavity and unique metal binding sites located on the surface of the protein, which presumably contributed to its exceedingly high thermostability.. |
| 14. |
Kohsei Tsuji, Ki-Seok Yoon, Seiji Ogo, Glyceraldehyde-3-phosphate dehydrogenase from Citrobacter sp. S-77 is post-translationally modified by CoA (protein CoAlation) under oxidative stress, FEBS Open Bio, 10.1002/2211-5463.12542, 9, 1, 53-73, 2019.01, Protein CoAlation (S-thiolation by coenzyme A) has recently emerged as an alternative redox-regulated post-translational modification by which protein thiols are covalently modified with coenzyme A (CoA). However, little is known about the role and mechanism of this post-translational modification. In the present study, we investigated CoAlation of glyceraldehyde-3-phosphate dehydrogenase (GAPDH) from a facultative anaerobic Gram-negative bacterium Citrobacter sp. S-77 (CbGAPDH). GAPDH is a key glycolytic enzyme whose activity relies on the thiol-based redox-regulated post-translational modifications of active-site cysteine. LC-MS/MS analysis revealed that CoAlation of CbGAPDH occurred in vivo under sodium hypochlorite (NaOCl) stress. The purified CbGAPDH was highly sensitive to overoxidation by H 2 O 2 and NaOCl, which resulted in irreversible enzyme inactivation. By contrast, treatment with coenzyme A disulphide (CoASSCoA) or H 2 O 2 /NaOCl in the presence of CoA led to CoAlation and inactivation of the enzyme; activity could be recovered after incubation with dithiothreitol, glutathione and CoA. CoAlation of the enzyme in vitro was confirmed by mass spectrometry. The presence of a substrate, glyceraldehyde-3-phosphate, fully protected CbGAPDH from inactivation by CoAlation, suggesting that the inactivation is due to the formation of mixed disulphides between CoA and the active-site cysteine Cys149. A molecular docking study also supported the formation of mixed disulphide without steric constraints. These observations suggest that CoAlation is an alternative mechanism to protect the redox-sensitive thiol (Cys149) of CbGAPDH against irreversible oxidation, thereby regulating enzyme activity under oxidative stress.. |
| 15. |
Yuki Mori, Tatsuya Ando, Takahiro Matsumoto, Takeshi Yatabe, Mitsuhiro Kikkawa, Ki-Seok Yoon, Seiji Ogo, Multifunctional Catalysts for H2O2-Resistant Hydrogen Fuel Cells, Angewandte Chemie - International Edition, 10.1002/anie.201810270, 57, 48, 15792-15796, 2018.11, The development of hydrogen fuel cells is greatly hindered by the unwanted generation of H2O2 at the cathode. A non-Pt cathode catalyst is now shown to be capable of simultaneously reducing both O2 and H2O2, thus rendering H2O2 a useful part of the feed stream. The applicability of this unique catalyst is demonstrated by employing it in a fuel cell running on H2/CO and O2/H2O2.. |
| 16. |
Makoto Takenaka, Mitsuhiro Kikkawa, Takahiro Matsumoto, Takeshi Yatabe, Tatsuya Ando, Ki-Seok Yoon, Seiji Ogo, Oxidation of Guanosine Monophosphate with O 2 via a Ru-peroxo Complex in Water, Chemistry - An Asian Journal, 10.1002/asia.201801267, 13, 21, 3180-3184, 2018.11, Oxidative damage of DNA by reactive oxygen species (ROS) is responsible for aging and cancer. Although many studies of DNA damage by ROS have been conducted, there have been no reports of the oxidation of RNA components, such as guanosine monophosphate, by metal-based species in water. Here, we report the first case of oxidation of guanosine monophosphate to 8-oxoguanosine monophosphate by a metal-based oxygen bound species, derived from O
2
and in water.. |
| 17. |
Noor Dina Muhd Noor, Hiroaki Matsuura, Koji Nishikawa, Hulin Tai, Shun Hirota, Jaehyun Kim, Jiyoung Kang, Masaru Tateno, Ki-Seok Yoon, Seiji Ogo, Shintaro Kubota, Yasuhito Shomura, Yoshiki Higuchi, Redox-dependent conformational changes of a proximal [4Fe-4S] cluster in Hyb-type [NiFe]-hydrogenase to protect the active site from O2, Chemical Communications, 10.1039/c8cc06261g, 54, 87, 12385-12388, 2018.10, Citrobacter sp. S-77 [NiFe]-hydrogenase harbors a standard [4Fe-4S] cluster proximal to the Ni-Fe active site. The presence of relocatable water molecules and a flexible aspartate enables the [4Fe-4S] to display redox-dependent conformational changes. These structural features are proposed to be the key aspects that protect the active site from O2 attack.. |
| 18. |
Takeshi Yatabe, Taisuke Tokunaga, Takahiro Matsumoto, Mitsuhiro Kikkawa, Ki-Seok Yoon, Seiji Ogo, A MnI model for the photoinhibited species of oxygen-evolving complex, Chemistry Letters, 10.1246/cl.170869, 47, 1, 34-36, 2018.01, We report the reactivity of a new MnI(cyclam) complex (cyclam: 1,4,8,11-tetraazacyclotetradecane) toward O2 and H2O as a model for the photoinhibited species of oxygen-evolving complex (OEC). The reactivity varies according to the number of CO ligands. A MnI dicarbonyl complex, [MnI(cyclam)(CO)2]+ reacts with O2, but not with H2O, to form a bis(μ-oxo)Mn2 III,IV complex, though a MnI tricarbonyl complex, [MnI(cyclam)(CO)3]+ does not react with either O2 or H2O. Newly synthesized MnI(cyclam) dicarbonyl complex was characterized by ESI mass spectrometry, UVvis absorption spectroscopy, IR spectroscopy, and X-ray analysis.. |
| 19. |
Taisuke Tokunaga, Takeshi Yatabe, Takahiro Matsumoto, Tatsuya Ando, Ki-Seok Yoon, Seiji Ogo, Mechanistic investigation of the formation of H2 from HCOOH with a dinuclear Ru model complex for formate hydrogen lyase, Science and Technology of Advanced Materials, 10.1080/14686996.2017.1379857, 18, 1, 870-876, 2017.12, We report the mechanistic investigation of catalytic H2 evolution from formic acid in water using a formate-bridged dinuclear Ru complex as a formate hydrogen lyase model. The mechanistic study is based on isotope-labeling experiments involving hydrogen isotope exchange reaction.. |
| 20. |
Mitsuhiro Kikkawa, Takeshi Yatabe, Takahiro Matsumoto, Ki-Seok Yoon, Kazuharu Suzuki, Takao Enomoto, Kenji Kaneko, Seiji Ogo, A Fusion of Biomimetic Fuel and Solar Cells Based on Hydrogenase, Photosystem II, and Cytochrome c Oxidase, ChemCatChem, 10.1002/cctc.201700995, 9, 21, 4024-4028, 2017.11, We report an Ir complex as an anode catalyst capable of switching between a hydrogenase-type fuel-cell mode and a photosystem II-type solar-cell mode. This catalyst is connected to carbon-black-supported platinum as a cathode catalyst, which reduces dioxygen in a manner analogous to cytochrome c oxidase. Together, they make a system capable of switching between the two modes.. |
| 21. |
Takahiro Matsumoto, Takahiro Kishima, Takeshi Yatabe, Ki-Seok Yoon, Seiji Ogo, Mechanistic Insight into Switching between H2- or O2-Activation by Simple Ligand Effects of [NiFe]hydrogenase Models, Organometallics, 10.1021/acs.organomet.7b00471, 36, 20, 3883-3890, 2017.10, We present a mechanistic investigation for the activation of H2 and O2, induced by a simple ligand effect within [NiFe] models for O2-tolerant [NiFe]hydrogenase. Kinetic study reveals Michaelis-Menten type saturation behaviors for both H2 and O2 activation, which is the same behavior as that found in O2-tolerant [NiFe]hydrogenase. Such saturation behavior is caused by H2 complexation followed by heterolytic cleavage of H2 by an outer-sphere base, resulting in the formation of a hydride species showing hydridic character.. |
| 22. |
Y. Shomura, M. Taketa, H. Nakashima, H. Tai, H. Nakagawa, Y. Ikeda, M. Ishii, Y. Igarashi, H. Nishihara, Ki-Seok Yoon, Seiji Ogo, S. Hirota, Y. Higuchi, Structural basis of the redox switches in the NAD+-reducing soluble [NiFe]-hydrogenase, Science, 10.1126/science.aan4497, 357, 6354, 928-932, 2017.09, NAD+(oxidized form of NAD: nicotinamide adenine dinucleotide)-reducing soluble [NiFe]-hydrogenase (SH) is phylogenetically related to NADH (reduced form of NAD):quinone oxidoreductase (complex I), but the geometrical arrangements of the subunits and Fe-S clusters are unclear. Here, we describe the crystal structures of SH in the oxidized and reduced states. The cluster arrangement is similar to that of complex I, but the subunits orientation is not, which supports the hypothesis that subunits evolved as prebuilt modules. The oxidized active site includes a six-coordinate Ni, which is unprecedented for hydrogenases, whose coordination geometry would prevent O2; from approaching. In the reduced state showing the normal active site structure without a physiological electron acceptor, the flavin mononucleotide cofactor is dissociated, which may be caused by the oxidation state change of nearby Fe-S clusters and may suppress production of reactive oxygen species.. |
| 23. |
Makoto Takenaka, Ki-Seok Yoon, Takahiro Matsumoto, Seiji Ogo, Acetyl-CoA production by encapsulated pyruvate ferredoxin oxidoreductase in alginate hydrogels, Bioresource Technology, 10.1016/j.biortech.2016.12.051, 227, 279-285, 2017.01, Pyruvate ferredoxin oxidoreductase from Citrobacter sp. S-77 (PFORS77) was purified in order to develop a method for acetyl-CoA production. Although the purified PFORS77showed high O2-sensitivity, the activity could be remarkably stabilized in anaerobic conditions. PFORS77was effectively immobilized on ceramic hydroxyapatite (PFORS77-HA) with an efficiency of more than 96%, however, after encapsulation of PFORS77-HA in alginate, the rate of catalytic acetyl-CoA production was highly reduced to 36% when compared to that of the free enzyme. However, the operational stability of the PFORS77-HA in alginate hydrogels was remarkable, retaining over 68% initial activity even after ten repeated cycles. The results suggested that the PFORS77-HA hydrogels have a high potential for biotechnological application.. |
| 24. |
Ki-Seok Yoon, Nga T. Nguyen, Kien Trung Tran, Kohsei Tsuji, Seiji Ogo, Nitrogen fixation genes and nitrogenase activity of the non-heterocystous cyanobacterium Thermoleptolyngbya sp. O-77, Microbes and Environments, 10.1264/jsme2.ME17015, 32, 4, 324-329, 2017.01, Cyanobacteria are widely distributed in marine, aquatic, and terrestrial ecosystems, and play an important role in the global nitrogen cycle. In the present study, we examined the genome sequence of the thermophilic non-heterocystous N2-fixing cyanobacterium, Thermoleptolyngbya sp. O-77 (formerly known as Leptolyngbya sp. O-77) and characterized its nitrogenase activity. The genome of this cyanobacterial strain O-77 consists of a single chromosome containing a nitrogen fixation gene cluster. A phylogenetic analysis indicated that the NifH amino acid sequence from strain O-77 was clustered with those from a group of mesophilic species: the highest identity was found in Leptolyngbya sp. KIOST-1 (97.9% sequence identity). The nitrogenase activity of O-77 cells was dependent on illumination, whereas a high intensity of light of 40 µmol m-2 s-1 suppressed the effects of illumination.. |
| 25. |
Seiji Ogo, Yuki Mori, Tatsuya Ando, Takahiro Matsumoto, Takeshi Yatabe, Ki-Seok Yoon, Hideki Hayashi, Masashi Asano, One Model, Two Enzymes Activation of Hydrogen and Carbon Monoxide, Angewandte Chemie - International Edition, 10.1002/anie.201704864, 56, 33, 9723-9726, 2017.01, The ability to catalyze the oxidation of both H2 and CO in one reaction pot would be a major boon to hydrogen technology since CO is a consistent contaminant of H2 supplies. Here, we report just such a catalyst, with the ability to catalyze the oxidation of either or both H2 and CO, based on the pH value. This catalyst is based on a NiIr core that mimics the chemical function of [NiFe]hydrogenase in acidic media (pH 4–7) and carbon monoxide dehydrogenase in basic media (pH 7–10). We have applied this catalyst in a demonstration fuel cell using H2, CO, and H2/CO (1/1) feeds as fuels for oxidation at the anode. The power density of the fuel cell depends on the pH value in the media of the fuel cell and shows a similar pH dependence in a flask. We have isolated and characterized all intermediates in our proposed catalytic cycles.. |
| 26. |
Yatabe Takeshi, Kishima Takahiro, Nagano Hideaki, Matsumoto Takahiro, Yamasaki Mikio, Yoon Ki-Seok, Ogo Seiji, Structure and Reactivity of a Ru-based Peroxide Complex as a Reactive Intermediate of O2-Promoted Activation of a C–H Bond in a Cp* Ligand, Chemistry Letters, 10.1246/cl.160909, 46, 1, 74-76, 2017.01, We report the first example of the characterization of a Ru-based peroxide intermediate of O2-promoted activation of a C–H bond of the pentamethylcyclopentadienyl (Cp*) ligand. The peroxide complex activates the C–H bond to form a tetramethylfulvene complex. We propose a proton-coupled electron-transfer (PCET) mechanism of the C–H bond activation based on the structures and properties of the peroxide and tetramethylfulvene complexes. . |
| 27. |
Tsuji Kohsei, Yoon Ki-Seok, Ogo Seiji, Biochemical characterization of a bifunctional acetaldehyde-alcohol dehydrogenase purified from a facultative anaerobic bacterium Citrobacter sp. S-77, Journal of bioscience and bioengineering, 10.1016/j.jbiosc.2015.06.019, 121, 3, 253-258, 2016.03, Acetaldehyde-alcohol dehydrogenase (ADHE) is a bifunctional enzyme consisting of two domains of an N-terminal acetaldehyde dehydrogenase (ALDH) and a C-terminal alcohol dehydrogenase (ADH). The enzyme is known to be important in the cellular alcohol metabolism. However, the role of coenzyme A-acylating ADHE responsible for ethanol production from acetyl-CoA remains uncertain. Here, we present the purification and biochemical characterization of an ADHE from Citrobacter sp. S-77 (ADHE_). Interestingly, the ADHE_ was unable to be solubilized from membrane with detergents either 1% Triton X-100 or 1% Sulfobetaine 3-12. However, the enzyme was easily dissociated from membrane by high-salt buffers containing either 1.0 M NaCl or (NH_4)_2SO_4 without detergents. The molecular weight of a native protein was estimated as approximately 400 kDa, consisting of four identical subunits of 96.3 kDa. Based on the specific activity and kinetic analysis, the ADHE_ tended to have catalytic reaction towards acetaldehyde elimination rather than acetaldehyde formation. Our experimental observation suggests that the ADHE_ may play a pivotal role in modulating intracellular acetaldehyde concentration.. |
| 28. |
Noor Dina Muhd Noor, Koji Nishikawa, Hirofumi Nishihara, Ki-Seok Yoon, Seiji Ogo, Yoshiki Higuchi, Improved purification, crystallization and crystallographic study of Hyd-2-type [NiFe]-hydrogenase from Citrobacter sp. S-77, Acta Crystallographica Section:F Structural Biology Communications, 10.1107/S2053230X15024152, 72, Pt 1, 53-58, 2016.01, The purification procedure of Hyd-2-type [NiFe]-hydrogenase from Citrobacter sp. S-77 was improved by applying treatment with trypsin before chromatography. Purified protein samples both with and without trypsin treatment were successfully crystallized using the sitting-drop vapour-diffusion method with polyethylene glycol as a precipitant. Both crystals belonged to space group P21, with unit-cell parameters a = 63.90, b = 118.89, c = 96.70Å, β = 100.61° for the protein subjected to trypsin treatment and a = 65.38, b = 121.45, c = 98.63Å, β = 102.29° for the sample not treated with trypsin. The crystal obtained from the trypsin-treated protein diffracted to 1.60Å resolution, which is considerably better than the 2.00Å resolution obtained without trypsin treatment. The [NiFe]-hydrogenase from Citrobacter sp. S-77 retained catalytic activity with some amount of O2, indicating that it has clear O2 tolerance.. |
| 29. |
Midori Taketa, Hanae Nakagawa, Mao Habukawa, Hisao Osuka, Kiyohito Kihira, Hirofumi Komori, Naoki Shibata, Masaharu Ishii, Yasuo Igarashi, Hirofumi Nishihara, Ki-Seok Yoon, Seiji Ogo, Yasuhito Shomura, Yoshiki Higuchi, Crystallization and preliminary X-ray analysis of the NAD+-reducing [NiFe] hydrogenase from Hydrogenophilus thermoluteolus TH-1, Acta Crystallographica Section F:Structural Biology Communications, 10.1107/S2053230X14026521, 71, 96-99, 2015.01, NAD+-reducing [NiFe] hydrogenases catalyze the oxidoreduction of dihydrogen concomitant with the interconversion of NAD+ and NADH. Here, the isolation, purification and crystallization of the NAD+-reducing [NiFe] hydrogenase from Hydrogenophilus thermoluteolus TH-1 are reported. Crystals of the NAD+-reducing [NiFe] hydrogenase were obtained within one week from a solution containing polyethylene glycol using the sitting-drop vapour-diffusion method and micro-seeding. The crystal diffracted to 2.58Å resolution and belonged to space group C2, with unit-cell parameters a = 131.43, b = 189.71, c = 124.59Å, β = 109.42°. Assuming the presence of two NAD+-reducing [NiFe] hydrogenase molecules in the asymmetric unit, V M was calculated to be 2.2Å3 Da-1, which corresponds to a solvent content of 43%. Initial phases were determined by the single-wavelength anomalous dispersion method using the anomalous signal from the Fe atoms.. |
| 30. |
Kajsa G.V. Sigfridsson, Nils Leidel, Oliver Sanganas, Petko Chernev, Oliver Lenz, Ki-Seok Yoon, Hirofumi Nishihara, Alison Parkin, Fraser A. Armstrong, Sébastien Dementin, Marc Rousset, Antonio L. De Lacey, Michael Haumann, Structural differences of oxidized iron-sulfur and nickel-iron cofactors in O2-tolerant and O2-sensitive hydrogenases studied by X-ray absorption spectroscopy, Biochimica et Biophysica Acta - Bioenergetics, 10.1016/j.bbabio.2014.06.011, 1847, 2, 162-170, 2015.01, The class of [NiFe]-hydrogenases comprises oxygen-sensitive periplasmic (PH) and oxygen-tolerant membrane-bound (MBH) enzymes. For three PHs and four MBHs from six bacterial species, structural features of the nickel-iron active site of hydrogen turnover and of the iron-sulfur clusters functioning in electron transfer were determined using X-ray absorption spectroscopy (XAS). Fe-XAS indicated surplus oxidized iron and a lower number of ∼ 2.7 Å Fe-Fe distances plus additional shorter and longer distances in the oxidized MBHs compared to the oxidized PHs. This supported a double-oxidized and modified proximal FeS cluster in all MBHs with an apparent trimer-plus-monomer arrangement of its four iron atoms, in agreement with crystal data showing a [4Fe3S] cluster instead of a [4Fe4S] cubane as in the PHs. Ni-XAS indicated coordination of the nickel by the thiol group sulfurs of four conserved cysteines and at least one iron-oxygen bond in both MBH and PH proteins. Structural differences of the oxidized inactive [NiFe] cofactor of MBHs in the Ni-B state compared to PHs in the Ni-A state included a ∼ 0.05 Å longer Ni-O bond, a two times larger spread of the Ni-S bond lengths, and a ∼ 0.1 Å shorter Ni-Fe distance. The modified proximal [4Fe3S] cluster, weaker binding of the Ni-Fe bridging oxygen species, and an altered localization of reduced oxygen species at the active site may each contribute to O2 tolerance.. |
| 31. |
Nga T. Nguyen, Yuki Mori, Takahiro Matsumoto, Takeshi Yatabe, Ryota Kabe, Hidetaka Nakai, Ki-Seok Yoon, Seiji Ogo, A [NiFe]hydrogenase model that catalyses the release of hydrogen from formic acid, Chemical Communications, 10.1039/c4cc05911e, 50, 87, 13385-13387, 2014.11, We report the decomposition of formic acid to hydrogen and carbon dioxide, catalysed by a NiRu complex originally developed as a [NiFe]hydrogenase model. This is the first example of H2 evolution, catalysed by a [NiFe]hydrogenase model, which does not require additional energy.. |
| 32. |
Harutaka Nakamori, Takahiro Matsumoto, Takeshi Yatabe, Ki-Seok Yoon, Hidetaka Nakai, Seiji Ogo, Synthesis and crystal structure of a dinuclear, monomeric MnIIp-semiquinonato complex, Chemical Communications, 10.1039/c4cc06055e, 50, 86, 13059-13061, 2014.11, Herein, we report the first crystal structure of a monomeric p-semiquinonato d-block complex and its reactivity toward dioxygen, closely associated with a biological system of an oxygen evolving centre of photosystem II. This journal is. |
| 33. |
Nga T. Nguyen, Takeshi Yatabe, Ki-Seok Yoon, Seiji Ogo, Molybdenum-containing membrane-bound formate dehydrogenase isolated from Citrobacter sp. S-77 having high stability against oxygen, pH, and temperature, Journal of Bioscience and Bioengineering, 10.1016/j.jbiosc.2014.03.011, 118, 4, 386-391, 2014.10, Membrane-bound formate dehydrogenase (FDH) was purified to homogeneity from a facultative anaerobic bacterium Citrobacter sp. S-77. The FDH from Citrobacter sp. S-77 (FDHS77) was a monomer with molecular mass of approximately 150kDa. On SDS-PAGE, the purified FDHS77 showed as three different protein bands with molecular mass of approximately 95, 87, and 32kDa, respectively. Based on the N-terminal amino acid sequence analysis, the sequence alignments observed for the 87kDa protein band were identical to that of the large subunit of 95kDa, indicating that the purified FDHS77 consisted of two subunits; a 95kDa large subunit and a 32kDa small subunit. The purified FDHS77 in this purification did not contain a heme b subunit, but the FDHS77 showed significant activity for formate oxidation, determined by the Vmax of 30.4U/mg using benzyl viologen as an electron acceptor. The EPR and ICP-MS spectra indicate that the FDHS77 is a molybdenum-containing enzyme, displaying a remarkable O2-stability along with thermostability and pH resistance. This is the first report of the purification and characterization of a FDH from Citrobacter species.. |
| 34. |
Takahiro Matsumoto, Shigenobu Eguchi, Hidetaka Nakai, Takashi Hibino, Ki-Seok Yoon, Seiji Ogo, Hydrogenase from citrobacter sp. S-77 surpasses platinum as an electrode for H2 oxidation reaction, Angewandte Chemie - International Edition, 10.1002/anie.201404701, 53, 34, 8895-8898, 2014.08, Reported herein is an electrode for dihydrogen (H2) oxidation, and it is based on [NiFe]Hydrogenase from Citrobacter sp. S-77 ([NiFe] S77). It has a 637 times higher mass activity than Pt (calculated based on 1 mg of [NiFe]S77 or Pt) at 50 mV in a hydrogen half-cell. The [NiFe]S77 electrode is also stable in air and, unlike Pt, can be recovered 100% after poisoning by carbon monoxide. Following characterization of the [NiFe]S77 electrode, a fuel cell comprising a [NiFe] S77 anode and Pt cathode was constructed and shown to have a a higher power density than that achievable by Pt.. |
| 35. |
Kyoshiro Nonaka, Ki-Seok Yoon, Seiji Ogo, Biochemical characterization of psychrophilic Mn-superoxide dismutase from newly isolated Exiguobacterium sp. OS-77, Extremophiles, 10.1007/s00792-013-0621-x, 18, 2, 363-373, 2014.01, Many types of superoxide dismutases have been purified and characterized from various bacteria, however, a psychrophilic Mn-superoxide dismutase (MnSOD) has not yet been reported. Here, we describe the purification and the biochemical characterization of the psychrophilic MnSOD from Exiguobacterium sp. strain OS-77 (EgMnSOD). According to 16S rRNA sequence analysis, a newly isolated bacterium strain OS-77 belongs to the genus Exiguobacterium. The optimum growth temperature of the strain OS-77 is 20 °C. The EgMnSOD is a homodimer of 23.5 kDa polypeptides determined by SDS-PAGE and gel filtration analysis. UV-Vis spectrum and ICP-MS analysis clearly indicated that the homogeneously purified enzyme contains only a Mn ion as a metal cofactor. The optimal reaction pH and temperature of the enzyme were pH 9.0 and 5 °C, respectively. Notably, the purified EgMnSOD was thermostable up to 45 °C and retained 50 % activity after 21.2 min at 60 °C. The differential scanning calorimetry also indicated that the EgMnSOD is thermostable, exhibiting two protein denaturation peaks at 65 and 84 °C. The statistical analysis of amino acid sequence and composition of the EgMnSOD suggests that the enzyme retains psychrophilic characteristics.. |
| 36. |
Harutaka Nakamori, Takeshi Yatabe, Ki-Seok Yoon, Seiji Ogo, Purification and characterization of an oxygen-evolving photosystem II from Leptolyngbya sp. strain O-77, Journal of Bioscience and Bioengineering, 10.1016/j.jbiosc.2014.01.009, 118, 2, 119-124, 2014.01, A new cyanobacterium of strain O-77 was isolated from a hot spring at Aso-Kuju National Park, Kumamoto, Japan. According to the phylogenetic analysis determined by 16S rRNA gene sequence, the strain O-77 belongs to the genus Leptolyngbya, classifying into filamentous non-heterocystous cyanobacteria. The strain O-77 showed the thermophilic behavior with optimal growth temperature of 55°C. Moreover, we have purified and characterized the oxygen-evolving photosystem II (PSII) from the strain O-77. The O2-evolving activity of the purified PSII from strain O-77 (PSIIO77) was 1275±255μmol O2 (mg Chl a)-1h-1. Based on the results of MALDI-TOF mass spectrometry and urea-SDS-PAGE analysis, the purified PSIIO77 was composite of the typical PSII components of CP47, CP43, PsbO, D2, D1, PsbV, PsbQ, PsbU, and several low molecular mass subunits. Visible absorption and 77K fluorescence spectra of the purified PSIIO77 were almost identical to those of other purified PSIIs from cyanobacteria. This report provides the successful example for the purification and characterization of an active PSII from thermophilic, filamentous non-heterocystous cyanobacteria.. |
| 37. |
Takeshi Yatabe, Takahiro Kikunaga, Takahiro Matsumoto, Hidetaka Nakai, Ki-Seok Yoon, Seiji Ogo, Synthesis of aqueous-stable and water-soluble mononuclear nonheme MnV-Oxo complexes using H2O2as an oxidant, Chemistry Letters, 10.1246/cl.140376, 43, 8, 1380-1382, 2014.01, We report the synthesis of mononuclear nonheme manganese(V)oxo complexes in aqueous acetonitrile solution from the reaction of manganese(III) complexes using hydrogen peroxide as an oxidant for the first time. A crystal structure of chloro derivative of manganese(V)oxo complex and its reactivity toward 3,5-di-tert-butyl-catechol are also reported.. |
| 38. |
Kyoshiro Nonaka, Nga T. Nguyen, Ki-Seok Yoon, Seiji Ogo, Novel H2-oxidizing [NiFeSe]hydrogenase from Desulfovibrio vulgaris Miyazaki F, Journal of Bioscience and Bioengineering, 10.1016/j.jbiosc.2012.10.011, 115, 4, 366-371, 2013.04, [NiFeSe]hydrogenases are promising biocatalysts in H2-based technology due to their high catalytic activity and O2-stability. Here, we report purification and characterization of a new membrane-associated [NiFeSe]hydrogenase from Desulfovibrio vulgaris Miyazaki F ([NiFeSe]DvMF). The [NiFeSe]DvMF was composed of two subunits, corresponding to a large subunit of 58.3 kDa and a small subunit of 29.3 kDa determined by SDS-PAGE. Unlike conventional [NiFeSe]hydrogenases having catalytic bias toward H2-production, the [NiFeSe]DvMF showed 11-fold higher specific activity of H2-oxidation (2444 U/mg) than that of H2-production (217 U/mg). At the optimal reaction temperature of the enzyme (65°C), the specific activity of H2-oxidation could reach up to 21,553 U/mg. Amperometric assays of the [NiFeSe]DvMF clearly indicated that the enzyme had a remarkable O2-stability. According to the amino acid sequence alignment, the conserved cysteine residue at position 281 in medial cluster of other [NiFeSe]hydrogenases was specifically replaced by a serine residue (Ser281) in the [NiFeSe]DvMF. These results indicate that the [NiFeSe]DvMF can play as a new H2-oxidizing and O2-stable biocatalyst, along with providing helpful insights into the structure-function relationship of [NiFeSe]hydrogenases.. |
| 39. |
Shigenobu Eguchi, Ki-Seok Yoon, Seiji Ogo, O 2-stable membrane-bound [NiFe]hydrogenase from a newly isolated Citrobacter sp. S-77, Journal of Bioscience and Bioengineering, 10.1016/j.jbiosc.2012.05.018, 114, 5, 479-484, 2012.11, Hydrogenases are of great interest due to their potential use in H 2-based technology. However, most hydrogenases are highly sensitive to O 2, which have been the major bottleneck in hydrogenase studies. Here we report an O 2-stable membrane-bound [NiFe]hydrogenase (MBH) purified from a newly isolated strain, S-77. According to the 16S rRNA gene sequence and phylogenetic analysis of the strain S-77, it belongs to the genus of Citrobacter. In vitro experiments using the cytoplasmic membrane of strain S-77 suggested that a cytochrome b acts as the physiological electron acceptor of the MBH. The purified MBH was composed of a dimer of heterodimers, consisting of two distinct subunits with the molecular weights of 58.5 and 38.5 kDa. The enzyme showed a specific activity for H 2-oxidation of 661U/mg, which is 35-fold greater than that for H 2-production of 18.7U/mg. Notably, the MBH showed a remarkable O 2-stability, maintaining almost 95% of its original activity even after incubation for 30 h in air at 4°C. These results suggest that the O 2-stable MBH may play an important role in the H 2-metabolic pathway under the aerobic conditions of Citrobacter sp. S-77. This is the first report of the purification and biochemical characterization of an O 2-stable MBH from the genus of Citrobacter.. |
| 40. |
Yasuhito Shomura, Ki-Seok Yoon, Hirofumi Nishihara, Yoshiki Higuchi, Structural basis for a [4Fe-3S] cluster in the oxygen-tolerant membrane-bound [NiFe]-hydrogenase, Nature, 10.1038/nature10504, 479, 7372, 253-256, 2011.11, Membrane-bound respiratory [NiFe]-hydrogenase (MBH), a H
2-uptake enzyme found in the periplasmic space of bacteria, catalyses the oxidation of dihydrogen: H
2 →2H
+ + 2e
- (ref. 1). In contrast to the well-studied O
2-sensitive [NiFe]-hydrogenases (referred to as the standard enzymes), MBH has an O
2-tolerant H
2 oxidation activity; however, the mechanism of O
2 tolerance is unclear. Here we report the crystal structures of Hydrogenovibrio marinus MBH in three different redox conditions at resolutions between 1.18 and 1.32Å We find that the proximal iron-sulphur (Fe-S) cluster of MBH has a [4Fe-3S] structure coordinated by six cysteine residues-in contrast to the [4Fe-4S] cubane structure coordinated by four cysteine residues found in the proximal Fe-S cluster of the standard enzymes-and that an amide nitrogen of the polypeptide backbone is deprotonated and additionally coordinates the cluster when chemically oxidized, thus stabilizing the superoxidized state of the cluster. The structure of MBH is very similar to that of the O
2-sensitive standard enzymes except for the proximal Fe-S cluster. Our results give a reasonable explanation why the O
2 tolerance of MBH is attributable to the unique proximal Fe-S cluster; we propose that the cluster is not only a component of the electron transfer for the catalytic cycle, but that it also donates two electrons and one proton crucial for the appropriate reduction of O
2 in preventing the formation of an unready, inactive state of the enzyme.. |
| 41. |
Takahiro Matsumoto, Ryota Kabe, Kyoshiro Nonaka, Tatsuya Ando, Ki-Seok Yoon, Hidetaka Nakai, Seiji Ogo, Model study of CO inhibition of [NiFe]hydrogenase, Inorganic Chemistry, 10.1021/ic200965t, 50, 18, 8902-8906, 2011.09, We propose a modified mechanism for the inhibition of [NiFe]hydrogenase ([NiFe]H 2ase) by CO. We present a model study, using a NiRu H 2ase mimic, that demonstrates that (i) CO completely inhibits the catalytic cycle of the model compound, (ii) CO prefers to coordinate to the Ru II center rather than taking an axial position on the Ni II center, and (iii) CO is unable to displace a hydrido ligand from the NiRu center. We combine these studies with a reevaluation of previous studies to propose that, under normal circumstances, CO inhibits [NiFe]H 2ase by complexing to the Fe II center.. |
| 42. |
Yasuhito Shomura, Keisuke Hagiya, Ki-Seok Yoon, Hirofumi Nishihara, Yoshiki Higuchi, Crystallization and preliminary X-ray diffraction analysis of membrane-bound respiratory [NiFe] hydrogenase from Hydrogenovibrio marinus, Acta Crystallographica Section F: Structural Biology and Crystallization Communications, 10.1107/S1744309111019804, 67, 7, 827-829, 2011.07, Membrane-bound respiratory [NiFe] hydrogenase is an H
2-uptake enzyme found in the periplasmic space of bacteria that plays a crucial role in energy-conservation processes. The heterodimeric unit of the enzyme from Hydrogeno-vibrio marinus was purified to homogeneity using chromatographic procedures. Crystals were grown using the sitting-drop vapour-diffusion method at room temperature. Preliminary crystallographic analysis revealed that the crystals belonged to space group P2
1, with unit-cell parameters a = 75.72, b = 116.59, c = 113.40 Å, β = 91.3°, indicating that two heterodimers were present in the asymmetric unit.. |
| 43. |
Ki-Seok Yoon, Keiichi Fukuda, Kiyoshi Fujisawa, Hirofumi Nishihara, Purification and characterization of a highly thermostable, oxygen-resistant, respiratory [NiFe]-hydrogenase from a marine, aerobic hydrogen-oxidizing bacterium Hydrogenovibrio marinus, International Journal of Hydrogen Energy, 10.1016/j.ijhydene.2011.03.049, 36, 12, 7081-7088, 2011.06, The membrane-bound [NiFe]-hydrogenase from Hydrogenovibrio marinus (HmMBH) was purified homogeneously under anaerobic conditions. Its molecular weight was estimated as 110 kDa, consisting of a heterodimeric structure of 66 kDa and 37 kDa subunits. The purified enzyme exhibited high activity in a wide temperature range: 185 U/mg at 30 °C and 615 U/mg at 85 °C (the optimum temperature). The Km and kcat/Km values for H2 were, respectively, 12 μM and 8.58 × 107 M-1 s-1. The optimum reaction pH was 7.8, but its stability was particularly high at pH 4.0-7.0. Results show that HmMBH was remarkably thermostable and oxygen-resistant: its half-life was 75 h at 80 °C under H2, and more than 72 h at 4 °C under air. The air-oxidized HmMBH for 72 h showed only weak EPR signals of Ni-B, suggesting a structural feature in which the active center is not easily oxidized.. |
| 44. |
Koji Ichikawa, Kyoshiro Nonaka, Takahiro Matsumoto, Bunsho Kure, Ki-Seok Yoon, Yoshiki Higuchi, Tatsuhiko Yagi, Seiji Ogo, Concerto catalysis - Harmonising [NiFe]hydrogenase and NiRu model catalysts, Dalton Transactions, 10.1039/b926061g, 39, 12, 2993-2994, 2010.01, This communication reports the successful merging of the chemical properties of a natural [NiFe]hydrogenase (Desulfovibrio vulgaris Miyazaki F) and our previously reported [NiRu] hydrogenase-mimic. The catalytic activity of both the natural enzyme and the mimic is almost identical, with the exception of working pH ranges, and this allows us to use them simultaneously in the same reaction flask. In such a manner, isotope exchange between D2 and H2O could be conducted over an extended pH range (about 2-10) in one pot under mild conditions at ambient temperature and pressure.. |
| 45. |
Ki-Seok Yoon, Yukiko Sakai, Natsuki Tsukada, Kiyoshi Fujisawa, Hirofumi Nishihara, Purification and biochemical characterization of a membrane-bound [NiFe]-hydrogenase from a hydrogen-oxidizing, lithotrophic bacterium, Hydrogenophaga sp. AH-24, FEMS microbiology letters, 10.1111/j.1574-6968.2008.01417.x, 290, 1, 114-120, 2009.01, Membrane-bound [NiFe]-hydrogenase from Hydrogenophaga sp. AH-24 was purified to homogeneity. The molecular weight was estimated as 100±10 kDa, consisting of two different subunits (62 and 37 kDa). The optimal pH values for H2 oxidation and evolution were 8.0 and 4.0, respectively, and the activity ratio (H2 oxidation/H2 evolution) was 1.61 × 102 at pH 7.0. The optimal temperature was 75 °C. The enzyme was quite stable under air atmosphere (the half-life of activity was c. 48 h at 4 °C), which should be important to function in the aerobic habitat of the strain. The enzyme showed high thermal stability under anaerobic conditions, which retained full activity for over 5 h at 50 °C. The activity increased up to 2.5-fold during incubation at 50 °C under H2. Using methylene blue as an electron acceptor, the kinetic constants of the purified membrane-bound homogenase (MBH) were Vmax=336 U mg -1, kcat=560 s-1, and kcat/K m=2.24 × 107 M-1 s-1. The MBH exhibited prominent electron paramagnetic resonance signals originating from [3Fe-4S]+ and [4Fe-4S]+ clusters. On the other hand, signals originating from Ni of the active center were very weak, as observed in other oxygen-stable hydrogenases from aerobic H2-oxidizing bacteria. This is the first report of catalytic and biochemical characterization of the respiratory MBH from Hydrogenophaga.. |
| 46. |
Ki-Seok Yoon, Natsuki Tsukada, Yukiko Sakai, Masaharu Ishii, Yasuo Igarashi, Hirofumi Nishihara, Isolation and characterization of a new facultatively autotrophic hydrogen-oxidizing Betaproteobacterium, Hydrogenophaga sp. AH-24, FEMS microbiology letters, 10.1111/j.1574-6968.2007.00983.x, 278, 1, 94-100, 2008.01, A hydrogen-oxidizing bacterium strain AH-24 was isolated, which was classified in the genus Hydrogenophaga, based on the 16S rRNA gene sequence. The isolate possessed a typical yellow pigment of Hydrogenophaga species. Its closest relative was Hydrogenophaga pseudoflava, but the assimilation profile of sugar compounds resembled that of no species of Hydrogenophaga. The optimum temperature and pH for autotrophic growth were, respectively, 33-35°C and 7.0. Most hydrogenase activity (benzyl viologen reducing activity) was localized in the membrane fraction (MF), but NAD(P)-reducing hydrogenase activity was detected in neither the membrane nor the soluble fractions. Cytochromes b 561 and c551 were present in MF; both were reduced when hydrogen was supplied to the oxidized MF, suggesting involvement in respiratory H2 oxidation as electron carriers. Cytochrome b561 was inferred to function as the redox partner of the membrane-bound hydrogenase.. |
| 47. |
Masaki Ihara, Hirofumi Nishihara, Ki-Seok Yoon, Oliver Lenz, Bärbel Friedrich, Hitoshi Nakamoto, Kouji Kojima, Daisuke Honma, Toshiaki Kamachi, Ichiro Okura, Light-driven hydrogen production by a hybrid complex of a [NiFe]-hydrogenase and the cyanobacterial photosystem I, Photochemistry and Photobiology, 10.1562/2006-01-16-RA-778, 82, 3, 676-682, 2006.05, In order to generate renewable and clean fuels, increasing efforts are focused on the exploitation of photosynthetic microorganisms for the production of molecular hydrogen from water and light. In this study we engineered a 'hard-wired' protein complex consisting of a hydrogenase and photosystem I (hydrogenase-PSI complex) as a direct light-to-hydrogen conversion system. The key component was an artificial fusion protein composed of the membrane-bound [NiFe] hydrogenase from the β-proteobacterium Ralstonia eutropha H16 and the peripheral PSI subunit PsaE of the cyanobacterium Thermosynechococcus elongatus. The resulting hydrogenase-PsaE fusion protein associated with PsaE-free PSI spontaneously, thereby forming a hydrogenase-PSI complex as confirmed by sucrose-gradient ultracentrifuge and immunoblot analysis. The hydrogenase-PSI complex displayed light-driven hydrogen production at a rate of 0.58 μmol H 2·mg chlorophyll -1·h -1. The complex maintained its accessibility to the native electron acceptor ferredoxin. This study provides the first example of a light-driven enzymatic reaction by an artificial complex between a redox enzyme and photosystem I and represents an important step on the way to design a photosynthetic organism that efficiently converts solar energy and water into hydrogen.. |
| 48. |
Ki-Seok Yoon, Cedric Bobst, Craig F. Hemann, Russ Hille, F. Robert Tabita, Spectroscopic and Functional Properties of Novel 2[4Fe-4S] Cluster-containing Ferredoxins from the Green Sulfur Bacterium Chlorobium tepidum, Journal of Biological Chemistry, 10.1074/jbc.M107852200, 276, 47, 44027-44036, 2001.11, Two distinct ferredoxins, Fd I and Fd II, were isolated and purified to homogeneity from photoautotrophically grown Chlorobium tepidum, a moderately thermophilic green sulfur bacterium that assimilates carbon dioxide by the reductive tricarboxylic acid cycle. Both ferredoxins serve a crucial role as electron donors for reductive carboxylation, catalyzed by a key enzyme of this pathway, pyruvate synthase/pyruvate ferredoxin oxidoreductase. The reduction potentials of Fd I and Fd II were determined by cyclic voltammetry to be -514 and -584 mV, respectively, which are more electronegative than any previously studied Fds in which two [4Fe-4S] clusters display a single transition. Further spectroscopic studies indicated that the CD spectrum of oxidized Fd I closely resembled that of Fd II; however, both spectra appeared to be unique relative to ferredoxins studied previously. Double integration of the EPR signal of the two Fds yielded approximately ∼2.0 spins per molecule, compatible with the idea that C. tepidum Fd I and Fd II accept 2 electrons upon reduction. These results suggest that the C. tepidum Fd I and Fd II polypeptides each contain two bound [4Fe-4S] clusters. C. tepidum Fd I and Fd II are novel 2[4Fe-4S] Fds, which were shown previously to function as biological electron donors or acceptors for C. tepidum pyruvate synthase/pyruvate ferredoxin oxidoreductase (Yoon, K.-S., Hille, R., Hemann, C. F., and Tabita, F. R. (1999) J. Biol. Chem. 274, 29772-29778). Kinetic measurements indicated that Fd I had ∼2.3-fold higher affinity than Fd II. The results of amino acid sequence alignments, molecular modeling, oxidation-reduction potentials, and spectral properties strongly indicate that the C. tepidum Fds are chimeras of both clostridial-type and chromatium-type Fds, suggesting that the two Fds are likely intermediates in the evolutional development of 2[4Fe-4S] clusters compared with the well described clostridial and chromatium types.. |
| 49. |
Ki-Seok Yoon, Russ Hille, Craig Hemann, F. Robert Tabita, Rubredoxin from the green sulfur bacterium Chlorobium tepidum functions as an electron acceptor for pyruvate ferredoxin oxidoreductase, Journal of Biological Chemistry, 10.1074/jbc.274.42.29772, 274, 42, 29772-29778, 1999.10, Rubredoxin (Rd) from the moderately thermophilic green sulfur bacterium Chlorobium tepidum was found to function as an electron acceptor for pyruvate ferredoxin oxidoreductase (PFOR). This enzyme, which catalyzes the conversion of pyruvate to acetyl-CoA and CO2, exhibited an absolute dependence upon the presence of Rd. However, Rd was incapable of participating in the pyruvate synthase or CO2 fixation reaction of C. tepidum PFOR, for which two different reduced ferredoxins are employed as electron donors. These results suggest a specific functional role for Rd in pyruvate oxidation and provide the initial indication that the two important physiological reactions catalyzed by PFOPJ pyruvate synthase are dependent on different electron carriers in the cell. The UV-visible spectrum of oxidized Rd, with a monomer molecular weight of 6500, gave a molar absorption coefficient at 492 nm of 6.89 mM-1 cm-1 with an A492/A280 ratio of 0.343 and contained one iron atom/molecule. Further spectroscopic studies indicated that the CD spectrum of oxidized C. tepidum Rd exhibited a unique absorption maximum at 385 nm and a shoulder at 420 nm. The EPR spectrum of oxidized Rd also exhibited unusual anisotropic resonances at g = 9.675 and g = 4.322, which is composed of a narrow central feature with broader shoulders to high and low field. The midpoint reduction potential of C. tepidum Rd was determined to be -87 mV, which is the most electronegative value reported for Rd from any source.. |
| 50. |
Masaharu Ishii, Ki-Seok Yoon, Yasufumi Ueda, Toshihiro Ochiai, Nare Yun, Seiichi Takishita, Tohru Kodama, Yasuo Igarashi, Reductive TCA cycle in an aerobic bacterium, Hydrogenobacter thermophilus strain TK-6, Studies in Surface Science and Catalysis, 114, 613-616, 1998.01. |
| 51. |
Ki-Seok Yoon, Masaharu Ishii, Tohru Kodama, Yasuo Igarashi, Carboxylation reactions of pyruvate Ferredoxin oxidoreductase and 2-oxoglutarate: Ferredoxin oxidoreductase from Hydrogenobacter thermophilus TK-6, Bioscience, Biotechnology and Biochemistry, 61, 3, 510-513, 1997.06, Enzymatic reactions involving pyruvate:ferredoxin oxidoreductase and 2-oxoglutarate:ferredoxin oxidoreductase from a thermophilic, aerobic, chemolithoautotrophic, and hydrogen-oxidizing bacterium, Hydrogenobacter thermophilus TK-6, were investigated as the CO2 exchange reaction and CO2 fixation reaction using ferredoxin isolated from the same organism as a reductant. The reduced ferredoxin was required in the pyruvate synthetic reaction and the 2-oxoglutarate synthetic reaction by a cell extract that had been treated with a PD-10 column to remove the low molecular weight substances. [14C]Pyruvate and [14C]2-oxoglutarate were detected as products of pyruvate synthetic and 2-oxoglutarate synthetic reactions, respectively. Further evidence for the operation of pyruvate: ferredoxin oxidoreductase and 2-oxoglutarate:ferredoxin oxidoreductase was obtained from experiments on CO2 exchange reactions using the purified enzymes.. |
| 52. |
Ki-Seok Yoon, Masaharu Ishii, Tohru Kodama, Yasuo Igarashi, Purification and characterization of pyruvate:ferredoxin oxidoreductase from hydrogenobacter thermophilus TK-6, Archives of Microbiology, 10.1007/s002030050443, 167, 5, 275-279, 1997.04, Pyruvate:ferredoxin oxidoreductase was purified to electrophoretic homogeneity from an aerobic, thermophilic, obligately chemolithoautotrophic, hydrogenoxidizing bacterium, Hydrogenobacter thermophilus TK-6, by precipitation with ammonium sulfate and fractionation by DEAE-Sepharose CL-GB, polyacrylate-quaternary amine, hydroxyapatite, and Superdex-200 chromatography. The native enzyme had a molecular mass of 135 kDa and was composed of four different subunits with apparent molecular masses of 46, 31.5, 29, and 24.5 kDa, respectively, indicating that the enzyme has an αβγδ-structure. The activity was detected with pyruvate, coenzyme A, and one of the following electron accepters in substrate amounts: ferredoxin isolated from H. thermophilus, FAD, FMN, triphenyltetrazolium chloride, or methyl viologen. NAD, NADP, ana ferredoxins from Chlorella spp. and Clostridium pasteurianum were ineffective as the electron acceptor. The temperature optimum for pyruvate oxidation was approximately 80°C. The pH optimum was 7.6-7.8. The apparent K(m) values for pyruvate and coenzyme A at 70°C were 3.45 mM and 54 μM, respectively. The enzyme was extremely thermostable under anoxic conditions; the time for a 50% loss of activity (t(50%)) at 70°C was approximately 8 h.. |
| 53. |
Ki-Seok Yoon, Yasufumi Ueda, Masaharu Ishii, Yasuo Igarashi, Tohru Kodama, NADH:ferredoxin reductase and NAD-reducing hydrogenase activities in Hydrogenobacter thermophilus strain TK-6, FEMS microbiology letters, 10.1016/0378-1097(96)00132-2, 139, 2-3, 139-142, 1996.06, NADH:ferredoxin reductase (EC 1.18.13) and NAD-reducing hydrogenase (EC 1.12.1.2) activities were detected in the cytoplasm of Hydrogenobacter thermophilus TK-6. NADH:ferredoxin reductase activity was detected using metronidazole, an artificial electron acceptor, which reacts specifica1ly with reduced ferredoxin. Soluble NAD-reducing hydrogenase activity was detected after extended preincubation. The lag disappeared when cell-free extract was incubated anaerobically for more than 30 min. The electron transport system of this chemolithoautotrophic bacterium is discussed.. |
| 54. |
Ki-Seok Yoon, Masaharu Ishii, Yasuo Igarashi, Tohru Kodama, Purification and characterization of 2-oxoglutarate Ferredoxin oxidoreductase from a thermophilic, obligately chemolithoautotrophic bacterium, Hydrogenobacter thermophilus TK-6, Journal of bacteriology, 10.1128/jb.178.11.3365-3368.1996, 178, 11, 3365-3368, 1996.01, 2-Oxoglutarate:ferredoxin oxidoreductase from a thermophilic, obligately autotrophic, hydrogen-oxidizing bacterium, Hydrogenobacter thermophilus TK- 6, was purified to homogeneity by precipitation with ammonium sulfate and by fractionation by DEAE-Sepharose CL-6B, polyacrylate-quaternary amine, hydroxyapatite, and Superdex-200 chromatography. The purified enzyme had a molecular mass of about 105 kDa and comprised two subunits (70 kDa and 35 kDa). The activity of the 2-oxoglutarate:ferredoxin oxidoreductase was detected by the use of 2-oxoglutarate, coenzyme A, and one of several electron acceptors in substrate amounts (ferredoxin isolated from H. thermophilus, flavin adenine dinucleotide, flavin mononucleotide, or methyl viologen). NAD, NADP, and ferredoxins from Chlorella spp. and Clostridium pasteurianum were ineffective. The enzyme was extremely thermostable; the temperature optimum for 2-oxoglutarate oxidation was above 80°C, and the time for a 50% loss of activity at 70°C under anaerobic conditions was 22 h. The optimum pH for a 2-oxoglutarate oxidation reaction was 7.6 to 7.8. The apparent K(m) values for 2-oxoglutarate and coenzyme A at 70°C were 1.42 mM and 80 μM, respectively.. |
| 55. |
ISHII Masaharu, UEDA Yasufumi, YOON Ki-Seok, IGARASHI Yasuo, KODAMA Tohru, Purification and Characterization of Ferredoxin from Hydrogenobacter thermophilus Strain TK-6, Bioscience, biotechnology, and biochemistry, 10.1271/bbb.60.1513, 60, 9, 1513-1515, 1996.01, Ferredoxin was purified from cells of Hydrogenobacter thermophilus strain TK-6. Purification was performed aerobically by the addition of octyl-β-glucoside to the buffers. The purified ferredoxin had a molecular mass of 13,000 and contained a [4Fe-4S] cluster. The protein had a long stretch at the N-terminal region; however, the sequence was not similar to the sequences of ferredoxins with a long stretch from Archaebacteria.. |
| 56. |
Tetsuya Ono, Masaharu Ishii, Ki-Seok Yoon, Yasuo Igarashi, Tohru Kodama, Purification and Characterization of Membrane-bound Hydrogenase from a Thermophilic Hydrogen-Oxidizing Bacterium, Pseudomonas hydrogenothermophila Strain TH-1, Bioscience, Biotechnology, and Biochemistry, 10.1271/bbb.59.917, 59, 5, 917-919, 1995.01, A membrane-bound hydrogenase was purified aerobically by one step using a hydroxyapatite column after solubilization by acetone treatment from a thermophilic hydrogen-oxidizing bacterium, Pseudomonas hydrogenothermophila strain TH-1. The enzyme consists of two polypeptides of 63 and 31 kDa, respectively. The amino-terminal amino acid sequences of both subunits were homologous to membrane-bound type [Ni-Fe] hydrogenases from other origins. The thermostability under a hydrogen gas atmosphere is highly stable at 50°C, which is the optimum temperature for the cell growth.. |
| 57. |
Tetsuya Ono, Masaharu Ishii, Ki-Seok Yoon, Yasuo Igarashi, Tohru Kodama, Purification and characterization of membrane-bound hydrogenase from a thermophilic hydrogen-oxidizing bacterium, pseudomonas hydrogenothermophila strain th-1, Bioscience, Biotechnology and Biochemistry, 10.1080/bbb.59.917, 59, 5, 917-919, 1995.01, A membrane-bound hydrogenase was purified aerobically by one step using a hydroxyapatite column after solubilization by acetone treatment from a thermophilic hydrogen-oxidizing bacterium, Pseudomonas hydrogenothermophila strain TH-l. The enzyme consists of two polypeptides of 63 and 31 kDa, respectively. The amino-terminal amino acid sequences of both subunits were homologous to membrane-bound type [Ni–Fe] hydrogenases from other origins. The thermostability under a hydrogen gas atmosphere is highly stable at 50°C, which is the optimum temperature for the cell growth.. |
