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1.
Takahiro Inoue Kyosuke Takao Takashi Yoshida Kei Wada Takashi Daifuku Yasuko Yoneda Keiichi Fukuyama Yoshihiko Sako 《Biochemical and biophysical research communications》2013
A unique [Ni–Fe–S] cluster (C-cluster) constitutes the active center of Ni-containing carbon monoxide dehydrogenases (CODHs). His261, which coordinates one of the Fe atoms with Cys295, is suggested to be the only residue required for Ni coordination in the C-cluster. To evaluate the role of Cys295, we constructed CODH-II variants. Ala substitution for the Cys295 substitution resulted in the decrease of Ni content and didn’t result in major change of Fe content. In addition, the substitution had no effect on the ability to assemble a full complement of [Fe–S] clusters. This strongly suggests Cys295 indirectly and His261 together affect Ni-coordination in the C-cluster. 相似文献
2.
《BBA》2020,1861(7):148188
Ni-containing CO-dehydrogenases (CODHs) allow some microorganisms to couple ATP synthesis to CO oxidation, or to use either CO or CO2 as a source of carbon. The recent detailed characterizations of some of them have evidenced a great diversity in terms of catalytic properties and resistance to O2. In an effort to increase the number of available CODHs, we have heterologously produced in Desulfovibrio fructosovorans, purified and characterized the two CooS-type CODHs (CooS1 and CooS2) from the hyperthermophilic archaeon Thermococcus sp. AM4 (Tc). We have also crystallized CooS2, which is coupled in vivo to a hydrogenase. CooS1 and CooS2 are homodimers, and harbour five metalloclusters: two [Ni4Fe-4S] C clusters, two [4Fe-4S] B clusters and one interfacial [4Fe-4S] D cluster. We show that both are dependent on a maturase, CooC1 or CooC2, which is interchangeable. The homologous protein CooC3 does not allow Ni insertion in either CooS. The two CODHs from Tc have similar properties: they can both oxidize and produce CO. The Michaelis constants (Km) are in the microM range for CO and in the mM range (CODH 1) or above (CODH 2) for CO2. Product inhibition is observed only for CO2 reduction, consistent with CO2 binding being much weaker than CO binding. The two enzymes are rather O2 sensitive (similarly to CODH II from Carboxydothermus hydrogenoformans), and react more slowly with O2 than any other CODH for which these data are available. 相似文献
3.
Sisler EC 《Plant physiology》1979,64(4):538-542
Tobacco leaves were exposed to 14C-labeled ethylene (3.7 × 10−2 microliters per liter) in the presence and absence of unlabeled ethylene and other compounds. Most of the [14C]ethylene appears to be bound to displaceable sites. Lineweaver-Burk plots for a one-half maximum response in a tobacco leaf respiration test gave a value of 0.3 microliter per liter for ethylene, 50 microliters per liter for propylene, and 266 microliters per liter for carbon monoxide. Scatchard plots for displacement of [14C]ethylene from the site gave 0.27 microliters per liter for ethylene, 42 microliters per liter for propylene, and 746 microliters per liter for carbon monoxide. At 2%, CO2 displaces about 35% of the bound ethylene, but increasing the concentration to 10% does not displace the remaining [14C]ethylene. A value of 3.5 nanomolar was calculated for the concentration of ethylene-binding sites available to exogenous ethylene. This does not account for the sites occupied by endogenous ethylene, and the total number of binding sites is probably somewhat higher. Using tissue culture material, the system was shown to be stable to freezing and thawing; and the π-acceptors, carbon monoxide, cyanide, n-butyl isocyanide, phosphorous trifluoride, and tetrafluoroethylene, were shown to compete with ethylene for binding. 相似文献
4.
C–N bond activation of tert-butyl isocyanide in methanol using 2,6-bis(di-tert-butylphosphinito)pyridine (PONOP) metal (Ni, Pd, Pt) complexes and (dippe)NiCl2 are reported. t-BuOMe and t-BuCl were detected as organic products by GC–MS. Substitution of the metal-chloride by one molecule of tert-butyl isocyanide followed by carbonium ion loss/nucleophilic attack by chloride anion or methanol led to formation of a metal-cyanide bond. 相似文献
5.
Won Bae Jeon Steven W. Singer Paul W. Ludden Luis M. Rubio 《Journal of biological inorganic chemistry》2005,10(8):903-912
Carbon monoxide dehydrogenase (CODH) from Rhodospirillum rubrum catalyzes the oxidation of CO to CO2. A unique [NiFe4S4] cluster, known as the C-cluster, constitutes the active site of the enzyme. When grown in Ni-deficient medium R. rubrum accumulates a Ni-deficient apo form of CODH that is readily activated by Ni. It has been previously shown that activation
of apo-CODH by Ni is a two-step process involving the rapid formation of an inactive apo-CODH•Ni complex prior to conversion
to the active holo-CODH. We have generated CODH variants with substitutions in cysteine residues involved in the coordination
of the [Fe3S4] portion of the C-cluster. Analysis of the variants suggests that the cysteine residues at positions 338, 451, and 481 are
important for CO oxidation activity catalyzed by CODH but not for Ni binding to the C-cluster. C451S CODH is the only new
variant that retains residual CO oxidation activity. Comparison of the kinetics and pH dependence of Ni activation of the
apo forms of wild-type, C451S, and C531A CODH allowed us to develop a model for Ni insertion into the C-cluster of CODH in
which Ni reversibly binds to the C-cluster and subsequently coordinates Cys531 in the rate-determining step. 相似文献
6.
Sigurd D. Süssmuth Anne D. Sperfeld Albert C. Ludolph Hayrettin Tumani 《Neurochemical research》2010,35(7):1071-1074
Elevated cerebrospinal fluid (CSF)/serum quotients of albumin (QAlb) may occur in motor neuron diseases (MND) including amyotrophic lateral sclerosis (ALS), but the pathophysiologic mechanisms
underlying these alterations are unclear. Evidence from animal experiments suggests that the arterial carbon dioxide level
might affect the QAlb, i.e. the function of the blood-CSF barrier (BCB). We therefore compared basic CSF parameters in different forms of MND (ALS,
n = 105; lower motor neuron diseases, n = 12; and upper motor neuron diseases, n = 7) and investigated the relationship between elevated QAlb and the arterial partial pressure of carbon dioxide (pCO2) in ALS where respiratory insufficiency leads to hypercapnia in the course of the disease. Pathologic elevations of QAlb occurred in 32 of 124 MND patients. In ALS, QAlb significantly correlated with the arterial pCO2 (r = 0.454; P = 0.001; n = 45). These data indicate that BCB dysfunction is a frequent finding in different forms of MND and may reflect distinct
pathophysiological mechanisms. In ALS, an important underlying mechanism might be the influence of the arterial pCO2 which may alter the CSF flow. 相似文献
7.
1. The oxidation of methanol to carbon dioxide by Candida N–16 grown on methanol was investigated. The presence of enzymes which catalyze the following reaction was found in the cell-free extract of the yeast employed; CH3OH→HCHO→HCOOH→CO2. 2. Methanol was oxidized to formaldehyde by an alcohol oxidase. The reaction was as follows; CH3OH+O2→HCHO+H2O2. The alcohol oxidase was crystallized after purification by ammonium sulfate-precipitation and column chromatography using DEAE-Sephadex A-50. A prosthetic group of the enzyme was proved to be FAD. The enzyme possessed a broad specificity for alcohols such as methanol, ethanol, n-propanol, n-butanol and n-amylalcohol. The enzyme was inducibly formed only by the addition of methanol. 3. The oxidation of formaldehyde to formate was catalyzed by a NAD-linked dehydrogenase dependent on GSH. 4. Formate was oxidized by a NAD-linked dehydrogenase. 5. Catalase was also found in the extract, and methanol was chemically oxidized by the reaction of catalase and hydrogen peroxide which was generated by the alcohol oxidase system. 6. The oxidation pathway from methanol to carbon dioxide was also found in other methanol-utilizing yeasts such as Candida N-17, Saccharomyces H-1 and Torulopsis M-1. 相似文献
8.
Chunli Zheng Yanfei Zhang Yuandong Liu Anna Wu Lexian Xia Jia Zeng Jianshe Liu Guanzhou Qiu 《Current microbiology》2009,58(6):586-592
Adenosine 5′-phosphosulfate (APS) reductase is a key enzyme involved in the pathways of sulfate reduction and sulfide oxidation
in the biological sulfur cycle. In this study, the gene of APS reductase from Acidithiobacillus ferrooxidans was cloned and expressed in Escherichia coli, the soluble protein was purified by one-step affinity chromatography to apparent homogeneity. The molecular mass of the
recombinant APS reductase was determined to be 28 kDa using SDS-PAGE. According to optical and EPR spectra results of the
recombinant protein confirmed that the iron–sulfur cluster inserted into the active site of the protein. Site-directed mutation
for the enzyme revealed that Cys110, Cys111, Cys193, and Cys196 were in ligation with the iron–sulfur cluster. The [Fe4S4] cluster could be assembled in vitro, and exhibited electron transport and redox catalysis properties. As we know so far,
this is the first report of expression in E. coli of APS reductase from A. ferrooxidans. 相似文献
9.
10.
《Free radical research》2013,47(3-6):197-204
Carbon dioxide radical adducts of the spin trapping agent, α-phenyl N-t-butyl nitrone (PBN), have been observed to occur in the urine and bile of rats exposed to carbon tetrachloride as well as in perfusates of liver in which the perfusion medium contained carbon tetrachloride (Connor er al., J. Biol. Chem., 261, 4542, (1986)). The carbon dioxide adduct was proven to be derived from CCI, by use of 13-C-labelled compound. These adducts were not observed in the liver itself suggesting that they might be rapidly secreted from the liver. However, using isolated hepatocytes, we have demonstrated that the carbon dioxide radical adduct can be observed directly in the liver cells as it is formed. Since this water-soluble adduct cannot be extracted by non-aqueous solvents such as chloroform or toluene, its formation in liver in vivo or in perfused livers was not detected. Lowering the oxygen tension in the system diminished the intensity of production of the carbon dioxide adduct, consistent with the adduct being produced as a result of ·OOCCl3 generation. It is not clear the extent to which this adduct is formed as a result of the ·CO2 radical or is produced by metabolic oxidation of the trichloromethyl radical adduct of PBN per se to the carbon dioxide radical adduct. The intensity of the signal of the carbon dioxide radical adduct suggests that adduct conversion may be the route of formation since it seems unlikely that a sufficient amount of the halocarbon could be metabolized to ·COCl or ·CO2 radicals to generate a signal of the magnitude involved. The ·CO2 adduct is readily observed in intact hepatocytes, but the ·CCl3 adduct is not (although we know the ·CCl3 adduct has been produced in these cells), indicating that the ·CO2 adduct is present in considerable abundance compared to the ·CCl3 adduct. 相似文献
11.
A model of the C
3 photosynthetic system is developed which describes the sensitivity of the steadystate rate of carbon dioxide assimilation to changes in the activity of several enzymes of the system. The model requires measurements of the steady-state rate of carbon dioxide assimilation, the concentrations of several intermediates in the photosynthetic system, and the concentration of the active site of ribulose 1,5-bisphosphate carboxyalse/oxygenase (Rubisco). It is shown that in sunflowers (Helianthus annuus L.) at photon flux densities that are largely saturating for the rate of photosynthesis, the steady-stete rate of carbon dioxide assimilation is most sensitive to Rubisco activity and, to a lesser degree, to the activities of the stromal fructose, 6-bisphosphatase and the enzymes catalysing sucrose synthesis. The activities of sedoheptulose 1,7-bisphosphatase, ribulose 5-phosphate kinase, ATP synthase and the ADP-glucose pyrophosphorylase are calculated to have a negligible effect on the flux under the high-light conditions. The utility of this analysis in developing simpler models of photosynthesis is also discussed.Abbreviations
c
i
intercellular CO2 concentration
-
C
infP
supJ
control coefficient for enzyme P with respect to flux J
- DHAP
dihydroxyacetonephosphate
- E4P
erythrose 4-phosphate
- F6P
fructose 6-phosphate
- FBP
fructose 1,6-bisphosphate
- FBPase
fructose 1,6-bisphosphatase
- G3P
glyceraldehyde 3-phosphate
- G1P
glucose 1-phosphate
- G6P
glucose 6-phosphate
- Pi
inorganic phosphate
- PCR
photosynthetic carbon reduction
- PGA
3-phosphoglyceric acid
- PPFD
photosynthetically active photon flux density
-
R
n
J
response coefficient for effector n with respect to flux J
- R5P
ribose 5-phosphate
- Rubisco
ribulose 1,5-bisphosphate carboxylase/oxygenase
- Ru5P
ribulose 5-phosphate
- RuBP
ribulose 1,5-bisphosphate
- S7P
sedoheptulose 7-phosphate
- SBP
sedoheptulose 1,7-bisphosphate
- SBPase
sedoheptulose 1,7-bisphosphatase
- SPS
sucrose-phosphate synthase
- Xu5P
xylulose 5-phosphate
-
n
P
elasticity coefficient for effector n with respect to the catalytic velocity of enzyme P
This research was funded by an Australian Research Council grant to I.E.W. and was undertaken during a visity by K.A.M. to the James Cook University of North Queensland. The expert help of Glenys Hanley and Mick Kelly is greatly appreciated. 相似文献
12.
Marcus Resch Holger Dobbek Ortwin Meyer 《Journal of biological inorganic chemistry》2005,10(5):518-528
Carbon monoxide dehydrogenase from the bacterium Oligotropha carboxidovorans catalyzes the oxidation of CO to CO2 at a unique [CuSMoO2] cluster. In the bacteria the cluster is assembled post-translational. The integration of S, and particularly of Cu, is rate limiting in vivo, which leads to CO dehydrogenase preparations containing the mature and fully functional enzyme along with forms of the enzyme deficient in one or both of these elements. The active sites of mature and immature forms of CO dehydrogenase were converted into a [MoO3] centre by treatment with potassium cyanide. We have established a method, which rescues 50% of the CO dehydrogenase activity by in vitro reconstitution of the active site through the supply of sulphide first and subsequently of Cu(I) under reducing conditions. Immature forms of CO dehydrogenase isolated from the bacterium, which were deficient in S and/or Cu at the active site, were similarly activated. X-ray crystallography and electron paramagnetic resonance spectroscopy indicated that the [CuSMoO2] cluster was properly reconstructed. However, reconstituted CO dehydrogenase contains mature along with immature forms. The chemical reactions of the reconstitution of CO dehydrogenase are summarized in a model, which assumes resulphuration of the Mo-ion at both equatorial positions at a 1:1 molar ratio. One equatorial Mo–S group reacts with Cu(I) in a productive fashion yielding a mature, functional [CuSMoO2] cluster. The other Mo–S group reacts with Cu(I), then Cu2S is released and an oxo group is introduced from water, yielding an inactive [MoO3] centre. 相似文献
13.
Eddy?Van der?Linden Tanja?Burgdorf Michael?Bernhard Boris?Bleijlevens B?rbel?Friedrich Simon?P.?J.?Albracht
Infrared spectra of 15N-enriched preparations of the soluble cytoplasmic NAD+-reducing [NiFe]-hydrogenase from Ralstonia eutropha are presented. These spectra, together with chemical analyses, show that the Ni-Fe active site contains four cyanide groups and one carbon monoxide molecule. It is proposed that the active site is a (RS)2(CN)Ni(-RS)2Fe(CN)3(CO) centre (R=Cys) and that H2 activation solely takes place on nickel. One of the two FMN groups (FMN-a) in the enzyme can be reversibly released upon reduction of the enzyme. It is now reported that at longer times also one of the cyanide groups, the one proposed to be bound to the nickel atom, could be removed from the enzyme. This process was irreversible and induced the inhibition of the enzyme activity by oxygen; the enzyme remained insensitive to carbon monoxide. The Ni-Fe active site was EPR undetectable under all conditions tested. It is concluded that the Ni-bound cyanide group is responsible for the oxygen insensitivity of the enzyme.Abbreviations BV benzyl viologen - DCIP 2,6-dichlorophenol-indophenol - EXAFS extended X-ray absorption fine structure - FTIR Fourier transform infrared - MV methyl viologen - SH soluble NAD+-reducing hydrogenase - XAS X-ray absorption spectroscopy 相似文献
14.
15.
Christopher R. McCullough Phani Kumar Pullela Sang-Choul Im Lucy Waskell Daniel S. Sem 《Journal of biomolecular NMR》2009,43(3):171-178
The cytochromes P450 (CYPs) play a central role in many biologically important oxidation reactions, including the metabolism
of drugs and other xenobiotic compounds. Because they are often assayed as both drug targets and anti-targets, any tools that
provide: (a) confirmation of active site binding and (b) structural data, would be of great utility, especially if data could
be obtained in reasonably high throughput. To this end, we have developed an analog of the promiscuous heme ligand, cyanide,
with a 13CH3-reporter attached. This 13C-methyl isocyanide ligand binds to bacterial (P450cam) and membrane-bound mammalian (CYP2B4) CYPs. It can be used in a rapid
1D experiment to identify binders, and provides a qualitative measure of structural changes in the active site.
Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. 相似文献
16.
Candida lipolytica was cultured batchwise using n-hexadecane as the main carbon source. Biomass production, n-hexadecane consumption, oxygen consumption, and carbon dioxide evolution were measured to follow the fermentation. The consistency of the measured data was examined using integrated and instantaneous available electron and carbon balances. Values of the “true” growth yield, ηmax, and maintenance coefficient, me were estimated using three different sets of data (biomass and n-hexadecane, oxygen and biomass, and CO2 and biomass), and the results were compared with estimates obtained from literature data. Hysteresis patterns were observed in plots of specific rates of oxygen consumption and carbon dioxide evolution versus specific growth rate. 相似文献
17.
《Systematic and applied microbiology》2020,43(2):126064
The ability to grow by anaerobic CO oxidation with production of H2 from water is known for some thermophilic bacteria, most of which belong to Firmicutes, as well as for a few hyperthermophilic Euryarchaeota isolated from deep-sea hydrothermal habitats. A hyperthermophilic, neutrophilic, anaerobic filamentous archaeon strain 1505 = VKM B-3180 = KCTC 15798 was isolated from a terrestrial hot spring in Kamchatka (Russia) in the presence of 30% CO in the gas phase. Strain 1505 could grow lithotrophically using carbon monoxide as the energy source with the production of hydrogen according to the equation CO + H2O → CO2 + H2; mixotrophically on CO plus glucose; and organotrophically on peptone, yeast extract, glucose, sucrose, or Avicel. The genome of strain 1505 was sequenced and assembled into a single chromosome. Based on 16S rRNA gene sequence analysis and in silico genome-genome hybridization, this organism was shown to be closely related to the Thermofilum adornatum species. In the genome of Thermofilum sp. strain 1505, a gene cluster (TCARB_0867-TCARB_0879) was found that included genes of anaerobic (Ni,Fe-containing) carbon monoxide dehydrogenase and genes of energy-converting hydrogenase ([Ni,Fe]-CODH–ECH gene cluster). Compared to the [Ni,Fe]-CODH–ECH gene clusters occurring in the sequenced genomes of other H2-producing carboxydotrophs, the [Ni,Fe]-CODH–ECH gene cluster of Thermofilum sp. strain 1505 presented a novel type of gene organization. The results of the study provided the first evidence of anaerobic CO oxidation coupled with H2 production performed by a crenarchaeon, as well as the first documented case of lithotrophic growth of a Thermofilaceae representative. 相似文献
18.
Hydrologic gradient and vegetation controls on CH4 and CO2 fluxes in a spring-fed forested wetland 总被引:2,自引:0,他引:2
Four different habitats in a spring-fed forested wetland (Clear Springs Wetland, Panola County, Mississippi, USA) varying
in hydrologic regime were examined for methane and carbon dioxide fluxes from soils over 15 and 9 months, respectively. There
was an increasing gradient of CH4 flux rates from an unflooded upper-elevation forest site to an occasionally flooded bottomland forest site to a shallow permanently
flooded site, and then to a deeper-water permanently flooded site. Depending on the time of year, all sites were sources of
methane but only at the upper-elevation forest site, when gravimetric soil moisture content fell below 54%, was atmospheric
methane consumed. On average, summer CH4 emission rates were higher than those in other seasons. A multiple regression model with soil temperature and soil redox
potential as independent variables could explain 65% of the variation in CH4 flux rates. In the flooded zone, variation in CH4 flux rates was correlated with aboveground plant biomass and stem density of emergent vascular plants, and plant-mediated
CH4 transport depended on plant type. The efflux of CH4 to plant biomass (Eff:B) ratio was generally lower in Hydrocotyle umbellata compared to Festuca
obtusa. Compared to several other freshwater forested wetlands in the southeastern USA, this spring-fed forested wetland ecosystem
was a strong source of atmospheric CH4, likely due to a long hydroperiod and high soil organic matter content. Carbon dioxide fluxes show a reverse spatial pattern
than CH4 fluxes with highest CO2 emissions in the non-flooded zone at all times of the year, indicating the dominance of aerobic soil respiration. A multiple
regression model also revealed a strong dependency of CO2 fluxes (r
2 = 0.73) on soil temperature and soil redox potential.
Handling editor: J. M. Melack 相似文献
19.
Binding of exogenously added carbon monoxide at the active site of the iron-only hydrogenase (CpI) from Clostridium pasteurianum. 总被引:1,自引:0,他引:1
A site for the binding of exogenously added carbon monoxide has been identified at the active site of the Fe-only hydrogenase (CpI) from Clostridium pasteurianum. The binding and inhibition of carbon monoxide have been exploited in biochemical and spectroscopic studies to gain mechanistic insights. In the present study, we have taken advantage of the ability to generate an irreversibly carbon monoxide bound state of CpI. The crystallization and structural characterization of CpI inhibited in the presence of carbon monoxide indicates the addition of a single molecule of carbon monoxide. The ability to generate crystals of the carbon monoxide bound state of the hydrogenase that are isomorphous to those of the native enzyme has allowed for a direct comparison of the crystallographic data and an unambiguous identification of the site of carbon monoxide binding at the active site of CpI. Carbon monoxide binds to an Fe atom of the 2Fe subcluster at the site of a terminally bound water molecule in the as crystallized native state of CpI that has been previously suggested to be a potential site of reversible hydrogen oxidation. Binding of carbon monoxide at this site results in an active site that is coordinately saturated with strong ligands (S, CO, and CN), providing a rational potential mechanism for inhibition of reversible hydrogen oxidation at the active site of CpI. 相似文献
20.
Lopes Ferreira N Mathis H Labbé D Monot F Greer CW Fayolle-Guichard F 《Applied microbiology and biotechnology》2007,75(4):909-919
Mycobacterium austroafricanum IFP 2012, which grows on methyl tert-butyl ether (MTBE) and on tert-butyl alcohol (TBA), the main intermediate of MTBE degradation, also grows on a broad range of n-alkanes (C2 to C16). A single alkB gene copy, encoding a non-heme alkane monooxygenase, was partially amplified from the genome of this bacterium. Its expression
was induced after growth on n-propane, n-hexane, n-hexadecane and on TBA but not after growth on LB. The capacity of other fast-growing mycobacteria to grow on n-alkanes (C1 to C16) and to degrade TBA after growth on n-alkanes was compared to that of M. austroafricanum IFP 2012. We studied M. austroafricanum IFP 2012 and IFP 2015 able to grow on MTBE, M. austroafricanum IFP 2173 able to grow on isooctane, Mycobacterium sp. IFP 2009 able to grow on ethyl tert-butyl ether (ETBE), M. vaccae JOB5 (M. austroaafricanum ATCC 29678) able to degrade MTBE and TBA and M. smegmatis mc2 155 with no known degradation capacity towards fuel oxygenates. The M. austroafricanum strains grew on a broad range of n-alkanes and three were able to degrade TBA after growth on propane, hexane and hexadecane. An alkB gene was partially amplified from the genome of all mycobacteria and a sequence comparison demonstrated a close relationship
among the M. austroafricanum strains. This is the first report suggesting the involvement of an alkane hydroxylase in TBA oxidation, a key step during
MTBE metabolism. 相似文献