model of a complex between the tetrahemic cytochrome c3 and the ferredoxin i from desulfovibrio desulfuricans (norway strain).a three-dimensional model of an electron-transfer complex between the tetrahemic cytochrome c3 and the ferredoxin i from the sulfate-reducing bacterium desulfovibrio desulfuricans (norway strain) has been generated through computer graphics methods. the model is based on the known x-ray structure of the cytochrome and on a model of the ferredoxin that has been derived through computer graphics modeling and energy minimization methods, from the x-ray structure of the homologous ferredoxin from pe ...19882847143
pyruvate dehydrogenase and the path of lactate degradation in desulfovibrio vulgaris miyazaki f.pyruvate dehydrogenase from desulfovibrio vulgaris miyazaki f was partially purified from the soluble fraction of the bacterial sonicate, and characterized. the enzyme catalyzes oxidative decarboxylation of pyruvate to produce acetyl-coa, in contrast to statements in current review articles in which acetyl phosphate is indicated to be a direct decomposition product of pyruvate in sulfate-reducing bacteria. the established reaction stoichiometry is: pyruvate + coa + fmn----acetyl-coa + co2 + fmnh ...19863023304
cytochrome components of nitrate- and sulfate-respiring desulfovibrio desulfuricans atcc 27774.three multiheme c-type cytochromes--the tetraheme cytochrome c3 (molecular weight [mw] 13,500), a dodecaheme cytochrome c (mw 40,800), and a "split-soret" cytochrome c (mw 51,540), which is a dimer with 2 hemes per subunit (mw 26,300)--were isolated from the soluble fraction of desulfovibrio desulfuricans (atcc 27774) grown under nitrate- or sulfate-respiring conditions. two of them, the dodecaheme and the split-soret cytochromes, showed no similarities to any of the c-type cytochromes isolated ...19882848008
on the active sites of the [nife] hydrogenase from desulfovibrio gigas. mössbauer and redox-titration studies.the [nife] hydrogenase isolated from desulfovibrio gigas was poised at different redox potentials and studied by mössbauer spectroscopy. the data firmly establish that this hydrogenase contains four prosthetic groups: one nickel center, one [3fe-xs], and two [4fe-4s] clusters. in the native enzyme, both the nickel and the [3fe-xs] cluster are epr-active. at low temperature (4.2 k), the [3fe-xs] cluster exhibits a paramagnetic mössbauer spectrum typical for oxidized [3fe-xs] clusters. at higher t ...19873027068
low-spin sulfite reductases: a new homologous group of non-heme iron-siroheme proteins in anaerobic bacteria.two new low molecular weight proteins with sulfite reductase activity, isolated from methanosarcina barkeri (dsm 800) and desulfuromonas acetoxidans (strain 5071), were studied by epr and optical spectroscopic techniques. both proteins have visible spectra similar to that of the low-spin sulfite reductase of desulfovibrio vulgaris strain hildenborough and no band at 715 nm, characteristic of high-spin fe3+ complexes in isobacteriochlorins is observed. epr shows that as isolated the siroheme is i ...19863028382
epr-detectable redox centers of the periplasmic hydrogenase from desulfovibrio vulgaris.the periplasmic hydrogenase of desulfovibrio vulgaris (hildenbourough ncib 8303) belongs to the category of [fe] hydrogenase which contains only iron-sulfur clusters as its prosthetic groups. amino acid analyses were performed on the purified d. vulgaris hydrogenase. the amino acid composition obtained compared very well with the result derived from the nucleotide sequence of the structural gene (voordouw, g., brenner, s. (1985) eur. j. biochem. 148, 515-520). detailed epr reductive titration st ...19882848804
analysis of the active center of hydrogenase from desulfovibrio vulgaris miyazaki by magnetic measurements.hydrogenase [hydrogen: ferricytochrome c3 oxidoreductase, ec] solubilized and purified from the particulate fraction of desulfovibrio vulgaris miyazaki f (iam 12604) contains 8 iron and 8 labile sulfide ions in one molecule which is composed of two unequal subunits (mr: 60,000 + 29,000). it does not contain nickel atoms. the epr (electron paramagnetic resonance) spectrum has an isotropic signal at g = 2.017 which is independent of the temperature. the peak-to-peak width of the signal is ...19852987196
electron paramagnetic resonance studies on the mechanism of activation and the catalytic cycle of the nickel-containing hydrogenase from desulfovibrio gigas.desulfovibrio gigas hydrogenase (ec is a complex enzyme containing one nickel, one 3fe, and two [fe4s4] clusters (teixeira, m., moura, i., xavier, a. v., der vartanian, d. v., legall, j., peck, h. d., jr., huynh, b. h., and moura, j. j. g. (1983) eur. j. biochem. 130, 481-484). this hydrogenase belongs to a class of enzymes that are inactive "as isolated" (the so-called "oxygen-stable hydrogenases") and must go through an activation process in order to express full activity. the state ...19852991227
direct electron transfer reactions of cytochrome c553 from desulfovibrio vulgaris hildenborough at indium oxide electrodes.the direct, heterogeneous, electron transfer reactions of cytochrome c553 from desulfovibrio vulgaris hildenborough have been studied at indium oxide optically transparent electrodes. these reactions have been studied using cyclic voltammetry and derivative cyclic voltabsorptometry and the kinetics of heterogeneous electron transfer is quasi-reversible. the thermodynamics and kinetics of electron transfer by this molecule can be studied at this electrode surface without the need for surface modi ...19873036137
inhibition studies of three classes of desulfovibrio hydrogenase: application to the further characterization of the multiple hydrogenases found in desulfovibrio vulgaris hildenborough.the three types of hydrogenase hitherto characterized in genus desulfovibrio exhibit distinctive inhibition patterns of their proton-deuterium exchange activity by co, no and no2-. the (fe) and (nifese) hydrogenases are the most sensitive to all three inhibitors while the (nife) enzymes, relatively little inhibited by co, are still very sensitive to no but unaffected by no2-. these differences together with some specific catalytic properties, in particular the ph profile and the h2 to hd ratio i ...19873038102
characterization and complete amino acid sequence of ferredoxin ii from desulfovibrio vulgaris of 2 ferredoxins, fd ii, purified from desulfovibrio vulgaris miyazaki (dvm) has been characterized and its complete amino acid sequence established. fd ii is composed of 63 amino acid residues and contains 7 cysteinyl residues but has only 4 iron atoms in an iron-sulfur cluster of a standard redox potential of -405 mv. the arrangement of cysteinyl residues in the protein suggests that some cysteinyl residues are not directly involved in ligation to the iron-sulfur cluster. homology is recog ...19882855025
nucleotide sequence of the genetic loci encoding subunits of bradyrhizobium japonicum uptake indispensable part of the hydrogen-recycling system in bradyrhizobium japonicum is the uptake hydrogenase, which is composed of 34.5- and 65.9-kda subunits. the gene encoding the large subunit is located on a 5.9-kilobase fragment of the h2-uptake-complementing cosmid phu52 [zuber, m., harker, a.r., sultana, m.a. & evans, h.j. (1986) proc. natl. acad. sci. usa 83, 7668-7672]. we have now determined that the structural genes for both subunits are present on this fragment. two open reading fram ...19883054886
cloning and sequencing of the genes encoding the large and the small subunits of the h2 uptake hydrogenase (hup) of rhodobacter capsulatus.the structural genes (hup) of the h2 uptake hydrogenase of rhodobacter capsulatus were isolated from a cosmid gene library of r. capsulatus dna by hybridization of bradyrhizobium japonicum. the r. capsulatus genes were localized on a 3.5 kb hindiii fragment. the fragment, cloned onto plasmid pac76, restored hydrogenase activity and autotrophic growth of the r. capsulatus mutant jp91, deficient in hydrogenase activity (hup-). the nucleotide sequence, determined by the dideoxy chain termination me ...19883067084
metabolic diversity among the dissimilatory sulfate-reducing bacteria. albert jan kluyver memorial lecture. 19892679377
on the anomalous temperature behaviour of the epr signal of monovalent nickel in hydrogenase.the dependence on temperature in the range between 4.2 k and 20 k was measured for the epr signal of monovalent nickel in h2-reduced hydrogenase from chromatium vinosum and from methanobacterium thermoautotrophicum. in accordance with measurements on the hydrogenase from desulfovibrio gigas [teixeira, m., moura, i., xavier, a. v., huynh, b. h., dervartanian, d. v., peck, h. d., jr, legall, j. and moura, j. j. g. (1985) j. biol. chem. 260, 8942-8950; and cammack, r., patil, d. s. and fernandez, v ...19872826142
activation and deactivation of the membrane-bound hydrogenase from desulfovibrio desulfuricans, norway strain.the hydrogenase from d. desulfuricans, when isolated in air, had a low activity in the hydrogen-methyl viologen reductase assay, and no activity in the hydrogen-methylene blue reductase assay. the activity increased markedly during incubation under hydrogen. this process is interpreted in terms of conversion of the enzyme from a relatively inactive unready state to the active state. oxidation by dichloro-indophenol caused conversion to a state in which the hydrogen-uptake activity to methyl viol ...19863015248
isolation, amino acid analysis and n-terminal sequence determination of the two subunits of the nickel-containing hydrogenase of desulfovibrio gigas.the two subunits of the nickel-iron hydrogenase from desulfovibrio gigas have been purified by preparative sodium dodecyl sulfate polyacrylamide gel electrophoresis and their amino acid compositions have been determined. the n-terminal sequences for 15 residues of the large subunit (mr 62,000) and 25 residues of the small subunit (mr 26,000), respectively, were established. the occurrence of several cysteine residues in the small subunit is discussed in relation with their possible role in the b ...19883134950
cloning, nucleotide sequence, and expression of the flavodoxin gene from desulfovibrio vulgaris (hildenborough).the gene coding for the flavodoxin protein from desulfovibrio vulgaris (hildenborough) has been identified, cloned, and sequenced. dna fragments containing the flavodoxin gene were identified by hybridization of a mixed synthetic heptadecanucleotide probe to southern blots of sali-digested genomic dna. the nucleotide sequences of the probe were derived from the published protein primary structure (dubourdieu, m., legall, j., and fox, j. l. (1973) biochem. biophys. res. commun. 52, 1418-1425). th ...19883170590
the ph dependence of proton-deuterium exchange, hydrogen production and uptake catalyzed by hydrogenases from sulfate-reducing bacteria.different patterns have been found in the ph dependence of hydrogenase activity with enzymes purified from different species of desulfovibrio. with the cytoplasmic hydrogenase from desulfovibrio baculatus strain 9974, the ph optima in h2 production and uptake were respectively 4.0 and 7.5 with a higher activity in production than in uptake. the highest d2-h+ exchange activity was found also at ph 4.0 but the optima differed for the hd and the h2 components. both similarly rose when the ph decrea ...19863015249
occurrence of sulphate-reducing bacteria in human faeces and the relationship of dissimilatory sulphate reduction to methanogenesis in the large gut.sulphate-reducing bacteria (srb) were enumerated in 40 faecal samples obtained from two different human populations in the united kingdom and rural south africa. species able to metabolize acetate, lactate, propionate, butyrate, h2/co2, succinate, pyruvate, valerate, ethanol and a glutamate/serine/alanine mixture were found in faeces from both populations. although a variety of nutritionally and morphologically distinct species of srb belonging to the genera desulfotomaculum, desulfobacter, desu ...19883204069
[evolution of sulfate respiration and cytochrome]. 19852999878
crystallization and preliminary x-ray diffraction study of a protein with a high potential rubredoxin center and a hemerythrin-type fe center.a newly discovered iron-containing protein, isolated from the bacterium desulfovibrio vulgaris (hildenborough, ncib 8303), has been crystallized. the molecule appears to be a dimer of mass 44kda. this protein has iron centers with spectrascopic similarities to those in rubredoxins and in hemerythrins. the x-ray diffraction shows symmetry consistent with space group i222 or i212121. cell parameters are a = 49.2 a, b = 81.3 a, c = 100.1 a, and alpha, beta, gamma = 90 degrees. x-ray diffraction dat ...19883255104
purification of a hexaheme cytochrome c552 from escherichia coli k 12 and its properties as a nitrite reductase.anaerobic cytochrome c552 was purified to electrophoretic homogeneity by ion-exchange chromatography and gel filtration from a mutant of escherichia coli k 12 that synthesizes an increased amount of this pigment. several molecular and enzymatic properties of the cytochrome were investigated. its relative molecular mass was determined to be 69 000 by sodium dodecyl sulfate/polyacrylamide gel electrophoresis. it was found to be an acidic protein that existed in the monomeric form in the native sta ...19863002798
redox properties and activity studies on a nickel-containing hydrogenase isolated from a halophilic sulfate reducer desulfovibrio salexigens.a soluble hydrogenase from the halophilic sulfate reducing bacterium desulfovibrio salexigens, strain british guiana (ncib 8403) has been purified to apparent homogeneity with a final specific activity of 760 mumoles h2 evolved/min/mg (an overall 180-fold purification with 20% recovery yield). the enzyme is composed of two non-identical subunits of molecular masses 62 and 36 kda, respectively, and contains approximately 1 ni, 12-15 fe and 1 se atoms/mole. the hydrogenase shows a visible absorpti ...19863015250
reversible activation of hydrogenase from escherichia coli.hydrogenase from escherichia coli exhibited low activity when assayed for hydrogen:methyl viologen reductase activity and no activity when assayed for hydrogen-uptake activity with acceptors of high redox potential (dichloroindophenol, methylene blue). nor did the enzyme as isolated catalyse proton-tritium exchange activity. incubation under hydrogen resulted in an increase in hydrogen-uptake activity with methyl viologen and the appearance of hydrogen-uptake activity with dichloroindophenol and ...19873297695
activation and active sites of nickel-containing hydrogenases.hydrogenases that contain nickel and iron-sulphur clusters also have a regulatory mechanism, by which exposure to oxidants such as oxygen prevents their reaction with hydrogen. treatment with reducing agents then causes reactivation. in some hydrogenases from desulfovibrio species, there is evidence that there are at least two different deactivated states, which differ in their rates of reductive reactivation. the membrane-bound hydrogenase of d. desulfuricans, norway strain, the periplasmic hyd ...19863015251
hydrogenase activity in aged, nonviable desulfovibrio vulgaris cultures and its significance in anaerobic biocorrosion.batch cultures of desulfovibrio vulgaris stored at 32 degrees c for 10 months have been found to retain 50% of the hydrogenase activity of a 1-day culture. the hydrogenase found in old cultures needs reducing conditions for its activation. viable cell counts are negative after 6 months, showing that the hydrogenase activity does not depend on the presence of viable cells. these observations are of importance in the understanding of anaerobic biocorrosion of metals caused by depolarization phenom ...19873310883
cloning and sequencing of the genes encoding the large and small subunits of the periplasmic (nifese) hydrogenase of desulfovibrio baculatus.the genes coding for the large and small subunits of the periplasmic hydrogenase from desulfovibrio baculatus have been cloned and sequenced. the genes are arranged in an operon with the small subunit gene preceding the large subunit gene. the small subunit gene codes for a 32 amino acid leader sequence supporting the periplasmic localization of the protein, however no ferredoxin-like or other characteristic iron-sulfur coordination sites were observed. the periplasmic hydrogenases from d. bacul ...19873316183
uncommonly encountered, motile, anaerobic gram-negative bacilli associated with infection.motile, anaerobic gram-negative bacilli belonging to the genera butyrivibrio, succinimonas, succinivibrio, anaerovibrio, wolinella, campylobacter, desulfovibrio, selenomonas, and anaerobiospirillum are being recognized in clinical specimens with increasing frequency. over a 12.5-year period at the va wadsworth medical center, 13 clinical specimens yielded one of these organisms. six isolates were recovered from infected wounds, five from respiratory tract specimens obtained from patients with an ...19873321364
characterization of the soluble hydrogenase from desulfovibrio africanus.the soluble hydrogenase from desulfovibrio africanus has been isolated and characterized. the enzyme consists of two subunits of 65 kda and 27 kda. its absorption spectrum is typical of an iron-sulfur protein. the protein contains 12 iron atoms, 10 labile sulfur atoms and 0.9 nickel atom per molecule. d. africanus hydrogenase is rapidly activated under reducing conditions and exhibits a specific activity of 570 mumoles h2 evolved/min/mg. the epr spectrum of the oxidized enzyme shows no ni(iii) s ...19863021136
cloning, characterization, and sequencing of the genes encoding the large and small subunits of the periplasmic [nife]hydrogenase of desulfovibrio gigas.the structural genes for the large and small subunits of desulfovibrio gigas periplasmic [nife]hydrogenase were identified and isolated by immunological and oligonucleotide screening. the gene for the small subunit codes for a 266-amino-acid, 28,724-dalton polypeptide which is separated by 63 nucleotides from the large subunit gene that codes for a 560-amino-acid, 61,707-dalton polypeptide. a putative signal peptide precedes the small subunit coding region, which may direct transport of the enzy ...19873322743
cloning the ddei restriction-modification system using a two-step method.ddei, a type ii restriction-modification system from the gram-negative anaerobic bacterium desulfovibrio desulfuricans, recognizes the sequence ctnag. the system has been cloned into e. coli in two steps. first the methylase gene was cloned into pbr322 and a derivative expressing higher levels was constructed. then the endonuclease gene was located by southern blot analyses; bamhi fragments large enough to contain the gene were cloned into pacyc184, introduced into a host containing the methylas ...19863022241
preliminary x-ray studies of the tetra-heme cytochrome c3 and the octa-heme cytochrome c3 from desulfovibrio gigas.a tetra-heme and an octa-heme cytochrome c3 from the sulfate bacterium desulfovibrio gigas have been crystallized. diffraction quality crystals of the tetra-heme cytochrome are obtained from solution by the addition of polyethylene glycol at ph 6.5. the crystals are orthorhombic, space group p2(1)2(1)2 with unit cell parameters a = 42.27 a, b = 52.54 a and c = 52.83 a. the octa-heme cytochrome crystals develop from low ionic strength solutions of phosphate or tris-cl in the ph range 6.2-7.6. the ...19863025018
purification and characterization of desulfovibrio vulgaris (hildenborough) hydrogenase expressed in escherichia coli.hydrogenase from desulfovibrio vulgaris (hildenborough) is a heterologous dimer of molecular mass 46 + 13.5 kda. its two structural genes have been cloned on a 4664-base-pair fragment of known sequence in the vector puc9. expression of hydrogenase polypeptides in escherichia coli transformed with this plasmid is poor (approximately 0.1% w/w of total protein). deletion of up to 1.9 kb of insert dna brings the gene encoding for the large subunit in close proximity to the lac promotor of puc9 and r ...19873028789
characterization of the cytochrome system of a nitrogen-fixing strain of a sulfate-reducing bacterium: desulfovibrio desulfuricans strain berre-eau.two c-type cytochromes were purified and characterized by electron paramagnetic resonance (epr) and nuclear magnetic resonance (nmr) spectroscopic techniques, from the sulfate-reducer nitrogen-fixing organism, desulfovibrio desulfuricans strain berre-eau (ncib 8387). the purification procedures included several chromatographic steps on alumina, carboxymethylcellulose and gel filtration. a tetrahaem and a monohaem cytochrome were identified. the multihaem cytochrome has visible, epr and nmr spect ...19873030740
putative signal peptide on the small subunit of the periplasmic hydrogenase from desulfovibrio vulgaris.we sequenced the nh2 terminus of the large and small subunits of the periplasmic hydrogenase from the sulfate-reducing bacterium desulfovibrio vulgaris (hildenborough) and found that the small subunit lacks a region of 34 nh4-terminal amino acids coded by the gene for the small subunit (g. voordouw and s. brenner, eur. j. biochem. 148:515-520, 1985). we suggest that this region constitutes a signal peptide based on comparison with known procaryotic signal peptides.19863525521
cloning in escherichia coli of genes involved in the synthesis of proline and leucine in desulfovibrio desulfuricans norway.a library of desulfovibrio desulfuricans norway genomic dna was constructed in escherichia coli with pbr322 as vector and plasmids able to complement the proa and leub mutations of the host were screened. it was observed that all the plasmids studied were highly unstable, the insert dna being rapidly lost under non-selective growth conditions. a 2.75 kb dna fragment of d. desulfuricans norway was found to complement e. coli proa, prob and proc deficiencies. from the results of restriction analys ...19873033436
aerobic degradation of choline by proteus mirabilis: enzymatic requirements and pathway.cleavage of choline to trimethylamine and acetaldehyde by extracts of proteus mirabilis requires both particulate and soluble protein fractions, k+, and a bound divalent metal cation. the reaction shows a long lag period, abolished only by preincubation of the particulate fraction in the complete reaction system. the two-carbon fragment produced is acetaldehyde; choline cleavage appears to be tightly coupled to dismutation of the acetaldehyde to ethanol and acetate, as indicated by stimulation b ...19863536045
characterization of a trithionate reductase system from desulfovibrio vulgaris.a trithionate reductase system was isolated and purified from extracts of desulfovibrio vulgaris. this system reduced trithionate to thiosulfate and consisted of two proteins. one was bisulfite reductase, an enzyme that reduces bisulfite to trithionate, and the second component was designated tr-1. both enzymes were required to reduce trithionate to thiosulfate. flavodoxin and cytochrome c3 from d. vulgaris were tested for their ability to function as electron carriers during trithionate reducti ...19852991191
purification and properties of protoporphyrinogen oxidase from an anaerobic bacterium, desulfovibrio gigas.protoporphyrinogen oxidase has been solubilized from plasma membranes of desulfovibrio gigas. the enzyme was purified to apparent homogeneity with single silver-stained protein bands on isoelectric focusing and sodium dodecyl sulfate-polyacrylamide gels. this protoporphyrinogen oxidase has a molecular weight (mr) of 148,000 and is composed of three dissimilar subunits of mrs 12,000, 18,500, and 57,000, which are held together by sulfhydryl bonds. unlike other protoporphyrinogen oxidases, which u ...19873667528
interaction of cellular hydrogenase, cytochrome c3, and desulfoviridin in desulfovibrio vulgaris miyazaki with their antibodies.anti-sera for hydrogenase, cytochrome c3, and desulfoviridin (abbreviated as anti-hyd, anti-c3, and anti-dvn, respectively) were raised in mice, and used to locate these antigens in cells of desulfovibrio vulgaris miyazaki. the activity of the intact cells to absorb h2 with methyl viologen or sulfite as an electron acceptor was cumulatively inhibited by treating the cells with anti-hyd and anti-c3 but unaffected by anti-dvn treatment. the activity of the intact cells to produce h2 from formate w ...19882853157
nickel-[iron-sulfur]-selenium-containing hydrogenases from desulfovibrio baculatus (dsm 1743). redox centers and catalytic properties.the hydrogenase from desulfovibrio baculatus (dsm 1743) was purified from each of three different fractions: soluble periplasmic (wash), soluble cytoplasmic (cell disruption) and membrane-bound (detergent solubilization). plasma-emission metal analysis detected in all three fractions the presence of iron plus nickel and selenium in equimolecular amounts. these hydrogenases were shown to be composed of two non-identical subunits and were distinct with respect to their spectroscopic properties. th ...19873040402
purification and properties of thiosulfate reductase from desulfovibrio vulgaris, miyazaki f.thiosulfate reductase was purified to an almost homogeneous state from desulfovibrio vulgaris, strain miyazaki f, by ammonium sulfate precipitation, chromatography on deae-toyopearl, ultrogel aca 34, and hydroxylapatite, and disc electrophoresis. the specific activity was increased 580-fold over the crude extract. the molecular weight was determined by gel filtration to be 85,000-89,000, differing from those reported for thiosulfate reductases from other desulfovibrio strains. the enzyme had no ...19852993256
crystallographic study of cytochrome c553 from desulfovibrio vulgaris miyazaki.cytochrome c553 from the sulfate-reducing bacterium, desulfovibrio vulgaris miyazaki, has been crystallized. the combination of microdialysis and vapor diffusion allowed successful crystallization. the crystals were of good quality, and useful data were obtained that extended to the nominal resolution of 1.3 a. the space group is p4(3)2(1)2 with cell dimensions of a = b = 42.7 a, c = 103.4 a. more than twenty heavy-atom reagents were screened with the isomorphous replacement technique, and only ...19863009426
epr of a novel high-spin component in activated hydrogenase from desulfovibrio vulgaris (hildenborough).the epr of reoxidized hydrogenase from desulfovibrio vulgaris (h.) has been reinvestigated. in contrast to other workers [(1984) proc. natl. acad. sci. usa 81, 3728-3732] we find the axial signal with g = 2.06; 2.01 to be only a minor component of concentration 0.03 spin/mol. in the spectrum of fully active reoxidized enzyme this signal is overshadowed by a rhombic signal (0.1 spin/mol) with g = 2.11; 2.05; 2.00 reminiscent of the only signal found for other oxidized bidirectional hydrogenases. ...19863011503
the three classes of hydrogenases from sulfate-reducing bacteria of the genus desulfovibrio.three types of hydrogenases have been isolated from the sulfate-reducing bacteria of the genus desulfovibrio. they differ in their subunit and metal compositions, physico-chemical characteristics, amino acid sequences, immunological reactivities, gene structures and their catalytic properties. broadly, the hydrogenases can be considered as 'iron only' hydrogenases and nickel-containing hydrogenases. the iron-sulfur-containing hydrogenase ([fe] hydrogenase) contains two ferredoxin-type (4fe-4s) c ...19883078655
the crystal structure of the three-iron ferredoxin ii from desulfovibrio gigas.the crystal structure of oxidized ferredoxin ii from the sulfate-reducing bacterium desulfovibrio gigas has been determined and refined at 1.7 a resolution. the folding of the polypeptide chain is similar to that of the 2[4fe-4s] ferredoxin in peptococcus aerogenes, except for an extended helical segment near the c-terminus. the single [3fe-4s] cluster in d. gigas is similar to a [4fe-4s] cluster, but lacks one fe atom and is coordinated to cys-8, -14 and -50. the side chain of cys-11 is not bou ...19892920839
purification and properties of the membrane-associated coenzyme f420-reducing hydrogenase from methanobacterium formicicum.the membrane-associated coenzyme f420-reducing hydrogenase of methanobacterium formicicum was purified 87-fold to electrophoretic homogeneity. the enzyme contained alpha, beta, and gamma subunits (molecular weights of 43,000, 36,700, and 28,800, respectively) and formed aggregates (molecular weight, 1,020,000) of a coenzyme f420-active alpha 1 beta 1 gamma 1 trimer (molecular weight, 109,000). the hydrogenase contained 1 mol of flavin adenine dinucleotide (fad), 1 mol of nickel, 12 to 14 mol of ...19892738024
a reversible effect of low carbon monoxide concentrations on the epr spectra of the periplasmic hydrogenase from desulfovibrio vulgaris.the effect of low concentrations of co (0.93 - 5.58 microm) on the epr spectrum of the periplasmic non-heme iron hydrogenase from d. vulgaris has been investigated. the "g = 2.06" epr signal is maximally induced (0.94 spin/molecule) at 46.5 microm co and partial induction of the epr signal could be observed at 0.93 microm co. this effect is reversed by removal of the co or irradiation of the hydrogenase with white light.19863015136
on the novel h2-activating iron-sulfur center of the "fe-only" hydrogenases.the two hydrogenases (i and ii) of the anaerobic n2-fixing bacterium clostridium pasteurianum (cp) and the hydrogenases of the anaerobes megasphaera elsdenii (me) and desulfovibrio vulgaris (strain hildenborough, dv), contain iron-sulfur clusters but not nickel. they are the most active hydrogenases known. all four enzymes in their reduced states give rise to epr signals typical of [4fe-4s]1+ clusters but exhibit novel epr signals in their oxidized states. for example, cp hydrogenase i exhibits ...19863015247
amino acid sequence of ferredoxin i from desulfovibrio vulgaris miyazaki.the amino acid sequence of ferredoxin (fd) i, purified from desulfovibrio vulgaris miyazaki, has been established. fd i is strikingly similar to fd iii of d. africanus benghazi with 84% homology. both have the sequence, -cys-x-x-asp-x-x-cys-x-x-x-cys-pro- in the n-terminal half, and the sequence, -cys-x-x-cys-x-x-cys-x-x-x-cys-glu- in the c-terminal half of the molecule, instead of the common sequences for ligation to the usual [4fe-4s] clusters. fd i has 76% homology to fd ii of d. desulfurican ...19883182762
use of a three-stage continuous culture system to study the effect of mucin on dissimilatory sulfate reduction and methanogenesis by mixed populations of human gut bacteria.a mixed culture of human fecal bacteria was grown for 120 days in a three-stage continuous culture system. to reproduce some of the nutritional and ph characteristics of the large gut, each vessel had a different operating volume (0.3, 0.5, and 0.8 liter) and ph (6.0, 6.5, and 7.0). a mixture of polysaccharides and proteins was used as carbon and nitrogen sources. measurements of h2, ch4, s2-, sulfate reduction rates, sulfate-reducing bacteria (srb), and volatile fatty acids were made throughout ...19883214155
the base sequence of the niff gene of klebsiella pneumoniae and homology of the predicted amino acid sequence of its protein product to other flavodoxins.the nucleotide sequence of a 629 base-pair segment of dna spanning the niff gene of klebsiella pneumoniae is presented. the structural gene comprises 531 base-pairs (175 codons, excluding the translational initiator and terminator) encoding an acidic polypeptide of 18950 da. the niff product thus belongs to the long-chain class of flavodoxins. it shows some sequence homology to the short-chain flavodoxins from desulfovibrio vulgaris, clostridium mp and megasphaera elsdenii, and much stronger hom ...19853911951
electron transfer between the hydrogenase from desulfovibrio vulgaris (hildenborough) and viologens. 1. investigations by cyclic voltammetry.the electron transfer kinetics between the hydrogenase from desulvovibrio vulgaris (strain hildenborough) and three different viologen mediators has been investigated by cyclic voltammetry. the mediators methyl viologen, di(n-aminopropyl) viologen and propyl viologen sulfonate differ in redox potential and in net charge. dependent on the ph both the one- and two-electron-reduced forms or only the two-electron-reduced form of the viologens are effective in electron exchange with hydrogenase. calc ...19883289919
new perspectives on bacterial ferredoxin evolution.recent evidence indicates that a gene transposition event occurred during the evolution of the bacterial ferredoxins subsequent to the ancestral intrasequence gene duplication. in light of this new information, the relationships among the bacterial ferredoxins were reexamined and an evolutionary tree consistent with this new understanding was derived. the bacterial ferredoxins can be divided into several groups based on their sequence properties; these include the clostridial-type ferredoxins, t ...19853932661
electron transfer between the hydrogenase from desulfovibrio vulgaris (hildenborough) and viologens. 2. investigations by chronoamperometry.the electron transfer kinetics between the hydrogenase from desulfovibrio vulgaris (strain hildenborough) and the mediators methyl viologen, di-(n-aminopropyl) viologen and propyl viologen sulfonate have been investigated by chronoamperometry. second-order rate constants were calculated on basis of the theory for a simple catalytic mechanism and are compared with the results obtained before by cyclic voltammetry (preceding paper in this journal). from the ionic-strength dependence and the observ ...19883289920
crystallization, preliminary x-ray study and crystal activity of the hydrogenase from desulfovibrio gigas.hydrogenase (ec 1.12) from desulfovibrio gigas is a dimeric enzyme (26 and 62 (x 10(3) mr) that catalyzes the reversible oxidation of molecular hydrogen. single crystals of hydrogenase have been produced using the hanging drop method, with either peg (polyethylene glycol) 6000 or ammonium sulfate as precipitants at ph 6.5. x-ray examination of the crystals indicates that those obtained with ammonium sulfate are suitable for structure determination to at least 3.0 a resolution when synchrotron ra ...19873309347
oxidation of protoporphyrinogen in the obligate anaerobe desulfovibrio gigas.the anaerobic oxidation of protoporphyrinogen to protoporphyrin was demonstrated in extracts of desulfovibrio gigas. protoporphyrin formation occurred in the presence of nitrite, hydroxylamine, sulfite, thiosulfate, atp plus sulfate, nad+, nadp+, flavin adenine dinucleotide, flavin mononucleotide, fumarate, 2,6-dichlorophenol-indophenol, methyl viologen, and 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide. with dialyzed cell extracts, highest activities were observed with sulfite, n ...19854044523
identification of three classes of hydrogenase in the genus, desulfovibrio.a comparison of amino-terminal amino acid sequences from the large and small subunits of hydrogenases from desulfovibrio reveals significant differences. these results, in conjunction with antibody analyses, clearly indicate that the iron, iron + nickel, and iron + nickel + selenium containing hydrogenases represent three distinct classes of hydrogenase in desulfovibrio.19873322275
purification and characterization of ferredoxin from desulfovibrio vulgaris miyazaki.two ferredoxins, fd i and fd ii, were isolated and purified from desulfovibrio vulgaris miyazaki. the major component, fd i, is an iron-sulfur protein of mr 12,000, composed of two identical subunits. the absorption spectra of fd i and fd ii have a broad absorption shoulder near 400 nm characteristic of iron-sulfur proteins. the purity index, a400/a280, of fd i is 0.69, and its millimolar absorption coefficient at 400 nm is 3.73 per fe. it contains two redox centers with discrete redox behaviors ...19883360752
fine structural observations of desulfovibrio desulfuricans. 19734123231
morphology of bacteriophage-like particles from desulfovibrio vulgaris.phagelike particles obtained from a mitomycin c-induced lysate of desulfovibrio vulgaris are described. whether they can be classified as temperate bacteriophages or as bacteriocins has not been determined.19734125584
rubredoxin from desulfovibrio gigas. a molecular model of the oxidized form at 1.4 a resolution.the crystal structure of rubredoxin from the sulfate-reducing bacterium desulfovibrio gigas has been determined at 1.4 a resolution (1 a = 0.1 nm) by x-ray diffraction methods; starting with a model of the isostructural rubredoxin from desulfovibrio vulgaris. refinement of the molecular model has been carried out by restrained least-squares techniques and fourier series calculations. the present model includes a formyl at the n-terminal end and 121 possible sites for solvent molecules with full ...19873441010
contamination of chrome-tanned leather by desulfovibrio. 19664161880
n-terminal amino acid sequences of azotobacter vinelandii and rhodospirillum rubrum flavodoxins. 19744212186
dinitrophenol-stimulated adenosine triphosphatase activity in extracts of desulfovibrio gigas.a dinitrophenol (dnp)-stimulated adenosine triphosphatase (atpase) has been found in both the soluble and particulate fractions of the anaerobic sulfate-reducing bacterium, desulfovibrio gigas. as the soluble atpase was labile to storage, only the particulate enzyme was studied in detail. it was optimally stimulated by dnp at 4 mm, and activity was insensitive to inhibition by ouabain. the atpase was stimulated by both ca(2+) and mg(2+), but the magnitude of the stimulation was dependent upon ph ...19714254119
purification and properties of l-alanine dehydrogenase from desulfovibrio desulfuricans.the l-alanine dehydrogenase from cell-free extracts of desulfovibrio desulfuricans was purified approximately 56-fold. the michaelis constants for the substrates of the amination reaction and the ph optima for the reactions catalyzed by this enzyme closely agree with those reported for other l-alanine dehydrogenases. pyruvate was found to inhibit the amination reaction. the enzyme was absolutely specific for l-alanine and nicotinamide adenine dinucleotide. its sensitivity to para-chloromecuriben ...19684298732
[photochemical and enzymatic reduction of flavodoxin isolated from desulfovibrio gigas]. 19684302850
rubredoxin from a nitrogen-fixing variety of desulfovibrio desulfuricans. 19684303402
menadione reductase from desulfovibrio gigas. 19704318157
homology of ribosomal ribonucleic acid of desulfovibrio species with desulfovibrio vulgaris.three species of desulfovibrio were found to have a high degree of ribosomal ribonucleic acid homology with desulfovibrio vulgaris. desulfotomaculum nigrificans, which is also a sulfate-reducing anaerobe, had only 38% ribosomal ribonucleic acid homology with d. vulgaris. the homologies of six other unrelated genera were determined and found to be lower than 50%.19714326740
electron paramagnetic resonance and light absorption studies on c-type cytochromes of the anaerobic sulfate reducer desulfovibrio. 19714330153
evidence for the involvement of non-heme iron in the active site of hydrogenase from desulfovibrio vulgaris. 19714330154
electron paramagnetic resonance studies on the reaction of exogenous ligands with cytochrome c 3 from desulfovibrio vulgaris. 19714330631
the evolution of prokaryotic ferredoxins--with a general method correcting for unobserved substitutions in less branched lineages.thirty-one bacterial type ferredoxins were examined by means of the parsimony method for their phylogenetic implications. the results show reasonable relationships in that photosynthetic, thermophilic, and desulfovibrio groups are identifiable; but a number of interesting anomalies occur. these include a methanogen sequence that clusters among the desulfovibrios. there are several differences from the phylogeny of woese. at least two duplications producing paralogous genes are demonstrated, plus ...19873447013
electrophoretic characterization of atp-sulfate adenylytransferase (atp-sulfurylase) using acrylamide gels. 19724339369
biochemical studies on sulfate-reducing bacteria. xii. some properties of flavodoxin from desulfovibrio vulgaris. 19734350899
kinetic studies on hydrogenase. parahydrogen-orthohydrogen conversion and hydrogen-deuterium exchange reactions. 19734352847
an iron tetrahydroporphyrin prosthetic group common to both assimilatory and dissimilatory sulfite reductases. 19734354952
rapid electrocatalytic procedure for hydrogenase kinetic determination in the h2 evolution direction.the linear sweep voltammetric method is used as a new approach for kinetic determination with enzymes accepting reversible redox couples as cosubstrate. a monolayer of hydrogenase molecules is grafted onto a glassy carbon electrode which is both the support of the enzyme and the detector of the activity. reduced viologen concentration in the enzyme microenvironment is controlled by the electrode potential. the catalytic current produced by the enzyme allows an easy kinetic constant determination ...19863516152
a monomolecular electron transfer chain: structure and function of cytochrome c3. 19744364940
proton magnetic resonance studies of desulfovibrio cytochromes c3. 19744365252
biochemical studies on sulfate-ruducing bacteria. 8. sulfite reductase from desulfovibrio vulgaris--mechanism of trithionate, thiosulfate, and sulfide formation and enzymatic properties. 19744365884
the presence of multiple intrinsic membrane nickel-containing hydrogenases in desulfovibrio vulgaris (hildenborough).three intrinsic membrane proteins exhibiting oxygen stable hydrogenase activity have been isolated from d. vulgaris. in contrast to the periplasmic exclusively non-heme iron hydrogenase, all three hydrogenases contain ni in addition to non-heme iron, have low specific activities and are insensitive to inhibition by co. none of the three hydrogenases cross react with iga against the periplasmic hydrogenase of d. vulgaris but two of the new hydrogenases cross react with iga against the periplasmic ...19863533065
[partial purification and study of nad:rubredoxin oxidoreductase from d. gigas]. 19684384975
[study of the metabolism of dicarboxylic acids and of pyruvate in sulfo-reducing bacteria. i. study of the enzyme oxidation of fumarate in acetate]. 19704392009
reduction of alkyl hydroperoxides to alcohols: role of rubredoxin, an electron carrier in the bacterial hydroxylation of hydrocarbons. 19714399432
light induced h2 evolution in a hydrogenase-tio2 particle system by direct electron transfer or via rhodium complexes.three different hydrogenases (isolated from clostridium pasteurianum, desulfovibrio desulfuricans strain norway 4 and d. baculatus 9974) added to a suspension of tio2 (anatase) powder are able to catalyze h2 evolution under band gap illumination of the semiconducting particles, and in the presence of edta or methanol as electron donor. this h2 production can be obtained by the direct electron transfer from the conduction band of the tio2 particles to the active site of the enzyme at phs higher t ...19863089310
differential inhibition of catalytic sites in desulfovibrio gigas hydrogenase.the hydrogenase of desulfovibrio gigas has been shown to contain one nickel atom, a cluster with three irons and two clusters of the [4fe-4s] type in an 89 kda molecule. though evidence that the nickel ion is involved in the site of hydrogen activation has been presented for this and other hydrogenases, the role of nickel and of the other redox centres in the protein remains to be firmly identified. we have examined the effects of inhibitors of hydrogenase activity in an attempt to identify the ...19863089313
single crystals of hydrogenase from desulfovibrio vulgaris miyazaki f.the hydrogenase solubilized from the particulate fraction from desulfovibrio vulgaris miyazaki f (iam 12604) has been crystallized. although the solubilized hydrogenase purified by the previous method (yagi, t., kimura, k., daidoji, h., sakai, f., tamura, s., and inokuchi, h. (1976) j. biochem. (tokyo) 79,661-671) revealed a single band upon disc electrophoresis, it could not be crystallized. the apparently homogeneous hydrogenase has been separated into three components of similar molecular wei ...19873546297
spectroscopic properties of siroheme extracted from sulfite reductases.siroheme has been extracted from sulfite reductases and its properties in aqueous solution have been investigated by optical absorption, electron paramagnetic resonance (epr), and magnetic circular dichroism (mdc) spectroscopy. the absorption spectrum of siroheme exhibits a marked ph dependence, and two pk values, 4.2 and 9.0, were determined by ph titration in the range 2-12. the first pk (4.2) is thought to correspond to the ionization of the carboxylic acid side-chains on the tetrapyrrole rin ...19873668524
amino acid sequence of rubredoxin from desulfovibrio desulfuricans strain 27774.the amino acid sequence of a rubredoxin from desulfovibrio desulfuricans (strain 27774) has been determined. comparison with rubredoxins from other species reveals pervasive homology, including the regions known to provide the cysteine ligands to the iron atom in several rubredoxins. neither an extra cysteinyl residue nor a unique histidyl residue in the new sequence is located in the sequence in such a way that, by homology, a functional role in the structure is suggested.19863709804
leaching of 226ra from u mill tailings by sulfate-reducing bacteria.relatively insoluble sulfate precipitates appear to be a major host for ra in sulfuric acid-treated, u mill tailings. the dissolution of such precipitates by natural processes, such as metabolism by sulfate-reducing bacteria (srb), creates the potential for release of ra to contacting waters. significant leaching of ra by srb was achieved in the laboratory during the anaerobic incubation (1 to 119 days) of u mill tailings with pure cultures of desulfovibrio desulfuricans and mixed cultures conta ...19863759464
structure of rubredoxin from the bacterium desulfovibrio desulfuricans.the x-ray crystallographic structure of rubredoxin from desulfovibrio desulfuricans strain 27774 is described. this molecule is 15% smaller than previously studied rubredoxins, lacking a seven-residue loop of chain but containing a histidine and a free-sulfhydryl cysteine. except for solvent exposure of the single invariant tryptophan, no other major difference occurs in the molecule.19863770211
metabolism of polyethylene glycol by two anaerobic bacteria, desulfovibrio desulfuricans and a bacteroides sp.two anaerobic bacteria were isolated from polyethylene glycol (peg)-degrading, methanogenic, enrichment cultures obtained from a municipal sludge digester. one isolate, identified as desulfovibrio desulfuricans (strain dg2), metabolized oligomers ranging from ethylene glycol (eg) to tetraethylene glycol. the other isolate, identified as a bacteroides sp. (strain pg1), metabolized diethylene glycol and polymers of peg up to an average molecular mass of 20,000 g/mol [peg 20000; ho-(ch2-ch2-o-)nh]. ...19863777930
properties of the complexes of riboflavin 3',5'-bisphosphate and the apoflavodoxins from megasphaera elsdenii and desulfovibrio vulgaris.megasphaera elsdenii and desulfovibrio vulgaris apoflavodoxins have been reconstituted with riboflavin 3',5'-bisphosphate. several biochemical and biophysical properties of the complexes have been investigated and the results are compared with the properties of the native proteins. the dissociation constant of the modified complex of m. elsdenii flavodoxin is increased by a factor of about 23 by comparison with that of the native protein. the rate constant for the formation of the complex of m. ...19863792314
a comparative carbon-13, nitrogen-15, and phosphorus-31 nuclear magnetic resonance study on the flavodoxins from clostridium mp, megasphaera elsdenii, and azotobacter vinelandii.the flavodoxins from megasphaera elsdenii, clostridium mp, and azotobacter vinelandii were studied by 13c, 15n, and 31p nmr techniques by using various selectivity enriched oxidized riboflavin 5'-phosphate (fmn) derivatives. it is shown that the pi electron distribution in protein-bound flavin differs from that of free flavin and depends also on the apoflavoprotein used. in the oxidized state clostridium mp and m. elsdenii flavodoxins are very similar with respect to specific hydrogen bond inter ...19863801391
properties of a hydrogen-inhibited mutant of desulfovibrio desulfuricans atcc 27774.a mutant of desulfovibrio desulfuricans atcc 27774 has been obtained which is incapable of sulfate respiration with molecular hydrogen but which grows normally on lactate plus sulfate under argon. growth characteristics of the mutant suggest that the defect is involved in electron transfer to sulfate or nitrate but not thiosulfate.19873818548
cloning of the gene encoding the hydrogenase from desulfovibrio vulgaris (hildenborough) and determination of the nh2-terminal sequence.the gene encoding the hydrogenase from desulfovibrio vulgaris (hildenborough) has been cloned in escherichia coli. d. vulgaris dna was digested with the restriction endonucleases ecori and sali and ligated into the vector puc9 [vieira, j. & messing, j. (1982) gene 19, 259-268], which had been cut with these same enzymes. approximately 9000 recombinant clones were obtained by transformation of e. coli jm 101 followed by growth on rich plates with ampicillin for selection and isopropyl-beta-d-thio ...19853888620
nucleotide sequence of the gene encoding the hydrogenase from desulfovibrio vulgaris (hildenborough).the nucleotide sequence of the 4.7-kb sali/ecori insert of plasmid phv 15 containing the hydrogenase gene from desulfovibrio vulgaris (hildenborough) has been determined with the dideoxy chain-termination method. the structural gene for hydrogenase encodes a protein product of molecular mass 45820 da. the nh2-terminal sequence of the enzyme deduced from the nucleic acid sequence corresponds exactly to the amino acid sequence determined by edman degradation. the nucleic acid sequence indicates th ...19853888621
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