cloning and characterization of the flavodoxin gene from desulfovibrio desulfuricans.the gene coding for the flavodoxin protein from desulfovibrio desulfuricans [essex 6] (atcc 29577) has been cloned and sequenced. the gene was identified on southern blots of hindiii-digested genomic dna by hybridization to the coding region for the flavodoxin from desulfovibrio vulgaris [hildenborough] (krey, g.d., vanin, e.f. and swenson, r.p. (1988) j. biol. chem. 263, 15436-15443). ultimately, a 1.8 kb taqi fragment was cloned which contains an open reading frame of 447 nucleotides coding fo ...19911859847
enzymatic redox chemistry: a proposed reaction pathway for the six-electron reduction of so3(2-) to s2- by the assimilatory-type sulfite reductase from desulfovibrio vulgaris (hildenborough).a detailed reaction pathway for the six-electron reduction of so3(2-) to s2- by the assimilatory-type sulfite reductase (sir) from desulfovibrio vulgaris (hildenborough) has been deduced from experiments with 35s-labeled enzyme and the relative reaction rates of nitrogenous substrates. the ligand bridging the prosthetic [fe4s4]-siroheme center is apparently exchanged by 35s2- in both oxidized and reduced enzyme. this 35s2- label was retained in the course of so3(2-) reduction, implicating substr ...19911888748
possible involvement of a l-delta 1-pyrroline-5-carboxylate (p5c) reductase in the synthesis of proline in desulfovibrio desulfuricans norway.a l-delta 1-pyrroline-5-carboxylate reductase activity has been detected in crude extracts of desulfovibrio desulfuricans norway. this p5c reductase activity is also found when a 2.5 kb d. desulfuricans dna fragment is introduced into an escherichia coli proc mutant. although it restores growth of the proc mutant, the prodd enzyme might be detrimental to the e. coli host since the plasmid carrying the cognate prodd gene is segregated at high rate by the cells but is stabilized by small deletions ...19911898390
cloning, expression, and sequence analysis of the genes for carbon monoxide dehydrogenase of methanothrix soehngenii.the cdha and cdhb genes that code for the large and the small subunits of carbon monoxide dehydrogenase (cdh), respectively, were isolated from a genomic library of methanothrix soehngenii dna in escherichia coli, using polyclonal antibodies raised against purified cdh. after introduction in e. coli or desulfovibrio vulgaris, the cdh genes appeared to be expressed irrespective of their orientation, yielding immunoreactive proteins of 79 and 19 kda, corresponding in size to the known subunits of ...19911901858
primary structure of hydrogenase i from clostridium pasteurianum.peptides obtained by cleavage of clostridium pasteurianum hydrogenase i have been sequenced. the data allowed design of oligonucleotide probes which were used to clone a 2310-bp sau3a fragment containing the hydrogenase encoding gene. the latter has been sequenced and was found to translate into a protein composed of 574 amino acids (mr = 63,836), including 22 cysteines. c. pasteurianum hydrogenase is homologous to, but longer than, the large subunit of desulfovibrio vulgaris (hildenborough) [fe ...19911911757
primary structure of the assimilatory-type sulfite reductase from desulfovibrio vulgaris (hildenborough): cloning and nucleotide sequence of the reductase gene.the nucleotide sequence encoding the structural gene (651 bp) and flanking regions for the assimilatory-type sulfite reductase from the sulfate-reducing bacterium desulfovibrio vulgaris (hildenborough) was determined after cloning a 1.4 kb hindiii/sali genomic fragment possessing the gene into bluescript pbs(+)ks. the primary structure of the protein was deduced, and the molecular mass of the apoprotein was estimated as 24 kda. the amino acid sequence of the polypeptide shows some similarities a ...19911911781
direct evidence of the metal-free nature of sirohydrochlorin in desulfoviridin.we have obtained direct evidence that the majority of the sirohydrochlorin chromophore in the dissimilatory sulfite reductase desulfoviridin from desulfovibrio gigas, is not associated with any metal. the evidence comes from resonance raman measurements of native and deuterated samples of desulfoviridin. the breathing mode v4 (or v4*) at 1336 cm-1 in the native enzyme is downshifted to 1326 cm-1 upon deuteration. this mode is not sensitive to deuteration if a metal is present at the center of th ...19911911825
in vivo 31p-nmr studies of desulfovibrio species. detection of a novel phosphorus-containing compound.the phosphorus metabolism of sulfate-reducing bacteria was, for the first time, probed by in vivo 31p nmr. a novel phosphoric anhydride diester compound was detected in desulfovibrio desulfuricans atcc 27774 at intracellular concentrations up to 5 mm. the compound has been extracted and partially purified by anion-exchange chromatography and analysed by 31p, 13c and 1h nmr. these studies show that the novel phosphorus-containing compound is formed by five carbon atoms and is probably cyclic, wit ...19911915373
simultaneous combined microbial removal of sulfur dioxide and nitric oxide from a gas stream.a program is under way at the university of tulsa to develop a viable process concept whereby a microbial process can impact on the problem of flue gas desulfurization and nox removal. we have previously reported studies of so2 reduction by desulfovibrio desulfuricans and nox reduction by thiobacillus denitrificans. one potential process concept is the simultaneous combined removal of so2 and nox from cooled flue gas by contact with cultures of sulfate-reducing bacteria (so2----h2s) and t. denit ...19911929381
an economic analysis of microbial reduction of sulfur dioxide as a means of byproduct recovery from regenerable processes for flue gas desulfurization. 19911929382
calcium is required for the reduction of sulfite from hydrogen in a reconstituted electron transfer chain from the sulfate reducing bacterium, desulfovibrio gigas.calcium is found a strong stimulator of sulfite reduction from hydrogen. a coupling protein of molecular weight 65,000 can be isolated from desulfovibrio gigas. it functions in a reconstituted electron transfer chain between hydrogenase and sulfite reductase. its n-terminal sequence shows high homologies with calcium or magnesium binding sites from other calcium-binding proteins.19911930220
cloning and sequencing of the gene for rubrerythrin from desulfovibrio vulgaris (hildenborough).the gene coding for rubrerythrin from the sulfate-reducing bacterium desulfovibrio vulgaris (hildenborough) has been cloned and sequenced. rubrerythrin is known to contain two types of iron sites: one rubredoxin-like fes4 center in each of the two identical subunits and one hemerythrin-like diiron site per dimer [legall, j., et al. (1988) biochemistry 27, 1636-1642]. the gene encodes a polypeptide of 191 amino acids, and a normal ribosome binding site is located 11-6 base pairs upstream from the ...19911932032
marker exchange mutagenesis of the hydn genes in desulfovibrio fructosovorans.a strain of desulfovibrio fructosovorans deleted from the hydn [nife]hydrogenase structural gene was constructed. a plasmid carrying a 7 kb dna fragment on which the hydn gene had been replaced by the npt reporter gene (kanamycin-resistant, knr) was introduced into d. fructosovorans by electroporation. southern analysis of one knr clone demonstrated that the hydn gene had been eliminated by marker exchange. this mutant, which was devoid of the [nife]hydrogenase gene, still showed a 10% residual ...19911943706
intrapeptide sequence homology in rubrerythrin from desulfovibrio vulgaris: identification of potential ligands to the diiron site.two regions in the amino acid sequence of the 21.5 kda subunit of rubrerythrin from desulfovibrio vulgaris (hildenborough) are shown to be homologous. rubrerythrin contains a non-heme, non-sulfur diiron site, and the internally homologous regions share homology with at least one proposed iron binding region of the component a alpha subunit of methane monooxygenase, which also contains a non-heme, non-sulfur diiron site. comparison of the rubrerythrin sequences with those of the b2 subunit of e. ...19911958203
s-class cytochromes c have a variety of folding patterns: structure of cytochrome c-553 from desulfovibrio vulgaris determined by the multi-wavelength anomalous dispersion method.the three-dimensional structure of cytochrome c-553 isolated from sulfate-reducing bacterium, desulfovibrio vulgaris miyazaki f strain, has been determined by the multi-wavelength anomalous dispersion technique with use of synchrotron radiation. the result shows that bacterial s-class cytochromes c have a variety of folding patterns. the relative location of two a-helices at amino- and carboxyl-terminals and the style of bonding to the heme group show "cytochrome c folding," but other regions of ...19901964450
structure of rubredoxin from desulfovibrio vulgaris at 1.5 a resolution.the x-ray model of rubredoxin from desulfovibrio vulgaris has been refined against 1.5 a x-ray diffraction data collected on a diffractometer. the final model comprises 395 non-hydrogen protein atoms, and 180 solvent o atoms. the final r-value for the model with calculated h atom positions included as fixed contributions is 0.098 over all reflections greater than 2 sigma i from infinity to 1.5 a. the error in co-ordinates is estimated to be 0.08 a. the solvent model was twice redetermined during ...19911992166
comparison of the crystal structures of a flavodoxin in its three oxidation states at cryogenic temperatures.the focus of this study has been to determine the conformation of the holoprotein of recombinant flavodoxin from desulfovibrio vulgaris with the fmn in each of its three oxidation states. the structures of the oxidized state of the wild-type flavodoxin at 2.0 a from d. vulgaris was used as a starting model for refinement. diffraction experiments were conducted at low temperature (-150 degrees c) in order to maintain the oxidation state of interest throughout the intensity data collection. yellow ...19912002503
refined crystal structure of ferredoxin ii from desulfovibrio gigas at 1.7 a.the crystal structure of ferredoxin ii from desulfovibrio gigas has been determined using phasing from anomalous scattering data at a resolution of 1.7 a and refined to an r-factor of 0.157. the molecule has an overall chain fold similar to that of the other bacterial ferredoxins of known structure. the molecule contains a single 3fe-4s cluster with geometry indistinguishable from the 4fe-4s clusters, and a disulfide bond near the site corresponding to the position of the second cluster of two-c ...19912056535
redox process of iron-sulfur clusters of the soluble-domain of the membrane-bound hydrogenase from desulfovibrio vulgaris miyazaki f studied by resonance raman spectroscopy.resonance raman spectra of the soluble-domain of a membrane-bound hydrogenase from desulfovibrio vulgaris miyazaki f were recorded in different oxidation states. in the oxidized state, the raman band due to the totally symmetric stretching mode of the iron-sulfur cluster was observed at 341 cm-1, which was attributed to the 3fe-4s cluster. in the hydrogen-reduced state, only a weak and broad band was observed in its vicinity. during the process of reoxidation, a raman band assignable to the 4fe- ...19902081730
characterization of two sulfate-reducing bacteria from the gut of the soil-feeding termite, cubitermes speciosus.two sulfate-reducing bacteria (srb) were isolated from a mixed culture enriched with benzoate obtained from gut homogenate of the soil-feeding higher termite, cubitermes speciosus. the organisms were vibrioid rods, staining gram-negative, which performed incomplete substrate oxidation. they differed in several features. the smaller one, strain stp, was motile with a single polar flagellum. this strain differed from desulfovibrio desulfuricans only by its inability to oxidize malate and pentanol. ...19902082814
the structure of rubredoxin from desulfovibrio desulfuricans strain 27774 at 1.5 a resolution.the structure of a small rubredoxin from the bacterium desulfovibrio desulfuricans has been determined and refined at 1.5 a resolution. the hairpin loop containing seven residues in other rubredoxins is missing in this 45 residue molecule, and once that fact was determined by amino acid sequencing studies, refinement progressed smoothly to an r value of 0.093 for all reflections from 5 to 1.5 a resolution. nearly all of the water molecules in the well-ordered triclinic unit cell have been added ...19902091025
cytoplasmic and periplasmic expression of a synthetic gene for ferredoxin in escherichia coli.a synthetic gene coding for a modified ferredoxin ii of desulfovibrio desulfuricans norway strain was assembled from 10 oligonucleotides. this gene was cloned into various expression vectors allowing either cytoplasmic expression or export to the periplasmic space. in the latter case, two different constructs were made, each of which contained the ompa signal peptide: one of these constructs contained 3 additional n-terminal amino acids as compared to the wild-type ferredoxin (56 amino acid resi ...19902124144
soluble hydrogenase of anabaena cylindrica. cloning and sequencing of a potential gene encoding the tritium exchange subunit.a gene potentially encoding a subunit of the soluble hydrogenase of anabaena cylindrica was isolated from a genomic library by screening with a set of redundant oligonucleotides, the sequence of which was deduced from the amino acid sequence of the purified hydrogenase subunit that catalyses tritium exchange. the nucleotide sequence of the potential gene was determined from two overlapping dna fragments spanning 7237 bp of the a. cylindrica genome. the region sequenced contained an open reading ...19902129525
characterization of the nickel-iron periplasmic hydrogenase from desulfovibrio fructosovorans.the periplasmic hydrogenase from desulfovibrio fructosovorans grown on fructose/sulfate medium was purified to homogeneity. it exhibits a molecular mass of 88 kda and is composed of two different subunits of 60 kda and 28.5 kda. the absorption spectrum of the enzyme is characteristic of an iron-sulfur protein and its absorption coefficients at 400 and 280 nm are 50 and 180 mm-1 cm-1, respectively. d. fructosovorans hydrogenase contains 11 +/- 1 iron atoms, 0.9 +/- 0.15 nickel atom and 12 +/- 1 a ...19902154378
the active centers of adenylylsulfate reductase from desulfovibrio gigas. characterization and spectroscopic order to utilize sulfate as the terminal electron acceptor, sulfate-reducing bacteria are equipped with a complex enzymatic system in which adenylylsulfate (adopso4) reductase plays one of the major roles, reducing adopso4 (the activated form of sulfate) to sulfite, with release of amp. the enzyme has been purified to homogeneity from the anaerobic sulfate reducer desulfovibrio gigas. the protein is composed of two non-identical subunits (70 kda and 23 kda) and is isolated in a multimeric for ...19902158885
estimation of microscopic redox potentials of a tetraheme protein, cytochrome c3 of desulfovibrio vulgaris, miyazaki f, and partial assignments of heme groups.the microscopic formal redox potentials of a tetraheme protein, cytochrome c3 from desulfovibrio vulgaris, miyazaki f, were estimated from the chemical shifts of the heme methyl signals in its 1h nmr spectrum. all chemical shifts in the five macroscopic oxidation states were determined for eight of the heme methyl protons by the saturation-transfer method. the electron-distribution probability at each heme in each oxidation state was estimated directly from the chemical shifts. to minimize error ...19902159795
the iron-sulfur centers of the soluble [nifese] hydrogenase, from desulfovibrio baculatus (dsm 1743). epr and mössbauer characterization.the soluble (cytoplasmic plus periplasmic) ni/fe-s/se-containing hydrogenase from desulfovibrio baculatus (dsm 1743) was purified from cells grown in an 57fe-enriched medium, and its iron-sulfur centers were extensively characterized by mössbauer and epr spectroscopies. the data analysis excludes the presence of a [3fe-4s] center, either in the native (as isolated) or in the hydrogen-reduced states. in the native state, the non-heme iron atoms are arranged as two diamagnetic [4fe-4s]2+ centers. ...19902159882
coordination and redox properties of a novel triheme cytochrome from desulfovibrio vulgaris (hildenborough).a high molecular weight multiheme c-type cytochrome from the sulfate-reducing bacterium desulfovibrio vulgaris (hildenborough) has been spectroscopically characterized and compared with the tetraheme cytochrome c3. the protein contains a pentacoordinate high-spin heme (gz 6.0) and two hexacoordinate low-spin hemes (gz 2.95, gy 2.27, gx 1.48). from analysis of the g values for the low-spin hemes by the procedure of blumberg and peisach (palmer, 1983) and comparison with with the optical spectra f ...19902163671
purification and characterization of bisulfite reductase (desulfofuscidin) from desulfovibrio thermophilus and its complexes with exogenous ligands.a dissimilatory bisulfite reductase has been purified from a thermophilic sulfate-reducing bacterium desulfovibrio thermophilus (dsm 1276) and studied by epr and optical spectroscopic techniques. the visible spectrum of the purified bisulfite reductase exhibits absorption maxima at 578.5, 392.5 and 281 nm with a weak band around 700 nm. photoreduction of the native enzyme causes a decrease in absorption at 578.5 nm and a concomitant increase in absorption at 607 nm. when reduced, the enzyme reac ...19902165817
hexaheme nitrite reductase from desulfovibrio desulfuricans. mössbauer and epr characterization of the heme groups.mössbauer and epr spectroscopy were used to characterize the heme prosthetic groups of the nitrite reductase isolated from desulfovibrio desulfuricans (atcc 27774), which is a membrane-bound multiheme cytochrome capable of catalyzing the 6-electron reduction of nitrite to ammonia. at ph 7.6, the as-isolated enzyme exhibited a complex epr spectrum consisting of a low-spin ferric heme signal at g = 2.96, 2.28, and 1.50 plus several broad resonances indicative of spin-spin interactions among the he ...19902167315
purification and characterization of two proteins with inorganic pyrophosphatase activity from desulfovibrio vulgaris: rubrerythrin and a new, highly active, enzyme.the inorganic pyrophosphatase activity of a soluble extract from the strict anaerobe, sulfate-reducing, desulfovibrio vulgaris, is readily resolved into two peaks. after purification, two active proteins with very dissimilar properties are obtained. one is the non-heme iron-containing rubrerythrin, with a specific activity of 350 pyrophosphate hydrolyzed, min-1, mg protein-1. the other, a protein of mr = 39,000, with a specific activity of 12,000.19902168174
functional expression of desulfovibrio vulgaris hildenborough cytochrome c3 in desulfovibrio desulfuricans g200 after conjugational gene transfer from escherichia coli.plasmid pjrdc800-1, containing the cyc gene encoding cytochrome c3 from desulfovibrio vulgaris subsp. vulgaris hildenborough, was transferred by conjugation from escherichia coli dh5 alpha to desulfovibrio desulfuricans g200. the g200 strain produced an acidic cytochrome c3 (pi = 5.8), which could be readily separated from the hildenborough cytochrome c3 (pi = 10.5). the latter was indistinguishable from cytochrome c3 produced by d. vulgaris subsp. vulgaris hildenborough with respect to a number ...19902170341
single-crystal electron paramagnetic resonance study of cytochrome c3 from desulfovibrio desulfuricans norway strain. assignment of the heme midpoint redox potentials.a single crystal of cytochrome c3 from desulfovibrio desulfuricans norway is studied by electron paramagnetic resonance at low temperature. the orientation of the principal axis corresponding to the largest g value is determined for the 12 heme groups in the crystal unit cell. the comparison of these directions to the normals to the heme planes, determined from the crystallographic data at 2.5 a resolution, gives strong evidence for the following assignment of the midpoint redox potentials to th ...19902172551
the structure and mechanism of iron-hydrogenases.hydrogenases devoid of nickel and containing only fe-s clusters have been found so far only in some strictly anaerobic bacteria. four fe-hydrogenases have been characterized: from megasphaera elsdenii, desulfovibrio vulgaris (strain hildenborough), and two from clostridium pasteurianum. all contain two or more [4fe-4s]1+,2+ or f clusters and a unique type of fe-s center termed the h cluster. the h cluster appears to be remarkably similar in all the hydrogenases, and is proposed as the site of h2 ...19902173950
purification and characterization of desulfoferrodoxin. a novel protein from desulfovibrio desulfuricans (atcc 27774) and from desulfovibrio vulgaris (strain hildenborough) that contains a distorted rubredoxin center and a mononuclear ferrous center.a new type of non-heme iron protein was purified to homogeneity from extracts of desulfovibrio desulfuricans (atcc 27774) and desulfovibrio vulgaris (strain hildenborough). this protein is a monomer of 16-kda containing two iron atoms per molecule. the visible spectrum has maxima at 495, 368, and 279 nm and the epr spectrum of the native form shows resonances at g = 7.7, 5.7, 4.1 and 1.8 characteristic of a high-spin ferric ion (s = 5/2) with e/d = 0.08. mössbauer data indicates the presence of ...19902174880
effect of 17o2 and 13co on epr spectra of nickel in hydrogenase from chromatium vinosum.oxygen, either molecular oxygen or a reduction adduct, can tightly bind in the vicinity of the two forms of trivalent nickel occurring in hydrogenase from chromatium vinosum, as evident from studies with 17o-enriched o2. this oxygen is not in the first coordination sphere of nickel. as has been reported earlier for hydrogenase from desulfovibrio gigas (fernandez, v.m., hatchikian, a.c., patil, d.s. and cammack, r. (1986) biochim. biophys. acta 883, 145-154), also the relative activity of the c.v ...19902176104
the identification, characterization, sequencing and mutagenesis of the genes (hupsl) encoding the small and large subunits of the h2-uptake hydrogenase of azotobacter chroococcum.the structural genes (hupsl) of the membrane-bound nife-containing h2-uptake hydrogenase (hup) of azotobacter chroococcum were identified by oligonucleotide screening and sequenced. the small subunit gene (hups) encodes a signal sequence of 34 amino acids followed by a 310-amino-acid, 34156d protein containing 12 cysteine residues. the large subunit gene (hupl) overlaps hups by one base and codes for a predicted 601-amino-acid, 66433d protein. there are two regions of strong homology with other ...19902215219
a gas chromatographic-mass spectrometric technique for studying simultaneous hydrogen-deuteron exchange and para-orthohydrogen conversion in hydrogenases of desulfovibrio vulgaris original gas chromatographic-mass spectrometric technique is described for studying simultaneous dihydrogen-deuteron exchange and para-ortho h2 conversion catalyzed by different desulfovibrio hydrogenases. para and orthohydrogens are separated on an alumina column at the temperature of liquid nitrogen, but if both hd and ortho h2 are present, their retention times are too close to each other for total separation and only one peak is observed with a thermal conductivity detector. in order to r ...19902221393
cloning and sequencing of the locus encoding the large and small subunit genes of the periplasmic [nife]hydrogenase from desulfovibrio fructosovorans.the genetic locus encoding the periplasmic [nife]hydrogenase (hyd) from desulfovibrio fructosovorans was cloned and sequenced. the genes of this two-subunit enzyme have an operon organization in which the 0.94-kb gene encoding the small subunit precedes the 1.69-kb gene encoding the large subunit. a shine-dalgarno sequence is centered at -9 bp from the atg of both subunits. the possible presence of another open reading frame downstream from the large-subunit-encoding gene is considered. the n-te ...19902227457
the nucleotide sequence of the desulfovibrio gigas desulforedoxin gene indicates that the desulfovibrio vulgaris rbo gene originated from a gene fusion event.expression of the rbo gene from desulfovibrio vulgaris hildenborough in escherichia coli minicells and western blotting (immunoblotting) of desulfovibrio cell extracts with antibodies raised against a synthetic peptide indicated the presence of a 14-kda polypeptide product, as expected from the gene sequence. cloning and sequencing of the gene (dsr) for desulforedoxin, a 4-kda redox protein from desulfovibrio gigas, showed that it is formed by expression of an autonomous gene of 111 bp, not by p ...19902254288
microbial anaerobic respiration. 19902264524
regulation of the hexaheme nitrite/nitric oxide reductase of desulfovibrio desulfuricans, wolinella succinogenes and escherichia coli. a mass spectrometric study.dissimilatory nitrite reduction, carried out by hexaheme proteins, gives ammonia as the final product. representatives of this enzyme group from 3 bacterial species can also reduce no to either ammonia or n2o. the redox regulation of the nitrite/nitric oxide activities is discussed in the context of the denitrifying pathway.19902265715
cloning and sequencing of a [nife] hydrogenase operon from desulfovibrio vulgaris miyazaki f.a hydrogenase operon was cloned from chromosomal dna isolated from desulfovibrio vulgaris miyazaki f with the use of probes derived from the genes encoding [nife] hydrogenase from desulfovibrio vulgaris hildenborough. the nucleic acid sequence of the cloned dna indicates this hydrogenase to be a two-subunit enzyme: the gene for the small subunit (267 residues; molecular mass = 28763 da) precedes that for the large subunit (566 residues; molecular mass = 62495 da), as in other [nife] and [nifese] ...19902269874
time-resolved fluorescence studies of flavodoxin. fluorescence decay and fluorescence anisotropy decay of tryptophan in desulfovibrio flavodoxins.the time-resolved fluorescence characteristics of tryptophan in flavodoxin isolated from the sulfate-reducing bacteria desulfovibrio vulgaris and desulfovibrio gigas have been examined. by comparing the results of protein preparations of normal and fmn-depleted flavodoxin, radiationless energy transfer from tryptophan to fmn has been demonstrated. since the crystal structure of the d. vulgaris flavodoxin is known, transfer rate constants from the two excited states 1la and 1lb can be calculated ...19902307144
identification, sequence determination, and expression of the flavodoxin gene from desulfovibrio salexigens.restriction fragments of genomic dna from desulfovibrio salexigens (atcc 14822) containing the structural gene coding for the flavodoxin protein were identified using the entire coding region of the gene for the desulfovibrio vulgaris (hildenborough) flavodoxin as a probe (krey, g.d., vanin, e.f., and swenson, r.p. (1988) j. biol. chem. 263, 15436-15443). a 1.4-kb psti-hindiii fragment was ultimately identified which contains an open reading frame coding for a polypeptide of 146 amino acid resid ...19902334437
anaerobic degradation of 1,3-propanediol by sulfate-reducing and by fermenting bacteria.three strains of strictly anaerobic gram-negative, non-sporeforming, motile bacteria were enriched and isolated from freshwater sediments with 1,3-propanediol as sole energy and carbon source. strain ottpdl was a sulfate-reducing bacterium which grew also with lactate, ethanol, propanol, butanol, 1,4-butanediol, formate or hydrogen plus co2, the latter only in the presence of acetate. in the absence of sulfate, most of these substrates were fermented to the respective fatty acids in syntrophic c ...19902353806
diversity and origin of desulfovibrio species: phylogenetic definition of a family.the different nutritional properties of several desulfovibrio desulfuricans strains suggest that either the strains are misclassified or there is a high degree of phenotypic diversity within the genus desulfovibrio. the results of partial 16s rrna and 23s rrna sequence determinations demonstrated that desulfovibrio desulfuricans atcc 27774 and "desulfovibrio multispirans" are closely related to the type strain (strain essex 6) and that strains atcc 7757, norway 4, and el agheila z are not. there ...19902361938
effects of substituting asparagine for glycine-61 in flavodoxin from desulfovibrio vulgaris (hildenborough).gly-61 in flavodoxin from desulfovibrio vulgaris (hildenborough) has been changed to asn by site-directed mutagenesis of the cloned gene. values determined for the dissociation constant for the dissociation of the mutant protein into apoprotein and fmn, and for the redox potentials of the two 1-electron steps in the reduction of the bound flavin showed that fmn in all three redox states is bound more weakly in the mutant protein than in the wild-type flavodoxin. however, the greatest effect was ...19902369409
oxidation of benzaldehydes to benzoic acid derivatives by three desulfovibrio strains.desulfovibrio vulgaris marburg, "desulfovibrio simplex" xvi, and desulfovibrio sp. strain mp47 used benzaldehydes such as vanillin, 3,4,5-trimethoxybenzaldehyde, protocatechualdehyde, syringaldehyde, p-anisaldehyde, p-hydroxybenzaldehyde, and 2-methoxybenzaldehyde as electron donors for sulfate reduction and carbon dioxide and/or components of yeast extract as carbon sources for cell synthesis. the aldehydes were oxidized to their corresponding benzoic acids. the three sulfate reducers oxidized ...19902389937
natural relationship between bacteroides and flavobacteria.comparisons among 16s rrna sequences from various eubacteria reveal a natural relationship between the bacteroides (represented by the bacteroides fragilis sequence) and a phylogenetic unit that comprises the flavobacteria, cytophagae, flexibacteria, and others (represented by the flavobacterium heparinum sequence). although the relationship is not a close one, it is, nevertheless, specific. rrnas from these two organisms are not only closer to one another in overall sequence than they are to ou ...19852413007
nucleotide sequence of 5s ribosomal ribonucleic acid from a sulfate-reducing bacterium, desulfovibrio vulgaris. 19862435418
immunological relationship among hydrogenases.we examined the immunological cross-reactions of 11 different hydrogenase antigens with 9 different hydrogenase antibodies. included were antibodies and antigens of both subunits of the hydrogenases of bradyrhizobium japonicum and thiocapsa roseopersicina. the results showed a strong relationship among the ni-fe dimeric hydrogenases. the two subunits of ni-fe dimeric hydrogenases appeared immunologically distinct: specific interactions occurred only when antibodies to the 60- and 30-kilodalton s ...19892464579
characterization of sulfate transport in desulfovibrio desulfuricans.uptake of 35s-labelled sulfate was studied with a new isolate of desulfovibrio desulfuricans, strain csn. micromolar additions of sulfate (1-10 microm or nmol/mg protein) to cell suspensions incubated in 150 mm kcl at -1 degrees c were almost completely taken up and accumulated about 5,000-fold. accumulation was not influenced by incubation in nacl instead of kcl, by acidic ph (5.5) or by incubation under air for 10 min. in alkaline milieu (ph 8.5), after prolonged contact with air (2 h), or aft ...19892476099
natural relationships among sulfate-reducing eubacteria.phylogenetic relationships among 20 nonsporeforming and two endospore-forming species of sulfate-reducing eubacteria were inferred from comparative 16s rrna sequencing. all genera of mesophilic sulfate-reducing eubacteria except the new genus desulfomicrobium and the gliding desulfonema species were included. the sporeforming species desulfotomaculum ruminis and desulfotomaculum orientis were found to be gram-positive organisms sharing 83% 16s rrna sequence similarity, indicating that this genus ...19892480344
mass-spectrometric studies of the interrelations among hydrogenase, carbon monoxide dehydrogenase, and methane-forming activities in pure and mixed cultures of desulfovibrio vulgaris, desulfovibrio desulfuricans, and methanosarcina barkeri.the activities of pure and mixed cultures of desulfovibrio vulgaris and methanosarcina barkeri in the exponential growth phase were monitored by measuring changes in dissolved-gas concentration by membrane-inlet mass spectrometry. m. barkeri grown under h2-co2 or methanol produced limited amounts of methane and practically no hydrogen from either substrate. the addition of co resulted in a transient h2 production concomitant with co consumption. hydrogen was then taken up, and ch4 production inc ...19892508553
evidence for selenocysteine coordination to the active site nickel in the [nifese]hydrogenases from desulfovibrio and se x-ray absorption spectroscopic studies of the [nifese]hydrogenases from desulfovibrio baculatus are described. the ni site geometry is pseudo-octahedral with a coordinating ligand composition of 3-4 (n,o) at 2.06 a, 1-2 (s,cl) at 2.17 a, and 1 se at 2.44 a. the se coordination environment consists of 1 c at 2.0 a and a heavy scatterer m (m = ni or fe) at approximately 2.4 a. these results are interpreted in terms of a selenocysteine residue coordinated to the ni site. the possible role ...19892521386
epr studies with 77se-enriched (nifese) hydrogenase of desulfovibrio baculatus. evidence for a selenium ligand to the active site nickel.the periplasmic hydrogenase containing equivalent amounts of nickel and selenium plus non-heme iron [nifese) hydrogenase) has been purified from cells of the sulfate reducing bacterium desulfovibrio baculatus (dsm 1748) grown on a lactate/sulfate medium containing natural se isotopes and the nuclear isotope, 77se. both the 77se-enriched and unenriched hydrogenases were shown to be free of other hydrogenases and characterized with regard to their se contents. epr studies of the reduced nickel sig ...19892536719
comparative studies of polyhemic cytochromes c isolated from desulfovibrio vulgaris (hildenborough) and desulfovibrio desulfuricans (norway).cytochrome c3 (mr 26,000) has been characterized in desulfovibrio vulgaris (hildenborough) and its properties compared with polyhemic cytochromes c isolated from the same organism and from d. desulfuricans (norway). it can be described as an octaheme cytochrome c3 constituted of two identical subunits. absorption spectrum is similar to cytochrome c3 (mr 13,000) and individual redox potentials have an average value of -180 mv.3 the n terminal sequence is compared with an homologous cytochrome iso ...19892539120
cloning and sequencing of the gene encoding cytochrome c553 from desulfovibrio vulgaris hildenborough.the gene encoding cytochrome c553 from desulfovibrio vulgaris hildenborough was cloned by using two synthetic deoxyoligonucleotide probes. the amino acid sequence derived from the sequence of the gene differs from that reported by bruschi and legall (biochim. biophys. acta 271:48-60, 1972). renewed protein sequencing confirmed the correctness of the dna-derived sequence. the gene sequence indicates cytochrome c553 to be synthesized as a precursor protein with an nh2-terminal signal sequence of 2 ...19892542232
effects of acetylene on hydrogenases from the sulfate reducing and methanogenic bacteria.the effect of acetylene on the activity of the three types of hydrogenase from the anaerobic sulfate reducing bacteria has been investigated. the (fe) hydrogenase is resistant to inhibition by acetylene while the nickel-containing hydrogenases are inhibited by acetylene with the (nife) hydrogenase being 10-50 fold more sensitive than the (nifese) hydrogenase. in addition the ni(iii) epr signal (g approximately 2.3) of the "as isolated" (nife) hydrogenase was significantly decreased in intensity ...19892543405
epr study of the redox interactions in cytochrome c3 from desulfovibrio vulgaris miyazaki.we present a new examination of the epr redox titration data for the tetraheme cytochrome c3 from desulfovibrio vulgaris miyazaki. our analysis includes the contribution of the interaction potentials between the four redox sites and is based on the model previously developed for the study of cytochrome c3 from desulfovibrio desulfuricans norway. we observed, as for d. desulfuricans norway cytochrome c3, that the conformation of the heme with the lowest redox potential, heme 4, is sensitive to th ...19892543574
direct electron transfer of redox proteins at the bare glassy carbon electrode.a simple system is presented for the microscale, direct voltammetry of redox proteins, typically 25 micrograms, in the absence of mediators and/or modifiers. the sample consists of a droplet of anaerobic solution laid onto an oversized disc of nitric-acid-pretreated glassy carbon as the working electrode. very reproducible, nernstian responses are obtained with horse heart cytochrome c. the midpoint potential em (ph 7.0) is dependent on the ionic strength, ranging from $293 mv in 1 mm potassium ...19892546759
bioaccumulation and chemical modification of tc by soil bacteria.bioaccumulation and chemical modification of pertechnetate (tco4-) by aerobically and anaerobically grown soil bacteria and by pure cultures of sulfate-reducing bacteria (desulfovibrio sp.) were studied to gain insight on the possible mechanisms by which bacteria can affect the solubility of tc in soil. aerobically grown bacteria had no apparent effect on tco4-; they did not accumulate tc nor modify its chemical form. anaerobically grown bacteria exhibited high bioaccumulation and reduced tco4-, ...19892547734
analysis of the transcriptional unit encoding the genes for rubredoxin (rub) and a putative rubredoxin oxidoreductase (rbo) in desulfovibrio vulgaris hildenborough.the nucleotide sequence of a 2.0-kilobase-pair ecori restriction fragment upstream from the gene (rub, 162 base pairs) encoding rubredoxin from desulfovibrio vulgaris hildenborough indicates that it is part of a larger transcriptional unit, containing an additional 378-base-pair open reading frame which terminates 16 nucleotides from the translational start of the rub gene and could encode a polypeptide of 14 kilodaltons (kda). northern (rna) blotting of rna isolated from both d. vulgaris hilden ...19892549009
characterization of the flavoprotein moieties of nadph-sulfite reductase from salmonella typhimurium and escherichia coli. physicochemical and catalytic properties, amino acid sequence deduced from dna sequence of cysj, and comparison with nadph-cytochrome p-450 reductase.nadph-sulfite reductase flavoprotein (sir-fp) was purified from a salmonella typhimurium cysg strain that does not synthesize the hemoprotein component of the sulfite reductase holoenzyme. cysj, which codes for sir-fp, was cloned from s. typhimurium lt7 and escherichia coli b, and both genes were sequenced. physicochemical analyses and deduced amino acid sequences indicate that sir-fp is an octamer of identical 66-kda peptides and contains 4 fad and 4 fmn per octamer. potentiometric titrations o ...19892550423
redox intermediates of desulfovibrio gigas [nife] hydrogenase generated under hydrogen. mössbauer and epr characterization of the metal centers.the hydrogenase (ec of desulfovibrio gigas is a complex enzyme containing one nickel center, one [3fe-4s] and two [4fe-4s] clusters. redox intermediates of this enzyme were generated under hydrogen (the natural substrate) using a redox-titration technique and were studied by epr and mössbauer spectroscopy. in the oxidized states, the two [4fe-4s]2+ clusters exhibit a broad quadrupole doublet with parameters (apparent delta eq = 1.10 mm/s and delta = 0.35 mm/s) typical for this type of c ...19892550443
inhibition of desulfovibrio gigas hydrogenase with copper salts and other metal ions.the effect of several transition metals on the activity of desulfovibrio gigas hydrogenase has been studied. co(ii) and ni(ii) at a concentration of 1 mm did not modify the activity of the enzyme; nor did they affect the pattern of activation/deactivation. cu(ii) inhibited the active hydrogenase, prepared by treatment with hydrogen, but had little effect on the 'unready' enzyme unless a reductant such as ascorbate was present, in which case inactivation took place either in air or under argon. h ...19892555191
hydrodynamic, structural and magnetic properties of megasphaera elsdenii fe hydrogenase reinvestigated.megasphaera elsdenii hydrogenase has been purified to homogeneity using an fplc procedure as the final step. the protein gives a single band in sds/page with an apparent molecular mass of 57-59 kda. there is no second hydrogenase activity in the soluble fraction of m. elsdenii. the hydrodynamics of the enzyme have been compared to those of the two-subunit fe hydrogenase from desulfovibrio vulgaris (hildenborough) in the analytical ultracentrifuge using the absorption of the intrinsic iron-sulfur ...19892556270
electron transport in sulfate-reducing bacteria. molecular modeling and nmr studies of the rubredoxin--tetraheme-cytochrome-c3 complex.a hypothetical model of the complex formed between the iron-sulfur protein rubredoxin and the tetraheme cytochrome c3 from the sulfate-reducing bacteria desulfovibrio vulgaris (hildenborough) has been proposed utilizing computer graphic modeling, computational methods and nmr spectroscopy. the proposed complex appears feasible on the basis of complementary electrostatic interaction and steric factors and is consistent with the data from nmr experiments. in this model, the non-heme iron atom of r ...19892556275
electrochemical and spectroscopic characterization of the 7fe form of ferredoxin iii from desulfovibrio africanus.desulfovibrio africanus ferredoxin iii is a monomeric protein (mr 6585) containing seven cysteine residues and 7-8 iron atoms and 6-8 atoms of acid-labile sulphur. it is shown that reversible unmediated electrochemistry of the two iron-sulphur clusters can be obtained by using a pyrolytic-graphite-'edge' carbon electrode in the presence of an appropriate aminoglycoside, neomycin or tobramycin, as promoter. cyclic voltammetry reveals two well-defined reversible waves with e0' = -140 +/- 10 mv and ...19892557831
electrochemical and spectroscopic characterization of the conversion of the 7fe into the 8fe form of ferredoxin iii from desulfovibrio africanus. identification of a [4fe-4s] cluster with one non-cysteine ligand.desulfovibrio africanus ferredoxin iii is a protein (mr 6585) containing one [3fe-4s]1+,0 and one [4fe-4s]2+,1+ core cluster when aerobically isolated. the amino acid sequence contains only seven cysteine residues, the minimum required to ligand these two clusters. cyclic voltammery by means of direct electrochemistry at a pyrolytic-graphite-'edge' electrode promoted by neomycin shows that, when reduced, the [3fe-4s]0 centre reacts rapidly with fe(ii) ion to form a [4fe-4s]2+ cluster. the latter ...19892557832
expression of the gene encoding cytochrome c3 from desulfovibrio vulgaris (hildenborough) in escherichia coli: export and processing of the apoprotein.the expression of cytochrome c3 from desulfovibrio vulgaris (hildenborough) was examined in escherichia coli transformed with either of two plasmids, pj8 and pj81. the former has an 840 bp insert of d. vulgaris dna, containing the structural gene for cytochrome c3 (387 bp) and its promoter region. plasmid pj81 was generated from pj8 by deoxyoligonucleotide-directed mutagenesis to direct the synthesis of a protein with an altered signal peptidase cleavage site [ala(-1)----asp(-1)]. synthesis of t ...19892561288
amino acid sequence and function of rubredoxin from desulfovibrio vulgaris miyazaki.rubredoxin was purified from desulfovibrio vulgaris miyazaki. it was sequenced and some of its properties determined. rubredoxin is composed of 52 amino acids. it is highly homologous to that from d. vulgaris hildenborough. its n-terminal methionyl residue is partially formylated. the millimolar absorption coefficients of the rubredoxin at 489 nm and 280 nm are 8.1 and 18.5, respectively, and the standard redox potential is +5 mv, which is slightly higher than those of other rubredoxins. rubredo ...19892561345
cloning and sequencing of the nifh gene of desulfovibrio gigas.the desulfovibrio gigas nifh gene has been cloned and sequenced. it consists of an open-reading frame of 822 base pairs encoding a 274 amino acid polypeptide. a potential ntra-dependent promotor sequence is present. the gene lacks an upstream activator sequence homologous to those often found in nif genes subject to activation by nifa.19892599361
structure of [4fe-4s] ferredoxin from bacillus thermoproteolyticus refined at 2.3 a resolution. structural comparisons of bacterial ferredoxins.the structure of a low-potential ferredoxin isolated from bacillus thermoproteolyticus has been refined by a restrained least-squares method. the final crystallographic r factor is 0.204 for 2906 reflections with f greater than 3 sigma f in the 6.0 to 2.3 a resolution range. the model contains 81 amino acid residues, one [4fe-4s] cluster, and 59 water molecules. the root-mean-square deviation from ideal values for bond lengths is 0.018 a, and the mean coordinate error is estimated to be 0.25 a. ...19892600971
analysis and comparison of nucleotide sequences encoding the genes for [nife] and [nifese] hydrogenases from desulfovibrio gigas and desulfovibrio baculatus.the nucleotide sequences encoding the [nife] hydrogenase from desulfovibrio gigas and the [nifese] hydrogenase from desulfovibrio baculatus (n.k. menon, h.d. peck, jr., j. legall, and a.e. przybyla, j. bacteriol. 169:5401-5407, 1987; c. li, h.d. peck, jr., j. legall, and a.e. przybyla, dna 6:539-551, 1987) were analyzed by the codon usage method of staden and mclachlan. the reported reading frames were found to contain regions of low codon probability which are matched by more probable sequences ...19892651421
organization of the genes encoding [fe] hydrogenase in desulfovibrio vulgaris subsp. oxamicus monticello.the genes encoding the periplasmic [fe] hydrogenase from desulfovibrio vulgaris subsp. oxamicus monticello were cloned by exploiting their homology with the hydab genes from d. vulgaris subsp. vulgaris hildenborough, in which this enzyme is present as a heterologous dimer of alpha and beta subunits. nucleotide sequencing showed that the enzyme is encoded by an operon in which the gene for the 46-kilodalton (kda) alpha subunit precedes that of the 13.5-kda beta subunit, exactly as in the hildenbo ...19892661538
hyd gamma, a gene from desulfovibrio vulgaris (hildenborough) encodes a polypeptide homologous to the periplasmic hydrogenase.downstream of the genes for the structural alpha and beta subunits of the periplasmic desulfovibrio vulgaris (hildenborough) hydrogenase a dna fragment was detected with sequence homology to these genes. this fragment was cloned in escherichia coli and the nucleotide sequence was determined. a gene was detected on the fragment with coding capacity for a 65.8 kda polypeptide, hyd gamma. the central part of hyd gamma has an unusually high degree of homology with the alpha subunit and the c-termina ...19892663634
metabolic diversity among the dissimilatory sulfate-reducing bacteria. albert jan kluyver memorial lecture. 19892679377
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
distribution of delta-aminolevulinic acid biosynthetic pathways among phototrophic bacterial groups.two biosynthetic pathways are known for the universal tetrapyrrole precursor, delta-aminolevulinic acid (ala). in the ala synthase pathway which was first described in animal and some bacterial cells, the pyridoxal phosphate-dependent enzyme ala synthase catalyzes condensation of glycine and succinyl-coa to form ala with the loss of c-1 of glycine as co2. in the five-carbon pathway which was first described in plant and algal cells, the carbon skeleton of glutamate is converted intact to ala in ...19892789025
structural assignment of the heme potentials of cytochrome c3, using a specifically modified view of the assignment of the four redox potentials values to the four heme groups in the crystallographic structure of desulfovibrio desulfuricans norway cytochrome c3, a biochemical approach is reported. a singly modified cytochrome c3 on arginine 73 has been prepared. the study of the redox properties of the modified cytochrome by electrochemistry together with the graphic modelisation of the molecule allow to assign the highest redox potential (-165 mv) to the heme 4 in the three dimensio ...19872820417
the molybdenum iron-sulphur protein from desulfovibrio gigas as a form of aldehyde oxidase.the molybdenum iron-sulphur protein originally isolated from desulfovibrio gigas by moura, xavier, bruschi, le gall, hall & cammack [(1976) biochem. biophys. res. commun. 72, 782-789] has been further investigated by e.p.r. spectroscopy of molybdenum(v). the signal obtained on extended reduction of the protein with sodium dithionite has been shown, by studies at 9 and 35 hgz in 1h2o and 2h2o and computer simulations, to have parameters corresponding to those of the slow signal from the inactive ...19872821990
electrochemical study of the electron exchange between cytochrome c3 and hydrogenase from desulfovibrio desulfuricans norway.the kinetics of the reduction of the desulfovibrio desulfuricans norway cytochrome c3 by its physiological partner hydrogenase, in the presence of hydrogen, was investigated by an electrochemical method; from cyclic voltammetry experiments a value of 3 x 10(7) m-1 s-1 was obtained for the second-order rate constant. results are discussed in terms of specific interactions between physiological partner proteins.19872822044
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
thermodynamic parameters of cytochrome c3-ferredoxin complex formation.the complex formation between cytochrome c3 and ferredoxin i from desulfovibrio desulfuricans norway was studied by microcalorimetric and ph-stat titration measurements. the stoichiometry of the complex was found to be one molecule of cytochrome c3 per monomer of ferredoxin i. the association constant determined at t = 283 k in tris(hydroxymethyl)aminomethane hydrochloride (tris-hcl) buffer, 10(-2) m and ph 7.7, was ka = 1.3 x 10(6) m-1. though the enthalpy (delta h = 19 +/- 1 kj.mol-1) and the ...19872827754
amino acid sequences of cytochrome c-554(548) and cytochrome c' from a halophilic denitrifying bacterium of the genus paracoccus.the amino acid sequences of the cytochromes c-554(548) and c' from the moderately halophilic bacterium paracoccus sp., i.a.m. 203 (= a.t.c.c. 12084, n.c.i.b. 8669) have been determined. cytochrome c-554(548) consists of a single polypeptide chain of 83 residues, and dimerizes strongly. the most similar protein of known sequence is the n-terminal half of the dihaem cytochrome c4, and other related proteins include the cytochrome c-554(547) of thiobacillus neapolitanus and the cytochrome c-553 of ...19872829828
the relationship between activity and the axial g = 2.06 epr signal induced by co in the periplasmic (fe) hydrogenase from desulfovibrio vulgaris.the effect of exposure to carbon monoxide on the activity of the (fe) hydrogenase from desulfovibrio vulgaris has been determined. concentrations of carbon monoxide which completely inhibit hydrogenase activity and induce formation of the axial g = 2.06 epr signal up to 0.8 spin/molecule do not cause irreversible inhibition of the (fe) hydrogenase.19882830138
magnetization of the oxidized and reduced three-iron cluster of desulfovibrio gigas ferredoxin ii.the saturation magnetizations of the three iron cluster of ferredoxin ii of desulfovibrio gigas in both the oxidized and reduced states have been studied at fixed magnetic fields up to 4.5 tesla over the temperature range from 1.8 to 200 k. the low field (0.3 tesla) susceptibility of oxidized ferredoxin ii obeys the curie law over this entire temperature range. this establishes -2jox greater than 200 cm-1 as the lower limit for the antiferromagnetic exchange coupling of oxidized ferredoxin ii. t ...19882831199
purification of vibrio fischeri nitrite reductase and its characterization as a hexaheme c-type cytochrome.dissimilatory nitrite reductase was isolated from anaerobically nitrate-grown vibrio fischeri cells and purified to electrophoretic homogeneity. the enzyme catalyzes the six-electron reduction of nitrite to ammonia. upon sodium dodecyl sulfate-polyacrylamide gel electrophoresis, under either nonreducing or reducing conditions, the purified nitrite reductase migrated as a single protein band of mr 57,000. gel filtration chromatography revealed a native molecular weight of 58,000, indicating the e ...19882833168
isolation and characterization of rubrerythrin, a non-heme iron protein from desulfovibrio vulgaris that contains rubredoxin centers and a hemerythrin-like binuclear iron cluster.a new non-heme iron protein from the periplasmic fraction of desulfovibrio vulgaris (hildenbourough ncib 8303) has been purified to homogeneity, and its amino acid composition, molecular weight, redox potential, iron content, and optical, epr, and mössbauer spectroscopic properties have been determined. this new protein is composed of two identical subunits with subunit molecular weight of 21,900 and contains four iron atoms per molecule. the as-purified oxidized protein exhibits an optical spec ...19882835096
a hypothetical model of the flavodoxin-tetraheme cytochrome c3 complex of sulfate-reducing bacteria.a hypothetical model of the flavodoxin-tetraheme cytochrome c3 electron-transfer complex from the sulfate-reducing bacterium desulfovibrio vulgaris has been constructed by using interactive computer graphics based on electrostatic potential field calculations and previous nmr experiments. features of the proposed complex are (1) van der waals contact between the flavin mononucleotide prosthetic group of flavodoxin and one heme of the cytochrome, (2) unique complementarity of electrostatic fields ...19882838073
assignment of individual heme epr signals of desulfovibrio baculatus (strain 9974) tetraheme cytochrome c3. a redox equilibria epr redox titration was performed on the tetraheme cytochrome c3 isolated from desulfovibrio baculatus (strain 9974), a sulfate-reducer. using spectral differences at different poised redox states of the protein, it was possible to individualize the epr g-values of each of the four hemes and also to determine the mid-point redox potentials of each individual heme: heme 4 (-70 mv) at gmax = 2.93, gmed = 2.26 and gmin = 1.51; heme 3 (-280 mv) at gmax = 3.41; heme 2 (-300 mv) at gmax = 3.05, gme ...19882843371
cloning of genes encoding redox proteins of known amino acid sequence from a library of the desulfovibrio vulgaris (hildenborough) genome.a library of 900 recombinant phages has been constructed for the genome of desulfovibrio vulgaris hildenborough (1.7 x 10(6) bp) by cloning size-fractionated sau3a fragments (15-20 kb) into the replacement vector lambda-2001. when a hydrogenase gene probe, a 4.7-kb sali-ecori fragment of known nucleotide sequence, was used to screen the plaque lifted library, 23 positive clones were found, which together span 31 kb of d. vulgaris dna. to facilitate the cloning of genes with oligodeoxynucleotides ...19882843442
epr determination of interaction redox potentials in a multiheme cytochrome: cytochrome c3 from desulfovibrio desulfuricans cytochromes c3 which contain four hemes per molecule, the redox properties of each heme may depend upon the redox state of the others. this effect can be described in terms of interaction redox potentials between the hemes and must be taken into account in the characterization of the redox properties of the molecule. we present here a method of measurement of these interactions based on the epr study of the redox equilibria of the protein. the microscopic and macroscopic midpoint potentials a ...19882846296
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
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
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
a pulsed epr study of redox-dependent hyperfine interactions for the nickel centre of desulfovibrio gigas hydrogenase.the nickel centre of hydrogenase from desulfovibrio gigas was studied by electron spin echo envelope modulation (eseem) spectroscopy in the oxidized, unready (ni-a) and h2-reduced active (ni-c) states, both in h2o and 2h2o solutions. fourier transforms of the 3-pulse eseem, taken at 8.7 ghz, for ni-a and ni-c in h2o contained similar peaks with narrow linewidths at frequencies of 0.4, 1.2 and 1.6 mhz, and a broader peak centered at 4.5 mhz. at 11.6 ghz, the low frequency components showed small ...19882849556
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
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