reduction of cr, mo, se and u by desulfovibrio desulfuricans immobilized in polyacrylamide gels.intact cells of desulfovibrio desulfuricans, immobilized in polyacrylamide gel, removed cr, mo, se and u from solution by enzymatic-mediated reduction reactions. lactate or h2 served as the electron donor and the oxidized cr(vi), mo(vi), se(vi) and u(vi) served as electron acceptors. reduction of the oxidized metal species resulted in the precipitation of solid phases of the metals. metal removal efficiencies of 86-96% were achieved for initial concentrations of 1 mm mo, se, and u and 0.5 mm cr. ...19989565467
nmr determination of the global structure of the 113cd derivative of desulforedoxin: investigation of the hydrogen bonding pattern at the metal center.desulforedoxin (dx) is a simple homodimeric protein isolated from desulfovibrio gigas (dg) containing a distorted rubredoxin-like center with one iron coordinated by four cysteinyl residues (7.9 kda with 36 amino acids per monomer). in order to probe the geometry and the h-bonding at the active site of dx, the protein was reconstituted with 113cd and the solution structure determined using 2d nmr methods. the structure of this derivative was initially compared with the nmr solution structure of ...19989568899
altered specificity mutations define residues essential for substrate positioning in xanthine dehydrogenase.we describe the sequence changes of a number of mutations of the aspergillus nidulans xanthine dehydrogenase (xdh). we have located the amino acids affected by these changes in the three-dimensional (3d) structure of aldehyde oxido-reductase (mop) from desulfovibrio gigas, related to eukaryotic xdhs. of these, two are loss of function mutations, mapping, respectively, in the molybdenum-pterin co-factor (moco) domain and in the domain involved in substrate recognition. changes in two amino acids ...19989571062
photostable chlorophyll a conjugated with poly(vinylpyrrolidone)-smectite catalyzes photoreduction and hydrogen gas evolution by visible light.chlorophyll a was adsorbed to a synthetic smectite intercalated by poly(vinylpyrrolidone) (pvp) to form the chlorophyll-pvp-smectite conjugate (chl-pvp-sme) having an absorption maximum at 677 nm. the conjugate was found to be stable toward light illumination in comparison with chlorophyll-smectite, chlorophyll-pvp, and free chlorophyll a. chl-pvp-sme had a photoinduced activity for catalyzing the reduction of methyl viologen. furthermore, the evolution of hydrogen gas was observed when an aqueo ...19989576817
electrospray mass spectrometry studies of non-heme iron-containing proteins.the oligomeric state and the metal atom stoichiometry of a series of non-heme iron-containing, multimeric proteins have been measured using electrospray ionization (esi) in a time-of-flight (tof) mass spectrometer. the proteins were obtained both from natural sources and by overexpression of recombinant dna in escherichia coli. esi-tof mass spectra of the metalloproteins present in nondenaturing solutions exhibit peaks corresponding to the multimeric forms of the holoproteins containing the expe ...19989599583
structure of azotobacter vinelandii 7fe ferredoxin at 1.35 a resolution and determination of the [fe-s] bonds with 0.01 a accuracy.the crystal structure of azotobacter vinelandii ferredoxin i (fdi) at 100 k has been refined at 1.35 a resolution by full matrix block diagonal least-squares methods with anisotropic temperature factors for all non-hydrogen atoms and with hydrogen atoms included in the model. fe-s bonds within the [3fe-4s]+ and [4fe-4s]2+ clusters of the protein are determined with an accuracy of at least 0.01 a. analysis of metric parameters reveals greater variation in bonds and angles within the [3fe-4s]+ clu ...19989600844
mercury methylation by interspecies hydrogen and acetate transfer between sulfidogens and methanogens.cocultures of desulfovibrio desulfuricans and methanococcus maripaludis grew on sulfate-free lactate medium while vigorously methylating hg2+. individually, neither bacterium could grow or methylate mercury in this medium. similar synergistic growth of sulfidogens and methanogens may create favorable conditions for hg2+ methylation in low-sulfate anoxic freshwater sediments.19989603804
growth of geobacter sulfurreducens with acetate in syntrophic cooperation with hydrogen-oxidizing anaerobic partnerspure cultures of geobacter sulfurreducens and other fe(iii)-reducing bacteria accumulated hydrogen to partial pressures of 5 to 70 pa with acetate, butyrate, benzoate, ethanol, lactate, or glucose as the electron donor if electron release to an acceptor was limiting. g. sulfurreducens coupled acetate oxidation with electron transfer to an anaerobic partner bacterium in the absence of ferric iron or other electron acceptors. cocultures of g. sulfurreducens and wolinella succinogenes with nitrate ...19989603840
tyrosine 64 of cytochrome c553 is required for electron exchange with formate dehydrogenase in desulfovibrio vulgaris hildenborough.replacement of tyrosine 64 by alanine in cytochrome c553 from desulfovibrio vulgarishildenborough prevents electron transfer with the formate dehydrogenase. biophysical and biochemical studies show that the protein is correctly folded and that the oxidoreduction potential is not modified. the solution structure of the mutant cytochrome determined by two-dimensional (2d) nmr clearly establishes that the overall fold of the molecule is nearly identical to that of the wild-type cytochrome. the elec ...19989622485
modulation of the redox potentials of fmn in desulfovibrio vulgaris flavodoxin: thermodynamic properties and crystal structures of glycine-61 mutants.mutants of the electron-transfer protein flavodoxin from desulfovibrio vulgaris were made by site-directed mutagenesis to investigate the role of glycine-61 in stabilizing the semiquinone of fmn by the protein and in controlling the flavin redox potentials. the spectroscopic properties, oxidation-reduction potentials, and flavin-binding properties of the mutant proteins, g61a/n/v and l, were compared with those of wild-type flavodoxin. the affinities of all of the mutant apoproteins for fmn and ...19989622492
effect of surface modifiers on the electrode reactions and conformation of cytochrome c3 adsorbed on a silver electrode.surface-enhanced resonance raman scattering and electroreflectance voltammetry were used to investigate the effect of electrode surface modification on the structure and redox properties of cytochrome c3 immobilized on ag surfaces. it is shown that the redox reactions of cytochrome c3 are more reversible at an 11-mercaptoundecanoic acid modified ag electrode as compared to a bare metal surface. the heme of cytochrome c3 is in a mixed low and high spin state when adsorbed at the bare electrode, w ...19989639107
structure and function of molybdopterin containing enzymes.molybdopterin containing enzymes are present in a wide range of living systems and have been known for several decades. however, only in the past two years have the first crystal structures been reported for this type of enzyme. this has represented a major breakthrough in this field. the enzymes share common structural features, but reveal different polypeptide folding topologies. in this review we give an account of the related spectroscopic information and the crystallographic results, with e ...19979652170
the formate dehydrogenase-cytochrome c553 complex from desulfovibrio vulgaris hildenborough.the electron transfer between formate dehydrogenase and cytochrome c553 from the anaerobic bacteria desulfovibrio vulgaris hildenborough has been investigated. parameters of the electron transfer kinetics are reported. the ionic strength dependence of the complex formation has been evidenced. two mutants of cytochrome c553 have been obtained using site-directed mutagenesis with the substitutions k62e and k62e,k63e. according to one-dimensional and two-dimensional nmr analysis, the two variants w ...19989654061
a periplasmic and extracellular c-type cytochrome of geobacter sulfurreducens acts as a ferric iron reductase and as an electron carrier to other acceptors or to partner extracellular electron carrier excreted into the growth medium by cells of geobacter sulfurreducens was identified as a c-type cytochrome. the cytochrome was found to be distributed in about equal amounts in the membrane fraction, the periplasmic space, and the surrounding medium during all phases of growth with acetate plus fumarate. it was isolated from periplasmic preparations and purified to homogeneity by cation-exchange chromatography, gel filtration, and hydrophobic interaction chromat ...19989658015
a family of flavoproteins in the domains archaea and bacteria.a family of flavoproteins, called a-type flavoproteins, is described. it consists of 14 protein sequences of 385-597 amino acids in length, 7 from methanogens (domain: archaea), 5 from phototrophic prokaryotes, one from escherichia coli, and a partial sequence from the sulfate reducer desulfovibrio gigas (domain: bacteria). no similar sequence could be found in the domain eucarya. all sequences show significant similarity over a 385-400 amino acid portion overlapping a recognizable flavodoxin si ...19989660187
characterisation of a new rubredoxin isolated from desulfovibrio desulfuricans 27774: definition of a new family of rubredoxins.a new rubredoxin from the sulphate-reducing bacterium desulfovibrio desulfuricans atcc 27774, grown with nitrate as terminal electron acceptor, was isolated and characterised. the protein is an 8.5 kda monomer containing one iron atom per molecule, with a reduction potential of 25 +/- 5 mv at ph 7.6. like the recombinant rdl protein from d. vulgaris, expressed in escherichia coli [lumpio, h.l., shenvi, n.v., garg, r.p., summers, a.o. and kurtz, d.m., j. bacteriol. 179 (1997) 4607-4615], it conta ...19989662435
metabolism of explosive compounds by sulfate-reducing bacteria.the metabolism of various explosive compounds-1,3,5-trinitrobenzene (tnb), hexahydro-1,3,5-trinitro-1,3,5-triazine (rdx), and octahydro-1,3,5,7-tetranitro-1,3,5,7-tetraazocine (hmx)-by a sulfate-reducing bacterial consortium, desulfovibrio spp., was studied. the results indicated that the desulfovibrio spp. used all of the explosive compounds studied as their sole source of nitrogen for growth. the concentrations of tnb, rdx, and hmx in the culture media dropped to below the detection limit (<0. ...19989662613
iron-sulfur proteins: new roles for old clusters.several major advances in our understanding of the structure, function and properties of biological iron-sulfur clusters have occurred in the past year. these include a new structural type of cluster in the inappropriately named prismane protein, the establishment of redox-mediated [fe2s2]2+ <--> [fe4s4]2+ cluster conversions, and the characterization of valence-delocalized [fe2s2]+ and all ferrous clusters with [fe2s2]0, [fe3s4]2- and [fe4s4]0 cores. the emergence of novel types of redox, regul ...19989667933
deletion of the rbo gene increases the oxygen sensitivity of the sulfate-reducing bacterium desulfovibrio vulgaris hildenborough.the rbo gene of desulfovibrio vulgaris hildenborough encodes rubredoxin oxidoreductase (rbo), a 14-kda iron sulfur protein; forms an operon with the gene for rubredoxin; and is preceded by the gene for the oxygen-sensing protein dcra. we have deleted the rbo gene from d. vulgaris with the sacb mutagenesis procedure developed previously (r. fu and g. voordouw, microbiology 143:1815-1826, 1997). the absence of the rbo-gene in the resulting mutant, d. vulgaris l2, was confirmed by pcr and protein b ...19989687445
interaction of sulfate-reducing bacteria with molybdenum dissolved from sputter-deposited molybdenum thin films and pure molybdenum powder.when sputter-deposited mo thin films were exposed to sulfate-reducing bacterium desulfovibrio desulfuricans, dissolved mo markedly delayed the culture growth and reduced the rate of sulfate reduction. the interaction led to an orange coloration of the culture liquid. x-ray photoelectron spectroscopy of dried culture droplets revealed that mo dissolution products existed mostly in pentavalent state, and a smaller amount of molybdate and molybdenum disulfide. in contrast, mo dissolution in uninocu ...19989698401
the nadp-reducing hydrogenase of desulfovibrio fructosovorans: evidence for a native complex with hydrogen-dependent methyl-viologen-reducing activity.the nadp-reducing hydrogenase of desulfovibrio fructosovorans represents a novel class of [fe] hydrogenases which is encoded by the well-characterized hndabcd operon containing the genes hnda, hndb, hndc, and hndd. expression of this operon, monitored by measuring the nadp-reducing activity, was found to be maximum during the exponential phase of growth on fructose and then decreased when the concentration of the carbon and energy source became limiting. the optimum ph for the h2-driven nadp red ...19989703971
psychrotolerant sulfate-reducing bacteria from an oxic freshwater sediment, description of desulfovibrio cuneatus sp. nov. and desulfovibrio litoralis sp. nov.the most abundant culturable sulfate-reducing bacteria were isolated from the littoral sediment of the oligotrophic lake stechlin. the strains stl1 and stl4 were obtained from the oxic uppermost layer, while strain stl6 was isolated from the anoxic zone in 20 to 30 mm depth. the isolates showed a striking morphological feature in tapering off at one end of the cell. physiological characteristics related them to the genus desulfovibrio. they contained desulfoviridin. h2, formate, pyruvate, lactat ...19989704109
solution structure of desulfovibrio vulgaris (hildenborough) ferrocytochrome c3: structural basis for functional cooperativity.desulfovibrio vulgaris cytochrome c3 is a 14 kda tetrahaem cytochrome that plays a central role in energy transduction. the three-dimensional structure of the ferrocytochrome at ph 8.5 was solved through two-dimensional 1h-nmr. the structures were calculated using a large amount of experimental information, which includes upper and lower distance limits as well as dihedral angle restraints. the analysis allows for fast-flipping aromatic residues and flexibility in the haem plane. the structure w ...19989710542
replacement of lysine 45 by uncharged residues modulates the redox-bohr effect in tetraheme cytochrome c3 of desulfovibrio vulgaris (hildenborough).the structural basis for the ph dependence of the redox potential in the tetrahemic desulfovibrio vulgaris (hildenborough) cytochrome c3 was investigated by site-directed mutagenesis of charged residues in the vicinity of heme i. mutation of lysine 45, located in the neighborhood of the propionates of heme i, by uncharged residues, namely threonine, glutamine and leucine, was performed. the replacement of a conserved charged residue, aspartate 7, present in the n-terminal region and near heme i ...19989724528
ionic strength-dependent physicochemical factors in cytochrome c3 regulating the electron transfer rate.the effect of ionic strength on the macroscopic and microscopic redox potentials and the heme environment of cytochrome c3 from desulfovibrio vulgaris miyazaki f have been investigated by nmr and electrochemical methods. the redox potentials of this tetraheme protein are found to be ionic strength-dependent. especially, the microscopic redox potentials of hemes 2 and 3 at the fourth reduction step increase significantly with increasing ionic strength, which is in contraction to the theoretical e ...19989726950
the structural origin of nonplanar heme distortions in tetraheme ferricytochromes c3.resonance raman (rr) spectroscopy, molecular mechanics (mm) calculations, and normal-coordinate structural decomposition (nsd) have been used to investigate the conformational differences in the hemes in ferricytochromes c3. nsd analyses of heme structures obtained from x-ray crystallography and mm calculations of heme-peptide fragments of the cytochromes c3 indicate that the nonplanarity of the hemes is largely controlled by a fingerprint peptide segment consisting of two heme-linked cysteines, ...19989730815
high genetic and physiological diversity of sulfate-reducing bacteria isolated from an oligotrophic lake sediment.the community structure of sulfate-reducing bacteria in littoral and profundal sediments of the oligotrophic lake stechlin (germany) was investigated. a collection of 32 strains was isolated from the highest positive dilutions of most-probable-number series, and their partial 16s rrna gene sequences and genomic fingerprints based on eric (enterobacterial repetitive intergenic consensus)-pcr were analyzed. the strains fell into eight distinct phylogenetic lineages, and the majority (70%) showed a ...19989732438
isolation and characterization of desulfovibrio senezii sp. nov., a halotolerant sulfate reducer from a solar saltern and phylogenetic confirmation of desulfovibrio fructosovorans as a new speciesa new halotolerant desulfovibrio, strain cvlt (t = type strain), was isolated from a solar saltern in california. the curved, gram-negative, nonsporeforming cells (0.3 x 1.0-1.3 &mgr;m) occurred singly, in pairs, or in chains, were motile by a single polar flagellum and tolerated up to 12.5% nacl. strain cvlt had a generation time of 60 min when grown in lactate-yeast extract medium under optimal conditions (37 degreesc, ph 7.6, 2.5% nacl). it used lactate, pyruvate, cysteine, or h2/co2 + acetat ...19989732447
heterologous expression of the desulfovibrio gigas [nife] hydrogenase in desulfovibrio fructosovorans mr400.the ability of desulfovibrio fructosovorans mr400 deltahynabc to express the heterologous cloned [nife] hydrogenase of desulfovibrio gigas was investigated. the [nife] hydrogenase operon from d. gigas, hynabcd, was cloned, sequenced, and introduced into d. fructosovorans mr400. a portion of the recombinant heterologous [nife] hydrogenase was totally matured, exhibiting catalytic and spectroscopic properties identical to those of the native d. gigas protein. a chimeric operon containing hynab fro ...19989733707
growth of a human intestinal desulfovibrio desulfuricans in continuous cultures containing defined populations of saccharolytic and amino acid fermenting bacteria.ecological and physiological effects of the sulphate-reducing bacterium (srb) desulfovibrio desulfuricans on other intestinal organisms were investigated in anaerobic chemostats (dilution rate approximately 0.2 h-1). reproducible defined bacterial communities were used in these experiments, comprising 14 different saccharolytic and amino acid fermenting species: bifidobacterium longum, bif. adolescentis, bif. pseudolongum, bif. infantis, bacteroides thetaiotaomicron, bact. vulgatus, lactobacillu ...19989750310
[3fe-4s] to [4fe-4s] cluster conversion in desulfovibrio fructosovorans [nife] hydrogenase by site-directed mutagenesis.the role of the high potential [3fe-4s]1+,0 cluster of [nife] hydrogenase from desulfovibrio species located halfway between the proximal and distal low potential [4fe-4s]2+,1+ clusters has been investigated by using site-directed mutagenesis. proline 238 of desulfovibrio fructosovorans [nife] hydrogenase, which occupies the position of a potential ligand of the lacking fourth fe-site of the [3fe-4s] cluster, was replaced by a cysteine residue. the properties of the mutant enzyme were investigat ...19989751716
structural and functional dynamics of sulfate-reducing populations in bacterial biofilmswe describe the combined application of microsensors and molecular techniques to investigate the development of sulfate reduction and of sulfate-reducing bacterial populations in an aerobic bacterial biofilm. microsensor measurements for oxygen showed that anaerobic zones developed in the biofilm within 1 week and that oxygen was depleted in the top 200 to 400 &mgr;m during all stages of biofilm development. sulfate reduction was first detected after 6 weeks of growth, although favorable conditi ...19989758792
voltammetric studies of the reactions of iron-sulphur clusters ([3fe-4s] or [m3fe-4s]) formed in pyrococcus furiosus ferredoxin.reactions of the [3fe-4s] cluster and various metallated [m3fe-4s] adducts co-ordinated in the ferredoxin from the hyperthermophile pyrococcus furiosus have been studied by protein-film voltammetry, bulk-solution voltammetry, solution kinetics and magnetic cd (mcd). the [3fe-4s] cluster exhibits two couples, [3fe-4s]+/0 and [3fe-4s]0/2-. film voltammetry is possible over a wide ph range (2-8), revealing that the [3fe-4s]+/0 couple shows a complex ph dependence with pkred1=2.8, pkox=4.9 and pkred ...19989761735
the relationship between microbial metabolic activity and biocorrosion of carbon steel.the effect of metabolic activity (expressed by generation time, rate of h2s production and the activity of hydrogenase and adenosine phosphosulphate (aps)-reductase enzymes) of the 8 wild strains of desulfovibrio desulfuricans and of their resistance to metal ions (hg2+, cu2+, mn2+, zn2+, ni2+, cr3+) on the rate of corrosion of carbon steel was studied. the medium containing lactate as the carbon source and sulphate as the electron acceptor was used for bacterial metabolic activity examination a ...19979765862
structural bases for the catalytic mechanism of [nife] hydrogenases. 19989765886
characterization of the complex of isofmn and apoflavodoxin from desulfovibrio vulgaris (hildenborough). 19989765934
enzymatic recovery of elemental palladium by using sulfate-reducing bacteriaworldwide usage of platinum group metals is increasing, prompting new recovery technologies. resting cells of desulfovibrio desulfuricans reduced soluble pd2+ to elemental, cell-bound pd0 supported by pyruvate, formate, or h2 as the electron donor without biochemical cofactors. pd reduction was o2 insensitive, opening the way for recycling and recovery of pd under oxic conditions.19989797331
in situ detection of bacteria in continuous-flow cultures of seawater sediment suspensions with fluorescently labelled rrna-directed oligonucleotide probes.rrna-targeted and fluorescently labelled oligonucleotide probes were used to study the composition of natural bacterial populations in continuous-flow cultures of seawater sediment suspensions. the cultures were run as enrichment cultures with increasing dilution rates, and hexadecane as the sole carbon source. total cell numbers were analysed by counting dapi (4',6-diamidino-2-phenylindole)-stained cells. to differentiate the population composition, oligonucleotide probes for eubacteria, for cy ...19989802019
mass balance studies with 14c-labeled 2,4,6-trinitrotoluene (tnt) mediated by an anaerobic desulfovibrio species and an aerobic serratia species.investigations were carried out to evaluate the level of incorporation of radiolabeled 2,4,6-trinitrotoluene (tnt) and metabolites into the bacterial biomass of two different bacterial species after cometabolically mediated tnt transformation. biotransformation experiments with 14c-tnt indicated that tnt was not mineralized; however, carbon derived from tnt became associated with the cells. it was found that more than 42% of the initially applied radiolabel was associated with the cell biomass a ...19989806975
atp sulfurylases from sulfate-reducing bacteria of the genus desulfovibrio. a novel metalloprotein containing cobalt and zinc.adenosine triphosphate sulfurylase catalyzes the formation of adenosine 5'-phosphosulfate from adenosine triphosphate and sulfate. the enzyme plays a crucial role in sulfate activation, the key step for sulfate utilization, and has been purified from crude extracts of desulfovibrio desulfuricans atcc 27774 and desulfovibrio gigas. both proteins are homotrimers [141 kda (3 x 47) for d. desulfuricans and 147 kda (3 x 49) for d. gigas] and have been identified, for the first time, as metalloprotein ...19989819214
identification of a gene for a rubrerythrin/nigerythrin-like protein in spirillum volutans by using amino acid sequence data from mass spectrometry and nh2-terminal sequencing.a hydrogen peroxide-resistant mutant of the catalase-negative microaerophile, spirillum volutans, constitutively expresses a 21.5 kda protein that is undetectable and non-inducible in the wild-type cells. part of the gene that encodes the protein was cloned using amino acid sequence data obtained by both mass spectrometry and nh2-terminal sequencing. the deduced 158 amino acid polypeptide shows high relatedness to rubrerythrin and nigerythrin previously described in the anaerobes clostridium per ...19989830123
products of mercury demethylation by sulfidogens and methanogens. 19989841732
functional and mechanistic studies of cytochrome c3 from desulfovibrio gigas: thermodynamics of a "proton thruster".nuclear magnetic resonance and visible spectroscopies were used to determine the thermodynamic parameters of the four hemes in cytochrome c3 from desulfovibrio gigas at 298 and 277 k and to investigate the mechanism of electron/proton energy transduction. data obtained in the ph range from 5 to 9 were analyzed according to a model in which the hemes interact with each other (redox cooperativities) and with an ionizable center (redox-bohr cooperativities). the results obtained at the two temperat ...19989843386
kinetics and interaction studies between cytochrome c3 and fe-only hydrogenase from desulfovibrio vulgaris hildenborough.hydrogenases from desulfovibrio are found to catalyze hydrogen uptake with low potential multiheme cytochromes, such as cytochrome c3, acting as acceptors. the production of fe-only hydrogenase from desulfovibrio vulgaris hildenborough was improved with respect to the growth phase and media to determine the best large-scale bacteria growth conditions. the interaction and electron transfer from fe-only hydrogenase to multiheme cytochrome has been studied in detail by both blacore and steady-state ...19989849942
a membrane-bound nad(p)+-reducing hydrogenase provides reduced pyridine nucleotides during citrate fermentation by klebsiella pneumoniae.during anaerobic growth of klebsiella pneumoniae on citrate, 9.4 mmol of h2/mol of citrate (4-kpa partial pressure) was formed at the end of growth besides acetate, formate, and co2. upon addition of nicl2 (36 microm) to the growth medium, hydrogen formation increased about 36% to 14.8 mmol/mol of citrate (6 kpa), and the cell yield increased about 15%. cells that had been harvested and washed under anoxic conditions exhibited an h2-dependent formation of nad(p)h in vivo. the reduction of intern ...19999864336
energetic aspects of co oxidation in desulfovibrio desulfuricansin cell suspension of desulfovibrio desulfuricans b-1388, oxidation of co as the only energy source is associated with reduction of so42-. after a 2-h incubation of cells in 8% co, 81% of the gas is converted. oxidation of 1 mole co results in formation of 0.23 mole h2s. intracellular atp content increases from 2.5 (control) to 8.3 nmoles/mg (during co conversion). dinitrophenol inhibits sulfate reduction and co oxidation. co dehydrogenase was detected in cytoplasmic and membrane cell fractions ...19989864447
x-ray crystal structure of the desulfovibrio vulgaris (hildenborough) apoflavodoxin-riboflavin complex.the apoprotein of flavodoxin from desulfovibrio vulgaris forms a complex with riboflavin. the ability to bind riboflavin distinguishes this flavodoxin from other short-chain flavodoxins which require the phosphate of fmn for flavin binding. the redox potential of the semiquinone/hydroquinone couple of the bound riboflavin is 180 mv less negative than the corresponding complex with fmn. to elucidate the binding of riboflavin, the complex has been crystallized and the crystal structure solved by m ...19989874201
a low-spin iron with cn and co as intrinsic ligands forms the core of the active site in [fe] this report the first high-quality infrared spectra of [fe]-hydrogenase are presented. analyses of these spectra obtained under a variety of redox conditions strongly indicate that [fe]-hydrogenases contain a low-spin fe ion in the active site with one cn- group and one co molecule as intrinsic, non-protein ligands. when in the ferric state, the presence of such an ion can explain the enigmatic epr properties (the rhombic 2.10 signal) of the active, oxidised enzyme. to account for other, well ...19989874225
key role of phenylalanine 20 in cytochrome c3: structure, stability, and function studies.aromatic residues in c-type cytochromes might have an important function in the folding and/or electron transferring properties of the molecule. in the tetraheme cytochrome c3 (mr 13 000) from desulfovibrio vulgaris hildenborough, phe20, is located between heme 1 and heme 3 with its aromatic ring close and almost parallel to the ring plane of heme 1. we replaced this residue by a nonaromatic hydrophobe residue, leucine, and analyzed the effects in terms of functional, structural, and physicochem ...19999890880
syntrophus aciditrophicus sp. nov., a new anaerobic bacterium that degrades fatty acids and benzoate in syntrophic association with hydrogen-using microorganisms.strain sbt is a new, strictly anaerobic, gram-negative, nonmotile, non-sporeforming, rod-shaped bacterium that degrades benzoate and certain fatty acids in syntrophic association with hydrogen/formate-using microorganisms. strain sbt produced approximately 3 mol of acetate and 0.6 mol of methane per mol of benzoate in coculture with methanospirillum hungatei strain jf1. saturated fatty acids, some unsaturated fatty acids, and methyl esters of butyrate and hexanoate also supported growth of strai ...19999914307
desulfovibrio gigas neelaredoxin. a novel superoxide dismutase integrated in a putative oxygen sensory operon of an anaerobe.neelaredoxin, a small non-heme blue iron protein from the sulfate-reducing bacterium desulfovibrio gigas [chen, l., sharma, p., legall, j., mariano, a.m., teixeira m. and xavier, a.v. (1994) eur. j. biochem. 226, 613-618] is shown to be encoded by a polycistronic unit which contains two additional open reading frames (orf-1 and orf-2) coding for chemotaxis-like proteins. orf-1 has domains highly homologous with those structurally and functionally important in methyl-accepting chemotaxis proteins ...19999914498
the reductive half-reaction of xanthine oxidase. reaction with aldehyde substrates and identification of the catalytically labile oxygen.the kinetics of xanthine oxidase has been investigated with the aim of addressing several outstanding questions concerning the reaction mechanism of the enzyme. steady-state and rapid kinetic studies with the substrate 2,5-dihydroxybenzaldehyde demonstrated that (kcat/km)app and kred/kd exhibit comparable bell-shaped ph dependence with pka values of 6.4 +/- 0.2 and 8.4 +/- 0.2, with the lower pka assigned to an active-site residue of xanthine oxidase (possibly glu-1261, by analogy to glu-869 in ...19999920873
carbon monoxide and cyanide as intrinsic ligands to iron in the active site of [nife]-hydrogenases. nife(cn)2co, biology's way to activate h2.infrared-spectroscopic studies on the [nife]-hydrogenase of chromatium vinosum-enriched in 15n or 13c, as well as chemical analyses, show that this enzyme contains three non-exchangeable, intrinsic, diatomic molecules as ligands to the active site, one carbon monoxide molecule and two cyanide groups. the results form an explanation for the three non-protein ligands to iron detected in the crystal structure of the desulfovibrio gigas hydrogenase (volbeda, a., garcin, e., piras, c., de lacey, a. i ...19999920874
desulfovibrio aminophilus sp. nov., a novel amino acid degrading and sulfate reducing bacterium from an anaerobic dairy wastewater lagoon.a mesophilic strain of sulfate-reducing bacterium, designated ala-3t (t = type strain), was isolated from an anaerobic lagoon of a dairy wastewater treatment plant. the curved, gram-negative, non-sporeforming cells (0.2 x 3.0-4.0 microns) existed singly or in chains, and were motile by single polar flagella. optimum growth occurred at 35 degrees c and ph 7.5 on a medium containing lactate and sulfate. thiosulfate or sulfite but not elemental sulfur, nitrate, or fumarate could also replace sulfat ...19989924817
hydrogenase sophistication. 19999930693
isolation of highly performant sulfate reducers from sulfate-rich environments.eleven pure strains of sulfate-reducing bacteria have been isolated from lab-scale bioreactors or gypsum disposal sites, all featuring relatively high concentrations of sulfate, and from natural environments in order to produce sulfide from gypsum using hydrogen as energy source. the properties of the eleven strains have been investigated and compared to these of three collection strains i.e. desulfovibrio desulfuricans and dv. vulgaris and desulfotomaculum orientis. particular attention was pai ...199810022071
formaldehyde ferredoxin oxidoreductase from pyrococcus furiosus: the 1.85 a resolution crystal structure and its mechanistic implications.crystal structures of formaldehyde ferredoxin oxidoreductase (for), a tungstopterin-containing protein from the hyperthermophilic archaeon pyrococcus furiosus, have been determined in the native state and as a complex with the inhibitor glutarate at 1.85 a and 2. 4 a resolution, respectively. the native structure was solved by molecular replacement using the structure of the homologous p. furiosus aldehyde ferredoxin oxidoreductase (aor) as the initial model. residues are identified in for that ...199910024458
crystal structures of the key anaerobic enzyme pyruvate:ferredoxin oxidoreductase, free and in complex with pyruvate.oxidative decarboxylation of pyruvate to form acetyl-coenzyme a, a crucial step in many metabolic pathways, is carried out in most aerobic organisms by the multienzyme complex pyruvate dehydrogenase. in most anaerobes, the same reaction is usually catalyzed by a single enzyme, pyruvate:ferredoxin oxidoreductase (pfor). thus, pfor is a potential target for drug design against certain anaerobic pathogens. here, we report the crystal structures of the homodimeric desulfovibrio africanus pfor (data ...199910048931
liberation of hydrogen sulfide during the catalytic action of desulfovibrio hydrogenase under the atmosphere of hydrogen.the active site of [nife] hydrogenase from desulfovibrio species is composed of a binuclear ni-fe complex bearing three diatomic nonprotein ligands to fe and three bridges between the two metals, two of which are thiolate side chains of the protein moiety. the third bridging atom in the enzyme isolated from d. vulgaris miyazaki f was suggested to be sulfur species, but was suggested to be oxygen species in d. gigas enzyme. when the hydrogenase from d. vulgaris miyazaki f was incubated under the ...199910049702
nadh peroxidase activity of rubrerythrin.p. s. alban et al. (j. appl. microbiol. (1998) 85, 875-882) reported that a mutant h2o2-resistant strain of spirullum (s.) volutans showed constitutive overexpression of a protein whose amino acid sequence and molecular weight closely resembled that of a subunit of rubrerythrin, a non-heme iron protein with no known function. they also reported that the mutant strain, but not the wild-type, showed nadh peroxidase activity. here we demonstrate that rubrerythrin and nigerythrin from desulfovibrio ...199910049706
diversity of dissimilatory bisulfite reductase genes of bacteria associated with the deep-sea hydrothermal vent polychaete annelid alvinella pompejana.a unique community of bacteria colonizes the dorsal integument of the polychaete annelid alvinella pompejana, which inhabits the high-temperature environments of active deep-sea hydrothermal vents along the east pacific rise. the composition of this bacterial community was characterized in previous studies by using a 16s rrna gene clone library and in situ hybridization with oligonucleotide probes. in the present study, a pair of pcr primers (p94-f and p93-r) were used to amplify a segment of th ...199910049872
isolation from estuarine sediments of a desulfovibrio strain which can grow on lactate coupled to the reductive dehalogenation of 2,4, 6-tribromophenol.strain tbp-1, an anaerobic bacterium capable of reductively dehalogenating 2,4,6-tribromophenol to phenol, was isolated from estuarine sediments of the arthur kill in the new york/new jersey harbor. it is a gram-negative, motile, vibrio-shaped, obligate anaerobe which grows on lactate, pyruvate, hydrogen, and fumarate when provided sulfate as an electron acceptor. the organism accumulates acetate when grown on lactate and sulfate, contains desulfoviridin, and will not grow in the absence of nacl ...199910049873
cross-linking between cytochrome c3 and flavodoxin from desulfovibrio gigas.tetraheme cytochrome c3 (13 kda) and flavodoxin (16 kda), are small electron transfer proteins that have been used to mimic, in vitro, part of the electron-transfer chain that operates between substract electron donors and respiratory electron acceptors partners in desulfovibrio species (palma, n., moura, i., legall, j., van beeumen, j., wampler, j., moura, j. j. g. (1994) biochemistry 33, 6394-6407). the electron transfer between these two proteins is believed to occur through the formation of ...199910079190
dissimilatory sulfite reductase from archaeoglobus profundus and desulfotomaculum thermocisternum: phylogenetic and structural implications from gene sequences.the genes encoding the alpha- and beta-subunits of dissimilatory sulfite reductase, dsrab, from the hyperthermophilic archaeon archaeoglobus profundus and the thermophilic gram-positive bacterium desulfotomaculum thermocisternum were cloned and sequenced. the dsrab genes are contiguous, and most probably comprise an operon also including a dsrd homolog, a conserved gene of unknown function located downstream of dsrab in all four sulfate reducers so far sequenced. sequence comparison confirms tha ...199910086846
ab initio structure determination of a small protein, rubredoxin, by direct methods.the direct-methods program saytan has been applied successfully to a known protein, rubredoxin, which contains 52 amino-acid residues including an fes4 unit, a sulfate ion and 102 solvent water molecules. starting with initially random phases, useful sets can be obtained from multiple trials and selected by figures of merit at different resolutions. phase extension followed by weighted fourier recycling reveals a recognizable structure of rubredoxin. the model is refined against 1 a resolution d ...199910089313
crystallization and preliminary x-ray analysis of a nitrate reductase from desulfovibrio desulfuricans atcc 27774.periplasmic nitrate reductase from the sulfate-reducing bacterium desulfovibrio desulfuricans atcc 27774 contains two molybdopterin guanine dinucleotide cofactors and one [4fe-4s] cluster as prosthetic groups and catalyzes the conversion of nitrate to nitrite. crystals of the oxidized form of this enzyme were obtained using peg as precipitant and belong to space group p3121 or p3221, with unit-cell dimensions a = b = 106.3, c = 135.1 a. there is one monomer of 80 kda in the asymmetric unit, whic ...199910089321
structure determination of rubredoxin from desulfovibrio vulgaris miyazaki f in two crystal forms.the structures of two crystal forms (form i, p3221, a = b = 43.7, c = 50.7 a; form ii, p21, a = 27.3, b = 44.9, c = 51.2 a and beta = 90. 6 degrees ) of the rubredoxin from desulfovibrio vulgaris miyazaki f have been solved by the molecular-replacement method. form i has been refined at a resolution of 2.0 a to an r value of 20.8% and includes 32 water molecules. form ii includes 86 water molecules and has been refined at 1.9 a resolution to an r value of 17.5%. in form ii, there are three molec ...199910089348
crystallization and preliminary crystallographic analysis of the pyruvate-ferredoxin oxidoreductase from desulfovibrio africanus.for the first time, crystals of a pyruvate-ferredoxin oxidoreductase (pfor) suitable for x-ray analysis have been obtained. this enzyme catalyzes, in anaerobic organisms, the crucial energy-yielding reaction of pyruvate decarboxylation to acetylcoa. polyethylene glycol and divalent metal cations have been used to crystallize the pfor from the sulfate-reducing bacterium desulfovibrio africanus. two different orthorhombic (p212121 ) crystal forms have been grown with unit-cell dimensions a = 86.1, ...199910089441
ph-dependent spectroscopic changes associated with the hydroquinone of fmn in flavodoxins.photoreduction with a 5-deazaflavin as the catalyst was used to convert flavodoxins from desulfovibrio vulgaris, megasphaera elsdenii, anabaena pcc 7119, and azotobacter vinelandii to their hydroquinone forms. the optical spectra of the fully reduced flavodoxins were found to vary with ph in the ph range of 5.0-8.5. the changes correspond to apparent pka values of 6.5 and 5.8 for flavodoxins from d. vulgaris and m. elsdenii, respectively, values that are similar to the apparent pka values report ...199910090764
a unified model describing the role of hydrogen in the growth of desulfovibrio vulgaris under different environmental conditionsa unified model for the growth of desulfovibrio vulgaris under different environmental conditions is presented. the model assumes the existence of two electron transport mechanisms functioning simultaneously. one mechanism results in the evolution and consumption of hydrogen, as in the hydrogen-cycling model. the second mechanism assumes a direct transport of electrons from the donor to the acceptor, without the participation of h2. a combination of kinetic and thermodynamic conditions control t ...199810099394
removal of u and mo from water by immobilized desulfovibrio desulfuricans in column reactors.intact cells of desulfovibrio desulfuricans were immobilized in polyacrylamide gel and used to remove soluble u and mo from water by enzymatically mediated reduction reactions in column reactors. formate or lactate served as the electron donor and oxidized u(vi) and mo(vi) species served as electron acceptors. greater than 99% removal efficiencies were achieved for both metals with initial concentrations of 5 mg/l u and 10 mg/l mo. hydraulic residence times in the columns were between 24 and 36 ...199810099409
15n-labelling and preliminary heteronuclear nmr study of desulfovibrio vulgaris hildenborough cytochrome c553.when using heteronuclear nmr, 15n-labelling is necessary for structural analysis, dynamic studies and determination of complex formation. the problems that arise with isotopic labelling of metalloproteins are due to their complex maturation process, which involves a large number of factors. cytochromes c are poorly expressed in escherichia coli and the overexpression that is necessary for 15n-labelling, requires an investigation of the expression host and special attention to growth conditions. ...199910215849
the superoxide dismutase activity of desulfoferrodoxin from desulfovibrio desulfuricans atcc 27774.desulfoferrodoxin (dfx), a small iron protein containing two mononuclear iron centres (designated centre i and ii), was shown to complement superoxide dismutase (sod) deficient mutants of escherichia coli [pianzzola, m.j., soubes m. & touati, d. (1996) j. bacteriol. 178, 6736-6742]. furthermore, neelaredoxin, a protein from desulfovibrio gigas containing an iron site similar to centre ii of dfx, was recently shown to have a significant sod activity [silva, g., oliveira, s., gomes, c.m., pacheco, ...199910215854
crystallization and preliminary crystallographic studies of fmn-binding protein from desulfovibrio vulgaris miyazaki f.the flavin mononucleotide binding protein from desulfovibrio vulgaris (miyazaki f) was crystallized using the vapour-diffusion method. the crystal belongs to the monoclinic space group p21 with unit-cell parameters a = 37.2, b = 84.6, c = 41.1 a, beta = 94.1 degrees, contains two molecules per asymmetric unit and diffracts beyond 1.2 a resolution with a synchrotron radiation x-ray source.199910216314
carboxy-terminal processing of the large subunit of [fe] hydrogenase from desulfovibrio desulfuricans atcc 7757.hyda and hydb, the genes encoding the large (46-kda) and small (13. 5-kda) subunits of the periplasmic [fe] hydrogenase from desulfovibrio desulfuricans atcc 7757, have been cloned and sequenced. the deduced amino acid sequence of the genes product showed complete identity to the sequence of the well-characterized [fe] hydrogenase from the closely related species desulfovibrio vulgaris hildenborough (g. voordouw and s. brenner, eur. j. biochem. 148:515-520, 1985). the data show that in addition ...199910217791
molecular phylogenetic and biogeochemical studies of sulfate-reducing bacteria in the rhizosphere of spartina alterniflorathe population composition and biogeochemistry of sulfate-reducing bacteria (srb) in the rhizosphere of the marsh grass spartina alterniflora was investigated over two growing seasons by molecular probing, enumerations of culturable srb, and measurements of so42- reduction rates and geochemical parameters. so42- reduction was rapid in marsh sediments with rates up to 3.5 &mgr;mol ml-1 day-1. rates increased greatly when plant growth began in april and decreased again when plants flowered in late ...199910224021
isolation and characterization of desulfovibrio burkinensis sp. nov. from an african ricefield, and phylogeny of desulfovibrio alcoholivorans.a sulfate-reducing bacterium, strain hdvt (t = type strain), was isolated from an anoxic ricefield soil. cells were gram-negative, non-sporulating curved rods motile by means of a single polar flagellum. cytochrome c3 and desulfoviridin were present. in the presence of sulfate, glycerol, 1,2- and 1,3-propanediol, dihydroxyacetone, pyruvate, lactate, fumarate, maleate, malate and succinate were incompletely oxidized mainly to acetate. sulfite, thiosulfate, elemental sulfur, fumarate, maleate and ...199910319487
desulfovibrio zosterae sp. nov., a new sulfate reducer isolated from surface-sterilized roots of the seagrass zostera marina.a sulfate-reducing bacterium, designated strain lact, was isolated from surface-sterilized roots of the benthic macrophyte zostera marina. cells were motile by means of a single polar flagellum. strain lact utilized lactate, pyruvate, malate, ethanol, l-alanine, fumarate, choline and fructose with sulfate as electron acceptor. in addition, fumarate, pyruvate and fructose were also degraded without an external electron acceptor. sulfate could be substituted with thiosulfate, sulfite and elemental ...199910319511
electrochemical study of reversible hydrogenase reaction of desulfovibrio vulgaris cells with methyl viologen as an electron electrode modified with immobilized whole cells of desulfovibrio vulgaris (hildenborough) produces an s-shaped voltammogram with both cathodic- and anodic-catalytic-limiting currents in a methyl viologen-containing buffer saturated with h2. methyl viologen penetrates into the bacterial cells to serve as an electron carrier in the reversible reaction of hydrogenase in the cells and functions as an electron-transfer mediator between the bacterial cells and the electrode, thus producing the cata ...199910330906
reduction of technetium by desulfovibrio desulfuricans: biocatalyst characterization and use in a flowthrough bioreactor.resting cells of desulfovibrio desulfuricans coupled the oxidation of a range of electron donors to tc(vii) reduction. the reduced technetium was precipitated as an insoluble low-valence oxide. the optimum electron donor for the biotransformation was hydrogen, although rapid rates of reduction were also supported when formate or pyruvate was supplied to the cells. technetium reduction was less efficient when the growth substrates lactate and ethanol were supplied as electron donors, while glycer ...199910347062
study of the interaction of sulphate-reducing bacteria exopolymers with iron using x-ray photoelectron spectroscopy and time-of-flight secondary ionisation mass spectrometry.time-of-flight secondary ionisation mass spectrometry and x-ray photoelectron spectroscopy were employed to determine the interaction of crude extracellular polymeric substances recovered from static batch cultures of two isolates of marine sulphate-reducing bacteria of the genus desulfovibrio, grown in the presence of and without mild steel surfaces, with fe ions released from steel. the results demonstrated that exopolymers synthesised by different strains of sulphate-reducers varied in their ...199910353794
simulation of electron-proton coupling with a monte carlo method: application to cytochrome c3 using continuum electrostatics.a new method is presented for simulating the simultaneous binding equilibrium of electrons and protons on protein molecules, which makes it possible to study the full equilibrium thermodynamics of redox and protonation processes, including electron-proton coupling. the simulations using this method reflect directly the ph and electrostatic potential of the environment, thus providing a much closer and realistic connection with experimental parameters than do usual methods. by ignoring the full b ...199910354425
desulfovibrio desulfuricans iron hydrogenase: the structure shows unusual coordination to an active site fe binuclear center.many microorganisms have the ability to either oxidize molecular hydrogen to generate reducing power or to produce hydrogen in order to remove low-potential electrons. these reactions are catalyzed by two unrelated enzymes: the ni-fe hydrogenases and the fe-only hydrogenases.199910368269
the primary and three-dimensional structures of a nine-haem cytochrome c from desulfovibrio desulfuricans atcc 27774 reveal a new member of the hmc family.haem-containing proteins are directly involved in electron transfer as well as in enzymatic functions. the nine-haem cytochrome c (9hcc), previously described as having 12 haem groups, was isolated from cells of desulfovibrio desulfuricans atcc 27774, grown under both nitrate- and sulphate-respiring conditions.199910368280
crystal structure of the first dissimilatory nitrate reductase at 1.9 a solved by mad methods.the periplasmic nitrate reductase (nap) from the sulphate reducing bacterium desulfovibrio desulfuricans atcc 27774 is induced by growth on nitrate and catalyses the reduction of nitrate to nitrite for respiration. nap is a molybdenum-containing enzyme with one bis-molybdopterin guanine dinucleotide (mgd) cofactor and one [4fe-4s] cluster in a single polypeptide chain of 723 amino acid residues. to date, there is no crystal structure of a nitrate reductase.199910368307
removal of the bridging ligand atom at the ni-fe active site of [nife] hydrogenase upon reduction with h2, as revealed by x-ray structure analysis at 1.4 a resolution.the active site of [nife] hydrogenase, a heterodimeric protein, is suggested to be a binuclear ni-fe complex having three diatomic ligands to the fe atom and three bridging ligands between the fe and ni atoms in the oxidized form of the enzyme. two of the bridging ligands are thiolate sidechains of cysteinyl residues of the large subunit, but the third bridging ligand was assigned as a non-protein monatomic sulfur species in desulfovibrio vulgaris miyazaki f hydrogenase.199910378274
the crystal structure of a reduced [nifese] hydrogenase provides an image of the activated catalytic center.[nifese] hydrogenases are metalloenzymes that catalyze the reaction h2<-->2h+ + 2e-. they are generally heterodimeric, contain three iron-sulfur clusters in their small subunit and a nickel-iron-containing active site in their large subunit that includes a selenocysteine (secys) ligand.199910378275
isolation of desulfovibrio intestinalis sp. nov. from the hindgut' of the lower termite mastotermes darwiniensis.a gram-negative, anaerobic sulfate-reducing bacterium was isolated from hindgut contents of the lower termite mastotermes darwiniensis froggatt (strain kms2). strain kms2 is motile by a single polar flagellum. the isolate possesses desulfoviridin and catalase activity. the g+c content of its dna is in the range of 54.5-55.5 mol% (strain kms2). it respires hydrogen and different low molecular weight organic compounds in the presence of sulfate, thiosulfate, and sulfite, and also oxygen. the isola ...199910380647
biochemical and spectroscopic characterization of overexpressed fuscoredoxin from escherichia coli.fuscoredoxin is a unique iron containing protein of yet unknown function originally discovered in the sulfate reducers of the genus desulfovibrio. it contains two iron-sulfur clusters: a cubane [4fe-4s] and a mixed oxo- and sulfido-bridged 4fe cluster of unprecedented structure. the recent determination of the genomic sequence of escherichia coli (e. coli) has revealed a homologue of fuscoredoxin in this facultative microbe. the presence of this gene in e. coli raises interesting questions regar ...199910381368
crystal structure of the oxidised and reduced acidic cytochrome c3from desulfovibrio africanus.unique among sulphate-reducing bacteria, desulfovibrio africanus has two periplasmic tetraheme cytochromes c3, one with an acidic isoelectric point which exhibits an unusually low reactivity towards hydrogenase, and another with a basic isoelectric point which shows the usual cytochrome c3reactivity. the crystal structure of the oxidised acidic cytochrome c3of desulfovibrio africanus (dva.a) was solved by the multiple anomalous diffraction (mad) method and refined to 1.6 a resolution. its struct ...199910398589
specific detection of different phylogenetic groups of chemocline bacteria based on pcr and denaturing gradient gel electrophoresis of 16s rrna gene fragments.specific amplification of 16s rrna gene fragments in combination with denaturing gradient gel electrophoresis (dgge) was used to generate fingerprints of chromatiaceae, green sulfur bacteria, desulfovibrionaceae, and beta-proteobacteria. sequencing of the gene fragments confirmed that each primer pair was highly specific for the respective phylogenetic group. applying the new primer sets, the bacterial diversity in the chemoclines of a eutrophic freshwater lake, a saline meromictic lake, and a l ...199910415169
crystallization and preliminary diffraction data analysis of both single and pseudo-merohedrally twinned crystals of rubredoxin oxygen oxidoreductase from desulfovibrio gigas.crystals of rubredoxin oxygen oxidoreductase have been obtained and characterized. they belong to space group p2(1)2(1)2, with unit-cell dimensions a = 88.24 (15), b = 101.25 (7), c = 90.80 (3) a. the homodimer (86 kda) in the asymmetric unit is related by a non-crystallographic twofold rotation axis parallel to the ab 'diagonal' direction, as shown by the self-rotation maximum in the section with chi = 180 degrees. this pseudo-crystallographic symmetry element was also found to be the twinning ...199910417417
equilibrium unfolding of a small low-potential cytochrome, cytochrome c553 from desulfovibrio understand general aspects of stability and folding of c-type cytochromes, we have studied the folding characteristics of cytochrome c553 from desulfovibrio vulgaris (hildenborough). this cytochrome is structurally similar but lacks sequence homology to other heme proteins; moreover, it has an abnormally low reduction potential. unfolding of oxidized and reduced cytochrome c553 by guanidine hydrochloride (guhcl) was monitored by circular dichroism (cd) and soret absorption; the same unfolding ...199910422842
structural studies by x-ray diffraction on metal substituted desulforedoxin, a rubredoxin-type protein.desulforedoxin (dx), isolated from the sulfate reducing bacterium desulfovibrio gigas, is a small homodimeric (2 x 36 amino acids) protein. each subunit contains a high-spin iron atom tetrahedrally bound to four cysteinyl sulfur atoms, a metal center similar to that found in rubredoxin (rd) type proteins. the simplicity of the active center in dx and the possibility of replacing the iron by other metals make this protein an attractive case for the crystallographic analysis of metal-substituted d ...199910422844
culturable populations of sporomusa spp. and desulfovibrio spp. in the anoxic bulk soil of flooded rice microcosms.most-probable-number (mpn) counts were made of homoacetogenic and other bacteria present in the anoxic flooded bulk soil of laboratory microcosms containing 90- to 95-day-old rice plants. mpn counts with substrates known to be useful for the selective enrichment or the cultivation of homoacetogenic bacteria (betaine, ethylene glycol, 2, 3-butanediol, and 3,4,5-trimethoxybenzoate) gave counts of 2.3 x 10(3) to 2.8 x 10(5) cells per g of dry soil. homoacetogens isolated from the terminal positive ...199910427044
crystal structure and mechanism of co dehydrogenase, a molybdo iron-sulfur flavoprotein containing dehydrogenase from the aerobic bacterium oligotropha carboxidovorans catalyzes the oxidation of co with h(2)o, yielding co(2), two electrons, and two h(+). its crystal structure in the air-oxidized form has been determined to 2.2 a. the active site of the enzyme, which contains molybdenum with three oxygen ligands, molybdopterin-cytosine dinucleotide and s-selanylcysteine, delivers the electrons to an intramolecular electron transport chain composed of two types of [2fe-2s] clusters and flavi ...199910430865
a phylogenetic analysis of microbial communities associated with methane hydrate containing marine fluids and sediments in the cascadia margin (odp site 892b).methane hydrates represent an enormous carbon and energy source in many low temperature deep marine sediments. however, little information is available concerning the nature of the microbial communities associated with these structures. here, we describe a phylogenetic analysis based on ribosomal dna (rdna) sequences obtained from sediment and fluid samples present in a region of gas hydrate formation in shallow sediments within the cascadia margin in and around ocean drilling program (odp) site ...199910436927
effects of protein-protein interactions on electron transfer: docking and electron transfer calculations for complexes between flavodoxin and c-type cytochromes.theoretical studies of protein-protein association and electron transfer were performed on the binary systems formed by desulfovibrio vulgaris hildenborough (d. v. h.) flavodoxin and d. v. h. cytochrome c553 and by flavodoxin and horse heart cytochrome c. initial structures for the complexes were obtained by rigid-body docking and were refined by md to allow for molecular flexibility. the structures thus obtained were analysed in terms of their relative stability through the calculation of exces ...199910439082
third human isolate of a desulfovibrio sp. identical to the provisionally named desulfovibrio fairfieldensis.desulfovibrio fairfieldensis was isolated from the urine sample of a patient with a urinary tract infection and meningoencephalitis. it was identified by 16s rrna gene amplification and sequencing.199910449514
sequencing the gene encoding desulfovibrio desulfuricans atcc 27774 nine-heme cytochrome c.contradicting early suggestions, the sequencing of the gene encoding the desulfovibrio desulfuricans (atcc 27774) nine-heme cytochrome c proves that this cytochrome is not the product of the degradation of the 16-heme containing cytochrome c [coelho et al. (1996) acta cryst. d52, 1202-1208]. however, preliminary data indicate that the cytochrome gene is part of an operon similar to the dvh hmc operon, which contains the gene coding for the 16-heme cytochrome c [rossi et al. (1993) j. bacteriol. ...199910471375
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