Publications
| Title | Abstract | Year Filter | PMID(sorted ascending) Filter |
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| application of a tetrazolium dye as an indicator of viability in anaerobic bacteria. | the use of the redox dye 5-cyano-2,3,-ditolyl tetrazolium chloride (ctc) for evaluating the metabolic activity of aerobic bacteria has gained wide application in recent years. in this study, we examined the utility of ctc in capturing the metabolic activity of anaerobic bacteria. in addition, the factors contributing to abiotic reduction of ctc were also examined. ctc was used in conjunction with the fluorochrome 5-(4,6-dichlorotriazinyl) aminofluorescein (dtaf), that targets bacterial cell wall ... | 1999 | 10480267 |
| combination of methods used in the structure solution of pyruvate:ferredoxin oxidoreductase from two crystal forms. | the structure of the homodimeric 267 kda pyruvate:ferredoxin oxidoreductase (pfor) of desulfovibrio africanus was solved with data from two crystals forms, both containing two monomers per asymmetric unit. phases were obtained from multiwavelength anomalous dispersion (mad), solvent flattening (sf), molecular replacement (mr) using a 5 a resolution electron-density search model, multiple isomorphous replacement (mir) and, finally, electron-density averaging (da) procedures. it is shown how the c ... | 1999 | 10489442 |
| structural and kinetic studies of the pyruvate-ferredoxin oxidoreductase/ferredoxin complex from desulfovibrio africanus. | the pyruvate-ferredoxin oxidoreductase (pfor)/ferredoxin (fd) system of desulfovibrio africanus has been investigated with the aim of understanding more fully protein-protein interaction and the kinetic characteristics of electron transfer between the two redox partners. d. africanus contains three fds (fd i, fd ii and fd iii) able to function as electron acceptors for pfor. the complete amino acid sequence of fd ii was determined by automatic edman degradation. it revealed a striking similarity ... | 1999 | 10491097 |
| degradation of maltose by proliferating cells of desulfovibrio desulfuricans 2198. | desulfovibrio desulfuricans 2198 can grow on maltose-based medium only in the presence of yeast extract. the results of kinetic measurements of maltose consumption by the cells show that there is no marked difference in km and vmax values for this bacterium versus other carbohydrate-utilizing microorganisms. the determination of some enzymes of sugar metabolism in d. desulfuricans 2198 suggests that maltose degradation occurs by the embden--meyerhof pathway. the cell extract also contains glucos ... | 1999 | 10498814 |
| ab initio structure solution of a dimeric cytochrome c3 from desulfovibrio gigas containing disulfide bridges. | the 1.2 a resolution crystal structure of the 29 kda di-tetrahaem cytochrome c3 from the sulfate reducing bacterium desulfovibrio gigas was solved by ab initio methods, making this the largest molecule to be solved by this procedure. the actual refined model of the cysteine-linked dimeric molecule reveals that this molecule is very similar to the non-covalently linked symmetrical dimer of the di-tetrahaem cytochrome c3 from desulfomicrobium norvegicum. each monomer has the typical polypeptide fo ... | 1999 | 10499086 |
| comparative redox and pka calculations on cytochrome c3 from several desulfovibrio species using continuum electrostatic methods. | a comparative study of the ph-dependent redox mechanisms of several members of the cytochrome c3 family has been carried out. in a previous work, the molecular determinants of this dependency (the so-called redox-bohr effect) were investigated for one species using continuum electrostatic methods to find groups with a titrating range and strength of interaction compatible with a mediating role in the redox-bohr effect. here we clarify these aspects in the light of new and improved pka calculatio ... | 1999 | 10499105 |
| inhibiting sulfate-reducing bacteria in biofilms on steel with antimicrobial peptides generated in situ. | in batch and continuous fermentations, the reduction in corrosion of sae 1018 mild steel and 304 stainless steel caused by inhibition of the reference sulfate-reducing bacterium (srb) desulfovibrio vulgaris by a protective, antimicrobial-producing bacillus brevis biofilm was investigated. the presence of d. vulgaris produced a thick black precipitate on mild steel and a higher corrosion rate in batch cultures than that seen in a mono-culture of non-antimicrobial-producing pseudomonas fragi k upo ... | 1999 | 10499267 |
| sulfonates as terminal electron acceptors for growth of sulfite-reducing bacteria (desulfitobacterium spp.) and sulfate-reducing bacteria: effects of inhibitors of sulfidogenesis. | this study demonstrates the ability of desulfitobacterium spp. to utilize aliphatic sulfonates as terminal electron acceptors (tea) for growth. isethionate (2-hydroxyethanesulfonate) reduction by desulfitobacterium hafniense resulted in acetate as well as sulfide accumulation in accordance with the expectation that the carbon portion of isethionate was oxidized to acetate and the sulfur was reduced to sulfide. the presence of a polypeptide, approximately 97 kda, was evident in isethionate-grown ... | 1999 | 10508097 |
| epr spectroscopy: a powerful technique for the structural and functional investigation of metalloproteins. | numerous metal centers in proteins can be prepared in a redox state in which their ground state is paramagnetic. complementary data provided by epr, mössbauer, electron nuclear double resonance, magnetic circular dichroism, and nmr spectroscopies have therefore played a major role in the elucidation of the structure and function of these centers. among those techniques the most commonly used is certainly epr spectroscopy. in this article various aspects of the current applications of epr to the ... | 1999 | 10512534 |
| first isolation of desulfovibrio species as part of a polymicrobial infection from a brain abscess. | 1999 | 10517202 | |
| adhesion of biodegradative anaerobic bacteria to solid surfaces. | in order to exploit the ability of anaerobic bacteria to degrade certain contaminants for bioremediation of polluted subsurface environments, we need to understand the mechanisms by which such bacteria partition between aqueous and solid phases, as well as the environmental conditions that influence partitioning. we studied four strictly anaerobic bacteria, desulfomonile tiedjei, syntrophomonas wolfei, syntrophobacter wolinii, and desulfovibrio sp. strain g11, which theoretically together can co ... | 1999 | 10543826 |
| analyses of spatial distributions of sulfate-reducing bacteria and their activity in aerobic wastewater biofilms. | the vertical distribution of sulfate-reducing bacteria (srb) in aerobic wastewater biofilms grown on rotating disk reactors was investigated by fluorescent in situ hybridization (fish) with 16s rrna-targeted oligonucleotide probes. to correlate the vertical distribution of srb populations with their activity, the microprofiles of o(2), h(2)s, no(2)(-), no(3)(-), nh(4)(+), and ph were measured with microelectrodes. in addition, a cross-evaluation of the fish and microelectrode analyses was perfor ... | 1999 | 10543829 |
| acetogenic and sulfate-reducing bacteria inhabiting the rhizoplane and deep cortex cells of the sea grass halodule wrightii. | recent declines in sea grass distribution underscore the importance of understanding microbial community structure-function relationships in sea grass rhizospheres that might affect the viability of these plants. phospholipid fatty acid analyses showed that sulfate-reducing bacteria and clostridia were enriched in sediments colonized by the sea grasses halodule wrightii and thalassia testudinum compared to an adjacent unvegetated sediment. most-probable-number analyses found that in contrast to ... | 1999 | 10543830 |
| orientation-selected endor of the active center in chromatium vinosum [nife] hydrogenase in the oxidized "ready" state. | electron nuclear double resonance (endor) was applied to study the active site of the oxidized "ready" state, ni(r), in the [nife] hydrogenase of chromatium vinosum. the magnetic field dependence of the epr was used to select specific subsets of molecules contributing to the endor response by stepping through the epr envelope. three hyperfine couplings could be clearly followed over the complete field range. two protons, h1 and h2, display a very similar large isotropic coupling of 12.5 and 12.6 ... | 1999 | 10555572 |
| the solution structure of a [3fe-4s] ferredoxin: oxidised ferredoxin ii from desulfovibrio gigas. | the use of standard 2d nmr experiments in combination with 1d noe experiments allowed the assignment of 51 of the 58 spin systems of oxidised [3fe4s] ferredoxin isolated from desulfovibrio gigas. the nmr solution structure was determined using data from 1d noe and 2d noesy spectra, as distance constraints, and information from the x-ray structure for the spin systems not detected by nmr in torsion angle dynamics calculations to produce a family of 15 low target function structures. the quality o ... | 1999 | 10555576 |
| nine-haem cytochrome c from desulfovibrio desulfuricans atcc 27774:primary sequence determination, crystallographic refinement at 1.8 and modelling studies of its interaction with the tetrahaem cytochrome c3. | a monomeric nine-haem cytochrome c (9hcc) with 292 amino acid residues was isolated from cells of the sulfate- and nitrate-reducing bacterium desulfovibrio desulfuricans atcc 27774 grown under both nitrate- and sulfate-respiring conditions. the nucleotide sequence encoding the 292 residues was determined, allowing the correction of about 10% of the previous primary structure, determined from 1.8 a electron density maps. the refinement at 1.8 a resolution of the structural model was completed, gi ... | 1999 | 10555582 |
| carbon monoxide and cyanide ligands in a classical organometallic complex model for fe-only hydrogenase. | the fe(i) organometallic complex [(µ-sch(2)ch(2)ch(2)s)fe(2)(co)(6)] provides a structural model for the cyano-carbonyl diiron site of fe-only hydrogenase as characterized by x-ray crystallography (the picture shows the structure (black) of the model overlaid with that of the fe-fe dimetallic site in the hydrogenase isolated from desulfovibrio desulfuricans). cyanide substitution of co occurs readily and provides spectroscopic references for the active site. | 1999 | 10556894 |
| a proton-nmr investigation of the fully reduced cytochrome c7 from desulfuromonas acetoxidans. comparison between the reduced and the oxidized forms. | the solution structure via 1h nmr of the fully reduced form of cytochrome c7 has been obtained. the protein sample was kept reduced by addition of catalytic amounts of desulfovibrio gigas iron hydrogenase in h2 atmosphere after it had been checked that the presence of the hydrogenase did not affect the nmr spectrum. a final family of 35 conformers with rmsd values with respect to the mean structure of 8.7 +/- 1.5 nm and 12.4 +/- 1.3 nm for the backbone and heavy atoms, respectively, was obtained ... | 1999 | 10561607 |
| microbial reduction of technetium by escherichia coli and desulfovibrio desulfuricans: enhancement via the use of high-activity strains and effect of process parameters. | escherichia coli and desulfovibrio desulfuricans reduce tc(vii) (tco(4)(-)) with formate or hydrogen as electron donors. the reaction is catalyzed by the hydrogenase component of the formate hydrogenlyase complex (fhl) of e. coli and is associated with a periplasmic hydrogenase activity in d. desulfuricans. tc(vii) reduction in e. coli by h(2) and formate was either inhibited or repressed by 10 mm nitrate. by contrast, tc(vii) reduction catalyzed by d. desulfuricans was less sensitive to nitrate ... | 1999 | 10567070 |
| mapping the cytochrome c553 interacting site using 1h and 15n nmr. | cytochrome c553 is the electron transfer partner of formate dehydrogenase and of [fel-hydrogenase, two metalloenzymes essential in the metabolism of sulfate reducing bacteria. these two enzymes contain a 'ferredoxin-like' domain which presents 30% identity with desulfovibrio desulfuricans norway ferredoxin 1. this was chosen as a model for the 'ferredoxin-like' domain involved in the electron transfer reaction with cytochrome c553. id nmr titration of complex formation gave us the stoichiometry ... | 1999 | 10571064 |
| amino acid replacements at the h2-activating site of the nad-reducing hydrogenase from alcaligenes eutrophus. | the role of amino acid residues in the h(2)-activating subunit (hoxh) of the nad-reducing hydrogenase (sh) from alcaligenes eutrophus has been investigated by site-directed mutagenesis. conserved residues in the n-terminal l1 (rgxe) and l2 (rxcgxcx(3)h) and the c-terminal l5 (dpcx(2)cx(2)h/r) motifs of the active site-harboring subunit were chosen as targets. crystal structure analysis of the [nife] hydrogenase from desulfovibrio gigas uncovered two pairs of cysteines (motifs l2 and l5) as coord ... | 1999 | 10572008 |
| purification and characterization of a tungsten-containing formate dehydrogenase from desulfovibrio gigas. | an air-stable formate dehydrogenase (fdh), an enzyme that catalyzes the oxidation of formate to carbon dioxide, was purified from the sulfate reducing organism desulfovibrio gigas (d. gigas) ncib 9332. d. gigas fdh is a heterodimeric protein [alpha (92 kda) and beta (29 kda) subunits] and contains 7 +/- 1 fe/protein and 0.9 +/- 0.1 w/protein. selenium was not detected. the uv/visible absorption spectrum of d. gigas fdh is typical of an iron-sulfur protein. analysis of pterin nucleotides yielded ... | 1999 | 10587462 |
| a sequential electron transfer from hydrogenases to cytochromes in sulfate-reducing bacteria. | a central step in the energy metabolism of sulfate-reducing bacteria is the oxidation of molecular hydrogen, catalyzed by a periplasmic hydrogenase. the resulting electrons are then transferred to various electron transport chains and used for cytoplasmic sulfate reduction. the complex formation between [nifese] hydrogenase and the soluble periplasmic polyheme cytochromes from desulfomicrobium norvegicum was characterized by cross-linking experiments, biacore and kinetics analysis. analysis of e ... | 2000 | 10606770 |
| structure and mechanism of iron-only hydrogenases. | the recent elucidation of the structures of iron-only hydrogenases from the microorganisms clostridium pasteurianum and desulfovibrio desulfuricans has revealed that the presumed site of reversible hydrogen oxidation exists as a unique, protein-associated organometallic prosthetic group. details of the hydrogenase structures provide insight into the chemical mechanism of this highly evolved catalyst. | 1999 | 10607666 |
| comparisons of wild-type and mutant flavodoxins from anacystis nidulans. structural determinants of the redox potentials. | the long-chain flavodoxins, with 169-176 residues, display oxidation-reduction potentials at ph 7 that vary from -50 to -260 mv for the oxidized/semiquinone (ox/sq) equilibrium and are -400 mv or lower for the semiquinone/hydroquinone (sq/hq) equilibrium. to examine the effects of protein interactions and conformation changes on fmn potentials in the long-chain flavodoxin from anacystis nidulans (synechococcus pcc 7942), we have determined crystal structures for the semiquinone and hydroquinone ... | 1999 | 10610792 |
| axenic aerobic biofilms inhibit corrosion of copper and aluminum. | the corrosion behavior of unalloyed copper and aluminum alloy 2024 in modified baar's medium has been studied with continuous reactors using electrochemical impedance spectroscopy. an axenic aerobic biofilm of either pseudomonas fragi k or bacillus brevis 18 was able to lessen corrosion as evidenced by a consistent 20-fold increase in the low-frequency impedance value of copper as well as by a consistent four- to seven-fold increase in the polarization resistance of aluminum 2024 after six days ... | 1999 | 10616712 |
| reaction of the desulfoferrodoxin from desulfoarculus baarsii with superoxide anion. evidence for a superoxide reductase activity. | desulfoferrodoxin is a small protein found in sulfate-reducing bacteria that contains two independent mononuclear iron centers, one ferric and one ferrous. expression of desulfoferrodoxin from desulfoarculus baarsii has been reported to functionally complement a superoxide dismutase deficient escherichia coli strain. to elucidate by which mechanism desulfoferrodoxin could substitute for superoxide dismutase in e. coli, we have purified the recombinant protein and studied its reactivity toward o- ... | 2000 | 10617593 |
| purification and characterization of an iron superoxide dismutase and a catalase from the sulfate-reducing bacterium desulfovibrio gigas. | the iron-containing superoxide dismutase (fesod; ec 1.15.1.1) and catalase (ec 1.11.1.6) enzymes constitutively expressed by the strictly anaerobic bacterium desulfovibrio gigas were purified and characterized. the fesod, isolated as a homodimer of 22-kda subunits, has a specific activity of 1,900 u/mg and exhibits an electron paramagnetic resonance (epr) spectrum characteristic of high-spin ferric iron in a rhombically distorted ligand field. like other fesods from different organisms, d. gigas ... | 2000 | 10633116 |
| two new arsenate/sulfate-reducing bacteria: mechanisms of arsenate reduction. | two sulfate-reducing bacteria, which also reduce arsenate, were isolated; both organisms oxidized lactate incompletely to acetate. when using lactate as the electron donor, one of these organisms, desulfomicrobium strain ben-rb, rapidly reduced (doubling time = 8 h) 5.1 mm arsenate at the same time it reduced sulfate (9.6 mm). sulfate reduction was not inhibited by the presence of arsenate. arsenate could act as the terminal electron acceptor in minimal medium (doubling time = 9 h) in the absenc ... | 2000 | 10648104 |
| the hybrid-cluster protein ('prismane protein') from escherichia coli. characterization of the hybrid-cluster protein, redox properties of the [2fe-2s] and [4fe-2s-2o] clusters and identification of an associated nadh oxidoreductase containing fad and [2fe-2s]. | hybrid-cluster proteins ('prismane proteins') have previously been isolated and characterized from strictly anaerobic sulfate-reducing bacteria. these proteins contain two types of fe/s clusters unique in biological systems: a [4fe-4s] cubane cluster with spin-admixed s = 3/2 ground-state paramagnetism and a novel type of hybrid [4fe-2s-2o] cluster, which can attain four redox states. genomic sequencing reveals that genes encoding putative hybrid-cluster proteins are present in a range of bacter ... | 2000 | 10651802 |
| cytochrome c(3) mutants of desulfovibrio desulfuricans. | to explore the physiological role of tetraheme cytochrome c(3) in the sulfate-reducing bacterium desulfovibrio desulfuricans g20, the gene encoding the preapoprotein was cloned, sequenced, and mutated by plasmid insertion. the physical analysis of the dna from the strain carrying the integrated plasmid showed that the insertion was successful. the growth rate of the mutant on lactate with sulfate was comparable to that of the wild type; however, mutant cultures did not achieve the same cell dens ... | 2000 | 10653734 |
| bacteremia caused by a strain of desulfovibrio related to the provisionally named desulfovibrio fairfieldensis. | eight isolates of desulfovibrio spp. have been obtained over 5 years from abdominal or brain abscesses or blood. seven isolates were part of a mixed flora [corrected]. one strain was isolated in pure culture from the blood of a patient with peritonitis of appendicular origin. according to the 16s rrna gene sequences, this strain was close to desulfovibrio fairfieldensis. the present report describes the fourth isolate of this recently described species to be isolated in pure culture or as a pred ... | 2000 | 10655421 |
| crystallization and preliminary x-ray analysis of a membrane-bound nitrite reductase from desulfovibrio desulfuricans atcc 27774. | nitrite reductase from the sulfate-reducing bacterium desulfovibrio desulfuricans atcc 27774 is a multihaem (type c) membrane-bound enzyme that catalyzes the dissimilatory conversion of nitrite to ammonia. crystals of the oxidized form of this enzyme were obtained using peg and cacl(2) as precipitants in the presence of 3--(decylmethylammonium)propane-1-sulfonate and belong to the space group p2(1)2(1)2(1), with unit-cell parameters a = 78.94, b = 104.59, c = 143.18 a. a complete data set to 2.3 ... | 2000 | 10666610 |
| adaptation of pregnant ewes to an exclusive onion diet. | a diet consisting entirely of cull onions fed to pregnant ewes produced heinz body hemolytic anemia in all sheep after 21 d. after 28 d of daily consumption of 20 kg of onions/ewe, the anemia stabilized, and for the remaining 74 d the packed cell volume increased in the majority of sheep, although it did not return to normal. compared to control ewes fed an alfalfa and grain diet, the onion-fed ewes had comparable body condition scores and fleece weights. there was no significant difference (alp ... | 2000 | 10670075 |
| resonance raman study of multihemic c-type cytochromes from desulfuromonas acetoxidans. | two multihemic cytochromes c from the sulfur reducing bacteria desulfuromonas acetoxidans have been studied by optical and resonance raman spectroscopy: cytochrome c551.5, a trihemic cytochrome and cytochrome c mr 50 000, a recently isolated high molecular mass cytochrome. the redox and raman characteristics of cytochrome c551.5 are compared to those of the tetrahemic cytochromes c3 from desulfovibrio. while the redox behavior, followed by spectroelectrochemistry, is similar to that of cytochrom ... | 2000 | 10672013 |
| ferredoxin iii of desulfovibrio africanus: sequencing of the native gene and characterization of a histidine-tagged form. | desulfovibrio africanus ferredoxin iii (da fdiii) contains one [4fe-4s](2+/1+) cluster and one [3fe-4s](1+/0) cluster, bound by seven cys residues, in which the [3fe-4s] cluster is co-ordinated by the unusual sequence, cys(11)-xaa-xaa-asp(14)-xaa-xaa-cys(17)-xaa(n)-cys(51)-glu. the [3fe-4s] core of this ferredoxin is so far unique in showing rapid bi-directional [3fe-4s]<-->[4fe-4s] cluster interconversion with a wide range of metal ions. in order to obtain protein for mutagenesis studies da fdi ... | 2000 | 10677356 |
| formation of aniline as a transient metabolite during the metabolism of tetryl by a sulfate-reducing bacterial consortium. | a laboratory study was conducted to determine whether tetryl (2,4,6-trinitrophenylmethylnitramine) can be degraded by an anaerobic process. the results indicated that the metabolic conversion of tetryl to aniline is possible by a sulfate-reducing bacterial (srb) consortium. this srb consortium metabolized tetryl by co-metabolism with pyruvate as a growth substrate. for every mole of tetryl metabolized, 1 mole of aniline was produced, and the aniline was further metabolized. this metabolic conver ... | 2000 | 10679052 |
| expression of a desulfovibrio tetraheme cytochrome c in escherichia coli. | a tetraheme cytochrome c was successfully overexpressed for the first time in escherichia coli. desulfovibrio desulfuricans atcc 27774 tetraheme cytochrome c(3) was expressed in aerobically grown escherichia coli cotransformed with escherichia coli ccm gene cluster (arslan et al. (1998) bioch. biophys. res. commun. 251, 744-747). the analysis of the produced cytochrome showed that the signal peptide was correctly cleaved, the four heme groups were inserted and the electronic structure around the ... | 2000 | 10679266 |
| biochemical/spectroscopic characterization and preliminary x-ray analysis of a new aldehyde oxidoreductase isolated from desulfovibrio desulfuricans atcc 27774. | aldehyde oxidoreductase (aor) activity has been found in different sulfate reducing organisms (moura, j. j. g., and barata, b. a. s. (1994) in methods in enzymology (peck, h. d., jr., and legall, j., eds.), vol. 243, chap. 4. academic press; romão, m. j., knäblein, j., huber, r., and moura, j. j. g. (1997) prog. biophys. mol. biol. 68, 121-144). the enzyme was purified to homogeneity from extracts of desulfovibrio desulfuricans (dd) atcc 27774, a sulfate reducer that can use sulfate or nitrate a ... | 2000 | 10679276 |
| characterization of novel proteins based on known protein structures. | the genome sciences face the challenge to characterize structure and function of a vast number of novel genes. sequence search techniques are used to infer functional and structural information from similarities to experimentally characterized genes or proteins. the persistent goal is to refine these techniques and to develop alternative and complementary methods to increase the range of reliable inference.here, we focus on the structural and functional assignments that can be inferred from the ... | 2000 | 10686110 |
| slow formation of [3fe-4s](1+) clusters in mutant forms of desulfovibrio africanus ferredoxin iii. | desulfovibrio africanus ferredoxin iii (da fdiii) readily interconverts between a 7fe and an 8fe form with asp-14 believed to provide a cluster ligand in the latter form. to investigate the factors important for cluster interconversion in fe/s cluster-containing proteins we have studied two variants of da fdiii produced by site-directed mutagenesis, asp14glu and asp14his, with cluster incorporation performed in vitro. characterisation of these proteins by uv/visible, epr and (1)h nmr spectroscop ... | 2000 | 10692579 |
| competitive pcr-dgge analysis of bacterial mixtures: an internal standard and an appraisal of template enumeration accuracy. | analysis of polymerase chain reaction (pcr) amplified 16s rdna fragments from environmental samples by denaturing gradients of chemicals or heat [denaturing gradient gel electrophoresis (dgge) and thermal gradient gel electrophoresis (tgge)] within polyacrylamide gels is a popular tool in microbial ecology. difficulties in acceptance of the technique and interpretation of the results remain, due to its qualitative nature. in this study we have addressed this problem by the construction and evalu ... | 2000 | 10699667 |
| construction of multicomponent catalytic films based on avidin-biotin technology for the electroenzymatic oxidation of molecular hydrogen. | two methods based on the avidin-biotin technology were developed for the multimonolayer immobilization of desulfovibrio gigas hydrogenase on glassy carbon or gold electrodes. in both methods the molecular structure of the modified interface was the result of a step-by-step process. the first method alternates monolayers of avidin and biotinylated hydrogenase, the mediator (methyl viologen) being free to diffuse in the structure. in the second method, the avidin monolayers were used to immobilize ... | 2000 | 10699866 |
| structures of the superoxide reductase from pyrococcus furiosus in the oxidized and reduced states. | superoxide reductase (sor) is a blue non-heme iron protein that functions in anaerobic microbes as a defense mechanism against reactive oxygen species by catalyzing the reduction of superoxide to hydrogen peroxide [jenney, f. e., jr., verhagen, m. f. j. m., cui, x. , and adams, m. w. w. (1999) science 286, 306-309]. crystal structures of sor from the hyperthermophilic archaeon pyrococcus furiosus have been determined in the oxidized and reduced forms to resolutions of 1.7 and 2.0 a, respectively ... | 2000 | 10704199 |
| heteronuclear nmr and soft docking: an experimental approach for a structural model of the cytochrome c553-ferredoxin complex. | the combination of docking algorithms with nmr data has been developed extensively for the studies of protein-ligand interactions. however, to extend this development for the studies of protein-protein interactions, the intermolecular noe constraints, which are needed, are more difficult to access. in the present work, we describe a new approach that combines an ab initio docking calculation and the mapping of an interaction site using chemical shift variation analysis. the cytochrome c553-ferre ... | 2000 | 10704202 |
| analysis of the electron paramagnetic resonance properties of the [2fe-2s]1+ centers in molybdenum enzymes of the xanthine oxidase family: assignment of signals i and ii. | molybdoenzymes of the xanthine oxidase family contain two [2fe-2s](1+,2+) clusters that are bound to the protein by very different cysteine motifs. in the x-ray crystal structure of desulfovibrio gigas aldehyde oxidoreductase, the cluster ligated by a ferredoxin-type motif is close to the protein surface, whereas that ligated by an unusual cysteine motif is in contact with the molybdopterin [romao, m. j., archer, m., moura, i., moura, j. j. g., legall, j., engh, r., schneider, m., hof, p., and h ... | 2000 | 10704221 |
| gene sequence and crystal structure of the aldehyde oxidoreductase from desulfovibrio desulfuricans atcc 27774. | the aldehyde oxidoreductase (mod) isolated from the sulfate reducer desulfovibrio desulfuricans (atcc 27774) is a member of the xanthine oxidase family of molybdenum-containing enzymes. it has substrate specificity similar to that of the homologous enzyme from desulfovibrio gigas (mop) and the primary sequences from both enzymes show 68 % identity. the enzyme was crystallized in space group p6(1)22, with unit cell dimensions of a=b=156.4 a and c=177.1 a, and diffraction data were obtained to bey ... | 2000 | 10704312 |
| how do the x-ray structure and the nmr structure of fmn-binding protein differ? | the crystal structure of fmn-binding protein (fmn-bp) from desulfovibrio vulgaris miyazaki f was solved by the multiple isomorphous replacement method and refined to an r factor of 15.1% at 1.3 a resolution. fmn-bp exists in a dimeric form in the crystal, in contrast to the monomeric structure determined by nmr. r.m.s. deviations between the crystal structure and the solution structure are more than 2 a, which implies significant differences. there are some hydrophobic residues in the interface ... | 2000 | 10713530 |
| aldehyde oxidoreductase activity in desulfovibrio alaskensis ncimb 13491 epr assignment of the proximal [2fe-2s] cluster to the mo site. | a novel molybdenum iron-sulfur-containing aldehyde oxidoreductase (aor) belonging to the xanthine oxidase family was isolated and characterized from the sulfate-reducing bacterium desulfovibrio alaskensis ncimb 13491, a strain isolated from a soured oil reservoir in purdu bay, alaska. d. alaskensis aor is closely related to other aors isolated from the desulfovibrio genus. the protein is a 97-kda homodimer, with 0.6 +/- 0.1 mo, 3.6 +/- 0.1 fe and 0.9 +/- 0.1 pterin cytosine dinucleotides per mon ... | 2000 | 10727945 |
| evidence for the presence of an f-type atp synthase involved in sulfate respiration in desulfovibrio vulgaris. | using a library of genomic dna from desulfovibrio vulgaris miyazaki f, a strict anaerobe, and two synthetic deoxyoligonucleotide probes designed for f-type atpases, the genes for open reading frames (orfs) 1 to 5 were cloned and sequenced. the predicted protein sequences of the gene products indicate that they are composed of 172, 488, 294, 471, and 134 amino acids, respectively, and that they share considerable identity at the amino acid level with delta, alpha, gamma, beta, and epsilon subunit ... | 2000 | 10735863 |
| sediment microbial community structure and mercury methylation in mercury-polluted clear lake, california. | spatial and temporal variations in sediment microbial community structure in a eutrophic lake polluted with inorganic mercury were identified using polar lipid fatty acid (plfa) analysis. microbial community structure was strongly related to mercury methylation potential, sediment organic carbon content, and lake location. pore water sulfate, total mercury concentrations, and organic matter c/n ratios showed no relationships with microbial community structure. seasonal changes and changes potent ... | 2000 | 10742230 |
| desulfovibrio desulfuricans bacteremia in a dog. | desulfovibrio desulfuricans was isolated from the blood of a dog presenting with fever, anorexia, and rear limb stiffness. the isolate was identified by 16s rrna gene amplification and sequencing. | 2000 | 10747176 |
| structural model of the fe-hydrogenase/cytochrome c553 complex combining transverse relaxation-optimized spectroscopy experiments and soft docking calculations. | fe-hydrogenase is a 54-kda iron-sulfur enzyme essential for hydrogen cycling in sulfate-reducing bacteria. the x-ray structure of desulfovibrio desulfuricans fe-hydrogenase has recently been solved, but structural information on the recognition of its redox partners is essential to understand the structure-function relationships of the enzyme. in the present work, we have obtained a structural model of the complex of fe-hydrogenase with its redox partner, the cytochrome c(553), combining docking ... | 2000 | 10748163 |
| structural basis for the network of functional cooperativities in cytochrome c(3) from desulfovibrio gigas: solution structures of the oxidised and reduced states. | cytochrome c(3) is a 14 kda tetrahaem protein that plays a central role in the bioenergetic metabolism of desulfovibrio spp. this involves an energy transduction mechanism made possible by a complex network of functional cooperativities between redox and redox/protolytic centres (the redox-bohr effect), which enables cytochrome c(3) to work as a proton activator. the three-dimensional structures of the oxidised and reduced desulfovibrio gigas cytochrome c(3) in solution were solved using 2d (1)h ... | 2000 | 10756105 |
| hydroxyhydroquinone reductase, the initial enzyme involved in the degradation of hydroxyhydroquinone (1,2,4-trihydroxybenzene) by desulfovibrio inopinatus. | the recently isolated sulfate reducer desulfovibrio inopinatus oxidizes hydroxyhydroquinone (1,2,4trihydroxybenzene; hhq) to 2 mol acetate and 2 mol co2 (mol substrate)-1, with stoichiometric reduction of sulfate to sulfide. none of the key enzymes of fermentative hhq degradation, i.e. hhq-1,2,3,5-tetrahydroxybenzene transhydroxylase or phloroglucinol reductase, were detected in cell-free extracts of d. inopinatus, indicating that this bacterium uses a different pathway for anaerobic hhq degrada ... | 2000 | 10763753 |
| single crystal epr studies of the oxidized active site of [nife] hydrogenase from desulfovibrio vulgaris miyazaki f. | the ni-a and the ni-b forms of the [nife] hydrogenase from desulfovibrio vulgaris miyazaki f have been studied in single crystals by continuous wave and pulsed epr spectroscopy at different temperatures (280 k, 80 k, and 10 k). for the first time, the orientation of the g-tensor axes with respect to the recently published atomic structure of the active site at 1.8 a resolution was elucidated for ni-a and ni-b. the determined g-tensors have a similar orientation. the configuration of the electron ... | 2000 | 10766434 |
| characterization of the desulforubidin operons from desulfobacter vibrioformis and desulfobulbus rhabdoformis. | the genes encoding the desulforubidin type of dissimilatory sulfite reductase (dsr) from the sulfate-reducing bacteria desulfobacter vibrioformis and desulfobulbus rhabdoformis were cloned and sequenced. similar to the genes for dissimilatory sulfite reductase from the genera archaeoglobus, desulfovibrio and desulfotomaculum the dsr genes were found to form an operon, dsrabd, where dsra and dsrb encode the structural subunits, alpha and beta, of dsr, respectively. dsrd encodes a conserved unknow ... | 2000 | 10779710 |
| [effect of gas phase composition on formation of hydrocarbons by desulfovibrio desulfuricans]. | changes in the synthesis of extracellular metabolic products generated by sulfate-reducing bacteria desulfovibrio desulfuricans grown on a lactate-containing mineral medium in the presence of h2 and co2 at various volume ratios in the gaseous phase were studied. an increase in the amount of extracellular products synthesized by the bacteria was observed at an h2/co2 ratio of 3:1. high concentrations of molecular hydrogen (80-95%) in the presence of 5-20% co2 facilitated the synthesis of hydrocar ... | 2000 | 10780008 |
| thermostabilization of proteins by diglycerol phosphate, a new compatible solute from the hyperthermophile archaeoglobus fulgidus. | diglycerol phosphate accumulates under salt stress in the archaeon archaeoglobus fulgidus (l. o. martins, r. huber, h. huber, k. o. stetter, m. s. da costa, and h. santos, appl. environ. microbiol. 63:896-902, 1997). this solute was purified after extraction from the cell biomass. in addition, the optically active and the optically inactive (racemic) forms of the compound were synthesized, and the ability of the solute to act as a protecting agent against heating was tested on several proteins d ... | 2000 | 10788369 |
| molecular ecological analysis of the succession and diversity of sulfate-reducing bacteria in the mouse gastrointestinal tract. | intestinal sulfate-reducing bacteria (srb) growth and resultant hydrogen sulfide production may damage the gastrointestinal epithelium and thereby contribute to chronic intestinal disorders. however, the ecology and phylogenetic diversity of intestinal dissimilatory srb populations are poorly understood, and endogenous or exogenous sources of available sulfate are not well defined. the succession of intestinal srb was therefore compared in inbred c57bl/6j mice using a pcr-based metabolic molecul ... | 2000 | 10788396 |
| secondary structure analysis of the dissimilatory sulphite reductase in desulfovibrio desulfuricans. | the complete sequences of the dsra and dsrb genes coding for the alpha- and beta-subunits, respectively, of the sulphite reductase enzyme in desulfovibrio desulfuricans were determined. analyses of the amino acid sequences indicated a number of serohaem/fe4s4 binding consensus sequences whilst predictive secondary structure analysis revealed a similar pattern of alpha-helix and beta-strand structures between the two subunits which was indicative of gene duplication. | 2000 | 10792666 |
| adenylylsulfate reductases from archaea and bacteria are 1:1 alphabeta-heterodimeric iron-sulfur flavoenzymes--high similarity of molecular properties emphasizes their central role in sulfur metabolism. | highly active adenylylsulfate (aps) reductase was isolated under n(2)/h(2) from sulfate-reducing and sulfide-oxidizing bacteria and archaea. it was a 1:1 alphabeta-heterodimer of molecular mass approximately 95 kda, and two subunits (alpha approximately 75, beta approximately 20 kda). the specific activity was 11-14 micromol (min mg)(-1); cofactor analysis revealed 0.96+/-0.05 fad, 7.5+/-0.1 fe and 7.9+/-0.25 s(2-). the photochemically reduced enzyme had a multiline epr spectrum resulting from t ... | 2000 | 10802060 |
| sensitivity enhancement in (hca)conh experiments. | a novel sensitivity-enhancement technique is proposed for experiments which correlate protein backbone resonances and start with magnetization from 13calpha-1halpha groups. the technique is based on replenishing magnetization lost by dipole-csa cross-correlated relaxation of the 13calpha spin with 13calpha steady state magnetization. the principle is demonstrated for the (hca)conh experiment, resulting in 1.6-fold sensitivity enhancement compared to the hn(ca)co experiment. furthermore, other ve ... | 2000 | 10805129 |
| preliminary x-ray crystallographic study of dsrd protein from the sulfate-reducing bacterium desulfovibrio vulgaris. | dsrd (dissimilatory sulfite reductase d) protein encoded by the dsr operon of the sulfate-reducing bacterium desulfovibrio vulgaris hildenborough has been crystallized using the vapour-diffusion method with ammonium sulfate as a precipitating agent. the crystals diffract to 1.7 a resolution and belong to the orthorhombic space group p2(1)2(1)2(1), with unit-cell parameters a = 60.54 (6), b = 65. 20 (4), c = 46.41 (3) a. the crystal contains two dsrd molecules per asymmetric unit, giving a matthe ... | 2000 | 10818354 |
| a hemerythrin-like domain in a bacterial chemotaxis protein. | hemerythrin (hr) is an o(2)-carrying protein found in some marine invertebrates. a conserved sequence motif in all hrs provides five histidine and two carboxylate ligands to an oxo-/hydroxo-bridged diiron active site, as well as a hydrophobic o(2) binding pocket. database searches located a previously unrecognized hr-like sequence motif at the 3' end of the gene, dcrh, from the anaerobic sulfate-reducing bacterium, desulfovibrio (d.) vulgaris (hildenborough). this gene encodes a putative methyl- ... | 2000 | 10819979 |
| isolation and characterization of desulfovibrio dechloracetivorans sp. nov., a marine dechlorinating bacterium growing by coupling the oxidation of acetate to the reductive dechlorination of 2-chlorophenol. | strain sf3, a gram-negative, anaerobic, motile, short curved rod that grows by coupling the reductive dechlorination of 2-chlorophenol (2-cp) to the oxidation of acetate, was isolated from san francisco bay sediment. strain sf3 grew at concentrations of nacl ranging from 0.16 to 2.5%, but concentrations of kcl above 0. 32% inhibited growth. the isolate used acetate, fumarate, lactate, propionate, pyruvate, alanine, and ethanol as electron donors for growth coupled to reductive dechlorination. am ... | 2000 | 10831418 |
| sulfate-reducing bacteria methylate mercury at variable rates in pure culture and in marine sediments. | differences in methylmercury (ch(3)hg) production normalized to the sulfate reduction rate (srr) in various species of sulfate-reducing bacteria (srb) were quantified in pure cultures and in marine sediment slurries in order to determine if srb strains which differ phylogenetically methylate mercury (hg) at similar rates. cultures representing five genera of the srb (desulfovibrio desulfuricans, desulfobulbus propionicus, desulfococcus multivorans, desulfobacter sp. strain bg-8, and desulfobacte ... | 2000 | 10831421 |
| a bacterioferritin from the strict anaerobe desulfovibrio desulfuricans atcc 27774. | a bacterioferritin was isolated from the anaerobic bacterium desulfovibrio desulfuricans atcc 27774, grown with nitrate as the terminal electron acceptor, which is the first example of a bacterioferritin from a strict anaerobic organism. this new bacterioferritin was isolated mainly as a 24-mer of 20 kda identical subunits, containing 0.5 noncovalently bound heme and 2 iron atoms per monomer. although its n-terminal sequence is significantly homologous with ferritins from other microorganisms an ... | 2000 | 10841764 |
| behavior of sulfate reducing bacteria under oligotrophic conditions and oxygen stress in particle-free systems related to drinking water. | the response of sulfate reducing bacteria (srb) to oxygen stress under oligotrophic conditions in particle-free systems was studied in (i) sterile berlin drinking water; (ii) mineral medium; and (iii) in coculture experiments with aerobic bacteria. using a polyphasic approach including anaerobic cultivation, fluorescent in situ hybridization (fish) and digital image analysis, the behavior of the strains zt3l and zt10e, isolated from berlin groundwater and affiliated to the family desulfovibriona ... | 2000 | 10858580 |
| molecular cloning of the gene encoding flavoredoxin, a flavoprotein from desulfovibrio gigas. | sulfate-reducing bacteria are rich in unique redox proteins and electron carriers that participate in a variety of essential pathways. several studies have been carried out to characterize these proteins, but the structure and function of many are poorly understood. many desulfovibrio species can grow using hydrogen as the sole energy source, indicating that the oxidation of hydrogen with sulfite as the terminal electron acceptor is an energy-conserving mechanism. flavoredoxin is an fmn-binding ... | 2000 | 10860809 |
| no cofactor effect on equilibrium unfolding of desulfovibrio desulfuricans flavodoxin. | flavodoxins are proteins with an alpha/beta doubly wound topology that mediate electron transfer through a non-covalently bound flavin mononucleotide (fmn). the fmn moiety binds strongly to folded flavodoxin (k(d)=0.1 nm, oxidized fmn). to study the effect of this organic cofactor on the conformational stability, we have characterized apo and holo forms of desulfovibrio desulfuricans flavodoxin by guhcl-induced denaturation. the unfolding reactions for both holo- and apo-flavodoxin are reversibl ... | 2000 | 10862971 |
| [effect of various organic compounds on the growth and hydrocarbon production by sulfur-reducing bacteria]. | the effects of lactate, pyruvate and ethanol on growth and formation of extracellular hydrocarbons by desulfovibrio desulfuricans 1799 cultivated in h2 + co2 atmosphere were studied. it was shown that sulfate reducing bacteria grow and produce hydrocarbons on all studied carbon and energy sources. substitution of lactate in the medium for pyruvate or ethanol decreased only insignificantly the amount of synthesized hydrocarbons with concomitant increase in the content of isoform. | 2000 | 10868066 |
| neelaredoxin, an iron-binding protein from the syphilis spirochete, treponema pallidum, is a superoxide reductase. | treponema pallidum, the causative agent of venereal syphilis, is a microaerophilic obligate pathogen of humans. as it disseminates hematogenously and invades a wide range of tissues, t. pallidum presumably must tolerate substantial oxidative stress. analysis of the t. pallidum genome indicates that the syphilis spirochete lacks most of the iron-binding proteins present in many other bacterial pathogens, including the oxidative defense enzymes superoxide dismutase, catalase, and peroxidase, but d ... | 2000 | 10874033 |
| correlation of empirical magnetic susceptibility tensors and structure in low-spin haem proteins. | experimental magnetic susceptibility tensors are reported for eight haems c with bis-his coordination. these data, obtained by fitting the dipolar shifts of backbone protons in the tetrahaem cytochromes c(3) from desulfovibrio vulgaris and d. gigas, are analysed together with published values for other haem proteins. the x and y axes are found to rotate in the opposite sense to the axial ligands and are also counter-rotated with respect to the frontier molecular orbitals of the haem. the magneti ... | 2000 | 10877019 |
| production of volatile derivatives of metal(loid)s by microflora involved in anaerobic digestion of sewage sludge. | gases released from anaerobic wastewater treatment facilities contain considerable amounts of volatile methyl and hydride derivatives of metals and metalloids, such as arsine (ash(3)), monomethylarsine, dimethylarsine, trimethylarsine, trimethylbismuth (tmbi), elemental mercury (hg(0)), trimethylstibine, dimethyltellurium, and tetramethyltin. most of these compounds could be shown to be produced by pure cultures of microorganisms which are representatives of the anaerobic sewage sludge microflor ... | 2000 | 10877769 |
| development of oligonucleotide probes and pcr primers for detecting phylogenetic subgroups of sulfate-reducing bacteria. | pcr primer sets for the 16s rrna gene of six phylogenetic groups of sulfate-reducing bacteria (srb) were designed. their application in conjunction with group-specific internal oligonucleotide probes was used to detect srb dna in samples of landfill leachate. six generic/suprageneric groups could be differentiated: desulfotomaculum:; desulfobulbus:; desulfobacterium:; desulfobacter:; desulfococcus:-desulfonema:-desulfosarcina:; desulfovibrio:-desulfomicrobium: the predicted specificities of the ... | 2000 | 10878133 |
| cloning of the cdnas coding for two novel molybdo-flavoproteins showing high similarity with aldehyde oxidase and xanthine oxidoreductase. | the cdnas coding for two novel mouse molybdo-flavoproteins, aoh1 and aoh2 (aldehyde oxidase homolog 1 and 2), were isolated. the aoh1 and aoh2 cdnas code for polypeptides of 1336 amino acids. the two proteins have similar primary structure and show striking amino acid identity with aldehyde oxidase and xanthine oxidoreductase, two other molybdo-flavoenzymes. aoh1 and aoh2 contain consensus sequences for a molybdopterin-binding site and two distinct 2fe-2s redox centers. in its native conformatio ... | 2000 | 10893244 |
| a dna fragment of desulfovibrio gigas genome containing replication origin related genes. | the nucleotide sequence of a 10,772 base pair (bp) region from desulfovibrio gigas genome was determined. this sequence, which is adjacent to the region containing the coding units for the metalloproteins rubredoxin-oxygen oxidoreductase (roo) and rubredoxin, includes the flavodoxin gene. additionally, it also contains four open reading frames (orfs) related to genes frequently found in replication origin regions of prokaryotes. these hypothetical encoded polypeptides are: the response regulator ... | 2000 | 10902918 |
| x-ray structure of escherichia coli pyridoxine 5'-phosphate oxidase complexed with fmn at 1.8 a resolution. | escherichia coli pyridoxine 5'-phosphate oxidase (pnpox) catalyzes the terminal step in the biosynthesis of pyridoxal 5'-phosphate (plp), a cofactor used by many enzymes involved in amino acid metabolism. the enzyme oxidizes either the 4'-hydroxyl group of pyridoxine 5'-phosphate (pnp) or the 4'-primary amine of pyridoxamine 5'-phosphate (pmp) to an aldehyde. pnpox is a homodimeric enzyme with one flavin mononucleotide (fmn) molecule non-covalently bound to each subunit. a high degree of sequenc ... | 2000 | 10903950 |
| investigation of exchange couplings in [fe3s4]+ clusters by electron spin-lattice relaxation. | we have studied four proteins containing oxidized 3fe clusters ([fe3s4]+, s=1/2, composed of three, antiferromagnetically coupled high-spin ferric ions) by continuous wave (cw) and pulsed epr techniques: azotobacter vinelandii ferredoxin i, desulfovibrio gigas ferredoxin ii, and the 3fe forms of pyrococcus furiosus ferredoxin and aconitase. the 35 ghz (q-band) cw epr signals are simulated to yield experimental g tensors, which either had not been reported, or had been reported only at x-band mic ... | 2000 | 10907748 |
| optical and tdpac spectroscopy of hg(ii)-rubredoxin: model for a mononuclear tetrahedral [hg(cyss)4]2- center. isolde collaboration. | rubredoxins possess a well-defined mononuclear tetrahedral tetrathiolate metal binding site, a feature exploited by several investigations to study the spectroscopic characteristics and the coordination chemistry of different metal ions at this binding site. in the present work, hg(ii)-substituted rubredoxin (rd) from desulfovibrio gigas has been studied by electronic absorption, circular dichroism (cd), magnetic circular dichroism (mcd), and time differential perturbed angular correlation of ga ... | 2000 | 10907750 |
| purification and characterization of cytochrome c-553 from helicobacter pylori. | helicobacter pylori, a microaerophilic gram-negative spiral bacterium residing in the human stomach, contains a small size soluble cytochrome c. this cytochrome c was purified from the soluble fraction of h. pylori by conventional chromatographies involving octyl-cellulose and cm-toyopearl. its reduced form gave an alpha absorption band at 553 nm, and thus the cytochrome was named h. pylori cytochrome c-553. the cytochrome, giving a band below 10,000 da upon sds-page, was determined to have a ma ... | 2000 | 10965034 |
| modeling reduction of uranium u(vi) under variable sulfate concentrations by sulfate-reducing bacteria. | the kinetics for the reduction of sulfate alone and for concurrent uranium [u(vi)] and sulfate reduction, by mixed and pure cultures of sulfate-reducing bacteria (srb) at 21 +/- 3 degrees c were studied. the mixed culture contained the srb desulfovibrio vulgaris along with a clostridium sp. determined via 16s ribosomal dna analysis. the pure culture was desulfovibrio desulfuricans (atcc 7757). a zero-order model best fit the data for the reduction of sulfate from 0.1 to 10 mm. a lag time occurre ... | 2000 | 10966381 |
| expression of a tetraheme protein, desulfovibrio vulgaris miyazaki f cytochrome c(3), in shewanella oneidensis mr-1. | cytochrome c(3) from desulfovibrio vulgaris miyazaki f was successfully expressed in the facultative aerobe shewanella oneidensis mr-1 under anaerobic, microaerophilic, and aerobic conditions, with yields of 0.3 to 0.5 mg of cytochrome/g of cells. a derivative of the broad-host-range plasmid prk415 containing the cytochrome c(3) gene from d. vulgaris miyazaki f was used for transformation of s. oneidensis mr-1, resulting in the production of protein product that was indistinguishable from that p ... | 2000 | 10966450 |
| cytochrome c(553), a small heme protein that lacks misligation in its unfolded state, folds with rapid two-state kinetics. | cytochrome c(553) (cyt c(553)) from desulfovibrio vulgaris is a small helical heme protein that displays apparent two-state equilibrium-unfolding behavior. the covalently attached heme is low-spin, ligated by met and his residues, in the native state but becomes high-spin upon unfolding at ph 7. here, we show that in contrast to other c-type heme proteins, where misligations in the unfolded states are prominent, cyt c(553) refolding kinetics at ph 7 proceeds rapidly without detectable intermedia ... | 2000 | 10966783 |
| characterisation of oxidised 7fe dicluster ferredoxins with nmr spectroscopy. | dicluster ferredoxins (fds) from sulfolobus acidocaldarius and desulfovibrio africanus (fdiii) have been studied using 1h nmr. both wild-type proteins contain a [3fe-4s]+/0 and a [4fe-4s]2+/+ cluster as isolated. the [4fe-4s]2+/+ cluster (cluster ii) is bound by cysteine residues arranged in a classic ferredoxin motif: cysi-(xaa)2-cysii-(xaa)2-cysiii-(xaa)n-cysiv-pro , whilst the binding motif of the [3fe-4s]+/0 cluster (cluster i) has a non-ligating aspartic acid (asp14) at position ii, i.e. cy ... | 2000 | 10968614 |
| the 1.9 a crystal structure of the "as isolated" rubrerythrin from desulfovibrio vulgaris: some surprising results. | rubrerythrin is a non-heme iron dimeric protein isolated from the sulfate-reducing bacterium desulfovibrio vulgaris. each monomer has one mononuclear iron center similar to rubredoxin and one dinuclear metal center similar to hemerythrin or ribonucleotide reductase. the 1.88 a x-ray structure of the "as isolated" molecule and a uranyl heavy atom derivative have been solved by molecular replacement techniques. the resulting model of the native "as isolated" molecule, including 164 water molecules ... | 2000 | 10968622 |
| efficient measurement of (3)j(n,cgamma) and (3)j(c',cgamma) coupling constants of aromatic residues in (13)c, (15)n-labeled proteins. | an nmr pulse sequence is proposed for the simultaneous determination of side chain chi1 torsion-angle related (3)j(n,cgamma) and (3)j(c', cgamma) couplings in aromatic amino acid spin systems. the method is of the quantitative j correlation type and takes advantage of attenuated (15)n and (1)h transverse relaxation by means of the trosy principle. unlike previously developed schemes for the measurement of either of the two coupling types, spectra contain internal reference peaks that are usually ... | 2000 | 10968965 |
| the presence of a so molecule in [nife] hydrogenase from desulfovibrio vulgaris miyazaki as detected by mass spectrometry. | the active site of [nife] hydrogenase is a binuclear metal complex composed of fe and ni atoms and is called the ni-fe site, where the fe atom is known to be coordinated to three diatomic ligands. two mass spectrometric techniques, pyrolysis-ms (pyrolysis-mass spectrometry) and tof-sims (time-of-flight secondary ion mass spectrometry), were applied to several proteins, including native and denatured forms of [nife] hydrogenase from desulfovibrio vulgaris miyazaki f, [fe4s4]2-ferredoxin from clos ... | 2000 | 11001090 |
| cloning, sequencing and expression of the tetraheme cytochrome c(3) from desulfovibrio gigas. | the gene encoding the tetraheme cytochrome c(3) from desulfovibrio gigas was cloned and sequenced from a 2.7-kb ecori-psti insert of d. gigas dna. the derived amino acid sequence showed that the d. gigas cytochrome c(3) is synthesized as a precursor protein with an n-terminal signal peptide sequence of 25 residues and allowed the correction of the previous reported amino acid sequence (matias et al. protein science 5 (1996) 1342-1354). expression in d. vulgaris (hildenborough) was possible by co ... | 2000 | 11004501 |
| escherichia coli is able to produce heterologous tetraheme cytochrome c(3) when the ccm genes are co-expressed. | the production of desulfovibrio vulgaris hildenborough cytochrome c(3) (m(r) 13000), which is a tetraheme cytochrome, in escherichia coli was examined. this cytochrome was successfully produced in an e. coli strain co-expressing the ccmabcdefgh genes involved in the cytochrome c maturation process. the apocytochrome c(3) was matured in either anaerobic or aerobic conditions, but aerobic growth in the presence of delta-aminolevulinic acid was found to be best for cytochrome c(3) production. site- ... | 2000 | 11004576 |
| characterization of a heme c nitrite reductase from a non-ammonifying microorganism, desulfovibrio vulgaris hildenborough. | a cytochrome c nitrite reductase (nir) was purified for the first time from a microorganism not capable of growing on nitrate, the sulfate-reducing bacterium desulfovibrio vulgaris hildenborough. it was isolated from the membranes as a large heterooligomeric complex of 760 kda, containing two cytochrome c subunits of 56 and 18 kda. this complex has nitrite and sulfite reductase activities of 685 micromol nh(4)(+)/min/mg and 1.0 micromol h(2)/min/mg. the enzyme was studied by uv-visible and elect ... | 2000 | 11004582 |
| microbial sulfate reduction in a liquid-solid fluidized bed reactor. | a liquid-solid fluidized bed reactor was used to carry out sulfate reduction with a mixed culture of sulfate reducing bacteria. the bacteria were immobilized on porous glass beads. stable fluidized bed operation with these biofilm-coated beads was possible. the low specific gravity of the hydrated beads allowed operation at low liquid recirculation rates. h(2)s level in the reactor was controlled by n(2) sparging, which also served as the location for liquid feed and removal. ethanol was used as ... | 2000 | 11005919 |
| oxygen respiration by desulfovibrio species. | throughout the first 90 years after their discovery, sulfate-reducing bacteria were thought to be strict anaerobes. during the last 15 years, however, it has turned out that they have manifold properties that enable them to cope with oxygen. sulfate-reducing bacteria not only survive oxygen exposure for at least days, but many of them even reduce oxygen to water. this process can be a true respiration process when it is coupled to energy conservation. various oxygen-reducing systems are present ... | 2000 | 11018146 |
| kinetic characterization of desulfovibrio gigas hydrogenase upon selective chemical modification of amino acid groups as a tool for structure-function relationships. | the effect of amino acid residues modification of desulfovibrio gigas hydrogenase on different activity assays is reported. the first method consisted in the modification of glutamic and aspartic acid residues of the enzyme with ethylenediamine in order to change the polarity of certain regions of the protein surface. the second method consisted in the modification of histidine residues with a ru complex in order to change the acid-base properties of the histidine residues. the implication of th ... | 2000 | 11018729 |
| iron-coproporphyrin iii is a natural cofactor in bacterioferritin from the anaerobic bacterium desulfovibrio desulfuricans. | a bacterioferritin was recently isolated from the anaerobic sulphate-reducing bacterium desulfivibrio desulfuricans atcc 27774 [romão et al. (2000) biochemistry 39, 6841-6849]. although its properties are in general similar to those of the other bacterioferritins, it contains a haem quite distinct from the haem b, found in bacterioferritins from aerobic organisms. using visible and nmr spectroscopies, as well as mass spectrometry analysis, the haem is now unambiguously identified as iron-copropo ... | 2000 | 11034331 |
| deletion of the hmc operon of desulfovibrio vulgaris subsp. vulgaris hildenborough hampers hydrogen metabolism and low-redox-potential niche establishment. | the hmc operon of desulfovibrio vulgaris subsp. vulgaris hildenborough encodes a transmembrane redox protein complex (the hmc complex) that has been proposed to catalyze electron transport linking periplasmic hydrogen oxidation to cytoplasmic sulfate reduction. we have replaced a 5-kb dna fragment containing most of the hmc operon by the cat gene. the resulting chloramphenicol-resistant mutant d. vulgaris h801 grows normally when lactate or pyruvate serve as electron donors for sulfate reduction ... | 2000 | 11041344 |
| ethanol utilization by sulfate-reducing bacteria: an experimental and modeling study. | a mixed culture of sulfate-reducing bacteria containing the species desulfovibrio desulfuricans was used to study sulfate-reduction stoichiometry and kinetics using ethanol as the carbon source. growth yield was lower, and kinetics were slower, for ethanol compared to lactate. ethanol was converted into acetate and no significant carbon dioxide production was observed. a mathematical model for growth of sulfate-reducing bacteria on ethanol was developed, and simulations of the growth experiments ... | 2000 | 11042550 |
| miniaturized metalloproteins: application to iron-sulfur proteins. | the miniaturization process applied to rubredoxins generated a class of peptide-based metalloprotein models, named metp (miniaturized electron transfer protein). the crystal structure of desulfovibrio vulgaris rubredoxin was selected as a template for the construction of a tetrahedral (s(gamma)-cys)(4) iron-binding site. analysis of the structure showed that a sphere of 17 a in diameter, centered on the metal, circumscribes two unconnected approximately c(2) symmetry related beta-hairpins, each ... | 2000 | 11050226 |
| crystal structure of oxidized bacillus pasteurii cytochrome c553 at 0.97-a resolution. | this article reports the first x-ray structure of the soluble form of a c-type cytochrome isolated from a gram-positive bacterium. bacillus pasteurii cytochrome c(553), characterized by a low reduction potential and by a low sequence homology with cytochromes from gram-negative bacteria or eukaryotes, is a useful case study for understanding the structure-function relationships for this class of electron-transfer proteins. diffraction data on a single crystal of cytochrome c(553) were obtained u ... | 2000 | 11052663 |