Publications

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 ...	1997	9652170
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 ...	1998	9639107
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 ...	1998	9622492
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 ...	1998	9622485
growth of geobacter sulfurreducens with acetate in syntrophic cooperation with hydrogen-oxidizing anaerobic partners	pure 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 ...	1998	9603840
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.	1998	9603804
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 ...	1998	9600844
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 ...	1998	9599583
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 ...	1998	9576817
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 ...	1998	9571062
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 ...	1998	9568899
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. ...	1998	9565467
cloning and expression of the gene encoding flavodoxin from desulfovibrio vulgaris (miyazaki f).	the gene encoding a flavodoxin of desulfovibrio vulgaris (miyazaki f) was cloned, and overexpressed in escherichia coli. a 1.6-kbp dna fragment, isolated from d. vulgaris (miyazaki f) by double digestion with sali and ecori, contained the flavodoxin gene and its regulatory region. an expression system for the flavodoxin gene under control of the t7 promoter was constructed in e. coli. the purified protein was soluble and exhibited a characteristic visible absorption spectrum. hplc analysis of th ...	1998	9562622
fractionation of sulfur isotopes during thiosulfate reduction by desulfovibrio desulfuricans	sulfur isotope fractionation during reduction of thiosulfate was investigated with growing batch cultures of desulfovibrio desulfuricans csn (dsm 9104) at 30 degreesc. the sulfide produced was depleted in 34s by 10 per thousand as compared to total thiosulfate sulfur. the depletion was equal to that during sulfate reduction under similar conditions. the two sulfur atoms of the thiosulfate molecule were affected differently by fractionation. sulfide produced from sulfonate sulfur was depleted by ...	1998	9560428
a primitive pathway of porphyrin biosynthesis and enzymology in desulfovibrio vulgaris.	culture of desulfovibrio vulgaris in a medium supplemented with 5-aminolevulinic acid and l-methionine-methyl-d3 resulted in the formation of porphyrins (sirohydrochlorin, coproporphyrin iii, and protoporphyrin ix) in which the methyl groups at the c-2 and c-7 positions were deuterated. a previously unknown hexacarboxylic acid was also isolated, and its structure was determined to be 12, 18-didecarboxysirohydrochlorin by mass spectrometry and 1h nmr. these results indicate a primitive pathway of ...	1998	9560192
the desulfuromonas acetoxidans triheme cytochrome c7 produced in desulfovibrio desulfuricans retains its metal reductase activity.	multiheme cytochrome c proteins that belong to class iii have been recently shown to exhibit a metal reductase activity, which could be of great environmental interest, especially in metal bioremediation. to get a better understanding of these activities, the gene encoding cytochrome c7 from the sulfur-reducing bacterium desulfuromonas acetoxidans was cloned from genomic dna by pcr and expressed in desulfovibrio desulfuricans g201. the expression system was based on the cyc transcription unit fr ...	1998	9546165
molecular dynamics simulation of cytochrome c3: studying the reduction processes using free energy calculations.	the tetraheme cytochrome c3 from desulfovibrio vulgaris hildenborough is studied using molecular dynamics simulation studies in explicit solvent. the high heme content of the protein, which has its core almost entirely made up of c-type heme, presents specific problems in the simulation. instability in the structure is observed in long simulations above 1 ns, something that does not occur in a monoheme cytochrome, suggesting problems in heme parametrization. given these stability problems, a par ...	1998	9545034
desulfovibrio aespoeensis sp. nov., a mesophilic sulfate-reducing bacterium from deep groundwater at aspö hard rock laboratory, sweden.	a sulfate-reducing bacterium, strain aspo-2, was isolated from granitic groundwater sampled at a depth of 600 m. this and other strains of srb frequently occur in the deep granitic rock aquifers studied. on the basis of its morphological, physiological and genotypical properties, and its unique habitat, we propose strain aspo-2 as a new species of the genus desulfovibrio, desulfovibrio aespoeensis (dsm 10631t).	1998	9542102
anaerobic degradation of glycerol by desulfovibrio fructosovorans and d. carbinolicus and evidence for glycerol-dependent utilization of 1,2-propanediol	the degradation of glycerol by desulfovibrio carbinolicus and desulfovibrio fructosovorans was tested in pure culture with sulfate and in coculture with methanospirillum hungatei. desulfovibrio carbinolicus degraded glycerol into 3-hydroxypropionate with the formation of sulfide in pure culture and methane in the coculture. the maximum growth rates were 0.063 h-1 in pure culture and 0.014 h-1 in coculture (corresponding growth yields: 8.9 and 6.0 g dry weight/mol glycerol). with d. fructosovoran ...	1998	9541565
determination of the structure of oxidised desulfovibrio africanus ferredoxin i by 1h nmr spectroscopy and comparison of its solution structure with its crystal structure.	the solution structure of the 64 amino acid fe4s4 ferredoxin i from desulfovibrio africanus has been determined using two-dimensional 1h nmr spectroscopy. sequence-specific assignments were obtained for 59 amino acid residues and the structure determined with the program diana on the basis of 549 nuclear overhauser enhancement (noe) upper distance limits, and four dihedral angle and 52 distance constraints for the fe4s4 cluster. the nmr structure was refined using the simulated annealing and ene ...	1998	9533888
unusual organization of the genes coding for hydsl, the stable [nife]hydrogenase in the photosynthetic bacterium thiocapsa roseopersicina bbs.	the characterization of a hyd gene cluster encoding the stable, bidirectional [nife]hydrogenase 1 enzyme in thiocapsa roseopersicina bbs, a purple sulfur photosynthetic bacterium belonging to the family chromatiaceae, is presented. the heterodimeric hydrogenase 1 had been purified to homogeneity and thoroughly characterized (k. l. kovacs et al., j. biol. chem. 266:947-951, 1991; c. bagyinka et al., j. am. chem. soc. 115:3567-3585, 1993). as an unusual feature, a 1,979-bp intergenic sequence (is) ...	1998	9515914
new shuttle vectors for the introduction of cloned dna in desulfovibrio.	the pbg1 replicon from the cryptic plasmid of desulfovibrio desulfuricans g100a was inserted into ptz18u derivatives to generate a new family of shuttle vectors. these plasmids are stable both in escherichia coli and in desulfovibrio, they present a large number of unique restriction sites, and colonies of recombinant clones can be identified by blue/white screening in e. coli. the pbmc, pbmk, and pbms series carry the cat, npt, or strab genes as selectable markers, respectively. the pbmc6, pbmk ...	1998	9514705
a dissimilatory sirohaem-sulfite-reductase-type protein from the hyperthermophilic archaeon pyrobaculum islandicum.	a sulfite-reductase-type protein was purified from the hyperthermophilic crenarchaeote pyrobaculum islandicum grown chemoorganoheterotrophically with thiosulfate as terminal electron acceptor. in common with dissimilatory sulfite reductases the protein has an alpha 2 beta 2 structure and contains high-spin sirohaem, non-haem iron and acid-labile sulfide. the oxidized protein exhibits absorption maxima at 280, 392, 578 and 710 nm with shoulders at 430 and 610 nm. the isoelectric point of ph 8.4 s ...	1998	9493389
the prismane protein resolved--mössbauer investigation of a 4fe cluster with an unusual mixture of bridging ligands and metal coordinations.	the prismane protein of desulfovibrio vulgaris, in its isolated, its one-electron-reduced and its oxidized states, was the subject of a detailed mössbauer investigation. measurements were recorded in the range 0.295-77 k and in the field range 0-6.2 t (parallel and perpendicular to the gamma beam). the paramagnetic parts of the magnetically split mössbauer spectra were analyzed with the spin-hamiltonian formalism, including the nuclear hamiltonian; the diamagnetic parts result from the nuclear h ...	1998	9492318
1h-nmr study of the structural influence of y64 substitution in desulfovibrio vulgaris hildenborough cytochrome c553.	y64 has been replaced in cytochrome c553 from desulfovibrio vulgaris hildenborough by phenylalanine, leucine, valine, serine and alanine residues. an nmr study of structural variation induced in both oxidoreduction states of the molecule has been carried out by analysing observed chemical-shift variations. dynamic changes were evidenced using nh exchange. we have observed that the substitution has a drastic effect on the stability of the molecule in the reduced state, although there is no effect ...	1998	9490053
macrorestriction analysis of desulfurella acetivorans and desulfurella multipotens.	the genomes of the phylogenetically and physiologically unique bacteria desulfurella acetivorans dsm 5264t and d. multipotens dsm 8415t were characterized and compared by pulsed field gel electrophoresis (pfge). macrorestriction patterns made of large pfge separated dna fragments were generated by digesting the genomic dnas of both strains with the rare cutting restriction endonucleases apai, asci, eagi, rsrii, sacii, sali as well as with the intron encoded endonuclease i-ceui. the sum of calcul ...	1998	9485604
spectroscopic characterization of a novel tetranuclear fe cluster in an iron-sulfur protein isolated from desulfovibrio desulfuricans.	mossbauer and epr spectroscopies were used to characterize the fe clusters in an fe-s protein isolated from desulfovibrio desulfuricans (atcc 27774). this protein was previously thought to contain hexanuclear fe clusters, but a recent x-ray crystallographic measurement on a similar protein isolated from desulfovibrio vulgaris showed that the protein contains two tetranuclear clusters, a cubane-type [4fe-4s] cluster and a mixed-ligand cluster of novel structure [lindley et al. (1997) abstract, ch ...	1998	9485434
purification and characterization of the hnda subunit of nadp-reducing hydrogenase from desulfovibrio fructosovorans overproduced in escherichia coli.	based on the dna sequence of its structural genes, clustered in the hnd operon, the nadp-reducing hydrogenase of desulfovibrio fructosovorans is thought to be a heterotetrameric complex in which hnda and hndc constitute the nadp-reducing unit and hndd constitutes the hydrogenase unit, respectively. the weak representativity of the enzyme among cell proteins has prevented its purification. this paper discusses the purification and characterization of the hnda subunit of this unique tetrameric iro ...	1998	9485416
structural and kinetic studies of the y73e mutant of octaheme cytochrome c3 (mr = 26 000) from desulfovibrio desulfuricans norway.	a combination of structural, kinetic, and interaction experiments has been used to study the role of a highly conserved aromatic residue, tyr73, parallel to the sixth heme axial ligand of heme 4 in multiheme cytochrome c3 (mr = 26 000), also called cytochrome cc3 or octaheme cytochrome, from desulfovibrio desulfuricans norway. this residue is expected to be involved in intermolecular electron transfer and protein-protein interaction, since heme 4 is described to be the interaction site between p ...	1998	9485359
hydrogenase: a hydrogen-metabolizing enzyme. what do the crystal structures tell us about its mode of action?	hydrogenases are proteins which metabolize the most simple of chemical compounds, molecular hydrogen, according to the reaction h2<-->2h+ + 2e-. these enzymes are found in many microorganisms of great biotechnological interest such as methanogenic, acetogenic, nitrogen fixing, photosynthetic or sulfate-reducing bacteria. the x-ray structure of a dimeric [nife] hydrogenase together with a wealth of biophysical, biochemical and genetic studies have revealed that the large subunit contains the bime ...	1997	9479448
nutritional aspects of dissimilatory sulfate reduction in the human large intestine.	in contrast to other anaerobic ecosystems, such as marine and estuarine sediments, there is a lack of information on the nutritional requirements of human gut sulfate-reducing bacteria (srb). various substrates stimulated sulfate reduction in mixed culture, including short-chain fatty acids and other organic acids, alcohols, and amino acids (but not sugars or aromatic compounds). however, the use of sodium molybdate as a specific inhibitor of sulfate reduction caused an accumulation of ethanol a ...	1997	9462959
common ancestor of serine proteases and flavin-binding domains.		1998	9461072
probable circular permutation in the flavin-binding domain.		1998	9461071
characterization of the cytochromes c from desulfovibrio desulfuricans g201.	a monoheme cytochrome c553 and a hexadecaheme high molecular weight cytochrome (hmc) have been isolated and characterized from the sulfate-reducing bacteria desulfovibrio desulfuricans g201, in addition to the tetraheme cytochrome c3 (mr 13000) that has been previously described. both cytochromes are homologous with respect to several biochemical properties to the corresponding cytochromes found in other desulfovibrio species. however, they are acidic proteins while the corresponding molecules, ...	1998	9439638
unusual ligand structure in ni-fe active center and an additional mg site in hydrogenase revealed by high resolution x-ray structure analysis.	the hydrogenase of desulfovibrio sp. catalyzes the reversible oxidoreduction of molecular hydrogen, in conjunction with a specific electron acceptor, cytochrome c3. the ni-fe active center of desulfovibrio hydrogenase has an unusual ligand structure with non-protein ligands. an atomic model at high resolution is required to make concrete assignment of the ligands which coordinate the ni-fe center. these in turn will provide insight into the mechanism of electron transfer, during the reaction cat ...	1997	9438867
isd1, an insertion element from the sulfate-reducing bacterium desulfovibrio vulgaris hildenborough: structure, transposition, and distribution.	insertion element isd1, discovered when its transposition caused the insertional inactivation of an introduced sacb gene, is present in two copies in the genome of desulfovibrio vulgaris hildenborough. southern blot analysis indicated at least two insertion sites in the sacb gene. cloning and sequencing of a transposed copy of isd1 indicated a length of 1,200 bp with a pair of 44-bp imperfect inverted repeats at the ends, flanked by a direct repeat of the 4-bp target sequence. aagg and aatt were ...	1998	9435062
isolation and evaluation of susceptibility to sulphasalazine of desulfovibrio desulfuricans strains from the human digestive tract.	various genera of sulphate reducing bacteria (srb) have been found in the human digestive tract. it is suggested that some of srb species may be responsible for the development of the clinical symptoms of ulcerative colitis and other disease of large intestine. sulphasalazine (salicyl-azo-sulphapyridine, sas) is commonly used to treat patients with ulcerative colitis and crohn disease. above 30 samples of faeces or biopsy specimens from 25 patients (age 45 +/- 14 years; m/f, 13/12) suffering fro ...	1997	9429289
determinant role of e. coli rnase iii in the decay of both specific and heterologous mrnas.	a comparative analysis of mrna decay was carried out in escherichia coli using the wild-type and an isogenic rnase iii deletion strain. we have studied the mrna degradation from the escherichia coli gene bola, the lactococcus lactis biovar diacetylactis citqrp operon and the desulfovibrio vulgaris hildenborough gene cyc. as seen by a dramatic stabilization of the specific mrnas in the mutant strain, rnase iii was crucial for the decay process of these three messages. since rnase iii, unlike rnas ...	1997	9418237
dynamics and unfolding pathways of a hyperthermophilic and a mesophilic rubredoxin.	molecular dynamics simulations in solution are performed for a rubredoxin from the hyperthermophilic archaeon pyrococcus furiosus (rdpf) and one from the mesophilic organism desulfovibrio vulgaris (rddv). the two proteins are simulated at four temperatures: 300 k, 373 k, 473 k (two sets), and 500 k; the various simulations extended from 200 ps to 1,020 ps. at room temperature, the two proteins are stable, remain close to the crystal structure, and exhibit similar dynamic behavior; the rms residu ...	1997	9416608
molecular epidemiology of rabies epizootics in texas.	texas is in the midst of two independent epizootics of rabies, involving coyotes (canis latrans) and domestic dogs (canis familiaris) in southern texas and grey foxes (urocyon cinereoargenteus) in west central texas. the domestic dog/coyote (ddc) and grey for (tf) rabies virus variants cannot be differentiated by antigenic typing with currently available monoclonal antibodies. these two variants also cannot be distinguished from a third variant, sonora dog (sd) rabies, that is not enzootic in te ...	1997	9406651
pathway of chymotrypsin evolution suggested by the structure of the fmn-binding protein from desulfovibrio vulgaris (miyazaki f)		1997	9406543
role of intestinal bacteria in nutrient metabolism.	the human large intestine contains a microbiota, the components of which are generically complex and metabolically diverse. its primary function is to salvage energy from carbohydrate not digested in the upper gut. this is achieved through fermentation and absorption of the major products, short chain fatty acids (scfa), which represent 40-50% of the available energy of the carbohydrate. the principal scfa, acetate, propionate and butyrate, are metabolized by the colonic epithelium (butyrate), l ...	1997	9406136
evaluation of the bbl crystal anaerobe identification system.	the bbl crystal anaerobe (anr) identification system was evaluated, and the results were compared with those from conventional anaerobic methods. we tested 322 clinically significant anaerobic bacteria according to the manufacturer's instructions. the system identified correctly 286 of 322 (88.8%) of the anaerobic bacteria tested. of these, 263 of 322 (81.7%) were identified correctly on initial testing and 49 were identified correctly only to the genus level; on repeat testing, 23 of 49 (46.9%) ...	1997	9399517
desulfovibrio inopinatus, sp. nov., a new sulfate-reducing bacterium that degrades hydroxyhydroquinone (1,2,4-trihydroxybenzene)		1998	9396841
further characterization of the two tetraheme cytochromes c3 from desulfovibiro africanus: nucleotide sequences, epr spectroscopy and biological activity.	the genes encoding the basic and acidic tetraheme cytochromes c3 from desulfovibrio africanus have been sequenced. the corresponding amino acid sequences of the basic and acidic cytochromes c3 indicate that the mature proteins consist of a single polypeptide chain of 117 and 103 residues, respectively. their molecular masses, 15102 and 13742 da, respectively, determined by mass spectrometry, are in perfect agreement with those calculated from their amino acid sequences. both d. africanus cytochr ...	1997	9392524
crystal structure and mechanism of action of the xanthine oxidase-related aldehyde oxidoreductase from desulfovibrio gigas.		1997	9388539
evidence for a tungsten-stimulated aldehyde dehydrogenase activity of desulfovibrio simplex that oxidizes aliphatic and aromatic aldehydes with flavins as coenzymes.	the aldehyde dehydrogenase activity of the sulfate-reducing bacterium desulfovibrio simplex strain dsm 4141 was characterized in cell-free extracts. oxygen-sensitive, constitutive aldehyde dehydrogenase activity was found in cells grown on l(+)-lactate, hydrogen, or vanillin with sulfate as the electron acceptor. a 1.83- to 2.6-fold higher specific activity was obtained in cells grown in media supplemented with 1 microm wo42-. the aldehyde dehydrogenase in cell-free extracts catalyzed the oxidat ...	1997	9385139
protein contributions to redox potentials of homologous rubredoxins: an energy minimization study.	the energetic contributions of the protein to the redox potential in an iron-sulfur protein are studied via energy minimization, comparing homologous rubredoxins from clostridium pasteurianum, desulfovibrio gigas, desulfovibrio vulgaris, and pyrococcus furiosus. the reduction reaction was divided into 1) the change in the redox site charge without allowing the protein to respond and 2) the relaxation of the protein in response to the new charge state, focusing on the latter. the energy minimizat ...	1997	9370467
characterization of the [nife] hydrogenase from the sulfate reducer desulfovibrio vulgaris hildenborough.	the [nife] hydrogenase from desulfovibrio vulgaris hildenborough was isolated from the cytoplasmic membranes and characterized by epr spectroscopy. it has a total molecular mass of 98.7 kda (subunits of 66.4 and 32.3 kda), and contains 1 nickel and 12 fe atoms per heterodimer. the catalytic activities for hydrogen consumption and production were determined to be 174 and 89 mumol h2.min-1.mg-1, respectively. as isolated, under aerobic conditions, this hydrogenase exhibits epr signals characterist ...	1997	9367885
enzymatic properties and effect of ionic strength on periplasmic nitrate reductase (nap) from desulfovibrio desulfuricans atcc 27774.	some sulfate reducing bacteria can induce nitrate reductase when grown on nitrate containing media being involved in dissimilatory reduction of nitrate, an important step of the nitrogen cycle. previously, it was reported the purification of the first soluble nitrate reductase from a sulfate-reducing bacteria desulfovibrio desulfuricans atcc 27774 (s.a. bursakov, m.-y. liu, w.j. payne, j. legall, i. moura, and j.j.g. moura (1995) anaerobe 1, 55-60). the present work provides further information ...	1997	9367852
genetic diversity and expression of the [nife] hydrogenase large-subunit gene of desulfovibrio spp. in environmental samples.	the genetic diversity and expression of the [nife] hydrogenase large-subunit gene of desulfovibrio spp. in environmental samples were determined in order to show in parallel the existing and active members of desulfovibrio populations. dna and total rna were extracted from different anaerobic bioreactor samples; rna was transcribed into cdna. subsequently, pcr was performed to amplify a ca.-440-bp fragment of the [nife] hydrogenase large-subunit gene and its mrna. denaturing gradient gel electro ...	1997	9361423
recombinant two-iron rubredoxin of pseudomonas oleovorans: overexpression, purification and characterization by optical, cd and 113cd nmr spectroscopies.	the gene (alk g) encoding the two-iron rubredoxin of pseudomonas oleovorans was amplified from genomic dna by pcr and subcloned into the expression vector pkk223-3. the vector directed the high-level production of rubredoxin in escherichia coli. a simple three-step procedure was used to purify recombinant rubredoxin in the 1fe form. 1fe-rubredoxin was readily converted to the 2fe, apoprotein and cadmium forms after precipitation with trichloroacetic acid and resolubilization in the presence or a ...	1997	9359843
evaluation of the role of specific acidic amino acid residues in electron transfer between the flavodoxin and cytochrome c3 from desulfovibrio vulgaris.	a hypothetical model for electron transfer complex between cytochrome c3 and the flavodoxin from the sulfate-reducing bacteria desulfovibrio vulgaris has been proposed, based on electrostatic potential field calculations and nmr data [stewart, d. e., legall, j. , moura, i., moura, j. j. g., peck, h. d., jr., xavier, a. v., weiner, p. k., & wampler, j. e. (1988) biochemistry 27, 2444-2450]. this modeled complex relies primarily on the formation of five ion pairs between lysine residues of the cyt ...	1997	9354631
a geographically widespread plasmid from thiobacillus ferrooxidans has genes for ferredoxin-, fnr-, prismane- and nadh-oxidoreductase-like proteins which are also located on the chromosome.	during a search for genes encoding electron transport proteins from a thiobacillus ferroxidans atcc 33020 gene bank, a 19.8 kb plasmid, ptf5, which conferred increased sensitivity to the antimicrobial agent metronidazole upon an escherichia coli mutant, was isolated and cloned in e. coli. the plasmid had an identical restriction enzyme map to a plasmid which has been found in t. ferrooxidans strains isolated from many different parts of the world. the plasmid was present at between two and four ...	1997	9353917
the primary structure of the split-soret cytochrome c from desulfovibrio desulfuricans atcc 27774 reveals an unusual type of diheme cytochrome c.	the complete amino acid sequence of the unusual diheme split-soret cytochrome c from the sulphate-reducing desulfovibrio desulfuricans strain atcc 27774 has been determined using classical chemical sequencing techniques and mass spectrometry. the 247-residue sequence shows almost no similarity with any other known diheme cytochrome c, but the heme-binding site of the protein is similar to that of the cytochromes c3 from the sulphate reducers. the cytochrome-c-like domain of the protein covers on ...	1997	9346301
identification of a putative histidine base and of a non-protein nitrogen ligand in the active site of fe-hydrogenases by one-dimensional and two-dimensional electron spin-echo envelope-modulation spectroscopy.	the active h-cluster of the fe-hydrogenases from megasphaera elsdenii and desulfovibrio vulgaris (strain hildenborough) has been investigated with one- and two-dimensional pulsed epr spectroscopy. in both complexes the coordination of a nitrogen-containing ligand was found. the unusual quadrupole interaction parameters (d. vulgaris: quadrupole coupling constant, k = 1.20 mhz, asymmetry parameter eta = 0.32, m. elsdenii: k = 1.23 mhz, eta = 0.25) indicate a non-protein type of nitrogen and are co ...	1997	9346288
backbone dynamics of oxidized and reduced d. vulgaris flavodoxin in solution.	recombinant desulfovibrio vulgaris flavodoxin was produced in escherichia coli. a complete backbone nmr assignment for the two-electron reduced protein revealed significant changes of chemical shift values compared to the oxidized protein, in particular for the flavine mononucleotide (fmn)-binding site. a comparison of homo- and heteronuclear noesy spectra for the two redox states led to the assumption that reduction is not accompanied by significant changes of the global fold of the protein. th ...	1997	9335116
a model for the unusual kinetics of thermal denaturation of rubredoxin.	the thermal denaturation of the simple, redox-active iron protein rubredoxin is characterized by a slow, irreversible decay of the characteristic red color of the iron center at elevated temperatures in the presence of oxygen at ph 7.8. the denaturation rate is essentially constant and the time period for complete bleaching is nearly independent of protein concentration. these two characteristics of the kinetics can be fit by a simple self-catalyzed kinetics model consisting of the combination o ...	1997	9330230
a mechanism for complementation of the soda sodb defect in escherichia coli by overproduction of the rbo gene product (desulfoferrodoxin) from desulfoarculus baarsii.	overexpression of rbo in escherichia coli prevents the inactivation of the [4fe-4s]-containing fumarases that otherwise occurs in the soda sodb strain. it similarly protects against the increased sensitivity toward h2o2, which is imposed by the lack of sod a and sod b. these results would be explained on the basis of scavenging of o-2 within the cells by rbo. this interpretation was supported by measurements of intracellular scavenging of o-2 by the lucigenin luminescence method. since sod activ ...	1997	9325275
towards the phylogeny of aps reductases and sirohaem sulfite reductases in sulfate-reducing and sulfur-oxidizing prokaryotes.	the genes for adenosine-5'-phosphosulfate (aps) reductase, aprba, and sirohaem sulfite reductase, dsrab, from the sulfur-oxidizing phototrophic bacterium chromatium vinosum strain d (dsmz 180(t)) were cloned and sequenced. statistically significant sequence similarities and similar physicochemical properties suggest that the aprba and dsrab gene products from chr. vinosum are true homologues of their counterparts from the sulfate-reducing chemotrophic archaeon archaeoglobus fulgidus and the sulf ...	1997	9308173
desulfovibrio inopinatus, sp. nov., a new sulfate-reducing bacterium that degrades hydroxyhydroquinone.	a new sulfate-reducing bacterium was isolated from marine sediment with hydroxyhydroquinone (1,2,4-trihydroxybenzene) as the sole electron and carbon source. strain hhq 20 grew slowly with doubling times of > 20 h and oxidized hydroxyhydroquinone, lactate, pyruvate, ethanol, fructose, and ribose incompletely to acetate and carbon dioxide, with concomitant reduction of sulfate to sulfide. cells were large, vibrio-shaped, and gram-negative with a g+c content of 49.7 mol%, and contained desulfoviri ...	1997	9297472
isolation and analysis of the gene encoding the pyruvate-ferredoxin oxidoreductase of desulfovibrio africanus, production of the recombinant enzyme in escherichia coli, and effect of carboxy-terminal deletions on its stability.	previous studies have shown that the pyruvate-ferredoxin oxidoreductase (por) of the sulfate-reducing bacterium desulfovibrio africanus is a homodimer that contains one thiamine pyrophosphate and three [4fe-4s]2+/1+ centers/subunit. interestingly, the enzyme isolated from a strictly anaerobic bacterium is highly stable in the presence of oxygen, in contrast to the other pors characterized in anaerobic organisms (l. pieulle, b. guigliarelli, m. asso, f. dole, a. bernadac, and e. c. hatchikian, bi ...	1997	9294422
oxygen-dependent growth of the obligate anaerobe desulfovibrio vulgaris hildenborough.	desulfovibrio vulgaris hildenborough, a sulfate-reducing bacterium classified as an obligate anaerobe, swam to a preferred oxygen concentration of 0.02 to 0.04% (0.24 to 0.48 microm), a level which also supported growth. oxygen concentrations of 0.08% and higher arrested growth. we propose that in zones of transition from an oxic to an anoxic environment, d. vulgaris protects anoxic microenvironments from intrusion of oxygen.	1997	9287020
studies on the redox centers of the terminal oxidase from desulfovibrio gigas and evidence for its interaction with rubredoxin.	rubredoxin-oxygen oxidoreductase (roo) is the final component of a soluble electron transfer chain that couples nadh oxidation to oxygen consumption in the anaerobic sulfate reducer desulfovibrio gigas. it is an 86-kda homodimeric flavohemeprotein containing two fad molecules, one mesoheme ix, and one fe-uroporphyrin i per monomer, capable of fully reducing oxygen to water. epr studies on the native enzyme reveal two components with g values at approximately 2.46, 2.29, and 1.89, which are assig ...	1997	9278402
biochemical and spectroscopic characterization of two new cytochromes isolated from desulfuromonas acetoxidans.	the multimeric cytochromes described to date in sulfate- and sulfur-reducing bacteria are associated with diverse respiratory modes involving the use of elemental sulfur or oxidized sulfur compounds as terminal acceptors. they exhibit no structural similarity with the other cytochrome c classes and are characterized by a bis-histidinyl axial iron coordination and low redox potentials. we have purified two new cytochromes c with markedly different molecular masses (10 000 and 50 000) from the bac ...	1997	9271490
gas access to the active site of ni-fe hydrogenases probed by x-ray crystallography and molecular dynamics.	the 2.54 a resolution structure of ni-fe hydrogenase has revealed the existence of hydrophobic channels connecting the molecular surface to the active site. a crystallographic analysis of xenon binding together with molecular dynamics simulations of xenon and h2 diffusion in the enzyme interior suggest that these channels serve as pathways for gas access to the active site.	1997	9228943
comparison of the 16s ribosomal dna sequences from the intracellular agents of proliferative enteritis in a hamster, deer, and ostrich with the sequence of a porcine isolate of lawsonia intracellularis.	proliferative enteritis is an enteric disease that affects a variety of animals. the causative agent in swine has been determined to be an obligate intracellular bacterium, lawsonia intracellularis, related to the sulfate-reducing bacterium desulfovibrio desulfuricans. the intracellular agents found in the lesions of different animal species are antigenically similar. in addition, strains from the pig, ferret, and hamster have been shown to be genetically similar. in this study we performed a pa ...	1997	9226893
a rubrerythrin operon and nigerythrin gene in desulfovibrio vulgaris (hildenborough).	rubrerythrin is a nonheme iron protein of unknown function isolated from desulfovibrio vulgaris (hildenborough). we have sequenced a 3.3-kbp sal1 fragment of d. vulgaris chromosomal dna containing the rubrerythrin gene, rbr, identified additional open reading frames (orfs) adjacent to rbr, and shown that these orfs are part of a transcriptional unit containing rbr. one orf, designated fur, lies just upstream of rbr and encodes a 128-amino-acid-residue protein which shows homology to fur (ferric ...	1997	9226272
regulation of oxidation-reduction potentials through redox-linked ionization in the y98h mutant of the desulfovibrio vulgaris [hildenborough] flavodoxin: direct proton nuclear magnetic resonance spectroscopic evidence for the redox-dependent shift in the pka of histidine-98.	flavodoxin from desulfovibrio vulgaris is a low molecular weight (15 000 da) acidic flavoprotein that contains a single flavin mononucleotide (fmn) cofactor. a distinguishing feature of the flavodoxin family is the exceptionally low midpoint potential of the semiquinone/hydroquinone couple. tyrosine-98, which flanks the outer or si face of the fmn, plays an important role in establishing the oxidation-reduction properties of the bound cofactor as demonstrated by the substitution of a number of a ...	1997	9220989
targeted gene-replacement mutagenesis of dcra, encoding an oxygen sensor of the sulfate-reducing bacterium desulfovibrio vulgaris hildenborough.	a gene-replacement mutagenesis method has been developed for the anaerobic, sulfate-reducing bacterium desulfovibrio vulgaris hildenborough and used to delete dcra, encoding a potential oxygen or redox sensor with homology to the methyl-accepting chemotaxis proteins. a suicide plasmid, containing a cat-marked dcra allele and a counter-selectable sacb marker was transferred from escherichia coli s17-1 to d. vulgaris by conjugation. following plasmid integration the desired dcra deletion mutant (d ...	1997	9202456
nature and electronic structure of the ni-x dinuclear center of desulfovibrio gigas hydrogenase. implications for the enzymatic mechanism.	the recent determination of the x-ray crystal structure of desulfovibrio gigas hydrogenase has revealed that the active site is a ni-x dinuclear center [volbeda, a., charon, m. h., piras, c., hatchikian, e. c., frey, m., & fontecilla-camps, j. c. (1995) nature 373, 580-587]. this unexpected result calls for a re-examination of the magnetic and redox properties that have been attributed previously to a mononuclear ni center. we have used a combination of dosimetric and electron paramagnetic reson ...	1997	9201928
bacteremia caused by a recently described novel desulfovibrio species.	an obligately anaerobic, fastidious, slowly growing, spiral, gram-negative bacterium was isolated from the blood of a 75-year-old man with acute onset of pyrexia. the patient responded rapidly to appropriate antibiotic therapy. extensive investigation failed to detect a focus for the infection. phenotypically, the organism was consistent with desulfovibrio species. microscopic investigation revealed an organism with a vibrioid or spirillioid morphology with rapidly progressive motility by means ...	1997	9196198
pathways for utilization of carbon reserves in desulfovibrio gigas under fermentative and respiratory conditions.	the sulfate-reducing bacterium desulfovibrio gigas accumulates large amounts of polyglucose as an endogenous carbon and energy reserve. in the absence of exogenous substrates, the intracellular polysaccharide was utilized, and energy was conserved in the process (h. santos, p. fareleira, a. v. xavier, l. chen, m.-y. liu, and j. legall, biochem. biophys. res. commun. 195:551-557, 1993). when an external electron acceptor was not provided, degradation of polyglucose by cell suspensions of d. gigas ...	1997	9190814
a single mutation in the heme 4 environment of desulfovibrio desulfuricans norway cytochrome c3 (mr 26,000) greatly affects the molecule reactivity.	the gene encoding desulfovibrio desulfuricans norway cytochrome c3 (mr 26,000), a dimeric octaheme cytochrome belonging to the polyheme cytochrome c3 superfamily, has been cloned and successfully expressed in another sulfate reducing bacteria, d. desulfuricans g201. the gene, named cycd, is monocistronic and encodes a cytochrome precursor of 135 amino acids with an extension at the nh2 terminus of 24 amino acids. this extension acts as a signal sequence which allows export across the cytoplasmic ...	1997	9182533
encapsulation of flavodoxin in reverse micelles.	the regulation of the properties of desulfovibrio gigas flavodoxin in aot/water/iso-octane micellar system was studied. uv-visible spectroscopic studies have shown that photoreduction of flavodoxin in the presence of edta leads to hydroquinone formation through the intermediate semiquinone. the [free fmn] - [bound to flavodoxin fmn] equilibrium (and hence, the amount of apoprotein) depends on redox state of fmn and on hydration degree which controls the micellar size. thus, a new method of rever ...	1997	9175769
[3fe-4s] <--> [4fe-4s] cluster interconversion in desulfovibrio africanus ferredoxin iii: properties of an asp14 --> cys mutant.	the 8fe ferredoxin iii from desulfovibrio africanus is a monomeric protein which contains two [4fe-4s]2+/1+ clusters, one of which is labile and can readily and reversibly lose one fe under oxidative conditions to yield a [3fe-4s]1+/0 cluster. this 4fe cluster has an s = 3/2 ground sping state insteaed of s = 1/2 in the reduced +1 state [george, armstrong, hatchikian and thomson (1989) biochem. j. 264, 275-284]. the co-ordination to this cluster is unusual in that an aspartate (asp14, d14, is fo ...	1997	9173907
evidence for the bacterial origin of genes encoding fermentation enzymes of the amitochondriate protozoan parasite entamoeba histolytica.	entamoeba histolytica is an amitochondriate protozoan parasite with numerous bacterium-like fermentation enzymes including the pyruvate:ferredoxin oxidoreductase (por), ferredoxin (fd), and alcohol dehydrogenase e (adhe). the goal of this study was to determine whether the genes encoding these cytosolic e. histolytica fermentation enzymes might derive from a bacterium by horizontal transfer, as has previously been suggested for e. histolytica genes encoding heat shock protein 60, nicotinamide nu ...	1997	9171424
one-electron photo-oxidation of reduced desulfovibrio vulgaris flavodoxin on laser excitation at 355 nm.	electron ejection from the reduced flavin in flavodoxin from desulfovibrio vulgaris was obtained on exposure of the protein to the third harmonic radiation (354.7 nm) generated from a pulsed nd/yag laser. the results indicate that the reaction is due to stepwise two-photon excitation of the reduced flavin via the excited singlet state. the absorption spectrum of the neutral flavosemiquinone radical formed in this process was obtained. this spectrum remains stable over the time of study (0.2 ms) ...	1997	9165104
deletion of two downstream genes alters expression of the hmc operon of desulfovibrio vulgaris subsp. vulgaris hildenborough.	the hmc operon of desulfovibrio vulgaris subsp. vulgaris hildenborough consists of six genes (hmca to hmcf) that encode structural components of the high-molecular-mass cytochrome redox protein complex (the hmc complex). two genes (rrf1 and rrf2) encoding regulatory proteins are present downstream of hmcf. expression of the hmc operon, monitored by incubating protein blots with hmca-specific or hmcf-specific antibodies, was found to be highest when hydrogen was the sole electron donor for sulfat ...	1997	9148780
taurine reduction in anaerobic respiration of bilophila wadsworthia rzatau.	organosulfonates are important natural and man-made compounds, but until recently (t. j. lie, t. pitta, e. r. leadbetter, w. godchaux iii, and j. r. leadbetter. arch. microbiol. 166:204-210, 1996), they were not believed to be dissimilated under anoxic conditions. we also chose to test whether alkane- and arenesulfonates could serve as electron sinks in respiratory metabolism. we generated 60 anoxic enrichment cultures in mineral salts medium which included several potential electron donors and ...	1997	9143131
genome sizes of desulfovibrio desulfuricans, desulfovibrio vulgaris, and desulfobulbus propionicus estimated by pulsed-field gel electrophoresis of linearized chromosomal dna.	pulsed-field gel electrophoresis (pfge) of linearized, full-length chromosomal dna was used to estimate the genome sizes of three species of sulfate-reducing bacteria. genome sizes of desulfovibrio desulfuricans, desulfovibrio vulgaris, and desulfobulbus propionicus were estimated to be 3.1, 3.6, and 3.7 mb, respectively. these values are double the genome sizes previously determined for two desulfovibrio species by two-dimensional agarose gel electrophoresis of dna cut with restriction enzymes. ...	1997	9142739
catalytic properties of adenylylsulfate reductase from desulfovibrio vulgaris miyazaki.	adenylylsulfate reductase (ec 1.8.99.2) isolated from desulfovibrio vulgaris miyazaki catalyzes electron transfer from dihydroflavin coenzyme (fadh2, fmnh2, or dihydroriboflavin) to adenylyl sulfate (aps), and catalyzes flavin-mediated oxidation of ferrocytochrome c3 with aps. the reaction with fad as an electron mediator was markedly stimulated in the presence of menadione. km of the enzyme was about 0.015 mm for riboflavin and fad in the presence of menadione. free flavin coenzyme was found to ...	1996	9116053
cloning and expression of the rubredoxin gene from desulfovibrio vulgaris (miyazaki f)--comparison of the primary structure of desulfoferrodoxin.	a gene encoding rubredoxin from desulfovibrio vulgaris (miyazaki f) was cloned and overexpressed in escherichia coli. a 1.1-kilobase pair dna fragment, isolated from d. vulgaris (miyazaki f) by double digestion with smai and sali, contained two genes, the rubredoxin gene (rub) and the desulfoferrodoxin gene (rbo) which was situated upstream of rub. the deduced amino acid sequence of desulfoferrodoxin was homologous to those from other strains and cys residues that are responsible to bind irons w ...	1997	9116039
use of paramagnetic nmr probes for structural analysis in cytochrome c3 from desulfovibrio vulgaris.	the dipolar field generated by each of the four haems in the tetrahaem ferricytochrome c3 from desulfovibrio vulgaris (hildenborough) (c3dvh) is determined by means of a novel procedure. in this method the 13c chemical shifts of the nuclei directly bound to the haems are used to determine the in-plane orientations of the rhombic perturbation in each of the four haems with respect to a model of molecular orbitals of e(g) symmetry which are subject to a rhombic perturbation [turner, d. l., salguei ...	1997	9108240
desulfovibrio profundus sp. nov., a novel barophilic sulfate-reducing bacterium from deep sediment layers in the japan sea.	several strains of a strictly anaerobic, vibrio-shaped or sigmoid, sulfate-reducing bacterium were isolated from deep marine sediments (depth, 80 and 500 m) obtained from the japan sea (ocean drilling program leg 128, site 798b). this bacterium was identified as a member of the genus desulfovibrio on the basis of the presence of desulfoviridin and characteristic phospholipid fatty acids (iso 17:1 omega 7 and iso 15:0), the small number of growth substrates utilized (lactate, pyruvate, and hydrog ...	1997	9103642
population structure of microbial communities associated with two deep, anaerobic, alkaline aquifers.	microbial communities of two deep (1,270 and 316 m) alkaline (ph 9.94 and 8.05), anaerobic (eh, -137 and -27 mv) aquifers were characterized by rrna-based analyses. both aquifers, the grande ronde (gr) and priest rapids (pr) formations, are located within the columbia river basalt group in south-central washington, and sulfidogenesis and methanogenesis characterize the gr and pr formations, respectively. rna was extracted from microorganisms collected from groundwater by ultrafiltration through ...	1997	9097447
conversion of desulforedoxin into a rubredoxin center.	rubredoxin and desulforedoxin both contain an fe(s-cys)4 center. however, the spectroscopic properties of the center in desulforedoxin differ from rubredoxin. these differences arise from a distortion of the metal site hypothesized to result from adjacent cysteine residues in the primary sequence of desulforedoxin. two desulforedoxin mutants were generated in which either a g or p-v were inserted between adjacent cysteines. both mutants exhibited optical spectra with maxima at 278, 345, 380, 480 ...	1997	9070870
the formate dehydrogenase isolated from the aerobe methylobacterium sp. rxm is a molybdenum-containing protein.	the formate dehydrogenase (fdh) isolated from cells of methylobacterium sp. rxm grown on molybdenum-containing mineral medium using methanol as carbon source, was partially purified (at least 90% pure as revealed by sds-page). the enzyme is unstable under oxygen and all the purification steps were conducted under strict anaerobic conditions. the molecular mass is 75 kda (gel exclusion 300 kda). the enzyme was characterized in terms of the kinetic parameters towards different substrates and elect ...	1997	9020054
barriers to heterologous expression of a selenoprotein gene in bacteria.	the specificity parameters counteracting the heterologous expression in escherichia coli of the desulfomicrobium baculatum gene (hydv) coding for the large subunit of the periplasmic hydrogenase which is a selenoprotein have been studied. hydv'-'lacz fusions were constructed, and it was shown that they do not direct the incorporation of selenocysteine in e. coli. rather, the uga codon is efficiently suppressed by some other aminoacyl-trna in an e. coli strain possessing a ribosomal ambiguity mut ...	1997	9006007
the cytochrome c3 superfamily: amino acid sequence of a dimeric octahaem cytochrome c3 (m(r) 26,000) isolated from desulfovibrio gigas.	cytochrome c3 (m(r) 26000) isolated from desulfovibrio gigas is a dimeric cytochrome consisting of two identical subunits of 109 amino acids, each of which contains four haem groups. on the basis of its amino acid sequence, this cytochrome clearly belongs to the cytochrome c3 superfamily, and will be classified in class iii of the c-type cytochromes as defined by ambler [(1980) in from cyclotrons to cytochromes (robinson, a. b. and kaplan, n. o., eds.), pp. 263-279, academic press, london]. it c ...	1996	9003383
physiological characteristics and growth behavior of single and double hydrogenase mutants of desulfovibrio fructosovorans.	the presence of one periplasmic [nife] hydrogenase, one periplasmic [fe] hydrogenase, and one cytoplasmic nadp-reducing hydrogenase has been previously established in desulfovibrio fructosovorans. in the present work, marker-exchange mutagenesis was performed to determine the function of the tetrameric nadp-reducing hydrogenase encoded by the hnda, b, c, and d genes. the mutations performed were not lethal to the cells, although the h2-dependent nadp reduction was completely abolished. the doubl ...	1997	9000340
desulfonatronovibrio hydrogenovorans gen. nov., sp. nov., an alkaliphilic, sulfate-reducing bacterium.	a new alkaliphilic, sulfate-reducing bacterium, strain z-7935t (t = type strain), was isolated from a soda-depositing lake, lake magadi in kenya. this organism is a motile vibrio which utilizes only hydrogen and formate as electron donors and sulfate, sulfite, and thiosulfate, but not sulfur, as electron acceptors. thiosulfate is dismutated. strain z-7935t is an obligately sodium-dependent alkaliphile which grows in sodium carbonate medium and does not grow at ph 7; the maximum ph for growth is ...	1997	8995816
characterization of partial anaerobic metabolic pathway for 2,4,6-trinitrotoluene degradation by a sulfate-reducing bacterial consortium.	the anaerobic degradative pathway for metabolism of 2,4,6-trinitrotoluene (tnt) by a consortium of desulfovibrio spp. isolated from a creek sediment was studied. this consortium has the metabolic capability to degrade tnt to fatty acids. the growth of the consortium and the metabolism of tnt were greatly enhanced in the presence of an additional carbon source like pyruvate. the optimal concentration of pyruvate for the maximum rate of tnt degradation was 15-20 mm. various intermediates of tnt me ...	1996	8989860
a new role for rnase ii in mrna decay: striking differences between rnase ii mutants and similarities with a strain deficient in rnase e.	the effect of escherichia coli ribonuclease ii and polynucleotide phosphorylase was analysed on the degradation of desulfovibrio vulgaris cytochrome c3 (cyc) mrna. in the absence of these exoribonucleolytic activities, cyc mrna was stabilised but the two enzymes had a different role in its decay. surprisingly, a temperature-sensitive mutation in ribonuclease ii gave a degradation pattern similar to what had been observed in the absence of endoribonuclease e activity. in an rnase ii deletion muta ...	1996	8978085
electron-dense granules in desulfovibrio gigas do not consist of inorganic triphosphate but of a glucose pentakis(diphosphate).	under certain growth conditions the sulfate-reducing bacterium desulfovibrio gigas forms electron-dense granules in the cells which had been claimed to consist of a magnesium triphosphate). we observed granules after cultivation in media with a low fe2+ or nh4+ concentration and reinvestigated the nature of the electron-dense bodies. energy-dispersive x-ray analysis of the granules in the cells showed that they contain large amounts of p, mg, and k. gel electrophoresis and chromatographic analys ...	1996	8973651
spin-spin interactions between the ni site and the [4fe-4s] centers as a probe of light-induced structural changes in active desulfovibrio gigas hydrogenase.	in typical nife hydrogenases like that from desulfovibrio gigas, the active state of the enzyme which is obtained by incubation under hydrogen gas gives a characteristic ni-c electron paramagnetic resonance (epr) signal at g = 2.19, 2.14, and 2.01. the ni-c species is light-sensitive, being converted upon illumination at temperatures below 100 k in a mixture of different ni-l species, the most important giving an epr signal at g = 2.30, 2.12, and 2.05. this photoprocess is considered to correspo ...	1996	8973216
the cumulative electrostatic effect of aromatic stacking interactions and the negative electrostatic environment of the flavin mononucleotide binding site is a major determinant of the reduction potential for the flavodoxin from desulfovibrio vulgaris [hildenborough].	flavodoxins are typified by the very low one-electron reduction potential for the semiquinone/hydroquinone couple (esq/hq) of the flavin mononucleotide (fmn) cofactor. in the desulfovibrio vulgaris flavodoxin, the elimination of the side chain of tyr98, which flanks the outer or si face of the flavin, through the y98a mutation results in a substantial increase in esq/hq of 139 mv, representing about one-half of the total shift in esq/hq in this flavodoxin [swenson, r. p., & krey, g. d. (1994) bi ...	1996	8973168
structural origins of redox potentials in fe-s proteins: electrostatic potentials of crystal structures.	redox potentials often differ dramatically for homologous proteins that have identical redox centers. for two types of iron-sulfur proteins, the rubredoxins and the high-potential iron-sulfur proteins (hipips), no structural explanations for these differences have been found. we calculated the classical electrostatic potential at the redox site using static crystal structures of four rubredoxins and four hipips to identify important structural determinants of their redox potentials. the contribu ...	1996	8968568
nmr characterization and solution structure determination of the oxidized cytochrome c7 from desulfuromonas acetoxidans.	the solution structure of the three-heme electron transfer protein cytochrome c7 from desulfuromonas acetoxidans is reported. the determination of the structure is obtained through nmr spectroscopy on the fully oxidized, paramagnetic form. the richness of structural motifs and the presence of three prosthetic groups in a protein of 68 residues is discussed in comparison with the four-heme cytochromes c3 already characterized through x-ray crystallography. in particular, the orientation of the th ...	1996	8962062
rubrerythrin from clostridium perfringens: cloning of the gene, purification of the protein, and characterization of its superoxide dismutase function.	the food-borne pathogen clostridium perfringens, which is an obligate anaerobe, showed growth under conditions of oxidative stress. in protein extracts we looked for superoxide dismutase (sod) activities which might scavenge highly toxic superoxide radicals evolving under such stress conditions. using the classical assay to detect sod activity on gels after electrophoresis of c. perfringens proteins, we obtained a pattern of three major bands indicating sod activity. the protein representing the ...	1996	8955396