Publications

desulfovibrio hydrothermalis sp. nov., a novel sulfate-reducing bacterium isolated from hydrothermal vents.	mesophilic, hydrogenotrophic, sulfate-reducing bacteria were isolated from a deep-sea hydrothermal chimney sample collected at 13 degrees n on the east-pacific rise at a depth of 2,600 m. two strains (bl5 and h9) were found to be phylogenetically similar to desulfovibrio profundus (similarity >99%), whereas two other strains (h1 and am13t) were found to be phylogenetically distinct (similarity 96.4%) from desulfovibrio zosterae, their closest relative. strain am13t was characterized further. it ...	2003	12656169
the effect of 5-aminosalicylic acid-containing drugs on sulfide production by sulfate-reducing and amino acid-fermenting bacteria.	the toxic, bacterial metabolite sulfide is implicated in ulcerative colitis. ulcerative colitis patients taking 5-aminosalicylic acid-containing drugs have lower fecal sulfide levels than those not taking these drugs. the effects of sulfasalazine, balsalazide, olsalazine, and 5-aminosalicylic acid on sulfide production were studied in a three-stage chemostat pulsed on days 1 to 3 with 5 g sulfasalazine (40 mm) and in pure cultures of amino acid-fermenting and sulfate-reducing bacteria. by the th ...	2003	12656132
1h, 13c and 15n assignment of the hydroquinone form of flavodoxin from desulfovibrio vulgaris (hildenborough) and comparison of the chemical shift differences with respect to the oxidized state.		2003	12652141
an engineered two-iron superoxide reductase lacking the [fe(scys)4] site retains its catalytic properties in vitro and in vivo.	superoxide reductases (sors) contain a characteristic square-pyramidal [fe(nhis)(4)(scys)] active site that catalyzes reduction of superoxide to hydrogen peroxide in several anaerobic bacteria and archaea. some sors, referred to as two-iron sors (2fe-sors), also contain a lower-potential [fe(scys)(4)] site that is presumed to have an electron transfer function. however, the intra- and inter-subunit distances between [fe(scys)(4)] and [fe(nhis)(4)(scys)] iron centers within the 2fe-sor homodimer ...	2003	12637682
the nature of the di-iron site in the bacterioferritin from desulfovibrio desulfuricans.	the first crystal structure of a native di-iron center in an iron-storage protein (bacterio)ferritin is reported. the protein, isolated from the anaerobic bacterium desulfovibrio desulfuricans, has the unique property of having fe-coproporphyrin iii as its heme cofactor. the three-dimensional structure of this bacterioferritin was determined in three distinct catalytic/redox states by x-ray crystallography (at 1.95, 2.05 and 2.35 a resolution), corresponding to different intermediates of the di- ...	2003	12627224
isolation of sulfate-reducing bacteria from human thoracoabdominal pus.	to evaluate the prevalence of sulfate-reducing bacteria in septic processes, we searched for these bacteria by culture in 100 consecutive abdominal and pleural pus specimens. twelve isolates were obtained from abdominal samples and were identified by a multiplex pcr as desulfovibrio piger (formerly desulfomonas pigra) (seven strains), desulfovibrio fairfieldensis (four strains), and desulfovibrio desulfuricans (one strain).	2003	12624073
activity of sulfate-reducing bacteria in human periodontal pocket.	samples of subgingival dental tissues were examined for the presence of sulfate-reducing bacteria (srb). using enrichment cultures, srbs were detected in 9 of 17 individuals. a pure culture of srb was obtained from one sample collected from a patient with type iv periodontal disease. the characterization of this isolate showed that it belongs to the genus desulfovibrio. the isolate used pyruvate, lactate, glucose, fructose, and ethanol as the sole source of carbon. however, the isolate was unabl ...	2002	12619823
cytochrome c nitrite reductase from desulfovibrio desulfuricans atcc 27774. the relevance of the two calcium sites in the structure of the catalytic subunit (nrfa).	the gene encoding cytochrome c nitrite reductase (nrfa) from desulfovibrio desulfuricans atcc 27774 was sequenced and the crystal structure of the enzyme was determined to 2.3-a resolution. in comparison with homologous structures, it presents structural differences mainly located at the regions surrounding the putative substrate inlet and product outlet, and includes a well defined second calcium site with octahedral geometry, coordinated to propionates of hemes 3 and 4, and caged by a loop non ...	2003	12618432
biological activity of desulfovibrio desulfuricans lipopolysaccharides evaluated via interleukin-8 secretion by caco-2 cells.	although desulfovibrio desulfuricans species, besides existing in the natural environment, is also found in the human digestive tract, no information is currently available on its role in the intestinal ecosystem and its activity in regard to the intestinal mucosa. bacterial products (lipopolysaccharides, lpss) are generally known for their ability to trigger inflammatory response by stimulating cytokine expression, such as interleukin-8 (il-8).	2003	12608468
mechanism of flavin mononucleotide cofactor binding to the desulfovibrio vulgaris flavodoxin. 2. evidence for cooperative conformational changes involving tryptophan 60 in the interaction between the phosphate- and ring-binding subsites.	a mechanism has been proposed for the binding of flavin mononucleotide (fmn) and riboflavin to the apoflavodoxin from desulfovibrio vulgaris [murray, t. a., and swenson, r. p. (2003) biochemistry 42, 2307-2316]. in this model, the binding of the flavin isoalloxazine ring is dependent on the presence of a phosphate moiety in the phosphate-binding subsite, suggesting a cooperative interaction between that region and the ring-binding subsite. in the absence of inorganic phosphate, fmn can bind thro ...	2003	12600199
mechanism of flavin mononucleotide cofactor binding to the desulfovibrio vulgaris flavodoxin. 1. kinetic evidence for cooperative effects associated with the binding of inorganic phosphate and the 5'-phosphate moiety of the cofactor.	the pathway(s) by which the flavin cofactor binds to the apoflavoprotein is the subject of some debate. the crystal and nmr structures of several different flavodoxins have provided some insight, although there is disagreement about the location of the initial interaction between the flavin mononucleotide (fmn) and the apoflavodoxin and the degree of protein conformational change associated with cofactor binding [genzor, c. g., perales-alcon, a., sancho, j., and romero, a. (1996) nat. struct. bi ...	2003	12600198
intraspecies variability of desulfovibrio desulfuricans strains determined by the genetic profiles.	fifteen (soil and intestinal) strains of desulfovibrio desulfuricans species were typed by pcr method with the use of primers specific for repetitive extragenic palindromic (rep) and enterobacterial repetitive intergenic consensus (eric) sequences. as a result, characteristic dna fingerprints for the strains were obtained. moreover, the genetic profiles were found to be useful for typing and distinguishing the strains of d. desulfuricans. according to cluster analysis, pcr with primers complemen ...	2003	12594025
a novel iron centre in the split-soret cytochrome c from desulfovibrio desulfuricans atcc 27774.	the facultative sulfate/nitrate-reducing bacterium desulfovibrio desulfuricans atcc 27774 harbours a split-soret cytochrome c. this cytochrome is a homodimeric protein, having two bis-histidinyl c-type haems per monomer. it has an unique architecture at the haem domain: each haem has one of the coordinating histidines provided by the other monomer, and in each monomer the haems are parallel to each other, almost in van der waals contact. this work reports the cloning and sequencing of the gene e ...	2003	12589573
formation of a stable cyano-bridged dinuclear iron cluster following oxidation of the superoxide reductases from treponema pallidum and desulfovibrio vulgaris with k(3)fe(cn)(6).	superoxide reductases catalyze the monovalent reduction of superoxide anion to hydrogen peroxide. spectroscopic evidence for the formation of a dinuclear cyano-bridged adduct after k(3)fe(cn)(6) oxidation of the superoxide reductases neelaredoxin from treponema pallidum and desulfoferrodoxin from desulfovibrio vulgaris was reported. oxidation with k(3)fe(cn)(6) reveals a band in the near-ir with lambda(max) at 1020 nm, coupled with an increase of the iron content by almost 2-fold. fourier transf ...	2003	12588121
electronic structure contributions to electron-transfer reactivity in iron-sulfur active sites: 3. kinetics of electron transfer.	the kinetics of electron transfer for rubredoxins are examined using density functional methods to determine the electronic structure characteristics that influence and allow for fast electron self-exchange in these electron-transport proteins. potential energy surfaces for [fex(4)](2-,1-) models confirm that the inner-sphere reorganization energy is inherently small for tetrathiolates ( approximately 0.1 ev), as evidenced by the only small changes in the equilibrium fe-s bond distance during re ...	2003	12562183
toxicity of lead in aqueous medium to desulfovibrio desulfuricans g20.	the toxicity of pb(ii) to sulfate-reducing bacteria (srb) was studied using desulfovibrio desulfuricans g20 in a medium specifically designed to assess metal toxicity. the effects of pb(ii) toxicity were observed in terms of longer lag times, lower specific growth rates, and in some cases no measurable growth. with an increase in medium ph from 6 to 8, pb(ii) toxicity decreased. at all ph values, in the presence of pb(ii) concentrations ranging from 3 to 15 microm, specific growth rates decrease ...	2003	12558154
diversity of microbial communities correlated to physiochemical parameters in a digestion basin of a zero-discharge mariculture system.	bacterial community structure and physiochemical parameters were examined in a sedimentation basin of a zero-discharge mariculture system. the system consisted of an intensively stocked fish basin from which water was recirculated through two separate treatment loops. surface water from the basin was pumped over a trickling filter in one loop while bottom-water was recirculated through a sedimentation basin followed by a fluidized bed reactor in the other. ammonia oxidation to nitrate in the tri ...	2003	12542713
nmr solution structures of two mutants of desulforedoxin.	the differences in geometry at the metal centres in the two known [fe-4s] proteins rubredoxin (rd) and desulforedoxin (dx) are postulated to be a result of the different spacing of the c-terminal cysteine pair in the two proteins. in order to address this question, two mutants of desulfovibrio gigas dx with modified cysteinyl spacing were prepared and their solution structures have been determined by nmr. mutant 1 of dx (dxm1) has a single glycine inserted between the adjacent cysteines (c28 and ...	2003	12538058
refinement of the nickel site structure in desulfovibrio gigas hydrogenase using range-extended exafs spectroscopy.	we have reexamined the ni exafs of oxidized, inactive (as-isolated) and h(2) reduced desulfovibrio gigas hydrogenase. better spatial resolution was achieved by analyzing the data over a 50% wider k-range than was previously available. a lower k(min) was obtained using the feff code for phase shifts and amplitudes. a higher k(max) was obtained by removing an interfering cu signal from the raw spectra using multiple energy fluorescence detection. the larger k-range allowed us to better resolve the ...	2003	12538051
single crystal epr studies of the reduced active site of [nife] hydrogenase from desulfovibrio vulgaris miyazaki f.	in the catalytic cycle of [nife] hydrogenase the paramagnetic ni-c intermediate is of key importance, since it is believed to carry the substrate hydrogen, albeit in a yet unknown geometry. upon illumination at low temperatures, ni-c is converted to the so-called ni-l state with markedly different spectroscopic parameters. it is suspected that ni-l has lost the "substrate hydrogen". in this work, both paramagnetic states have been generated in single crystals obtained from the [nife] hydrogenase ...	2003	12515509
molecular dynamics study of desulfovibrio africanus cytochrome c3 in oxidized and reduced forms.	a 5-ns molecular dynamics study of a tetraheme cytochrome in fully oxidized and reduced forms was performed using the charmm molecular modeling program, with explicit water molecules, langevin dynamics thermalization, particle mesh ewald long-range electrostatics, and quantum mechanical determination of heme partial charges. the simulations used, as starting points, crystallographic structures of the oxidized and reduced forms of the acidic cytochrome c(3) from desulfovibrio africanus obtained a ...	2002	12496077
new oxovanadium bis(1,2-dithiolate) compounds that mimic the hydrogen-bonding interactions at the active sites of mononuclear molybdenum enzymes.	reaction of vo(acac)(2) with 1,2-dithiols in the presence of triethylamine gives pentacoordinate oxovanadium complexes [hnet(3)](2)[vo(bdt)(2)] (1), [hnet(3)](2)[vo(tdt)(2)] (2), and [hnet(3)](2)[vo(bdtcl(2))(2)] (3) (where h(2)bdt = 1,2-benzenedithiol, h(2)tdt = 3,4-toluenedithiol, and h(2)bdtcl(2) = 3,6-dichloro-1,2-benzenedithiol). compounds 1-3 have been characterized by ir, uv/visible, epr, and mass spectroscopies. the x-ray crystal stuctures of 1 and 2 show hydrogen-bonding interactions be ...	2002	12495349
function of oxygen resistance proteins in the anaerobic, sulfate-reducing bacterium desulfovibrio vulgaris hildenborough.	two mutant strains of desulfovibrio vulgaris hildenborough lacking either the sod gene for periplasmic superoxide dismutase or the rbr gene for rubrerythrin, a cytoplasmic hydrogen peroxide (h(2)o(2)) reductase, were constructed. their resistance to oxidative stress was compared to that of the wild-type and of a sor mutant lacking the gene for the cytoplasmic superoxide reductase. the sor mutant was more sensitive to exposure to air or to internally or externally generated superoxide than was th ...	2003	12486042
the influence of fluid shear on the structure and material properties of sulphate-reducing bacterial biofilms.	biofilms of sulphate-reducing desulfovibrio sp. ex265 were grown in square section glass capillary flow cells under a range of fluid flow velocities from 0.01 to 0.4 m/s (wall shear stress, tau(w), from 0.027 to 1.0 n/m(2)). in situ image analysis and confocal scanning laser microscopy revealed biofilm characteristics similar to those reported for aerobic biofilms. biofilms in both flow cells were patchy and consisted of cell clusters separated by voids. length-to-width ratio measurements (l(c): ...	2002	12483477
a mechano-chemical model for energy transduction in cytochrome c oxidase: the work of a maxwell's god.	cytochrome c3 has a central role in the energetics of desulfovibrio sp., where it performs an electroprotonic energy transduction step. this process uses a network of cooperativities, largely based on anti-coulomb components, resulting from a mechano-chemical energy coupling mechanism. this mechanism provides a model coherent with the data available for the redox chemistry of haem a of cytochrome c oxidase and its link to the activation of protons. a crucial feature of the model is an anti-coulo ...	2002	12482576
the crystal structure of the hexadeca-heme cytochrome hmc and a structural model of its complex with cytochrome c(3).	sulfate-reducing bacteria contain a variety of multi-heme c-type cytochromes. the cytochrome of highest molecular weight (hmc) contains 16 heme groups and is part of a transmembrane complex involved in the sulfate respiration pathway. we present the 2.42 a resolution crystal structure of the desulfovibrio vulgaris hildenborough cytochrome hmc and a structural model of the complex with its physiological electron transfer partner, cytochrome c(3), obtained by nmr restrained soft-docking calculatio ...	2002	12467575
the nadp-reducing hydrogenase from desulfovibrio fructosovorans: functional interaction between the c-terminal region of hnda and the n-terminal region of hndd subunits.	the hndabcd operon from desulfovibrio fructosovorans encodes an uncommon heterotetrameric nadp-reducing iron hydrogenase. the presence of a [2fe-2s] cluster likely located in the c-terminal region of the hnda subunit has already been revealed. we have cloned and expressed the truncated hnda gene in escherichia coli to isolate the structural [2fe-2s] module. optical and epr spectra are found identical to that of the native hnda subunit and the midpoint redox potential (-385 mv) is similar to that ...	2002	12460679
crystal structure studies on rubrerythrin: enzymatic activity in relation to the zinc movement.	rubrerythrin (rr) is a non-heme iron protein isolated from anaerobic sulfate-reducing bacteria. rr is a dimeric molecule, each monomer contains a fe(scys)(4) center in the c-terminal domain and a binuclear metal center in the n-terminal domain. rr structures with different protein sources and/or preparation procedures have been studied. two rr crystal structures have been solved with significant differences in their binuclear metal centers. the first structure, which was obtained from expressed ...	2003	12459910
spectroscopic and kinetic characterization of active site mutants of desulfovibrio fructosovoransni-fe hydrogenase.	site-directed mutagenesis of amino acid residues proximate to the active site of the ni-fe hydrogenase of desulfovibrio fructosovorans has been done. the different mutants have been analyzed by ftir spectroscopy and compared with wild type enzyme. the changes observed in the spectra confirm that hydrogen bonds between the cn(-) ligands of the active site's fe atom and certain neighbor amino acid residues stabilize the active center within the protein matrix. however, kinetic analysis of the muta ...	2003	12459907
flavin thermodynamics explain the oxygen insensitivity of enteric nitroreductases.	bacterial nitroreductases are nad(p)h-dependent flavoenzymes which catalyze the oxygen-insensitive reduction of nitroaromatics, quinones, and riboflavin derivatives. despite their broad substrate specificity, their reactivity is very specific for two-electron, not one-electron, chemistry. we now describe the thermodynamic properties of the flavin mononucleotide cofactor of enterobacter cloacae nitroreductase (nr), determined under a variety of solution conditions. the two-electron redox midpoint ...	2002	12450383
bioremediation of chromate: thermodynamic analysis of the effects of cr(vi) on sulfate-reducing bacteria.	developing new bioremediation processes for soils and effluents polluted by cr(vi) requires the selection of the most efficient and the most heavy-metal-resistant bacteria. the effects of cr(vi) on bioenergetic metabolism in two sulfate-reducing bacteria (srb), desulfovibrio vulgaris hildenborough and desulfomicrobium norvegicum, were monitored using isothermal microcalorimetry. the complete reduction of cr(vi) to cr(iii) was studied by spectrophotometry and by speciation using a combination of ...	2002	12436319
thermodynamic and kinetic characterization of trihaem cytochrome c3 from desulfuromonas acetoxidans.	trihaem cytochrome c3 (also known as cytochrome c551.5 and cytochrome c7) is isolated from the periplasmic space of desulfuromonas acetoxidans, a sulfur-reducing bacterium. thermodynamic and kinetic data for the trihaem cytochrome c3 are presented and discussed in the context of the possible physiological implications of its functional properties with respect to the natural habitat of d. acetoxidans, namely as a symbiont with green sulfur bacteria working as a mini-sulfuretum. the thermodynamic ...	2002	12423372
stoichiometric redox titrations of complex metalloenzymes.		2002	12418235
mercury methylation by desulfovibrio desulfuricans nd132 in the presence of polysulfides.	the extracellular speciation of mercury may control bacterial uptake and methylation. mercury-polysulfide complexes have recently been shown to be prevalent in sulfidic waters containing zero-valent sulfur. despite substantial increases in total dissolved mercury concentration, methylation rates in cultures of desulfovibrio desulfuricans nd132 equilibrated with cinnabar did not increase in the presence of polysulfides, as expected due to the large size and charged nature of most of the complexes ...	2002	12406773
pulsed electron-electron double resonance on multinuclear metal clusters: assignment of spin projection factors based on the dipolar interaction.	the interaction between two paramagnetic metal centers, a [3fe-4s](+) cluster and a [nife] center, is investigated in the hydrogenase from desulfovibrio vulgaris miyazaki f by pulsed eldor (electron-electron double resonance). the distance between the metal centers is known from x-ray crystallography. the experimental dipolar spin-spin interaction deviates from the value expected for two point-dipoles located at the centers of the metal clusters. an extended spin-coupling model accounting for th ...	2002	12381206
carbon monoxide cycling by desulfovibrio vulgaris hildenborough.	sulfate-reducing bacteria, like desulfovibrio vulgaris hildenborough, use the reduction of sulfate as a sink for electrons liberated in oxidation reactions of organic substrates. the rate of the latter exceeds that of sulfate reduction at the onset of growth, causing a temporary accumulation of hydrogen and other fermentation products (the hydrogen or fermentation burst). in addition to hydrogen, d. vulgaris was found to produce significant amounts of carbon monoxide during the fermentation burs ...	2002	12374824
hydroxylamine reductase activity of the hybrid cluster protein from escherichia coli.	the hybrid cluster protein (hcp; formerly termed the prismane protein) has been extensively studied due to its unique spectroscopic properties. although the structural and spectroscopic characteristics are well defined, its enzymatic function, up to this point, has remained unidentified. while it was proposed that hcp acts in some step of nitrogen metabolism, a specific role for this enzyme remained unknown. recent studies of hcp purified from escherichia coli have identified a novel hydroxylami ...	2002	12374823
converting the nifes carbon monoxide dehydrogenase to a hydrogenase and a hydroxylamine reductase.	substitution of one amino acid for another at the active site of an enzyme usually diminishes or eliminates the activity of the enzyme. in some cases, however, the specificity of the enzyme is changed. in this study, we report that the changing of a metal ligand at the active site of the nifes-containing carbon monoxide dehydrogenase (codh) converts the enzyme to a hydrogenase or a hydroxylamine reductase. codh with alanine substituted for cys(531) exhibits substantial uptake hydrogenase activit ...	2002	12374822
sulfate respiration in desulfovibrio vulgaris hildenborough. structure of the 16-heme cytochrome c hmca at 2.5-a resolution and a view of its role in transmembrane electron transfer.	the crystal structure of the high molecular mass cytochrome c hmca from desulfovibrio vulgaris hildenborough is described. hmca contains the unprecedented number of sixteen hemes c attached to a single polypeptide chain, is associated with a membrane-bound redox complex, and is involved in electron transfer from the periplasmic oxidation of hydrogen to the cytoplasmic reduction of sulfate. the structure of hmca is organized into four tetraheme cytochrome c(3)-like domains, of which the first is ...	2002	12356749
isolation of the provisionally named desulfovibrio fairfieldensis from human periodontal pockets.	sulfate-reducing bacteria have recently been associated with periodontitis and proposed to play a role in the pathogenesis of this chronic inflammatory process. eight isolates of sulfate-reducing bacteria belonging to the genus desulfovibrio were obtained from the periodontal pockets of five out of seven patients presenting with active periodontitis. a multiplex pcr was devised for their identification at the species level. all isolates were identified as desulfovibrio fairfieldensis, a recently ...	2002	12354215
comparison of the refined crystal structures of wild-type (1.34 a) flavodoxin from desulfovibrio vulgaris and the s35c mutant (1.44 a) at 100 k.	engineered flavodoxins in which a surface residue has been replaced by an exposed cysteine are useful modules to link multi-domain redox proteins obtained by gene fusion to electrode surfaces. in the present work, the crystal structure of the s35c mutant of desulfovibrio vulgaris flavodoxin in the oxidized state has been determined and compared with a refined structure of the wild type (wt). the structure of wt flavodoxin (space group p4(3)2(1)2, unit-cell parameters a = 50.52, b = 50.52, c = 13 ...	2002	12351822
bioreduction and biocrystallization of palladium by desulfovibrio desulfuricans ncimb 8307.	the reduction of pd(ii) to pd(0) was accelerated by using the sulfate-reducing bacterium desulfovibrio desulfuricans ncimb 8307 at the expense of formate or h(2) as electron donors at ph 2-7. with formate no reduction occurred at ph 2, but with h(2) 50% of the activity was retained at ph 2, with the maximum rate (1.3-1.4 micromol min(-1) mg dry cells(-1)) seen at ph 3-7, which was similar to the rate with formate at neutral ph. excess nitrate was inhibitory to pd(ii) reduction using formate, but ...	2002	12325145
ammonia production by ruminal microorganisms and enumeration, isolation, and characterization of bacteria capable of growth on peptides and amino acids from the sheep rumen.	excessive nh(3) production in the rumen is a major nutritional inefficiency in ruminant animals. experiments were undertaken to compare the rates of nh(3) production from different substrates in ruminal fluid in vitro and to assess the role of asaccharolytic bacteria in nh(3) production. ruminal fluid was taken from four rumen-fistulated sheep receiving a mixed hay-concentrate diet. the calculated rate of nh(3) production from trypticase varied from 1.8 to 19.7 nmol mg of protein(-1) min(-1) dep ...	2002	12324340
structural studies of the carbon monoxide complex of [nife]hydrogenase from desulfovibrio vulgaris miyazaki f: suggestion for the initial activation site for dihydrogen.	the carbon monoxide complex of [nife]hydrogenase from desulfovibrio vulgaris miyazaki f has been characterized by x-ray crystallography and absorption and resonance raman spectroscopy. nine crystal structures of the [nife]hydrogenase in the co-bound and co-liberated forms were determined at 1.2-1.4 a resolution. the exogenously added co was assigned to be bound to the ni atom at the ni-fe active site. the co was not replaced with h(2) in the dark at 100 k, but was liberated by illumination with ...	2002	12296727
zinc-substituted desulfovibrio gigas desulforedoxins: resolving subunit degeneracy with nonsymmetric pseudocontact shifts.	desulfovibrio gigas desulforedoxin (dx) consists of two identical peptides, each containing one [fe-4s] center per monomer. variants with different iron and zinc metal compositions arise when desulforedoxin is produced recombinantly from escherichia coli. the three forms of the protein, the two homodimers [fe(iii)/fe(iii)]dx and [zn(ii)/zn(ii)]dx, and the heterodimer [fe(iii)/zn(ii)]dx, can be separated by ion exchange chromatography on the basis of their charge differences. once separated, the ...	2002	12237467
biochemical-genetic analysis and distribution of des-1, an ambler class a extended-spectrum beta-lactamase from desulfovibrio desulfuricans.	desulfovibrio spp. are gram-negative anaerobes phylogenetically related to bacteroides spp., which are rarely isolated and which are mostly isolated from intra-abdominal abscesses. desulfovibrio desulfuricans clinical isolate d3 had a clavulanic acid-inhibited beta-lactam resistance profile and was resistant to some expanded-spectrum cephalosporins. a beta-lactamase gene, bla(des-1), was cloned from whole-cell dna of isolate d3 and expressed in escherichia coli. purified beta-lactamase des-1, wi ...	2002	12234847
gene sequence and the 1.8 a crystal structure of the tungsten-containing formate dehydrogenase from desulfovibrio gigas.	desulfovibrio gigas formate dehydrogenase is the first representative of a tungsten-containing enzyme from a mesophile that has been structurally characterized. it is a heterodimer of 110 and 24 kda subunits. the large subunit, homologous to e. coli fdh-h and to d. desulfuricans nitrate reductase, harbors the w site and one [4fe-4s] center. no small subunit ortholog containing three [4fe-4s] clusters has been reported. the structural homology with e. coli fdh-h shows that the essential residues ...	2002	12220497
crystallographic investigation of the role of aspartate 95 in the modulation of the redox potentials of desulfovibrio vulgaris flavodoxin.	the side chain of aspartate 95 in flavodoxin from desulfovibrio vulgaris provides the closest negative charge to n(1) of the bound fmn in the protein. site-directed mutagenesis was used to substitute alanine, asparagine, or glutamate for this amino acid to assess the effect of this charge on the semiquinone/hydroquinone redox potential (e(1)) of the fmn cofactor. the d95a mutation shifts the e(1) redox potential positively by 16 mv, while a negative shift of 23 mv occurs in the oxidized/semiquin ...	2002	12206666
construction and physiological studies of hydrogenase depleted mutants of desulfovibrio fructosovorans.	desulfovibrio fructosovorans possesses two periplasmic hydrogenases (a nickel-iron and an iron hydrogenase) and a cytoplasmic nadp-dependent hydrogenase. the hydab genes encoding the periplasmic iron hydrogenase were replaced, in the wild-type strain as well as in single mutants depleted of one of the other two hydrogenases, by the acc1 gene encoding resistance to gentamycin. molecular characterization and remaining activity measurements of the resulting single and double mutants were performed. ...	2002	12204380
structure-function relationship in type ii cytochrome c(3) from desulfovibrio africanus: a novel function in a familiar heme core.	nmr and visible spectroscopy were used to characterize the type ii tetraheme cytochrome c(3) isolated from the periplasmic space of desulfovibrio africanus, a sulfate-reducing bacterium. although structurally similar to other cytochromes c(3), this protein displays distinct functional properties. proton nmr signals from the four hemes were assigned to the structure in the ferri- and ferrocytochromes using two-dimensional nmr experiments. the thermodynamic parameters of the hemes and of an acid-b ...	2002	12203018
diversity and abundance of bacteria in an underground oil-storage cavity.	microorganisms inhabiting subterranean oil fields have recently attracted much attention. since intact groundwater can easily be obtained from the bottom of underground oil-storage cavities without contamination by surface water, studies on such oil-storage cavities are expected to provide valuable information to understand microbial ecology of subterranean oil fields.	2002	12197947
susceptibility to antibiotics and biochemical properties of desulfovibrio desulfuricans strains.	susceptibility to several antibiotics and biochemical properties of intestinal and soil strains of desulfovibrio desulfuricans bacteria were investigated using the tests: atb ana, sceptor anaerobic mic/id and api zym. it was demonstrated that the d. desulfuricans strains were resistant to penicillin, cefoxitin, clindamycin, metronidazole, erythromycin, rifampicin and teicoplanin. the strains initially susceptible to imipenem became resistant to this drug following 72 h incubation with it. of 25 ...	2001	12197616
density functional calculations for modeling the active site of nickel-iron hydrogenases. 2. predictions for the unready and ready states and the corresponding activation processes.	zora relativistic dft calculations are presented which aim to model the geometric and electronic structure of the active site of nife hydrogenases in its epr-active oxidized states ni-a (unready state) and ni-b (ready state). starting coordinates are taken from the x-ray structure of a mutant of desulfovibrio fructosovorans hydrogenase refined at 1.81 a resolution. nine possible candidates for ni-a and ni-b are analyzed in terms of their geometric and electronic structure. comparison of calculat ...	2002	12184759
a highly selective direct method of detecting sulphate-reducing bacteria in crude oil.	the aim of this work was to develop a highly selective method of detecting sulphate-reducing bacteria (srb) in crude oil.	2002	12180949
x-ray crystal structures of reduced rubrerythrin and its azide adduct: a structure-based mechanism for a non-heme diiron peroxidase.	rubrerythrin (rbr) is a 44-kda homodimeric protein, found in many air-sensitive bacteria and archaea, which contains a unique combination of a rubredoxin-like [fe(scys)(4)] site and a non-sulfur, oxo/dicarboxylato-bridged diiron site. the diiron site structure resembles those found in o2-activating diiron enzymes. however, rbr instead appears to function as a hydrogen peroxide reductase (peroxidase). the diferrous site in all-ferrous rbr (rbr(red)) shows a much greater reactivity with h2o2 than ...	2002	12175244
redox-dependent structural changes in the superoxide reductase from desulfoarculus baarsii and treponema pallidum: a ftir study.	the redox-induced structural changes at the active site of the superoxide reductase (sor) from desulfoarculus baarsii and treponema pallidum have been monitored by means of ftir difference spectroscopy coupled to electrochemistry. with this technique, the structure and interactions formed by individual amino acids at a redox site can be detected. the infrared data on wild-type, glu47ala, and lys48ile mutants of the sor from d. baarsii provide experimental support for the conclusion that the two ...	2002	12162752
reclassification of the only species of the genus desulfomonas, desulfomonas pigra, as desulfovibrio piger comb. nov.	the growth characteristics, dna g+c content and sequences of 16s rdna and the transcribed 16s-23s rdna internal spacer were determined for desulfomonas pigra atcc 29098t, desulfovibrio desulfuricans subsp. desulfuricans strains essex 6t (= atcc 29577t) and mb (= atcc 27774) and 'desulfovibrio fairfieldensis' atcc 700045. despite phenotypic differences (shape and motility) between desulfomonas pigra and desulfovibrio strains, the molecular analysis suggests that desulfomonas pigra should be recla ...	2002	12148644
antioxidative enzymes of sulfate-reducing bacterium desulfovibrio desulfuricans: superoxide dismutase and peroxidases.	extracts of desulfovibrio desulfuricans b-1388 cells grown under anaerobic conditions displayed superoxide dismutase activity. the maximal activity was found during the stationary growth phase. the enzyme was virtually completely located in the periplasm fraction. d. desulfuricans b-1388 lacked catalase activity but contained active nadh- and nadph-peroxidases. the activity of nadh-peroxidase depended on the physiological state of the culture. on changing the growth conditions (the presence of 5 ...	2002	12139483
[transformation of cellulose nitro ester by the sulfate-reducing bacterium desulfovibrio desulfuricans].		2002	12138769
characterization of the bacterial consortium associated with black band disease in coral using molecular microbiological techniques.	the bacterial community associated with black band disease (bbd) of the scleractinian corals diploria strigosa, montastrea annularis and colpophyllia natans was examined using culture-independent techniques. two complementary molecular screening techniques of 16s rdna genes [amplified 16s ribosomal dna restriction analysis (ardra) of clone libraries and denaturing gradient gel electrophoresis (dgge)] were used to give a comprehensive characterization of the community. findings support previous s ...	2002	12123476
effect of complexing agents on reduction of cr(vi) by desulfovibrio vulgaris atcc 29579.	the reduction of cr(vi) at the expense of molecular hydrogen was studied using resting cells of desulfovibrio vulgaris atcc 29579 in anaerobic resting cell suspensions in mops buffer. bioreduction occurred only in the presence of ligands or chelating agents (co32-, citrate, nta, edta, dtpa). the stimulatory effect of these ligands on the rate of cr(vi) reduction was correlated (r = 0.988) with the strength of the ligand/chelate complex of cr(iii). the data are examined with respect to likely sol ...	2002	12115402
phylogenetic characterization of microbial communities that reductively dechlorinate tce based upon a combination of molecular techniques.	an anaerobic microbial consortium (referred to as anas) that reductively dechlorinates trichloroethene (tce) completely to ethene with the transient production of cisdichloroethene (cdce) and vinyl chloride was enriched from contaminated soil obtained from alameda naval air station. anas uses lactate as its electron donor and has been functionally stable for over 2 years. following a brief exposure to oxygen, a subculture (designated vcc) derived from anas could dechlorinate tce only to vinyl ch ...	2002	12099461
tuning the reduction potential of engineered cytochrome c-553.	cytochrome c-553 from desulfovibrio vulgaris exhibits a highly exposed heme and an unusually low reduction potential with respect to other c-type cytochromes. solvent heme exposure has been indicated as one of the most important factors in modulating the midpoint potential of the redox center. to test this hypothesis, a unique surface-exposed cysteine has been substituted for either m23 or g51 to produce the corresponding mutants and allow the formation of homodimers through a specific disulfide ...	2002	12093290
contribution of neelaredoxin to oxygen tolerance by treponema pallidum.		2002	12078490
superoxide scavenging by neelaredoxin: dismutation and reduction activities in anaerobes.	a superfamily of mononuclear iron proteins, originally named desulfoferrodoxin and neelaredoxin, has been identified by in vivo and in vitro studies as scavengers of the superoxide anion radical. these proteins, whose genes are present in all the so-far known genomes from anaerobes and in the microaerophilic pathogen treponema pallidum, show not only a considerable amino acid sequence identity but, most importantly, a common active iron site, fe[his(4)cysglu], in the oxidized state which loses t ...	2002	12072976
what is the ultimate fate of superoxide anion in vivo?	for three decades, oxidative stress and the role of reactive oxygen species in biology have been extensively studied. recently, a new interest in these areas has emerged with the discovery of superoxide reductases, a family of familiar bacterial metalloenzymes whose heretofore unknown function has now been apparently revealed. in a series of experiments utilizing genetic, molecular biological, and biochemical methods, these enzymes have been shown to be physiologically competent at removing supe ...	2002	12072975
sequential nmr assignment of the ferri-cytochrome c3 from desulfovibrio vulgaris hildenborough.		2002	12061720
redox-coupled conformational alternations in cytochrome c(3) from d. vulgaris miyazaki f on the basis of its reduced solution structure.	heteronuclear nmr spectroscopy was performed to determine the solution structure of (15)n-labeled ferrocytochrome c(3) from desulfovibrio vulgaris miyazaki f (dvmf). although the folding of the reduced cytochrome c(3) in solution was similar to that of the oxidized one in the crystal structure, the region involving hemes 1 and 2 was different. the redox-coupled conformational change is consistent with the reported solution structure of d. vulgaris hildenborough ferrocytochrome c(3), but is diffe ...	2002	12054869
characterization of microbial community in granular sludge treating brewery wastewater.	the diversity and distribution of microbes within brewery-degrading anaerobic sludge granules were studied using various molecular techniques. molecular cloning of small-subunit rrna gene sequences indicated that all archaeal clones were affiliated with methanosaeta concillii (>99% sequence similarity), and the bacterial clones were mostly affiliated with a not-yet-cultured clostridium cluster (48 out of 99 clones) in the low g + c gram-positive group, xanthomonas spp. in the gamma-subclass of p ...	2002	12044076
uranium reduction by desulfovibrio desulfuricans strain g20 and a cytochrome c3 mutant.	previous in vitro experiments with desulfovibrio vulgaris strain hildenborough demonstrated that extracts containing hydrogenase and cytochrome c3 could reduce uranium(vi) to uranium(iv) with hydrogen as the electron donor. to test the involvement of these proteins in vivo, a cytochrome c3 mutant of d. desulfuricans strain g20 was assayed and found to be able to reduce u(vi) with lactate or pyruvate as the electron donor at rates about one-half of those of the wild type. with electrons from hydr ...	2002	12039777
cadmium recovery by a sulfate-reducing magnetotactic bacterium, desulfovibrio magneticus rs-1, using magnetic separation.	cadmium recovery by a sulfate-reducing magnetotactic bacterium, desulfovibrio magneticus strain rs-1, was investigated. d. magneticus precipitated >95% of cadmium at an initial concentration of 1.3 ppm in the growth medium. electron microscopic analysis revealed that d. magneticus formed electron-dense particles on its surface when cultivated in the presence of cadmium ions (cd2+). sulfide was also found in the precipitate, and the composition ratio of sulfide/cadmium was 0.7. sixty percent of v ...	2002	12018305
active site structure and dynamics of cytochrome c3 from desulfovibrio gigas immobilized on electrodes.	cytochrome c3 from desulfovibrio gigas is electrostatically adsorbed on ag electrodes coated with self-assembled monolayers (sams) of 11-mercaptoundecanoic acid. the redox equilibria and electron transfer dynamics of the adsorbed four-heme protein are studied by surface enhanced resonance raman spectroscopy. immobilization on the coated electrodes does not cause any structural changes in the redox sites. the potential-dependent stationary experiments distinguish the redox potential of heme iv (- ...	2002	12012460
substrate recognition by 2-oxoacid:ferredoxin oxidoreductase from sulfolobus sp. strain 7.	2-oxoacid:ferredoxin oxidoreductase (ofor) catalyzes the coenzyme a-dependent oxidative decarboxylation of 2-oxoacids, at an analogous metabolic position to 2-oxoacid dehydrogenase multienzyme complex. the enzyme from sulfolobus sp. strain 7, a thermoacidophilic crenarchaeon, is a heterodimer comprising two subunits, a (632 amino acids) and b (305 amino acids). in contrast to other ofors, the sulfolobus enzyme shows a broad specificity for 2-oxoacids such as pyruvate and 2-oxoglutarate. based on ...	2002	12009405
methanogenesis from furfural by defined mixed cultures.	methanogenesis from furfural by defined mixed cultures was studied. under sulfate-reducing conditions, a desulfovibrio strain was used as the furfural-degrading species producing acetic acid. this sulfate-reducing bacterium (srb) desulfovibrio strain b is an incomplete oxidizer, unable to carry out the terminal oxidation of organic substrates, leaving acetic acid as the end product. introduction of acetate-utilizing methanogenic archaeon methanosarcina barkeri 227 converted acetic acid to methan ...	2002	12000990
anaerobic reduction of a sulfonated azo dye, congo red, by sulfate-reducing bacteria.	the capacity for anaerobic decolorization of a sulfonated azo dye, congo red, by a strain of a sulfate-reducing bacterium was evaluated. after optimizing the growth rate of the bacteria on a simple carbon source and terminal electron acceptor pair, lactate and sulfate, respectively, the effect of the dye concentration on their growth rate was analyzed. the decolorization rate was affected by the dye concentration in the growth medium. the azo-bond cleavage mechanism of reductive decolorization w ...	2002	11998840
presence of the cofactor speeds up folding of desulfovibrio desulfuricans flavodoxin.	flavodoxin is an alpha/beta protein with a noncovalently bound flavin-mononucleotide (fmn) cofactor. the apo-protein adopts a structure identical to that of the holo-form, although there is more dynamics in the fmn-binding loops. the equilibrium unfolding processes of azotobacter vinelandii apo-flavodoxin, and desulfovibrio desulfuricans atcc strain 27774 apo- and holo-flavodoxins involve rather stable intermediates. in contrast, we here show that both holo- and apo-forms of flavodoxin from d. d ...	2002	11967369
reduction of humic substances by halorespiring, sulphate-reducing and methanogenic microorganisms.	physiologically distinct anaerobic microorganisms were explored for their ability to oxidize different substrates with humic acids or the humic analogue, anthraquinone-2,6-disulphonate (aqds), as a terminal electron acceptor. most of the microorganisms evaluated including, for example, the halorespiring bacterium, desulfitobacterium pce1, the sulphate-reducing bacterium, desulfovibrio g11 and the methanogenic archaeon, methanospirillum hungatei jf1, could oxidize hydrogen linked to the reduction ...	2002	11966825
growth of sulfate-reducing bacteria with solid-phase electron acceptors.	hannebachite (caso3 x 0.5h2o), gypsum (caso4 x 2h2o), anglesite (pbso4), and barite (baso4) were tested as electron acceptors for sulfate-reducing bacteria with lactate as the electron donor. hannebachite and gypsum are commonly associated with flue gas desulfurization products, and anglesite is a weathering product found in lead mines. barite was included as the most insoluble sulfate. growth of sulfate-reducing bacteria was monitored by protein and sulfide (dissolved h2s and hs-) measurements. ...	2002	11954795
purification and characterization of a membrane-bound enzyme complex from the sulfate-reducing archaeon archaeoglobus fulgidus related to heterodisulfide reductase from methanogenic archaea.	heterodisulfide reductase (hdr) is a unique disulfide reductase that plays a key role in the energy metabolism of methanogenic archaea. the genome of the sulfate-reducing archaeon archaeoglobus fulgidus encodes several proteins of unknown function with high sequence similarity to the catalytic subunit of hdr. here we report on the purification of a multisubunit membrane-bound enzyme complex from a. fulgidus that contains a subunit related to the catalytic subunit of hdr. the purified enzyme is a ...	2002	11952791
anabaena sp. pcc 7119 flavodoxin as electron carrier from photosystem i to ferredoxin-nadp+ reductase. role of trp(57) and tyr(94).	the influence of the amino acid residues sandwiching the flavin ring in flavodoxin (fld) from the cyanobacterium anabaena sp. pcc 7119 in complex formation and electron transfer (et) with its natural partners, photosystem i (psi) and ferredoxin-nadp(+) reductase (fnr), was examined in mutants of the key residues trp(57) and tyr(94). the mutants' ability to form complexes with either fnr or psi is similar to that of wild-type fld. however, some of the mutants exhibit altered kinetic properties in ...	2002	11950835
a membrane-bound cytochrome c3: a type ii cytochrome c3 from desulfovibrio vulgaris hildenborough.	a new tetraheme cytochrome c3 was isolated from the membranes of desulfovibrio vulgaris hildenborough (dvh). this cytochrome has a molecular mass of 13.4 kda and a pi of 5.5 and contains four heme c groups with apparent reduction potentials of -170 mv, -235 mv, -260 mv and -325 mv at ph 7.6. the complete sequence of the new cytochrome, retrieved from the preliminary data of the dvh genome, shows that this cytochrome is homologous to the "acidic" cytochrome c3 from desulfovibrio africanus (da). a ...	2001	11948878
cooperativity between electrons and protons in a monomeric cytochrome c(3): the importance of mechano-chemical coupling for energy transduction.	to fully understand the structural bases for the mechanisms of biological energy transduction, it is essential to determine the microscopic thermodynamic parameters which describe the properties of each centre involved in the reactions, as well as its interactions with the others. these interactions between centres can then be interpreted in the light of structural features of the proteins. redox titrations of cytochrome c(3) from desulfovibrio desulfuricans atcc 27774 followed by nmr and visibl ...	2001	11948869
identification of the clostridium perfringens genes involved in the adaptive response to oxidative stress.	clostridium perfringens is a ubiquitous gram-positive pathogen that is present in the air, soil, animals, and humans. although c. perfringens is strictly anaerobic, vegetative and stationary cells can survive in a growth-arrested stage in the presence of oxygen and/or low concentrations of superoxide and hydroxyl radicals. indeed, it possesses an adaptive response to oxidative stress, which can be activated in both aerobic and anaerobic conditions. to identify the genes involved in this oxidativ ...	2002	11948145
the structure of cytochrome c'(3) from desulfovibrio gigas (ncib 9332).		1969	11947254
the amino acid sequence of cytochrome c(3) from desulfovibrio desulfuricans (strain el agheila z, ncib 8380).		1971	11946159
hybrid cluster proteins (hcps) from desulfovibrio desulfuricans atcc 27774 and desulfovibrio vulgaris (hildenborough): x-ray structures at 1.25 a resolution using synchrotron radiation.	the structures of the hybrid cluster proteins (hcps) from the sulfate-reducing bacteria desulfovibrio desulfuricans (atcc 27774) and desulfovibrio vulgaris (hildenborough) have been elucidated at a resolution of 1.25 a using x-ray synchrotron radiation techniques. in the case of the d. desulfuricans protein, protein isolation, purification, crystallization and x-ray data collection were carried out under strict anaerobic conditions, whereas for the d. vulgaris protein the conditions were aerobic ...	2002	11941509
the 1.25 a resolution structure of the diheme napb subunit of soluble nitrate reductase reveals a novel cytochrome c fold with a stacked heme arrangement.	the diheme cytochrome napb constitutes the small subunit of a periplasmic nitrate reductase found in a wide variety of bacterial species, including pathogens. the napb protein is essential in transferring electrons to the large catalytic subunit napa, which subsequently reduces nitrate to nitrite. here we present the crystal structure of a proteolyzed form of recombinant napb from haemophilus influenzae, which was determined by the multiple-wavelength anomalous dispersion (mad) method at 1.25 a ...	2002	11939777
ir spectroelectrochemical study of the binding of carbon monoxide to the active site of desulfovibrio fructosovorans ni-fe hydrogenase.	the binding of carbon monoxide, a competitive inhibitor of many hydrogenases, to the active site of desulfovibrio fructosovorans hydrogenase has been studied by infrared spectroscopy in a spectroelectrochemical cell. direct evidence has been obtained of which redox states of the enzyme can bind extrinsic co. redox states a, b and su do not bind extrinsic co; only after reductive activation of the hydrogenase can co bind to the active site. two states with bound extrinsic co can be distinguished ...	2002	11935356
evolution of nitrate reductase: molecular and structural variations on a common function.	the biological transformation of nitrogen oxyanions is widespread in nature and gives rise to a robust biogeochemical cycle. the first step in nitrate reduction is carried out by the enzyme nitrate reductase (nr). although nr always catalyzes the same chemical reaction (conversion of nitrate into nitrite), its location in the cell, structure, and function are organism-dependent. we use protein sequence data to determine phylogenetic relationships and to examine similarities in structure and func ...	2002	11921398
hydrogenases: hydrogen-activating enzymes.		2002	11921392
desulfovibrio sp. genes involved in the respiration of sulfate during metabolism of hydrogen and lactate.	to develop a better understanding of respiration by sulfate-reducing bacteria, we examined transcriptional control of respiratory genes during growth with lactate or hydrogen as an electron donor. rna extracts of desulfovibrio desulfuricans subsp. aestuarii were analyzed by using random arbitrarily primed pcr. rna was reverse transcribed under low-stringency conditions with a set of random primers, and candidate cdnas were cloned, sequenced, and characterized by blast analysis. putative differen ...	2002	11916715
a 6940 bp dna fragment from desulfovibrio gigas contains genes coding for lipoproteins, universal stress response and transcriptional regulator protein homologues.	the nucleotide sequence of a 6940 bp dna fragment from desulfovibrio gigas, containing seven orfs was determined. orf-1 encodes a probable lipoprotein having high similarities with lytic transglycosylases. orf-2 encodes a polypeptide that does not show homologies with proteins deposited in the database, but it contains the consensus pattern of class ii aminoacyl-trna synthetases. the putative protein encoded by orf-3 possesses high similarities with universal stress response proteins from the us ...	2001	11916257
kinetics and mechanism of superoxide reduction by two-iron superoxide reductase from desulfovibrio vulgaris.	superoxide reductases (sors) contain a novel square pyramidal ferrous [fe(nhis)(4)(scys)] site that rapidly reduces superoxide to hydrogen peroxide. here we report extensive pulse radiolysis studies on recombinant two-iron sor (2fe-sor) from desulfovibrio vulgaris. the results support and elaborate on our originally proposed scheme for reaction of the [fe(nhis)(4)(scys)] site with superoxide [coulter, e. d., emerson, j. e., kurtz, d. m., jr., and cabelli, d. e. (2000) j. am. chem. soc. 122, 1155 ...	2002	11914081
superoxide reductase activities of neelaredoxin and desulfoferrodoxin metalloproteins.	superoxide reductases have now been well characterized from several organisms. unique biochemical features include the ability of the reduced enzyme to react with o2- but not dioxygen (reduced sors are stable in an aerobic atmosphere for hours). future biochemical assays that measure the reaction of sor with o2- should take into account the difficulties of assaying o2- directly and the myriad of redox reactions that can take place between components in the assay, for example, direct electron tra ...	2002	11912914
characterization of a novel insertion sequence, is bp1, in burkholderia pseudomallei.	during screening for antigenic proteins in burkholderia pseudomallei, a novel insertion sequence, is bp1, was found by sequence similarity searches. is bp1 contains two overlapping orfs of 261 bp ( orfa) and 852 bp ( orfb), encoding 87 and 284 amino acid residues, respectively, and an imperfect inverted repeat. the putative protein encoded by orfa (orfa) is similar to the orfa in insertion sequences of the is 3 family in other bacteria, showing 49% and 76% amino acid identity and similarity, res ...	2002	11907683
dft investigation of structural, electronic, and catalytic properties of diiron complexes related to the [2fe](h) subcluster of fe-only hydrogenases.	hydrogenases catalyze the reversible oxidation of dihydrogen to protons and electrons. the structures of two fe-only hydrogenases have been recently reported [peters, j. w.; lanzilotta, w. n.; lemon, b. j.; seefeldt, l. c. science 1998, 282, 1853-1858. nicolet, y.; piras, c.; legrand, p.; hatchikian, e. c.; fontecilla-camps, j. c. structure 1999, 7, 13-23], showing that the likely site of dihydrogen activation is the so-called [2fe](h) cluster, where each fe ion is coordinated by co and cn(-) li ...	2002	11896710
a hydrogenosomal [fe]-hydrogenase from the anaerobic chytrid neocallimastix sp. l2.	the presence of a [fe]-hydrogenase in the hydrogenosomes of the anaerobic chytridiomycete fungus neocallimastix sp. l2 has been demonstrated by immunocytochemistry, subcellular fractionation, western-blotting and measurements of hydrogenase activity in the presence of various concentrations of carbon monoxide (co). since the hydrogenosomal hydrogenase activity can be inhibited nearly completely by low concentrations of co, it is likely that the [fe]-hydrogenase is responsible for at least 90% of ...	2002	11891051
successional development of sulfate-reducing bacterial populations and their activities in a wastewater biofilm growing under microaerophilic conditions.	a combination of fluorescence in situ hybridization, microprofiles, denaturing gradient gel electrophoresis of pcr-amplified 16s ribosomal dna fragments, and 16s rrna gene cloning analysis was applied to investigate successional development of sulfate-reducing bacteria (srb) community structure and in situ sulfide production activity within a biofilm growing under microaerophilic conditions (dissolved oxygen concentration in the bulk liquid was in the range of 0 to 100 microm) and in the presenc ...	2002	11872492
successional development of sulfate-reducing bacterial populations and their activities in an activated sludge immobilized agar gel film.	a combination of fluorescence in situ hybridization (fish), microprofiles, and denaturing gradient gel electrophoresis (dgge) analysis of pcr-amplified 16s rdna fragments followed by hybridization analysis with specific probes was applied to investigate successional development of sulfate-reducing bacteria (srb) community structure and in situ sulfide production activity within an activated sludge immobilized agar gel film. in this model biofilm system, since biases arising from biofilm heteroge ...	2002	11870602
studies of the reduction and protonation behavior of tetraheme cytochromes using atomic detail.	a comparative study of tetraheme cytochrome c3 molecules from several species was carried out using recently developed theoretical methods based on continuum electrostatics. the binding joint equilibrium of electrons and protons was simulated, revealing the complete thermodynamic aspects of electron-proton coupling in these molecules. the method yields excellent accuracy in terms of midpoint potentials, giving the correct reduction orders in all molecules examined, except for one heme site. the ...	2002	11862556