Publications

nitrate reductase from the magnetotactic bacterium magnetospirillum magnetotacticum ms-1: purification and sequence analyses.	we purified the nitrate reductase from the soluble fraction of magnetospirillum magnetotacticum ms-1. the enzyme was composed of 86- and 17-kda subunits and contained molybdenum, non-heme iron, and heme c. these properties are very similar to those of the periplasmic nitrate reductase found in paracoccus pantotrophus. the m. magnetotacticum nap locus was clustered in seven open reading frames, napfdaghbc. the phylogenetic analyses of napa, napb, and napc suggested a close relationship between m. ...	2003	12795406
maug, a novel diheme protein required for tryptophan tryptophylquinone biogenesis.	the biosynthesis of methylamine dehydrogenase (madh) from paracoccus denitrificans requires four genes in addition to those that encode the two structural protein subunits. none of these gene products have been previously isolated. one of these, maug, exhibits sequence similarity to diheme cytochrome c peroxidases and is required for the synthesis of the tryptophan tryptophylquinone (ttq) prosthetic group of madh. a system was developed for the homologous expression of maug in p. denitrificans. ...	2003	12809487
identification and characterization of transposable elements of paracoccus pantotrophus.	we studied diversity and distribution of transposable elements residing in different strains (dsm 11072, dsm 11073, dsm 65, and lmd 82.5) of a soil bacterium paracoccus pantotrophus (alpha-proteobacteria). with application of a shuttle entrapment vector pmec1, several novel insertion sequences (iss) and transposons (tns) have been identified. they were sequenced and subjected to detailed comparative analysis, which allowed their characterization (i.e., identification of transposase genes, termin ...	2003	12813068
electron transport to periplasmic nitrate reductase (napa) of wolinella succinogenes is independent of a napc protein.	the rumen bacterium wolinella succinogenes grows by respiratory nitrate ammonification with formate as electron donor. whereas the enzymology and coupling mechanism of nitrite respiration is well known, nitrate reduction to nitrite has not yet been examined. we report here that intact cells and cell fractions catalyse nitrate and chlorate reduction by reduced viologen dyes with high specific activities. a gene cluster encoding components of a putative periplasmic nitrate reductase system (napa, ...	2003	12823811
the proton pump of the mitochondrial bc1 complex.	the molecular mechanism of the proton pump activity by the respiratory chain bc1 complex is still unknown. this group has proposed since long time that protonation/deprotonation events in the apoproteins of the complex are cooperatively linked to the oxido-reduction reactions at the quinone catalytic centre. protolytic residues in the apoproteins can thus provide proton transfer pathways between the bulk aqueons phases and the redox centre. a series of experiments has been carried out aimed at d ...	2003	12833636
a novel enzyme, d-3-hydroxyaspartate aldolase from paracoccus denitrificans ifo 13301: purification, characterization, and gene cloning.	a novel enzyme, d-3-hydroxyaspartate aldolase (d-haa), catalyzing the conversion of d-3-hydroxyaspartate to glyoxylate plus glycine, was purified to homogeneity from paracoccus denitrificans ifo 13301. d-haa is strictly d-specific as to the alpha-position, whereas the enzyme does not distinguish between threo and erythro forms at the beta-position. in addition to d-3-hydroxyaspartate, the enzyme also acts on d-threonine, d-3-3,4-dihydroxyphenylserine, d-3-3,4-methylenedioxyphenylserine, and d-3- ...	2003	12835921
sequence analysis of a gene product synthesized by xanthomonas sp. during growth on natural rubber latex.	xanthomonas sp. secretes an extracellular protein (mr approximately 70+/-5 kda) during growth on purified natural rubber [poly(1,4-cis-isoprene)] but not during growth on water-soluble carbon sources such as glucose or gluconate. a 1.3 kbp dna fragment coding for an internal part of the structural gene of the 70 kda protein was amplified by nested polymerase chain reaction (pcr) using amino acid sequence information obtained after edman degradation of selected trypsin-generated peptides of the p ...	2003	12855168
atr-ftir spectroscopy of the p(m) and f intermediates of bovine and paracoccus denitrificans cytochrome c oxidase.	the structures of p(m) and f intermediates of bovine and paracoccus denitrificans cytochrome c oxidase were investigated by perfusion-induced attenuated total reflection-fourier transform infrared (atr-ftir) spectroscopy. transitions from the "fast" oxidized state to the p(m) or f states were initiated by perfusion with buffer containing either co/oxygen or h(2)o(2). intermediates were quantitated by simultaneous monitoring of visible absorption changes in the protein film. for both bovine and p ...	2003	12873142
role of tryptophan 121 in the soluble cua domain of cytochrome c oxidase: structure and electron transfer studies.	to investigate the contribution of tryptophan-121 (trp121) residue to the structure and function of soluble cua domain of cytochrome c oxidase, three mutant proteins, trp121tyr, trp121leu and trp121-deleted mutant of the soluble domain of paracoccus versutus cytochrome c oxidase, were constructed and expressed in escherichia coli bl21 (de3). optical spectral studies showed that both the coordination structure of the cua center and the secondary structure of the protein were changed significantly ...	2003	12874377
control of metalloprotein reduction potential: compensation phenomena in the reduction thermodynamics of blue copper proteins.	the reduction thermodynamics (delta h degrees '(rc) and delta s degrees '(rc)) for native paracoccus versutus amicyanin, for alcaligenes faecalis s-6 pseudoazurin, and for the g45p, m64e, and k27c variants of pseudomonas aeruginosa azurin were measured electrochemically. comparison with the data available for other native and mutated blue copper proteins indicates that the features of metal coordination and the electrostatic potential due to the protein matrix and the solvent control the reducti ...	2003	12885256
chloride dependence of growth in bacteria.	chloride is an abundant anion on earth but studies analyzing a possible function of chloride in prokaryotes are scarce. to address the question, we have tested 44 different gram-negative and gram-positive bacteria for a chloride dependence or chloride stimulation of growth. none required chloride for growth at their optimal growth (salt) conditions. however, in hyperosmotic media containing high concentrations of na+, 11 bacteria (aeromonas hydrophila, bacillus megaterium, bacillus subtilis, cor ...	2003	12900036
physiological role of s-formylglutathione hydrolase in c(1) metabolism of the methylotrophic yeast candida boidinii.	the methylotrophic yeast candida boidinii exhibits s-formylglutathione hydrolase activity (fgh, ec 3.1.2.12), which is involved in the glutathione-dependent formaldehyde oxidation pathway during growth on methanol as the sole carbon source. the structural gene, fgh1, was cloned from c. boidinii, and its predicted amino acid sequence showed more than 60 % similarity to those of fghs from paracoccus denitrificans and saccharomyces cerevisiae, and human esterase d. fgh from c. boidinii contained a ...	2003	12904537
steady-state kinetic analysis of substrate pair cycling between two enzymes: application to a mediated electron transport between the cytoplasmic membrane and the periplasmic nitrite reductase of paracoccus denitrificans.	an extended kinetic model is presented for the process catalysed by two enzymes mutually connected by the cycling of two reversibly interconvertible chemically relative species. expressions are derived for the steady-state velocity, limiting velocity (v) and the half-saturation concentration of the cycling substrate (a(0.5)). it is shown that the velocity depends on the total concentration of cycling substrate hyperbolically if both enzymes have equal activities. based on these theoretical consi ...	2003	12914907
unidirectional effect of lauryl sulfate on the reversible nadh:ubiquinone oxidoreductase (complex i).	lauryl sulfate inhibits the deltamu;(h)(+)-dependent reverse electron transfer reactions catalyzed by nadh:ubiquinone oxidoreductase (complex i) in coupled bovine heart submitochondrial particles and in vesicles derived from paracoccus denitrificans. the inhibitor affects neither nadh oxidase (coupled or uncoupled) nor nadh:ferricyanide reductase and succinate oxidase activities at the concentrations that selectively prevent the succinate-supported, rotenone-sensitive nad(+) or ferricyanide redu ...	2003	12914921
structure of the phenylhydrazine adduct of the quinohemoprotein amine dehydrogenase from paracoccus denitrificans at 1.7 a resolution.	the 109 kda quinohemoprotein amine dehydrogenase (qhndh) from paracoccus denitrificans contains a novel redox cofactor, cysteine tryptophylquinone (ctq). this cofactor is derived from a pair of gene-encoded amino acids by post-translational modification and was previously identified and characterized within an 82-residue subunit by chemical methods and crystallographic analysis at 2.05 a resolution. it contains an orthoquinone moiety bound to the indole ring and catalyzes the oxidation of alipha ...	2003	12925784
different interaction modes of two cytochrome-c oxidase soluble cua fragments with their substrates.	cytochrome-c oxidase is the terminal enzyme in the respiratory chains of mitochondria and many bacteria and catalyzes the formation of water by reduction of dioxygen. the first step in the cytochrome oxidase reaction is the bimolecular electron transfer from cytochrome c to the homobinuclear mixed-valence cua center of subunit ii. in thermus thermophilus a soluble cytochrome c552 acts as the electron donor to ba3 cytochrome-c oxidase, an interaction believed to be mainly hydrophobic. in paracocc ...	2003	12937163
isolation and characterization of novel halotolerant and/or halophilic denitrifying bacteria with versatile metabolic pathways for the degradation of trimethylamine.	four denitrifying bacteria capable of degrading trimethylamine under both aerobic and denitrifying conditions were newly isolated from coastal sediments and wastewater contaminated by marine water. all strains were in alpha-proteobacteria. strain gp43 was classified as a member of genus paracoccus, and strain ph32, ph34 and grp21 were novel organisms with remote phylogenetic position from other genus alpha-proteobacteria. among these four strains were the halophilic strains ph32, ph34 and grp21, ...	2003	12951251
growth and nitrite and nitrous oxide accumulation of paracoccus denitrificans atcc 19367 in the presence of selected pesticides.	the effects of the application of eight pesticides (aldrin, lindane, dimetoate, methylparathion, methidation, atrazine, simazine, and captan) on growth, respiratory activity (as co2 production), denitrifying activity (as n2o released), and nitrite accumulation in the culture medium by paracoccus denitrificans strain atcc 19367 were studied. the fungicide captan totally inhibited growth and biological activity of p. denitrificans, while the rest of the tested pesticides delayed the growth and co2 ...	2003	12959522
an engineered cua amicyanin capable of intermolecular electron transfer reactions.	the type i copper center of amicyanin was replaced with a binuclear cua center. to create this model cua protein, a portion of the amino acid sequence that contains three of the ligands to the native type i copper center of paracoccus denitrificans amicyanin was replaced with the corresponding portion of sequence that provides five ligands for the cua center of cytochrome c oxidase from p. denitrificans. uv-visible and electron paramagnetic resonance spectroscopy confirm that the engineered prot ...	2003	12970350
chemical and kinetic reaction mechanisms of quinohemoprotein amine dehydrogenase from paracoccus denitrificans.	quinohemoprotein amine dehydrogenase (qhndh) possesses a cysteine tryptophylquinone (ctq) prosthetic group that catalyzes the oxidative deamination of primary amines. in addition to ctq, two heme c cofactors are present in qhndh that mediate the transfer of the substrate-derived electrons from ctq to an external electron acceptor. steady-state kinetic assays yielded relatively small k(cat) values (<6 s(-1)), and the rate-limiting step appears to be the interprotein electron transfer from heme in ...	2003	12974623
x-ray structure of methanol dehydrogenase from paracoccus denitrificans and molecular modeling of its interactions with cytochrome c-551i.	the x-ray structure of methanol dehydrogenase (medh) from paracoccus denitrificans (medh-pd) was determined at 2.5 a resolution using molecular replacement based on the structure of medh from methylophilus methylotrophus w3a1 (medh-wa). the overall structures from the two bacteria are similar to each other except that the former has a longer c-terminal tail in each subunit and shows local differences in several insertion regions. the "x-ray sequence" of the segment alphagly444-alphaleu452 was es ...	2003	14505072
active/de-active transition of respiratory complex i in bacteria, fungi, and animals.	mammalian complex i (nadh:ubiquinone oxidoreductase) exists as a mixture of interconvertible active (a) and de-activated (d) forms. the a-form is capable of nadh:quinone-reductase catalysis, but not the d-form. complex i from the bacterium paracoccus denitrificans, by contrast, exists only in the a-form. this bacterial complex contains 32 fewer subunits than the mammalian complex. the question arises therefore if the structural complexity of complex i from higher organisms correlates with its ab ...	2003	14507430
electron transfer complexes of cytochrome c peroxidase from paracoccus denitrificans containing more than one cytochrome.	according to the model proposed in previous papers [pettigrew, g. w., prazeres, s., costa, c., palma, n., krippahl, l., and moura, j. j. (1999) the structure of an electron-transfer complex containing a cytochrome c and a peroxidase, j. biol. chem. 274, 11383-11389; pettigrew, g. w., goodhew, c. f., cooper, a., nutley, m., jumel, k., and harding, s. e. (2003) electron transfer complexes of cytochrome c peroxidase from paracoccus denitrificans, biochemistry 42, 2046-2055], cytochrome c peroxidase ...	2003	14556628
a mutant of paracoccus denitrificans with disrupted genes coding for cytochrome c550 and pseudoazurin establishes these two proteins as the in vivo electron donors to cytochrome cd1 nitrite reductase.	in paracoccus denitrificans, electrons pass from the membrane-bound cytochrome bc(1) complex to the periplasmic nitrite reductase, cytochrome cd(1). the periplasmic protein cytochrome c(550) has often been implicated in this electron transfer, but its absence, as a consequence of mutation, has previously been shown to result in almost no attenuation in the ability of the nitrite reductase to function in intact cells. here, the hypothesis that cytochrome c(550) and pseudoazurin are alternative el ...	2003	14563865
electrochemical and ftir spectroscopic characterization of the cytochrome bc1 complex from paracoccus denitrificans: evidence for protonation reactions coupled to quinone binding.	the cytochrome bc(1) complex from paracoccus denitrificans and soluble fragments of its cytochrome c(1) and rieske isp subunits are characterized by a combined approach of protein electrochemistry and ftir difference spectroscopy. the ftir difference spectra provide information about alterations in the protein upon redox reactions: signals from the polypeptide backbone, from the cofactors, and from amino acid side chains. we describe typical modes for conformational changes in the polypeptide an ...	2003	14567700
kinetic stability of the peroxidase activity of unfolded cytochrome c: heme degradation and catalyst inactivation by hydrogen peroxide.	unfolding converts paracoccus versutus cytochrome c-550 into a potent peroxidase (diederix, r. e. m.; ubbink, m.; canters, g. w. chembiochem 2002, 3, 110-112). the catalytic activity is accompanied by peroxide-driven inactivation that is prevented, in part, by reducing substrate. here, the kinetics of inactivation are described, and evidence is presented for the occurrence of a labile intermediate on the catalytic peroxidase pathway of unfolded cytochrome c-550. this intermediate represents a br ...	2003	14577794
amicyanin metal-site structure and interaction with madh: pac and nmr spectroscopy of ag-, cd-, and cu-amicyanin.	to investigate the structural control mechanisms in the metal site of amicyanin when interacting with madh, redox-inactive ag(+)- and cd(2+)-substituted amicyanins were studied with perturbed angular correlations of gamma-rays (pac) spectroscopy. pac experiments on (111m)cd-substituted amicyanin revealed two different metal-site structures, which are very likely in dynamic exchange on a ~5 ns timescale. only one structure binds to madh. the dissociation constants, k(d), are 9+/-2 microm with mad ...	2004	14605949
assembly of respiratory complexes i, iii, and iv into nadh oxidase supercomplex stabilizes complex i in paracoccus denitrificans.	stable supercomplexes of bacterial respiratory chain complexes iii (ubiquinol:cytochrome c oxidoreductase) and iv (cytochrome c oxidase) have been isolated as early as 1985 (berry, e. a., and trumpower, b. l. (1985) j. biol. chem. 260, 2458-2467). however, these assemblies did not comprise complex i (nadh:ubiquinone oxidoreductase). using the mild detergent digitonin for solubilization of paracoccus denitrificans membranes we could isolate nadh oxidase, assembled from complexes i, iii, and iv in ...	2004	14610094
investigation of protonatable residues in rhodothermus marinus caa3 haem-copper oxygen reductase: comparison with paracoccus denitrificans aa3 haem-copper oxygen reductase.	the rhodothermus marinus caa(3 )haem-copper oxygen reductase contains all the residues of the so-called d- and k-proton channels, with the notable exception of the helix vi glutamate residue (glu278(i) in paracoccus denitrificans aa(3)), being nevertheless a true oxygen reductase reducing o(2) to water, and an efficient proton pump. instead, in the same helix, but one turn below, it has a tyrosine residue (tyr256(i), r. marinus caa(3) numbering), whose hydroxyl group occupies the same spatial po ...	2004	14691678
use of stable-isotope probing, full-cycle rrna analysis, and fluorescence in situ hybridization-microautoradiography to study a methanol-fed denitrifying microbial community.	a denitrifying microbial consortium was enriched in an anoxically operated, methanol-fed sequencing batch reactor (sbr) fed with a mineral salts medium containing methanol as the sole carbon source and nitrate as the electron acceptor. the sbr was inoculated with sludge from a biological nutrient removal activated sludge plant exhibiting good denitrification. the sbr denitrification rate improved from less than 0.02 mg of no(3)(-)-n mg of mixed-liquor volatile suspended solids (mlvss)(-1) h(-1) ...	2004	14711691
energy-dependent transformation of f0.f1-atpase in paracoccus denitrificans plasma membranes.	f(0).f(1)-atp synthase in tightly coupled inside-out vesicles derived from paracoccus denitrificans catalyzes rapid respiration-supported atp synthesis, whereas their atpase activity is very low. in the present study, the conditions required to reveal the deltamu(h+)-generating atp hydrolase activity of the bacterial enzyme have been elucidated. energization of the membranes by respiration results in strong activation of the venturicidin-sensitive atp hydrolysis, which is coupled with generation ...	2004	14722115
isolation and biochemical characterization of two soluble iron(iii) reductases from paracoccus denitrificans.	two soluble enzymes (fera and ferb) catalyzing the reduction of a number of iron(iii) complexes by nadh, were purified to near homogeneity from the aerobically grown iron-limited culture of paracoccus denitrificans using a combination of anion-exchange chromatography (sepharose q), chromatofocusing (mono p), and gel permeation chromatography (superose 12). fera is a monomer with a molecular mass of 19 kda, whereas ferb exhibited a molecular mass of about 55 kda and consists of probably two ident ...	2004	14728682
crystallization and preliminary x-ray diffraction analysis of a dihaem cytochrome c peroxidase from paracoccus denitrificans.	cytochrome c peroxidase was isolated from paracoccus denitrificans and purified to homogeneity in three steps prior to crystallization. two different diffraction-quality crystal forms were obtained by the hanging-drop vapour-diffusion method using a number of screening conditions. the best (needle-shaped) crystal form is suitable for structural studies and was grown from solutions containing 20% peg 8000, 0.1 m tris ph 8.5 and 0.2 m mgcl(2). crystals grew to a maximum length of approximately 0.7 ...	2004	14747715
soluble cua domain of cyanobacterial cytochrome c oxidase.	the genomes of several cyanobacteria show the existence of gene clusters encoding subunits i, ii, and iii of aa(3)-type cytochrome c oxidase. the enzyme occurs on both plasma and thylakoid membranes of these oxygenic phototrophic prokaryotes. here we report the expression and purification of a truncated subunit ii copper a (cu(a)) domain (i.e. the electron entry and donor binding site) of cytochrome c oxidase from the cyanobacterium synechocystis pcc 6803 in high yield. the water-soluble purple ...	2004	14672950
lucigenin and coelenterazine as superoxide probes in mitochondrial and bacterial membranes.	the chemiluminescent superoxide indicators lucigenin and coelenterazine were compared in rat liver submitochondrial particles and cytoplasmic membranes from paracoccus denitrificans. qualitative monitoring is possible with both probes, but quantitative work with lucigenin is hampered by its dependence on one-electron reduction before the photon-emitting reaction. therefore, calibration of measurements on complex i, capable of efficient lucigenin prereduction with reduced nicotinamide adenine din ...	2004	14654044
[methanotrophs and methylobacteria are found in woody plant tissues within a winter period].	samples of tree seeds, buds, and needles collected within a winter period at ambient temperatures from -11 to -17 degrees c were analyzed for the presence of methylotrophic microflora. thin sections of blue spruce needles were found to contain bacteria morphologically close to pink-pigmented methylobacteria. the methylobacteria that were isolated in pure cultures from samples of linden seeds and buds, pine and blue spruce needles, as well as of lilac, maple, and apple buds, were classified into ...	2004	15688941
nitric oxide oscillations in paracoccus denitrificans: the effects of environmental factors and of segregating nitrite reductase and nitric oxide reductase into separate cells.	nitric oxide is a denitrification intermediate which is produced from nitrite and then further converted via nitrous oxide to nitrogen. here, the effect of low concentrations of the protonophore carbonylcyanide m-chlorophenylhydrazone on the time courses for dissolved gases was examined. while no was found to oscillate, n(2)o only increased gradually as the reduction of nitrite progressed. the frequency and shape of protonophore-induced no oscillations were influenced by temperature and the conc ...	2004	15313228
characterization and expression of genes from the rubisco gene cluster of the chemoautotrophic symbiont of solemya velum: cbblsqo.	chemoautotrophic endosymbionts residing in solemya velum gills provide this shallow water clam with most of its nutritional requirements. the cbb gene cluster of the s. velum symbiont, including cbbl and cbbs, which encode the large and small subunits of the carbon-fixing enzyme ribulose 1,5-bisphosphate carboxylase/oxygenase (rubisco), was cloned and expressed in escherichia coli. the recombinant rubisco had a high specific activity, approximately 3 micromol min(-1) mg protein (-1), and a kco2 ...	2004	15316720
direct immobilization of native yeast iso-1 cytochrome c on bare gold: fast electron relay to redox enzymes and zeptomole protein-film voltammetry.	cyclic voltammetry shows that yeast iso-1-cytochrome c (ycc), chemisorbed on a bare gold electrode via cys102, exhibits fast, reversible interfacial electron transfer (k(0) = 1.8 x 10(3) s(-1)) and retains its native functionality. vectorially immobilized ycc relays electrons to yeast cytochrome c peroxidase, and to both cytochrome cd(1) nitrite reductase (nir) and nitric oxide reductase from paracoccus denitrificans, thereby revealing the mechanistic properties of these enzymes. on a microelect ...	2004	15339197
protein composition of paracoccus denitrificans cells grown on various electron acceptors and in the presence of azide.	two-dimensional gel electrophoresis (2-de) with immobilized ph gradients was carried out on total cell lysates and membrane fractions of paracoccus denitrificans with the aim to characterize differences in protein expression during growth under aerobic and various anaerobic conditions (with nitrate, nitrite or nitrous oxide). comparative image analysis of the protein pattern revealed several subgroups of the total 800 protein spots resolved that were characteristically induced or repressed in re ...	2004	15352241
tyrosine 167: the origin of the radical species observed in the reaction of cytochrome c oxidase with hydrogen peroxide in paracoccus denitrificans.	determination of the three-dimensional structure of cytochrome c oxidase, the terminal enzyme of the respiratory chain, from paracoccus denitrificans offers the possibility of site-directed mutagenesis studies to investigate the relationship between the structure and the catalytic function of the enzyme. the mechanism of electron-coupled proton transfer is still, however, poorly understood. the p(m) intermediate of the catalytic cycle is an oxoferryl state the generation of which requires one ad ...	2004	15362855
paracoccus pantotrophus pseudoazurin is an electron donor to cytochrome c peroxidase.	the gene for pseudoazurin was isolated from paracoccus pantotrophus lmd 52.44 and expressed in a heterologous system with a yield of 54.3 mg of pure protein per liter of culture. the gene and protein were shown to be identical to those from p. pantotrophus lmd 82.5. the extinction coefficient of the protein was re-evaluated and was found to be 3.00 mm(-1) cm(-1) at 590 nm. it was confirmed that the oxidized protein is in a weak monomer/dimer equilibrium that is ionic-strength-dependent. the pseu ...	2004	15366931
a novel exopolymer-producing bacterium, paracoccus zeaxanthinifaciens subsp. payriae, isolated from a "kopara" mat located in rangiroa, an atoll of french polynesia.	an aerobic, mesophilic and heterotrophic marine bacterium designated ra19, able to produce two different exocellular polymers and zeaxanthin, was isolated from a french polynesian bacterial mat (localy named "kopara") situated in the atoll of rangiroa. this microorganism, on the basis of its phenotypical features and the genotypic investigations, can be clearly assigned to the parococcus zeaxanthinifaciens species and the name parococcus zeaxanthinifaciens subsp. payriae is proposed. optimal gro ...	2004	15386095
an oxo-ferryl tryptophan radical catalytic intermediate in cytochrome c and quinol oxidases trapped by microsecond freeze-hyperquenching (mhq).	the pre-steady state reaction kinetics of the reduction of molecular oxygen catalyzed by fully reduced cytochrome oxidase from escherichia coli and paracoccus denitrificans were studied using the newly developed microsecond freeze-hyperquenching mixing-and-sampling technique. reaction samples are prepared 60 and 200 micros after direct mixing of dioxygen with enzyme. analysis of the reaction samples by low temperature uv-vis spectroscopy indicates that both enzymes are trapped in the pm state. e ...	2004	15388346
paracoccus haeundaensis sp. nov., a gram-negative, halophilic, astaxanthin-producing bacterium.	an aerobic, non-motile, gram-negative, orange-pigmented, rod-shaped, astaxanthin-producing marine bacterium was isolated from the haeundae coast, korea. this strain, bc74171t, produced carotenoids, mainly astaxanthin. all the type strains of the genus paracoccus were compared with strain bc74171t using 16s rrna gene sequence analysis, fatty acid patterns and physiological reaction profiles. based on the results of these analyses, it is proposed that strain bc74171t represents a novel species, pa ...	2004	15388731
purification and some properties of isocitrate dehydrogenase from paracoccus denitrificans.	nadp-dependent isocitrate dehydrogenase (icdh) from the bacterium paracoccus denitrificans was purified to homogeneity. the purification procedure involved ammonium sulphate fractionation, ion exchange chromatography, and gel permeation chromatography. the specific activity of purified icdh was 801 nkat/mg, the yield of the enzyme 58%. the purity of the enzyme was checked by polyacrylamide gel electrophoresis in the presence of sodium dodecyl sulphate. icdh is a dimer composed of two probably id ...	2004	15461143
optimization of an escherichia coli system for cell-free synthesis of selectively n-labelled proteins for rapid analysis by nmr spectroscopy.	cell-free protein synthesis offers rapid access to proteins that are selectively labelled with [15n]amino acids and suitable for analysis by nmr spectroscopy without chromatographic purification. a system based on an escherichia coli cell extract was optimized with regard to protein yield and minimal usage of 15n-labelled amino acid, and examined for the presence of metabolic by-products which could interfere with the nmr analysis. yields of up to 1.8 mg of human cyclophilin a per ml of reaction ...	2004	15479237
no reductase from bacillus azotoformans is a bifunctional enzyme accepting electrons from menaquinol and a specific endogenous membrane-bound cytochrome c551.	bacillus azotoformans is a gram-positive denitrifying soil bacterium, which is capable of respiring nitrate, nitrite, nitric oxide, and nitrous oxide under anaerobic conditions. it contains a unique menaquinol-dependent nitric oxide reductase (qcu(a)nor) with a cu(a) center in its small subunit. the qcu(a)nor exhibits menaquinol-dependent no reductase activity, whereas reduced horse heart cytochrome c was inactive. here we describe the purification of three membrane-bound c cytochromes from b. a ...	2004	15491156
no binding and dynamics in reduced heme-copper oxidases aa3 from paracoccus denitrificans and ba3 from thermus thermophilus.	cytochrome c oxidase (cco) has a high affinity for nitric oxide (no), a property involved in the regulation of respiration. it has been shown that the recombination kinetics of photolyzed no with reduced cco from paracoccus denitrificans on the picosecond time scale depend strongly on the no/enzyme stoichiometry and inferred that more than one no can be accommodated by the active site, already at mildly suprastoichiometric no concentrations. we have largely extended these studies by monitoring r ...	2004	15518562
atr-ftir spectroscopy and isotope labeling of the pm intermediate of paracoccus denitrificans cytochrome c oxidase.	the structure of the p(m) intermediate of paracoccus denitrificans cytochrome c oxidase was investigated by perfusion-induced attenuated total reflection-fourier transform infrared (atr-ftir) spectroscopy. transitions from the oxidized to p(m) state were initiated by perfusion with co/oxygen buffer, and the extent of conversion was quantitated by simultaneously monitoring visible absorption changes. in prior work, tentative assignments of bands were proposed for heme a(3), a change in the enviro ...	2004	15533041
a copper protein and a cytochrome bind at the same site on bacterial cytochrome c peroxidase.	pseudoazurin binds at a single site on cytochrome c peroxidase from paracoccus pantotrophus with a k(d) of 16.4 microm at 25 degrees c, ph 6.0, in an endothermic reaction that is driven by a large entropy change. sedimentation velocity experiments confirmed the presence of a single site, although results at higher pseudoazurin concentrations are complicated by the dimerization of the protein. microcalorimetry, ultracentrifugation, and (1)h nmr spectroscopy studies in which cytochrome c550, pseud ...	2004	15544327
sulfide dehydrogenase activity of the monomeric flavoprotein soxf of paracoccus pantotrophus.	flavocytochrome c-sulfide dehydrogenases (fcsds) are complexes of a flavoprotein with a c-type cytochrome performing hydrogen sulfide-dependent cytochrome c reduction in vitro. the amino acid sequence analysis revealed that the phylogenetic relationship of different flavoproteins reflected the relationship of sulfur-oxidizing bacteria. the flavoprotein soxf of paracoccus pantotrophus is 29-67% identical to the flavoprotein subunit of fcsd of phototrophic sulfur-oxidizing bacteria. purification o ...	2004	15544340
redox-dependent open and closed forms of the active site of the bacterial respiratory nitric-oxide reductase revealed by cyanide binding studies.	the bacterial respiratory nitric-oxide reductase (nor) catalyzes the respiratory detoxification of nitric oxide in bacteria and archaea. it is a member of the well known super-family of heme-copper oxidases but has a [heme fe-non-heme fe] active site rather than the [heme fe-cu(b)] active site normally associated with oxygen reduction. paracoccus denitrificans nor is spectrally characterized by a ligand-to-metal charge transfer absorption band at 595 nm, which arises from the high spin ferric he ...	2004	14766741
examination of membrane protein expression in paracoccus denitrificans by two-dimensional gel electrophoresis.	the well-known metabolic versatility of the soil bacterium paracoccus denitrificans poses a challenge for modern proteomic approaches. we describe here improved preparation conditions that allow good separation and quantitative analyses of hundreds of membrane or periplasmic proteins. to illustrate this optimized procedure, the results of a screening for membrane proteins associated predominantly with aerobic or anaerobic (denitrifying) modes of growth are presented.	2004	14768023
microbial community structure of membrane fouling film in an intermittently and continuously aerated submerged membrane bioreactor treating domestic wastewater.	there was an observable difference in microbial community structure between suspended microorganisms and membrane biofouling film in intermittently and continuously aerated smbrs. the dominant quinone type of membrane biofouling film in an intermittently aerated smbr was ubiquinone (uqs)-8, -10 followed by menaquinone (mks)-8(h4) and -8(h2). but that of the continuously aerated smbr was uqs-10, -8 followed by mks-6 and -8(h4). the experimental results also showed that the conditions of an interm ...	2004	14982188
proton uptake upon anaerobic reduction of the paracoccus denitrificans cytochrome c oxidase: a kinetic investigation of the k354m and d124n mutants.	the kinetics and stoichiometry of the redox-linked protonation of the soluble paracoccus denitrificans cytochrome c oxidase were investigated at ph = 7.2-7.5 by multiwavelength stopped-flow spectroscopy, using the ph indicator phenol red. we compared the wild-type enzyme with the k354m and the d124n subunit i mutants, in which the k- and d-proton-conducting pathways are impaired, respectively. upon anaerobic reduction by ru-ii hexamine, the wild-type enzyme binds 3.3 +/- 0.6 h(+)/aa(3), i.e., ap ...	2004	15005632
subunit proximity in the h+-translocating nadh-quinone oxidoreductase probed by zero-length cross-linking.	the proton-translocating nadh-quinone oxidoreductase (ndh-1) of paracoccus denitrificans is composed of 14 different subunits (designated nqo1-14), seven of which are located in the membrane domain and the other seven in the peripheral domain. it has been previously reported that membrane domain subunit nqo7 (nd3) directly interacts with peripheral subunit nqo6 (psst) by using a cross-linker, m-maleimidobenzoyl-n-hydrosuccinimide ester, and heterologous expression [di bernardo, s., and yagi, t. ...	2004	15035646
dynamic water networks in cytochrome c oxidase from paracoccus denitrificans investigated by molecular dynamics simulations.	we present a molecular dynamics study of cytochrome c oxidase from paracoccus denitrificans in the fully oxidized state, embedded in a fully hydrated dimyristoylphosphatidylcholine lipid bilayer membrane. parallel simulations with different levels of protein hydration, 1.125 ns each in length, were carried out under conditions of constant temperature and pressure using three-dimensional periodic boundary conditions and full electrostatics to investigate the distribution and dynamics of water mol ...	2004	15041635
genetic organization of the basic replicon of plasmid pmth4 of a facultatively methylotrophic bacterium paracoccus methylutens dm12.	two functional regions within the basic replicon of plasmid pmth4 of paracoccus methylutens dm12 have been distinguished that are responsible for the replication of the plasmid (rep) and its stabilization (sta). in the rep region, a gene encoding the putative replication initiation protein repa has been identified, with the highest similarity to the replication protein of plasmid palc1 (paracoccus alcaliphilus). the potential origin of replication (oriv), consisting of five long repeated sequenc ...	2004	15057455
enzymes and genes of taurine and isethionate dissimilation in paracoccus denitrificans.	growth of the alpha-proteobacterium paracoccus denitrificans nknis with taurine or isethionate as sole source of carbon involves sulfoacetaldehyde acetyltransferase (xsc), which is presumably encoded by an xsc gene in subgroup 3, none of whose gene products has been characterized. the genome of the alpha-proteobacterium rhodobacter sphaeroides 2.4.1 was interpreted to contain a nine-gene cluster encoding the inducible dissimilation of taurine, and this deduced pathway included a regulator, a tri ...	2004	15073291
interaction of cytochrome c with cytochrome oxidase: two different docking scenarios.	cytochrome c is the specific and efficient electron transfer mediator between the two last redox complexes of the mitochondrial respiratory chain. its interaction with both partner proteins, namely cytochrome c(1) (of complex iii) and the hydrophilic cu(a) domain (of subunit ii of oxidase), is transient, and known to be guided mainly by electrostatic interactions, with a set of acidic residues on the presumed docking site on the cu(a) domain surface and a complementary region of opposite charges ...	2004	15100042
tryptophan or tyrosine? on the nature of the amino acid radical formed following hydrogen peroxide treatment of cytochrome c oxidase.	it has been reported that different amino acid radicals are formed following the addition of hydrogen peroxide to cytochrome c oxidase (cco) from bovine heart or from paracoccus denitrificans. a broad unresolved signal in the electron paramagnetic resonance (epr) spectra of bovine cco has been assigned to a tryptophan radical, probably trp126 [rigby et al. biochemistry 2000, 39, 5921-5928]. in the p. denitrificans enzyme, a similarly broad signal but with a well-resolved hyperfine structure was ...	2004	15100053
biotinylated polypyrrole films: an easy electrochemical approach for the reagentless immobilization of bacteria on electrode surfaces.	biotinylated bacteria were immobilized onto biotin/avidin modified electrode surfaces. firstly, an electrospotting deposition method, followed by fluorescence microscopy, showed that bacteria were specifically grafted onto a gold surface. fluorescence intensity versus the quantity of bacteria deposited on the surface was correlated, allowing determination of the microbial saturation point. secondly, biotinylated bacteria were immobilized onto a glassy carbon macro-electrode in order to assess im ...	2004	15110291
further insights into quinone cofactor biogenesis: probing the role of maug in methylamine dehydrogenase tryptophan tryptophylquinone formation.	paracoccus denitrificans methylamine dehydrogenase (madh) is an enzyme containing a quinone cofactor tryptophan tryptophylquinone (ttq) derived from two tryptophan residues (betatrp(57) and betatrp(108)) within the polypeptide chain. during cofactor formation, the two tryptophan residues become covalently linked, and two carbonyl oxygens are added to the indole ring of betatrp(57). expression of active madh from p. denitrificans requires four other genes in addition to those that encode the poly ...	2004	15122915
isolation and characterization of novel bacteria degrading polycyclic aromatic hydrocarbons from polluted greek soils.	three bacterial strains, designated as wphe1, sphe1, and ophe1, were isolated from greek soils contaminated with polycyclic aromatic hydrocarbon (pah)-containing waste from the wood processing, steel, and oil refinery industries. wphe1, sphe1, and ophe1 were characterized and identified as species of pseudomonas, microbacterium, and paracoccus, respectively, based on gram staining, biochemical tests, phospholipid analysis, fame analysis, g+c content and 16s rrna gene sequence analysis. the resul ...	2004	15133642
paracoccus pantotrophus napc can reductively activate cytochrome cd1 nitrite reductase.	the oxidized "as isolated" form of paracoccus pantotrophus cytochrome cd1 nitrite reductase has a bis-histidinyl coordinated c heme and a histidine/tyrosine coordinated d1 heme. this form of the enzyme has previously been shown to be kinetically incompetent. upon reduction, the coordination of both hemes changes and the enzyme is kinetically activated. here, we show that p. pantotrophus napc, a tetraheme c-type cytochrome belonging to a large family of such proteins, is capable of reducing, and ...	2004	15135051
investigation of the thermal stability of porin from paracoccus denitrificans by site-directed mutagenesis and fourier transform infrared spectroscopy.	the folding of membrane proteins was addressed using outer membrane protein porin from the soil bacterium paracoccus denitrificans (p. den.). ir spectroscopy and sodium dodecyl sulfate-polyacrylamide gel electrophoresis (sds-page) analysis were used to probe the effect of mutagenesis on the thermal stability of the protein. secondary structure analysis by amide i ir spectroscopy showed that the wild-type protein was predominantly composed of beta-sheet, which supports the x-ray crystal structure ...	2004	15137100
denitrification with epsilon-caprolactam by acclimated mixed culture and by pure culture of bacteria isolated from polyacrylonitrile fibre manufactured wastewater treatment system.	the aim of this study is to isolate denitrifying bacteria utilizing epsilon-caprolactam as the substrate, from a polyacrylonitrile fibre manufactured wastewater treatment system. the aim is also to compare the performance of pan (polyacrylonitrile) mixed bacteria cultures acclimated to epsilon-caprolactam and isolated pure strain for treating different initial epsilon-caprolactam concentrations from synthetic wastewater under anoxic conditions. the result showed that the pan mixed bacteria cultu ...	2004	15137443
catellibacterium nectariphilum gen. nov., sp. nov., which requires a diffusible compound from a strain related to the genus sphingomonas for vigorous growth.	a bacterial strain, designated ast4(t), was isolated from activated sludge. the bacterium did not show significant growth on nutrient broth, but growth was clearly stimulated by addition of supernatant from other bacterial cultures. culture filtrate of a strain related to the genus sphingomonas in particular increased the cell yield and growth rate of strain ast4(t). phylogenetic analysis based on the 16s rrna gene sequences showed that strain ast4(t) is located within the 'rhodobacter group' in ...	2004	15143049
phylogenetically diverse new sulfur chemolithotrophs of alpha-proteobacteria isolated from indian soils.	five facultative sulfur chemolithotrophs were isolated from soils to study the diversity of sulfur lithotrophy. phenotypic characteristics, including sulfur lithotrophic properties and chemotaxonomic features of the isolates, were similar to those of the members of the colorless sulfur bacteria. 16s rdna sequence analyses rendered placing the isolates to three distinct phylogenetic clusters of alpha-proteobacteria. three isolates, as001, as002, and kct002, were identified as members of the genus ...	2004	15170243
functional roles of four conserved charged residues in the membrane domain subunit nuoa of the proton-translocating nadh-quinone oxidoreductase from escherichia coli.	the h(+)(na(+))-translocating nadh-quinone (q) oxidoreductase (ndh-1) of escherichia coli is composed of 13 different subunits (nuoa-n). subunit nuoa (nd3, nqo7) is one of the seven membrane domain subunits that are considered to be involved in h(+)(na(+)) translocation. we demonstrated that in the paracoccus denitrificans ndh-1 subunit, nqo7 (nd3) directly interacts with peripheral subunits nqo6 (psst) and nqo4 (49 kda) by using cross-linkers (di bernardo, s., and yagi, t. (2001) febs lett. 508 ...	2004	15175326
use of sinorhizobium meliloti as an indicator for specific detection of long-chain n-acyl homoserine lactones.	population-density-dependent gene expression in gram-negative bacteria involves the production of signal molecules characterized as n-acyl homoserine lactones (ahls). the synthesis of ahls by numerous microorganisms has been identified by using biosensor strains based on the agrobacterium tumefaciens and chromobacterium violaceum quorum-sensing systems. the symbiotic nitrogen-fixing bacterium sinorhizobium meliloti is rapidly becoming a model organism for the study of quorum sensing. this organi ...	2004	15184178
a brownian dynamics study: the effect of a membrane environment on an electron transfer system.	during the past few years, three-dimensional crystal structures of many of the important integral membrane proteins responsible for the bioenergetic processes of photosynthesis and respiration have been determined. moreover, a few crystal structures of protein-protein complexes have become available that characterize the interaction between those membrane proteins and the electron carrier protein cytochrome c. here, we address the association kinetics for binding of cytochrome c to cytochrome c ...	2004	15240445
first comprehensively documented case of paracoccus yeei infection in a human.	paracoccus yeei was isolated in pure culture from an aerobic blood culture and bulla fluid from a 67-year-old male. the biochemical identification scheme for this recently described species is outlined. because of its reaction pattern it is not unlikely that p. yeei is underdiagnosed.	2004	15243119
characterisation of [cu4s], the catalytic site in nitrous oxide reductase, by epr spectroscopy.	the enzyme nitrous oxide reductase (n(2)or) has a unique tetranuclear copper centre [cu(4)s], called cu(z), at the catalytic site for the two-electron reduction of n(2)o to n(2). the x- and q-band epr spectra have been recorded from two forms of the catalytic site of the enzyme n(2)or from paracoccus pantotrophus, namely, a form prepared anaerobically, cu(z), that undergoes a one-electron redox cycle and cu(z)*, prepared aerobically, which cannot be redox cycled. the spectra of both species are ...	2004	15252678
structural studies of two mutants of amicyanin from paracoccus denitrificans that stabilize the reduced state of the copper.	mutation of pro94 to phenylalanine or alanine significantly alters the redox properties of the type i copper center of amicyanin. each mutation increases the redox midpoint potential (e(m)) value by at least 140 mv and shifts the pk(a) for the ph dependence of the e(m) value to a more acidic value. atomic resolution (0.99-1.1 a) structures of both the p94f and p94a amicyanin have been determined in the oxidized and reduced states. in each amicyanin mutant, an electron-withdrawing hydrogen bond t ...	2004	15260480
crystallographic and nmr investigation of cobalt-substituted amicyanin.	cobalt(ii) amicyanin was prepared by replacing the copper of the type i copper protein amicyanin from paracoccus denitrificans with cobalt. the structure of the protein and the metal center have been characterized by x-ray crystallography and paramagnetic nmr spectroscopy. the crystal structure indicates that met98, which provides an axial sulfur ligand in native amicyanin, is no longer bound to the metal in cobalt(ii) amicyanin and that a water molecule is recruited from solvent to form the fou ...	2004	15260481
metabolic engineering of ketocarotenoid formation in higher plants.	although higher plants synthesize carotenoids, they do not possess the ability to form ketocarotenoids. in order to generate higher plants capable of synthesizing combinations of ketolated and hydroxylated carotenoids the genes responsible for the carotene 4,4' oxygenase and 3,3' hydroxylase have been transformed into tomato and tobacco. the gene products were produced as a polyprotein. subsequent cleavage of the polyprotein, targeting of the two enzymes to the plastid and enzyme activities have ...	2004	15272869
a superfamily of voltage-gated sodium channels in bacteria.	nachbac, a six-alpha-helical transmembrane-spanning protein cloned from bacillus halodurans, is the first functionally characterized bacterial voltage-gated na(+)-selective channel. as a highly expressing ion channel protein, nachbac is an ideal candidate for high resolution structural determination and structure-function studies. the biological role of nachbac, however, is still unknown. in this report, another 11 structurally related bacterial proteins are described. two of these functionally ...	2004	14665618
cytochrome c551 from starkeya novella: characterization, spectroscopic properties, and phylogeny of a diheme protein of the soxax family.	cytochromes from the soxax family have a major role in thiosulfate oxidation via the thiosulfate-oxidizing multi-enzyme system (tomes). previously characterized soxax proteins from rhodovulum sulfidophilum and paracoccus pantotrophus contain three heme c groups, two of which are located on the soxa subunit. in contrast, the soxax protein purified from starkeya novella was found to contain only two heme groups. mass spectrometry showed that a disulfide bond replaced the second heme group found in ...	2004	14645228
expression profiles of polyhydroxyalkanoate synthesis-related genes in paracoccus denitrificans.	a facultative methylotrophic bacterium, paracoccus denitrificans can synthesize polyhydroxyalkanoate acids (pha) from various alcohols. recently, six genes, phaa, b, c, p, r, and z, related to pha synthesis have been cloned and characterized. pha synthesis and the expression of phaa, b, c, p, r, and z in p. denitrificans were examined at the transcriptional and translational levels under both nitrogen-sufficient and nitrogen-deficient conditions. the results showed that pha synthesis is not regu ...	2004	16233588
comparison of aerobic denitrifying activity among three cultural species with various carbon sources.	abilities of three aerobic denitrifiers such as alcaligenes faecalis, microvirgula aerodenitrificans and paracoccus pantotrophus were compared from the viewpoints of nitrate removal efficiency and organic matter utilization. first, the effect of carbon source was investigated. although nitrate reduction was observed in all strains under aerobic conditions, a change of carbon source considerably affected the denitrification ability. in the case of p. pantotrophus, nitrate and nitrite were complet ...	2004	15566182
in-situ characterization of microbial community in an a/o submerged membrane bioreactor with nitrogen removal.	the bacterial community involved in removing nitrogen from sewage and their preferred do environment within an anoxic/oxic membrane bioreactor (a/o mbr) was investigated. a continuously operated laboratory-scale a/o mbr was maintained for 360 d. at a sludge age of 150 d and a c/n ratio of 3.5, the system was capable of removing 88% of the influent nitrogen from raw wastewater through typical nitrogen removal transformations (i.e. aerobic ammonia oxidation and anoxic nitrate reduction). character ...	2004	15566185
evidence that the rhizobium regulatory protein rira binds to cis-acting iron-responsive operators (iros) at promoters of some fe-regulated genes.	mutations in rira of rhizobium have been shown to deregulate expression of several genes that are normally repressed by iron. a conserved sequence, the iron-responsive operator (iro), was identified near promoters of vbsc (involved in the synthesis of the siderophore vicibactin), rpoi (specifies an ecf sigma factor needed for vicibactin synthesis) and the two fhua genes (encoding vicibactin receptor). removal of these iro sequences abolished fe-responsive repression. most of these genes were con ...	2004	15583159
[biotransformation of organic substances by an immobilized associative bacterial culture].	bacterial strains were screened to transform to end-products (carbon monoxide and water) elevated concentrations of acetone, acidic acid, and ethanol in a biocatalyst with an immobilized bacterial association cultivated on solid foam polyvinyl acetate (fpva). the innocuous association amalgamated paracoccus denitrificans vkm v-1324, pseudomonas esterophilus vkm v-1736d and achromobacter parvulus vkm v-1541d. the biocatalyst was tested with the help of classic methods and equipment for microbes c ...	2004	15605736
development of nitrogen-removal bioreactor using poly(lactic acid) as an energy source.	to control nitrogen such as ammonia in a rearing water of aquatic animals, we developed new bioreactor capable of both nitrification and denitrification. it was consisted of gel-plate immobilized microorganisms and a biodegradable plastic plate composed of three kind of poly(lactic acid) as an energy source of denitrification. when batch treatment experiment by the bioreactor was continuously carried out with an artificial rearing water containing ammonia, nitrogen-removal rate of the bioreactor ...	2004	15858361
molecular dissection of diheme cytochrome c gene from soil isolate of a gram negative, facultative chemolithotrophic sulfur oxidizer.	a gram negative chemolithotrophic bacterium (rpi) with facultative mode of nutrition was isolated from the soil. enzymological studies confirmed presence of thiosulphate oxidase, sulphite oxidase and rhodanese, all of which play role in sulfur metabolism pathway. a set of degenerate oligonucleotide primer pairs was used for thermal amplification of a major part of the coding region of the cytochrome c gene locus of this bacterium. nucleotide and translated amino acid sequence revealed the gene t ...	2004	17240791
thermal stability of outer membrane protein porin from paracoccus denitrificans: ft-ir as a spectroscopic tool to study lipid-protein interaction.	lipid protein interactions play a key role in the stability and function of various membrane proteins. earlier we have reported the extreme thermal stability of porin from paracoccus denitrificans reconstituted into liposomes. here, we used fourier transform infrared spectroscopy for a label free analysis of the global secondary structural changes and local changes in the tyrosine microenvironment. our results show that a mixed lipid system (non-uniform bilayer) optimizes the thermal stability o ...	2005	15862288
sulfur dehydrogenase of paracoccus pantotrophus: the heme-2 domain of the molybdoprotein cytochrome c complex is dispensable for catalytic activity.	sulfur dehydrogenase, sox(cd)(2), is an essential part of the sulfur-oxidizing enzyme system of the chemotrophic bacterium paracoccus pantotrophus. sox(cd)(2) is a alpha(2)beta(2) complex composed of the molybdoprotein soxc (43 442 da) and the hybrid diheme c-type cytochrome soxd (37 637 da). sox(cd)(2) catalyzes the oxidation of protein-bound sulfur to sulfate with a unique six-electron transfer. amino acid sequence analysis identified the heme-1 domain of soxd proteins to be specific for sulfu ...	2005	15865447
soxrs-mediated regulation of chemotrophic sulfur oxidation in paracoccus pantotrophus.	paracoccus pantotrophus gb17 requires thiosulfate for induction of the sulfur-oxidizing (sox) enzyme system. the soxrs genes are divergently oriented to the soxvwxyza-h genes. soxr predicts a transcriptional regulator of the arsr family and soxs a periplasmic thioredoxin. the homogenate mutant gbomegas carrying a disruption of soxs by the omega-kanamycin-resistance-encoding interposon expressed a low thiosulfate-oxidizing activity under heterotrophic and mixotrophic growth conditions. this activ ...	2005	15870478
site-directed mutagenesis of proline 94 to alanine in amicyanin converts a true electron transfer reaction into one that is kinetically coupled.	amicyanin is a type i copper protein that mediates electron transfer (et) from methylamine dehydrogenase (madh) to cytochrome c-551i. pro(94) resides in the "ligand loop" of amicyanin, a sequence of amino acids that contains three of the four copper ligands. et from the reduced o-quinol tryptophan tryptophylquinone of madh to oxidized p94a amicyanin is a true et reaction that exhibits values of electronic coupling (h(ab)) and reorganization energy (lambda) that are the same as for the reaction o ...	2005	15882058
structural insight into soxc and soxd interaction and their role in electron transport process in the novel global sulfur cycle in paracoccus pantotrophus.	microbial oxidation of reduced inorganic sulfur compounds mainly sulfur anions in the environment is one of the major reactions of the global sulfur cycle mediated by phylogenetically diverse prokaryotes. the sulfur oxidizing gene cluster (sox) of alpha-proteobacteria comprises of at least 16 genes, which form two transcriptional units, viz., soxsrt and soxvwxyzabcdefgh. sequence analysis reveals that soxd gene product (soxd) belongs to the di-heme cytochrome c family of electron transport prote ...	2005	15882991
the effect of replacing the axial methionine ligand with a lysine residue in cytochrome c-550 from paracoccus versutus assessed by x-ray crystallography and unfolding.	the structure of cytochrome c-550 from the nonphotosynthetic bacteria paraccocus versutus has been solved by x-ray crystallography to 1.90 a resolution, and reveals a high structural homology to other bacterial cytochromes c(2). the effect of replacing the axial heme-iron methionine ligand with a lysine residue on protein structure and unfolding has been assessed using the m100k variant. from x-ray structures at 1.95 and 1.55 a resolution it became clear that the amino group of the lysine side c ...	2005	15885094
y25s variant of paracoccus pantotrophus cytochrome cd1 provides insight into anion binding by d1 heme and a rare example of a critical difference between solution and crystal structures.	tyr25 is a ligand to the active site d1 heme in as isolated, oxidized cytochrome cd1 nitrite reductase from paracoccus pantotrophus. this form of the enzyme requires reductive activation, a process that involves not only displacement of tyr25 from the d1 heme but also switching of the ligands at the c heme from bis-histidinyl to his/met. a y25s variant retains this bis-histidinyl coordination in the crystal of the oxidized state that has sulfate bound to the d1 heme iron. this y25s form of the e ...	2005	15901734
site-directed modifications indicate differences in axial haem c iron ligation between the related nrfh and napc families of multihaem c-type cytochromes.	during the last decade, a number of related bacterial membrane-bound multihaem c-type cytochromes, collectively referred to as the napc/nirt family, were identified. these proteins are generally thought to catalyse electron transport between the quinone/quinol pool and periplasmic oxidoreductases. the best-characterized members, the tetrahaem c-type cytochromes nrfh and napc, mediate electron transport to nrfa and napa respectively. amino acid sequence alignments suggest that the nature and posi ...	2005	15907193
miniaturized kinetic growth inhibition assay with denitrifying bacteria paracoccus denitrificans.	a method to cultivate anaerobic bacteria on standard 96-well microplates with automatic recording of growth curves is presented. the method was used as a kinetic growth inhibition assay with denitrifying bacteria paracoccus denitrificans, and applied to various heavy metal ions and selected agrochemicals. incorporated in a battery of other biotest the assay could take into account effects of toxicants on denitrifying organisms. the results (ec50) revealed that the assay was relatively sensitive. ...	2005	15910901
impact of the bacterial type i cytochrome c maturation system on different biological processes.	in the alpha-, beta- and gamma-proteobacteria, the so-called cytochrome c maturation (ccm) system is known to promote the covalent attachment of the haem to periplasmic apocytochrome c. however, in species of pseudomonas, rhizobium, paracoccus and legionella, mutations in ccm genes result in phenotypes that cannot be readily explained by the simple loss of a c-type cytochrome. these phenotypes include loss of siderophore production and utilization, reduced abilities to grow in low-iron condition ...	2005	15916594
elucidation of dominant effect on initial bacterial adhesion onto polymer surfaces prepared by radiation-induced graft polymerization.	surface-modified polyethylene (pe) membrane sheets were prepared by the radiation-induced graft polymerization (rigp) of an epoxy-group-containing monomer, glycidyl methacrylate (gma). the epoxy ring of gma was opened by introducing diethylamine (dea) or sodium sulfite (ss). we examined the properties of these sheets by measuring the amount of grafting polymer, surface roughness and membrane potential, and also investigated the adhesion of five gram-negative bacteria, escherichia coli, pseudomon ...	2005	15922579
maug-dependent in vitro biosynthesis of tryptophan tryptophylquinone in methylamine dehydrogenase.	tryptophan tryptophylquinone (ttq) is the prosthetic group of methylamine dehydrogenase (madh) and is synthesized through post-translational modification of two endogenous tryptophan residues. this modification involves two oxygenation reactions and one cross-linking reaction. it is clearly shown that the incorporation of the second oxygen into betatrp57 and the covalent cross-linking of betatrp57 to betatrp108 are maug-dependent processes. these reaction steps are severely compromised in vivo w ...	2005	15941239
amperometric detection of the bacterial metabolic regulation with a microbial array chip.	a microbial array chip with collagen gel spots entrapping living bacterial cells has been applied to investigate the metabolic regulation in paracoccus denitrificans. scanning electrochemical microscopy (secm) was used to monitor the ferrocyanide production that reflects the electron flow in the respiratory chain located within the internal membrane of p. denitrificans. the ferrocyanide production from p. denitrificans largely depends on the types of the carbon source (glucose or lactate), sugge ...	2005	15967362