Publications

sequence and expression of the gene encoding the respiratory nitrous-oxide reductase from paracoccus denitrificans. new and conserved structural and regulatory motifs.	the structural gene for the respiratory nitrous-oxide reductase from paracoccus denitrificans has been cloned using a probe derived from the structural gene, nosz, for this enzyme from pseudomonas stutzeri. the cloned gene could be expressed surprisingly well (presumably yielding an apo-protein) using an expression vector in escherichia coli. sequencing the nosz gene from p. denitrificans has shown that the periplasmic nitrous-oxide reductase of this organism is highly similar in sequence to pre ...	1993	8243476
synthesis of the rhodopseudomonas viridis holo-cytochrome c2 in paracoccus denitrificans.	the gene encoding the rhodopseudomonas viridis cytochrome c2 (cyca) has been introduced on a broad host range vector into paracoccus denitrificans, leading to high-level expression of the holo-cytochrome with the heme moiety covalently attached to the apoprotein. the cytochrome was demonstrated to reside in the periplasmic space of the host cell. in contrast to r. viridis, aerobic rather than anaerobic growth conditions led to higher production levels of the holo-cytochrome in p. denitrificans. ...	1993	8243979
soluble cua-binding domain from the paracoccus cytochrome c oxidase.	in cytochrome c oxidase the c-terminal part of subunit ii is outside the membrane and contains a copper center called cua. we have expressed this domain of the paracoccus denitrificans oxidase in a soluble form. data obtained by quantitative copper-to-protein measurements, electrospray mass spectrometry, and electron paramagnetic resonance spectroscopy show that the center contains two copper atoms probably in a mixed valence configuration. its absorbance spectrum is similar to that of the coppe ...	1993	8253767
is intracytoplasmic membrane structure a generic criterion? it does not coincide with phylogenetic interrelationships among phototrophic purple nonsulfur bacteria.	the 16s rrna or rrna gene sequences of the type strains of 5 species of rhodobacter, rhodopseudomonas blastica and paracoccus denitrificans were determined. the sequence analysis revealed that rhodobacter species, whose intracytoplasmic membrane systems were characteristically vesicular, composed a sole cluster. rhodopseudomonas blastica, whose intracytoplasmic membrane system was lamellar, was included in the cluster of rhodobacter. the phylogenetic co-clustering of these bacteria conformed to ...	1993	8257281
binding and electron transfer reactions between methanol dehydrogenase and its physiologic electron acceptor cytochrome c-551i: a kinetic and thermodynamic analysis.	the quinoprotein methanol dehydrogenase and cytochrome c-551i form a physiologic complex in which electrons are transferred from pyrroloquinoline quinone to heme. the reoxidation of methanol dehydrogenase by the cytochrome was studied by stopped-flow spectroscopy. the rate constant for the electron transfer reaction and the dissociation constant for complex formation were each determined at temperatures ranging from 20 to 50 degrees c. the electron transfer rates varied from 1.4 to 4.6 s-1. anal ...	1993	8260498
kinetics of photooxidation of soluble cytochromes, hipip, and azurin by the photosynthetic reaction center of the purple phototrophic bacterium rhodopseudomonas viridis.	the photosynthetic reaction center of rhodopseudomonas viridis contains a bound tetraheme cytochrome c subunit which is the primary electron donor to the photooxidized special pair bacteriochlorophyll. we have tested a variety of soluble electron-transfer proteins for their ability to serve as secondary electron donors to the bacteriochlorophyll via the bound cytochrome by measuring the kinetics of reaction center heme reduction following photooxidation by a laser flash, as a function of soluble ...	1993	8387812
mutants of methylobacterium extorquens and paracoccus denitrificans deficient in c-type cytochrome biogenesis synthesise the methylamine-dehydrogenase polypeptides but cannot assemble the tryptophan-tryptophylquinone group.	five mutants of methylobacterium extorquens and four mutants of paracoccus denitrificans that have a general defect in c-type cytochrome synthesis also failed to assemble an active methylamine dehydrogenase. in all cases methanol dehydrogenase, another periplasmic enzyme, was fully active. all nine mutant strains accumulated both the heavy and light subunits of methylamine dehydrogenase to essentially wild-type levels. in all nine mutants, the heavy-subunit and light-subunit polypeptides were pr ...	1993	8269962
reduction of nitric oxide by denitrifying bacteria.	two heterotrophic denitrifying bacteria, paracoccus denitrificans and pseudomonas denitrificans, have been shown to utilize nitric oxide (no) as a terminal electron acceptor and succinate, yeast extract, and heat/alkali pretreated municipal sewage sludge as carbon and energy sources. complete removal of no (0.50%) from a feed gas sparged into the cultures was observed. it is suggested that reduction of no may be a common feature of denitrifying bacteria and that a microbial process to dispose of ...	1993	8323271
binding constants for a physiologic electron-transfer protein complex between methylamine dehydrogenase and amicyanin. effects of ionic strength and bound copper on binding.	two soluble proteins, methylamine dehydrogenase and amicyanin, form a physiologically relevant complex in which intermolecular electron transfer occurs. to characterize and quantitate the binding of these two weakly-associating proteins, an ultrafiltration binding assay has been developed which involves brief centrifugation of mixtures of proteins in centrifuge concentrators followed by quantitation of proteins on each side of the filtration membrane by hplc. under low ionic strength conditions ...	1993	8347660
purification and properties of malate dehydrogenase from paracoccus denitrificans.	affinity chromatography on immobilized cibacron blue (matrex gel blue a) gel permeation chromatography on ultropac tsk g 3000 swg column and ion-exchange chromatography on "mono q" column were used to purify the malate dehydrogenase (mdh) from p. denitrificans to electrophoretic homogeneity. the last two purification steps were performed in fplc system. the enzyme having a specific activity of about 2300 nkat/mg protein was obtained with an approximate 70% yield. mdh is a dimer with a molecular ...	1993	8361952
a method for extracting rate constants from initial rates of stopped-flow kinetic data: application to a physiological electron-transfer reaction.	the most commonly used methods for analysis of stopped-flow kinetic data require performing a series of measurements in which one reactant is varied at concentrations significantly greater than the concentration of the other reactant. for enzyme-catalysed reactions this may not be possible, because the dissociation constants for the enzyme-substrate complex are often of the same order of magnitude as the high concentrations of enzyme that must frequently be used in stopped-flow studies. an alter ...	1993	8363574
isolation and characterization of the nd2 polypeptide of the bovine energy-transducing nadh-ubiquinone oxidoreductase (complex i).	the m(r) 30,000 polypeptide of the hydrophobic protein fraction of the energy-transducing nadh-ubiquinone oxidoreductase (complex i) of bovine heart mitochondria was identified as the nd2 gene product based on a comparison of amino acid analysis and partial n-terminal sequencing results with the known dna sequence of nd2 (anderson, s. et al. (1982) j. mol. biol. 156, 683-717). a simple purification procedure was devised for this nd2 gene product. the procedure, which is described, involves treat ...	1993	8364407
cloning, sequencing, and expression of the genes encoding subunits of paracoccus denitrificans electron transfer flavoprotein.	the genes encoding the two subunits of paracoccus denitrificans electron transfer flavoprotein (etf) were identified by screening a genomic library constructed in pbluescript ii sk+ with probes generated by amplification of genomic sequences by the polymerase chain reaction. primers for the polymerase chain reaction were designed based on peptide sequences from purified paracoccus etf subunits. the genes are arranged in tandem in the genomic dna with the deoxyadenylic acid residue in the tga ter ...	1993	8376381
preliminary crystal structure studies of a ternary electron transfer complex between a quinoprotein, a blue copper protein, and a c-type cytochrome.	a ternary electron transfer protein complex has been crystallized and a preliminary structure investigation has been carried out. the complex is composed of a quinoprotein, methylamine dehydrogenase (madh), a blue copper protein, amicyanin, and a c-type cytochrome (c551i). all three proteins were isolated from paracoccus denitrificans. the crystals of the complex are orthorhombic, space group c222(1) with cell dimensions a = 148.81 a, b = 68.85 a, and c = 187.18 a. two types of isomorphous cryst ...	1993	8382992
identification and characterization of the ctac (coxb) gene as part of an operon encoding subunits i, ii, and iii of the cytochrome c oxidase (cytochrome aa3) in the cyanobacterium synechocystis pcc 6803.	the gene (coxii = coxb = ctac) encoding subunit ii of synechocystis pcc 6803 cytochrome c oxidase has been isolated by screening a genomic dna library in puc18 with a 17-bp oligonucleotide probe (probe c) derived from coxi of paracoccus denitrificans after southern blots with a 19-kb oligonucleotide (probe a) derived from coxii of p. denitrificans had given equivocal results. a 2.2 kb psti-kpni restriction fragment was subcloned into puc 18 and the resulting plasmid pdauv26, which contained the ...	1993	8383492
proton slippage in cytochrome c oxidase of paracoccus denitrificans. membrane-potential measurements with the two-subunit and three-subunit enzyme.	isolated cytochrome c oxidase from paracoccus denitrificans, containing either two or three subunits, was reconstituted into liposomes and the membrane potential was measured at different rates of respiration using a triphenylmethylphosponium bromide electrode. both enzymes revealed a non-linear increase of the membrane potential with increasing respiratory rates. the ratios of the respiratory rates of the two proton pumps decreased with increasing membrane potential, suggesting slippage of prot ...	1993	8385014
identification of a two-component regulatory system controlling methanol dehydrogenase synthesis in paracoccus denitrificans.	upstream of the moxfjgir genes of paracoccus denitrificans a regulatory region involved in methanol oxidation was identified. the nucleotide sequence of this region was determined and revealed three genes, moxz, moxy and moxx, which are transcribed opposite to moxf and which encode proteins of 16.4, 48.2 and 24.5 kda, respectively. computer alignment analysis revealed that the gene products of moxy and moxx have homology with the protein histidine kinases and the response regulators, respectivel ...	1993	8392137
resonance raman spectroscopy of the cytochrome c oxidase from paracoccus denitrificans.	resonance raman spectra are reported for the fully reduced unliganded and cyanide-bound mixed-valence forms of the cytochrome c oxidases from bovine heart and paracoccus denitrificans in both detergent-solubilized forms and within their natural membrane environments. comparison of the vibrational patterns observed for these enzymes indicates that overall the heme environments are similar for both. the only major differences seen between the spectra of these two enzymes are for vibrations associa ...	1993	8392865
a new kinetic model for the steady-state reactions of the quinoprotein methanol dehydrogenase from paracoccus denitrificans.	the reactions of methanol dehydrogenase from paracoccus denitrificans with artificial electron acceptors, ammonia, cyanide, and substrates have been characterized by steady-state kinetic analysis. phenazine ethosulfate, a commonly used electron acceptor for this enzyme, was shown to exhibit pronounced substrate inhibition with a k(i) value approximately 20-fold lower than its km. wurster's blue exhibited only relatively mild substrate inhibition and was deemed a more appropriate electron accepto ...	1993	8386543
characterization of a cta/cde operon-like genomic region encoding subunits i-iii of the cytochrome c oxidase of the cyanobacterium synechocystis pcc 6803.	strong heterologous hybridization of a synthetic oligonucleotide probe of 17 bp originally used to clone subunit i of the paracoccus denitrificans cytochrome c oxidase (m. raitio, t. jalli and m. saraste (1987) embo j. 6, 2825-2833) to a single band was observed on southern blots of anacystis nidulans r2 (synechococcus pcc 7942), synechocystis pcc 6803, and nostoc mac pcc 8002 chromosomal dna digests. six pooled gene banks prepared from synechocystis pcc 6803 contained regions that hybridized to ...	1993	8387368
spectroscopic characterization of cytochrome c peroxidase from paracoccus denitrificans.	the cytochrome c peroxidase of paracoccus denitrificans is similar to the well-studied enzyme from pseudomonas aeruginosa. like the pseudomonas enzyme, the paracoccus peroxidase contains two haem c groups, one high potential and one low potential. the high-potential haem acts as a source of the second electron for h2o2 reduction, and the low-potential haem acts as a peroxidatic centre. reduction with ascorbate of the high-potential haem of the paracoccus enzyme results in a switch of the low-pot ...	1993	8397509
the bacterial energy-transducing nadh-quinone oxidoreductases.		1993	8435434
deuterium kinetic isotope effect and stopped-flow kinetic studies of the quinoprotein methylamine dehydrogenase.	stopped-flow kinetic studies of the reductive half-reaction of methylamine dehydrogenase from paracoccus denitrificans yielded kinetic constants for the reversible formation of the imine intermediate formed between the substrate and the tryptophan tryptophylquinone (ttq) prosthetic group and for the hydrogen abstraction step which occurs concomitantly with ttq reduction. when cd3nh2 was used as a substrate, deuterium kinetic isotope effects of 4.2 and 3.8, respectively, were measured for the rat ...	1993	8448129
characterization of a trypanosoma brucei nuclear gene encoding a protein homologous to a subunit of bovine nadh:ubiquinone oxidoreductase (complex i).	a trypanosoma brucei gene has been identified that encodes a protein predicted to be a component of the trypanosome homologue of mitochondrial nadh:ubiquinone oxidoreductase (complex i). high homology was found to a 20-kda component of the iron-sulfur protein fraction of bovine mitochondrial nadh:ubiquinone oxidoreductase and the products of the ndhk locus of paramecium tetraurelia mitochondria and the nqo6 locus of paracoccus denitrificans. the homology extends to several other proteins predict ...	1993	8459836
transfer of thiosphaera pantotropha to paracoccus denitrificans.	comparative sequence analysis of in vitro-amplified 16s rrna genes of thiosphaera pantotropha gb17t (t = type strain) and paracoccus denitrificans lmg 4218t revealed identical 16s rrna primary structures for the two organisms. the level of overall dna similarity of thiosphaera pantotropha gb17t and p. denitrificans dsm 65t is 85%, as determined by quantitative dna-dna hybridization. therefore, we propose the transfer of thiosphaera pantotropha to p. denitrificans. the closest relative of thiosph ...	1993	8494744
crystal structure analysis of amicyanin and apoamicyanin from paracoccus denitrificans at 2.0 a and 1.8 a resolution.	the crystal structure of amicyanin, a cupredoxin isolated from paracoccus denitrificans, has been determined by molecular replacement. the structure has been refined at 2.0 a resolution using energy-restrained least-squares procedures to a crystallographic residual of 15.7%. the copper-free protein, apoamicyanin, has also been refined to 1.8 a resolution with residual 15.5%. the protein is found to have a beta-sandwich topology with nine beta-strands forming two mixed beta-sheets. the secondary ...	1993	8495197
cdna cloning and mitochondrial import of the beta-subunit of the human electron-transfer flavoprotein.	we have isolated a cdna clone which encodes the entire beta-subunit of human electron-transferring flavoprotein (etf) by screening an expression library from human liver using polyclonal antibodies against porcine etf. this cdna encodes a protein of 255 amino-acid residues with a predicted molecular mass of 27,877 da which shows a high degree of similarity with partial amino-acid sequences obtained from both rat liver and paracoccus denitrificans beta-etf. northern-blot analysis shows that the h ...	1993	8504797
inhibition of mitochondrial and paracoccus denitrificans nadh-ubiquinone reductase by oxacarbocyanine dyes. a structure-activity study.	in this study, we determined that three structurally related oxacarbocyanine dyes, 3,3'-diethyloxacarbocyanine (dioc2(3)), 3,3'-dipentyloxacarbocyanine (dioc5(3)), and 3,3'-dihexyloxacarbocyanine (dioc6(3)), and one oxadicarbocyanine, 3,3'-diethyloxadicarbocyanine (dioc2(4)), inhibit bovine heart mitochondrial nadh oxidase activity and one of them, dioc6(3), inhibits paracoccus denitrificans nadh oxidase activity. the mitochondrial i50 values were 9 microm (dioc2(3)), approximately 1 microm (dio ...	1993	8512593
the genes in the thermophilic cyanobacterium synechococcus vulcanus encoding cytochrome-c oxidase.	it is still controversial whether cyanobacteria (blue-green algae) contain an aa3-type cytochrome-c oxidase. we have approached this problem using dna analysis. using a dna probe coding for the most conserved part of subunit i of the bacillus enzymes, structural genes for the oxidase of a thermophilic cyanobacterium synechococcus vulcanus were cloned and sequenced. we found genes for subunits ii, i, iii and iv of this order like those of the bacillus enzymes, and a terminator structure after the ...	1993	8399373
inhibitory effects of tannins on nadh dehydrogenases of various organisms.	we examined the effects of purified tannins and related compounds (33 species) on nadh-ubiquinone-1 oxidoreductase activity in four kinds of organism (paracoccus denitrificans, bacillus subtilis, photobacterium phosphoreum, and thermus thermophilus hb-8) and rat liver mitochondria. in addition to pentagalloylglucose, which was reported as a potent inhibitor of nadh dehydrogenases (ndh), sanguiin h-11, oolonghomobisflavan a, and polymerized procyanidin are potent inhibitors for both types of ndh ...	1993	8401410
cloning and sequencing of the gene coding for the large subunit of methylamine dehydrogenase from thiobacillus versutus.	the gene that codes for the alpha-subunit of methylamine dehydrogenase from thiobacillus versutus, mada, was cloned and sequenced. it codes for a protein of 395 amino acids preceded by a leader sequence of 31 amino acids. the derived amino acid sequence was confirmed by partial amino acid sequencing. the start of the mature protein could not be determined by direct sequencing, since the n terminus appeared to be blocked. instead, it was determined by electrospray mass spectrometry. confirmation ...	1993	8407797
dna sequencing of the seven remaining structural genes of the gene cluster encoding the energy-transducing nadh-quinone oxidoreductase of paracoccus denitrificans.	in our previous papers, seven structural genes (nqo1-7) of the energy-transducing nadh-quinone (q) oxidoreductase of paracoccus denitrificans were characterized [xu, x., matsuno-yagi, a., & yagi, t. (1991a) biochemistry 30, 8678-8684; (1991b) biochemistry 30, 6422-6428; (1992a) biochemistry 31, 6925-6932; (1992b) arch. biochem. biophys. 296, 40-48]. this paper reports the identification, cloning, and sequencing of seven additional structural genes in the same gene cluster (p. denitrificans enzym ...	1993	8422400
genetics of paracoccus denitrificans.	in bioenergetic research paracoccus denitrificans has been used as an interesting model to elucidate the mechanisms of bacterial energy transduction. genes for protein complexes of the respiratory chain and for proteins which are involved in periplasmic electron transport have been cloned and sequenced. conjugational gene transfer has allowed the construction of site-specific mutant strains. complementation experiments did not only open the field for site-directed mutagenesis and investigation o ...	1993	8431311
isolation, sequencing and mutational analysis of a gene cluster involved in nitrite reduction in paracoccus denitrificans.	by using the gene encoding the c-terminal part of the cd1-type nitrite reductase of pseudomonas stutzeri jm300 as a heterologous probe, the corresponding gene from paracoccus denitrificans was isolated. this gene, nirs, codes for a mature protein of 63144 da having high homology with cd1-type nitrite reductases from other bacteria. directly downstream from nirs, three other nir genes were found in the order nirecf. the organization of the nir gene cluster in pa. denitrificans is different from t ...	1994	7747927
import of a mitochondrial presequence into p. denitrificans. insight into the evolution of protein transport.	according to the endosymbiont hypothesis, mitochondria are descended from ancient aerobic bacteria that were engulfed by protoeukaryotic cells. experiments described here show that a synthetic peptide corresponding to a yeast mitochondrial targeting sequence can be imported into paracoccus denitrificans, a soil bacterium thought to be closely related to the protomitochondrion. the import is very similar to that observed with isolated yeast mitochondria. the results suggest that the protomitochon ...	1994	8276120
expression of the 25-kilodalton iron-sulfur subunit of the energy-transducing nadh-ubiquinone oxidoreductase of paracoccus denitrificans.	the energy-transducing nadh-ubiquinone (q) oxidoreductase of paracoccus denitrificans is composed of 14 dissimilar subunits and contains at least four iron-sulfur clusters [yagi, t. (1993) biochim. biophys. acta 1141, 1-17]. the complete dna sequence of the gene cluster encoding the energy-transducing nadh-q oxidoreductase of p. denitrificans has been determined. this paper reports the expression of the 25-kilodalton (kda) (nqo2) subunit of the p. denitrificans enzyme complex in escherichia coli ...	1994	8286379
studies on the proton-translocating nadh:ubiquinone oxidoreductases of mitochondria and escherichia coli using the inhibitor 1,10-phenanthroline.	mitochondrial nadh:ubiquinone oxidoreductase (complex i) is uncompetitively inhibited by 1,10-phenanthroline (op). epr spectroscopy of submitochondrial particles indicates that op, similarly to rotenone, inhibits electron transfer between the fe-s clusters of complex i and the ubiquinone pool. the proton-translocating nadh dehydrogenase (ndh1) of e. coli is more sensitive to op than is ndh1 of paracoccus. epr spectroscopy of membranous e. coli ndh1 shows that two slow- and one fast-relaxing fe-s ...	1994	8313963
cytochrome aa3 gene regulation in members of the family rhizobiaceae: comparison of copper and oxygen effects in bradyrhizobium japonicum and rhizobium tropici.	dithionite-reduced minus ferricyanide-oxidized difference spectra on membranes from rhizobium tropici (formerly rhizobium leguminosarum bv. phaseoli) incubated at progressively lower o2 concentrations showed only a slight concomitant decrease in a603, the alpha-peak of cytochrome aa3. in contrast to previous results on bradyrhizobium japonicum, r. tropici showed no significant o2-mediated reduction in the level of either coxa transcription or cytochrome aa3 activity (as measured by ascorbate-n,n ...	1994	8117073
the cupredoxin fold is found in the soluble cua and cyoa domains of two terminal oxidases.	the cd spectra of the cua domain from subunit ii of paracoccus cytochrome c oxidase and the cyoa domain of subunit ii from e. coli quinol oxidase have been recorded in the wavelength region 260-185 nm. a computer program based on a set of cd spectra of proteins with known structures, and employing the statistical method of variable selection, has been used to estimate the distribution of five forms of secondary structure. the analysis was improved by including the cd spectra of azurin and plasto ...	1994	8050583
molecular characterization of microbial alcohol dehydrogenases.	there is an astonishing array of microbial alcohol oxidoreductases. they display a wide variety of substrate specificities and they fulfill several vital but quite different physiological functions. some of these enzymes are involved in the production of alcoholic beverages and of industrial solvents, others are important in the production of vinegar, and still others participate in the degradation of naturally occurring and xenobiotic aromatic compounds as well as in the growth of bacteria and ...	1994	8185833
reevaluating the classification of paracoccus halodenitrificans with sequence comparisons of 16s ribosomal dna.	the results of phylogenetic analysis in which 16s ribosomal dna sequences were compared confirmed previous chemotaxonomic data which suggested that paracoccus halodenitrificans is inappropriately placed in the genus paracoccus, which belongs in the alpha subclass of the proteobacteria. p. halodenitrificans should be placed in the family halomonadaceae, which belongs in the gamma subclass of the proteobacteria.	1994	8186102
a mutation blocking the formation of membrane or periplasmic endogenous and exogenous c-type cytochromes in escherichia coli permits the cytoplasmic formation of hydrogenobacter thermophilus holo cytochrome c552.	a mutant of escherichia coli, jcb606, shown to be pleiotropically deficient in the formation of endogenous membrane and periplasmic c-type cytochromes, synthesised the apo form of the exogenous cytochrome c550 from paracoccus denitrificans, but not the holo form. in contrast, a cytoplasmically located holo form of hydrogenobacter thermophilus cytochrome c552 was found in e. coli jcb606. these findings support the proposition that the formation of the cytoplasmic h. thermophilus cytochrome c552 i ...	1994	8187885
characterization of cell surface material removed by water and nacl washing of paracoccus denitrificans grown under conditions of divalent cation deficiency and sufficiency.	paracoccus denitrificans grown on complex medium deficient in mg2+ and ca2+ are rendered lysozyme susceptible by washing with nacl, whereas cells grown in a succinate-salts medium (mg2+ and ca2+ sufficient) or complex medium supplemented with mg(2+)+ca2+ are not. the material released by water washing of cells grown on complex medium and complex medium supplemented with mg2+ and ca2+ was characterized by a high protein content. there was a high lipid: protein ratio and an appreciable amount of 3 ...	1994	8060122
properties of the iron-sulfur center in the 25-kilodalton subunit of the proton-translocating nadh-quinone oxidoreductase of paracoccus denitrificans.	the 25-kda subunit of the proton-translocating nadh-quinone oxidoreductase (ndh-1) of paracoccus denitrificans has been expressed in escherichia coli and purified to homogeneity. epr studies of the reduced recombinant protein indicated that the expressed subunit contains a single [2fe-2s] cluster (yano, t., sled', v. d., ohnishi, t., and yagi, t. (1994) biochemistry 33, 494-499). in this report, the electronic, magnetic, and vibrational properties of the [2fe-2s]2+,+ center have been investigate ...	1994	8063721
diphenyleneiodonium inhibits reduction of iron-sulfur clusters in the mitochondrial nadh-ubiquinone oxidoreductase (complex i).	diphenyleneiodonium (dpi) inhibits the mitochondrial nadh-ubiquinone oxidoreductase (complex i) on the substrate side of the fe-s clusters. in the inhibited nadh-supplemented state all of the fe-s clusters are oxidized, whereas the reduced minus oxidized difference spectrum of the protein-bound fmn can be visualized. it is characterized by troughs at 370 and 450 nm and a small increase of absorbance in the 500-700-nm region. dpi probably reacts irreversibly with fmn, because oxidation of fmn is ...	1994	8063722
thermodynamic and structural stability of cytochrome c oxidase from paracoccus denitrificans.	the structural stability of the integral membrane protein cytochrome c oxidase from paracoccus denitrificans has been measured by high-sensitivity differential scanning calorimetry and fourier transform infrared spectroscopy. contrary to the mammalian enzyme or the yeast enzyme, which are composed of 13 subunits, the bacterial enzyme has only three or four subunits, thus providing a unique opportunity to examine the magnitude of the forces that stabilize this enzyme and to establish accurate str ...	1994	8068652
replacement of enzyme-bound calcium with strontium alters the kinetic properties of methanol dehydrogenase.	methanol dehydrogenase (medh) possesses tightly bound ca2+ in addition to its pyrroloquinoline quinone (pqq) prosthetic group. ca2+ was replaced with sr2+ by growing the host bacterium, paracoccus denitrificans, in media in which ca2+ was replaced with sr2+. medh, which was purified from these cells (sr-medh), exhibited an increased absorption coefficient for the pqq chromophore, and displayed certain kinetic properties which were different from those of native medh. native medh exhibits an endo ...	1994	8198531
purification and characterization of the periplasmic nitrate reductase from thiosphaera pantotropha.	the periplasmic nitrate reductase of thiosphaera pantotropha has been purified from a mutant strain (m-6) that overproduces the enzyme activity under anaerobic growth conditions. the enzyme is a complex of a 93-kda polypeptide and a 16-kda nitrate-oxidizable cytochrome c552. the complex contains molybdenum; a fluorescent compound with spectral features of a pterin derivative can be extracted. in contrast to the dissimilatory membrane-bound nitrate reductases, the periplasmic nitrate reductase sh ...	1994	8119278
mechanism of proton translocation by the respiratory oxidases. the histidine cycle.		1994	8075101
bacterial genes and proteins involved in the biogenesis of c-type cytochromes and terminal oxidases.	a total of nine genes potentially concerned with the biosynthesis of c-type cytochromes have been identified recently in the bacteria bradyrhizobium japonicum and rhodobacter capsulatus, and homologous counterparts appear to be present also in escherichia coli. most of the respective gene products are membrane-bound, while others are located in the periplasmic space. as inferred from sequence analyses, several of these proteins may play roles in membrane transport or redox processes, both functi ...	1994	8075119
the kinetics of the oxidation of cytochrome c by paracoccus cytochrome c peroxidase.	in work that is complementary to our investigation of the spectroscopic features of the cytochrome c peroxidase from paracoccus denitrificans [gilmour, goodhew, pettigrew, prazeres, moura and moura (1993) biochem. j. 294, 745-752], we have studied the kinetics of oxidation of cytochrome c by this enzyme. the enzyme, as isolated, is in the fully oxidized form and is relatively inactive. reduction of the high-potential haem at ph 6 with ascorbate results in partial activation of the enzyme. full a ...	1994	8010977
influence of the lipid matrix on incorporation and function of lps-free porin from paracoccus denitrificans.	we have studied the role of lipopolysaccharide (lps) for the insertion of lps-free porin from paracoccus denitrificans into planar lipid bilayers and its function therein. for this, we reconstituted the porin into different asymmetric planar lipid bilayers with or without lps and into symmetric phospholipid bilayers. lps-free porin added to the various bilayer systems was found to induce a step-wise increase in membrane conductance with different incorporation rates, depending on the presence of ...	1994	8142421
denitrification and its control.	denitrification in bacteria comprises a series of four reduction reactions; for nitrate, nitrite, nitric oxide and nitrous oxide. nitrogen gas is the final product. the nature of the enzymes catalysing these reactions is described along with the the properties of the underlying electron transport systems. the factors influencing the expression of the reductases for the four reactions are reviewed along with the effect of oxygen on the activities of the enzymes of denitrification. the main emphas ...	1994	7747942
differential reduction in soluble and membrane-bound c-type cytochrome contents in a paracoccus denitrificans mutant partially deficient in 5-aminolevulinate synthase activity.	a mutant of paracoccus denitrificans, dp104, unable to grow anaerobically with nitrate as the terminal electron acceptor or aerobically with methanol as the electron donor and staining negatively in the dimethylphenylene diamine oxidation (nadi) test, was isolated by transposon tn5::phoa mutagenesis. p. denitrificans dp104 grown aerobically with succinate or choline had very low levels (2 to 3% of the wild-type levels) of spectroscopically detectable soluble c-type cytochromes. in contrast, memb ...	1994	7928952
ionic strength dependence of the reaction between methanol dehydrogenase and cytochrome c-551i: evidence of conformationally coupled electron transfer.	the quinoprotein methanol dehydrogenase and cytochrome c-551i are two soluble acidic proteins that form a physiological complex in which electrons are transferred from pyrroloquinoline quinone to heme. the oxidation of methanol dehydrogenase by the cytochrome was studied as a function of ionic strength using stopped-flow spectroscopy. the dissociation constant (kd) for complex formation decreased 2-fold with increasing ionic strength from 0.21 to 1.3 m and increased at higher ionic strengths. th ...	1994	7918485
secretion of human epidermal growth factor (egf) in autotrophic culture by a recombinant hydrogen-utilizing bacterium, pseudomonas pseudoflava, carrying broad-host-range egf secretion vector pksegf2.	we constructed the broad-host-range human epidermal growth factor (egf) secretion plasmid pksegf2 by inserting the escherichia coli tac promoter, the signal sequence of pseudomonas stutzeri amylase, and the synthesized egf gene into the broad-host-range vector pkt230. e. coli jm109 carrying pksegf2 secreted egf into the periplasm and the culture medium under the control of the tac promoter. pseudomonas aeruginosa pao1161 carrying pksegf2 and pseudomonas putida ac10 carrying pksegf2 secreted egf ...	1994	7944366
the gene encoding cytochrome-c oxidase subunit i from synechocystis pcc6803.	the gene (coxi or coxa) encoding subunit i (coi) of cytochrome-c oxidase (cytochrome aa3) of synechocystis pcc6803, synechococcus pcc7942 (anacystis nidulans r2) and nostoc pcc8002 (nostoc mac), was identified by heterologous hybridization of chromosomal digests with a 17-bp oligodeoxyribonucleotide (probe c) derived from the coxi of paracoccus denitrificans. a single genomic fragment was found to bind to probe c in all chromosomal digests. due to its favorable signal-to-noise ratio, the genome ...	1994	8125290
structure of an electron transfer complex: methylamine dehydrogenase, amicyanin, and cytochrome c551i.	the crystal structure of a ternary protein complex has been determined at 2.4 angstrom resolution. the complex is composed of three electron transfer proteins from paracoccus denitrificans, the quinoprotein methylamine dehydrogenase, the blue copper protein amicyanin, and the cytochrome c551i. the central region of the c551i is folded similarly to several small bacterial c-type cytochromes; there is a 45-residue extension at the amino terminus and a 25-residue extension at the carboxyl terminus. ...	1994	8140419
expression and characterization of human and chimeric human-paracoccus denitrificans electron transfer flavoproteins.	electron transfer flavoprotein (etf) is a heterodimer that contains a single equivalent of fad and accepts electrons from nine flavoprotein dehydrogenases in the mitochondrial matrix. human etf was expressed in escherichia coli using the expression vector previously employed to express paracoccus denitrificans etf (bedzyk, l. a., escudero, k. w., gill, r. e., griffin, k. j., and frerman, f. e. (1993) j. biol. chem. 268, 20211-20217). cdnas encoding the beta and alpha subunits of the human protei ...	1994	7798224
identification and sequence analysis of the soxb gene essential for sulfur oxidation of paracoccus denitrificans gb17.	the coding region for lithotrophic sulfur oxidation (sox) in paracoccus denitrificans gb17 was identified by isolation of a transposon tn5-mob mutant with a sox- phenotype (strain tp19). the corresponding wild-type region was cloned previously (g. mittenhuber, k. sonomoto, m. egert, and c. g. friedrich, j. bacteriol. 173:7340-7344, 1991). sequence analysis of a 2.5-kb subclone that complemented strain tp19 revealed that tn5-mob was inserted into a coding region for a 553-amino-acid polypeptide n ...	1994	7928987
thermal stability of methanol dehydrogenase is altered by the replacement of enzyme-bound ca2+ with sr2+.	methanol dehydrogenase (medh) possesses tightly bound ca2+ in addition to its pyrroloquinoline quinone prosthetic group. ca2+ was replaced with sr2+ by growing the host bacterium, paracoccus denitrificans, in media in which ca2+ was replaced with sr2+. at temperatures in the transition region for stability, the rate constants for inactivation of medh purified from these cells (sr-medh) were 2-fold lower than those for medh. however, arrhenius plots yielded an activation energy (ea) of 699 kj (16 ...	1994	7945232
expression of the mau genes involved in methylamine metabolism in paracoccus denitrificans is under control of a lysr-type transcriptional activator.	expression of methylamine dehydrogenase in paracoccus denitrificans and its concomitant ability to grow on methylamine is regulated by a substrate-induction mechanism as well as by a catabolite-repression-like mechanism. methylamine dehydrogenase is synthesized in cells growing on either methylamine or ethylamine, but not during growth on succinate, methanol or choline as sole sources of carbon and energy. the synthesis of methylamine dehydrogenase is repressed when succinate is added to the gro ...	1994	7957249
identification of amino acid residues associated with the [2fe-2s] cluster of the 25 kda (nqo2) subunit of the proton-translocating nadh-quinone oxidoreductase of paracoccus denitrificans.	in order to identify the ligand residues of the [2fe-2s] cluster of the 25 kda (nqo2) subunit of the proton-translocating nadh-quinone oxidoreductase of paracoccus denitrificans, we mutated individually all seven cysteine residues (c61, c96, c101, c104, c113, c137, and c141) and one conserved histidine residue (h92) to ser or ala and expressed them in e. coli. after purification of the mutated 25 kda subunits, the effect of mutations on the iron-sulfur cluster were characterized by chemical anal ...	1994	7957917
the fnr family of transcriptional regulators.	homologues of the transcriptional regulator fnr from escherichia coli have been identified in a variety of taxonomically diverse bacterial species. despite being structurally very similar, members of the fnr family have disparate regulatory roles. those from shewanella putrefaciens, pseudomonas aeruginosa, pseudomonas stutzeri and rhodopseudomonas palustris are functionally similar to fnr in that they regulate anaerobic respiration or carbon metabolism. four rhizobial proteins (from rhizobium me ...	1994	7747934
the terminal oxidases of paracoccus denitrificans.	three distinct types of terminal oxidases participate in the aerobic respiratory pathways of paracoccus denitrificans. two alternative genes encoding subunit i of the aa3-type cytochrome c oxidase have been isolated before, namely ctadi and ctadii. each of these genes can be expressed separately to complement a double mutant (delta ctadi, delta ctadii), indicating that they are isoforms of subunit i of the aa3-type oxidase. the genomic locus of a quinol oxidase has been isolated: cyoabc. this pr ...	1994	7984100
the effect of sulfite on the atp hydrolysis and synthesis activity of membrane-bound h(+)-atp synthase from various species.	the action of sulfite on atp hydrolysis and synthesis activities is investigated in membrane vesicles prepared from the cyanobacterium synechococcus 6716, chromatophores from the photosynthetic purple bacterium rhodospirillum rubrum, membrane vesicles from the related non-photosynthetic bacterium paracoccus denitrificans, and bovine heart submitochondrial particles. without any further pretreatment atp hydrolysis is stimulated by sulfite in all four membrane preparations. typically atp synthesis ...	1994	8002977
x-ray structure of the cytochrome c2 isolated from paracoccus denitrificans refined to 1.7-a resolution.	the cytochrome c2 (formerly c550) isolated from paracoccus denitrificans is one of the larger bacterial c-type proteins examined thus far. the molecular structure of this cytochrome has been redetermined and refined to 1.7-a resolution with a crystallographic r-factor of 17.5% for all measured x-ray data. like other, smaller c-type cytochromes, the molecule consists of five alpha-helices that wrap around the heme group. in addition, this bacterial cytochrome contains two strands of anti-parallel ...	1994	8179333
synthesis of holo paracoccus denitrificans cytochrome c550 requires targeting to the periplasm whereas that of holo hydrogenobacter thermophilus cytochrome c552 does not. implications for c-type cytochrome biogenesis.	expression from a plasmid of the complete gene, including the codons for the n-terminal periplasmic targeting signal, for cytochrome c550 of paracoccus denitrificans led to the formation of the holo protein in the periplasms of both p. denitrificans and escherichia coli. expression of the gene from which the region coding for the targeting signal had been specifically deleted resulted in formation of apo-protein in the cytoplasms of both organisms. these findings are consistent with haem attachm ...	1994	8119410
crystal structure analysis and refinement at 2.15 a resolution of amicyanin, a type i blue copper protein, from thiobacillus versutus.	the crystal structure of the type i blue copper protein amicyanin from thiobacillus versutus has been determined by patterson search techniques on the basis of the molecular model of amicyanin from paracoccus denitrificans, and refined by energy-restrained least-squares methods. amicyanin crystallizes in the trigonal space group p3(2) with unit cell dimensions of a = b = 87.40 a, c = 38.20 a. the asymmetric unit is composed of three independent molecules centred on the crystallographic 3(2) axes ...	1994	8120896
respiratory inhibitors activate an fnr-like regulatory protein in paracoccus denitrificans: implications for the regulation of the denitrification pathway.	unlike the uncoupler carbonyl cyanide 3-chlorophenyl-hydrazone, the respiratory inhibitors cn-, n3-, no2- and rotenone enhanced the formation of nitrate and nitrite reductases in highly aerated cultures of the paracoccus denitrificans ex-conjugant pd1222 (prw2a/ff). a maximal effect was observed at concentrations partly blocking electron transport to o2. the level of beta-galactosidase reporting the activity of an fnr-like regulatory protein showed a similar concentration dependency. it is concl ...	1994	8019429
a cytochrome ba3 functions as a quinol oxidase in paracoccus denitrificans. purification, cloning, and sequence comparison.	a quinol oxidase has been purified from the cytoplasmic membrane of paracoccus denitrificans; its heme composition and co binding properties identify it as a cytochrome ba3. on sds gels, the purified enzyme complex is separated into five polypeptides. using partial peptide sequence information for subunit ii, the gene locus has been cloned and sequenced. in a typical operon pattern, four genes were identified: qoxa, -b, -c, and -d, coding for subunits ii, i, iii, and iv. dna-derived amino acid s ...	1994	8083210
kinetic and thermodynamic analysis of a physiologic intermolecular electron-transfer reaction between methylamine dehydrogenase and amicyanin.	the quinoprotein methylamine dehydrogenase (madh) and a type i copper protein, amicyanin, form a physiologic complex in which electrons are transferred from tryptophan tryptophylquinone to copper. the reoxidation of madh by amicyanin has been studied by stopped-flow spectroscopy. the rate constant for the electron-transfer (et) reaction and the dissociation constant for the complex have been determined at different temperatures. marcus theory was used to calculate the distance, reorganizational ...	1994	8180195
genetic organization of the mau gene cluster in methylobacterium extorquens am1: complete nucleotide sequence and generation and characteristics of mau mutants.	the nucleotide sequence of the methylamine utilization (mau) gene region from methylobacterium extorquens am1 was determined. open reading frames for 11 genes (maufbedacjglmn) were found, all transcribed in the same orientation. the maub, maua, and mauc genes encode the periplasmic methylamine dehydrogenase (madh) large and small subunit polypeptides and amicyanin, respectively. the products of maud, maug, maul, and maum were also predicted to be periplasmic. the products of mauf, maue, and maun ...	1994	8021187
toxicity of 2-mercaptobenzothiazole towards bacterial growth and respiration.	active sludge systems containing benzothiazoles may be intoxicated by 2-mercaptobenzothiazole (mbt). this toxicity towards several bacteria is now confirmed and is situated at around 100 mg mbt l-1. octanol-water partition coefficients indicated that mbt might interact with membrane-bound systems. this was confirmed through experiments showing that bacterial cell respiration was inhibited using lactate or succinate as substrates. using these substrates and also nadh, it was found that their oxid ...	1994	7765737
sulfide dehydrogenase is identical with the soxb protein of the thiosulfate-oxidizing enzyme system of paracoccus denitrificans gb17.	thiosulfate induced cells of paracoccus denitrificans gb17 oxidize thiosulfate and sulfide to sulfate. a mutant carrying a tn5-mob insertion in the soxb gene is unable to oxidize thiosulfate or sulfide suggesting a linkage of both activities. to test this assumption we have separated the components of the thiosulfate-oxidizing enzyme system of the wild-type by ion exchange chromatography. the soxb protein coeluted with a highly active sulfide dehydrogenase. analysis by polyacrylamide gel electro ...	1994	8062925
cloning, sequence analysis, and expression of the genes encoding the two subunits of the methylotrophic bacterium w3a1 electron transfer flavoprotein.	the genes encoding the two different subunits of the electron transfer flavoprotein (etf) from the methylotrophic bacterium w3a1 have been identified, cloned, and sequenced. a 0.8-kilobase pair dna fragment was generated for use as a molecular probe by the amplification of genomic sequences using the polymerase chain reaction and a primer pair with degenerate sequences derived from the nh2-terminal amino acid sequences determined for the etf subunits purified from w3a1. the screening of a partia ...	1994	7798207
mo(v) electron paramagnetic resonance signals from the periplasmic nitrate reductase of thiosphaera pantotropha.	a mo(v) electron paramagnetic resonance (epr) study of the periplasmic respiratory nitrate reductase of the denitrifying bacterium thiosphaera pantotropha has revealed that the molybdenum centre of this enzyme is very similar to that in the assimilatory nitrate reductase of azotobacter vinelandii but is somewhat different from that of the membrane-bound bacterial respiratory nitrate reductases such as those of escherichia coli and paracoccus denitrificans. we have identified the mo(v) species mo ...	1994	7813468
characterisation and amino acid sequence of cytochrome c-550 from thiosphaera pantotropha.	a cytochrome c-550, with mid-point potential +265 mv, has been purified from thiosphaera pantotropha. the cytochrome was recognised by antibodies to paracoccus denitrificans cytochrome c-550, but the two proteins were not immunologically identical. amino acid sequencing of the cytochrome c-550 showed 85.9% and 95.5% identities, respectively, with the cytochromes c-550 of p. denitrificans and thiobacillus versutus; these are amongst the highest values reported for similarities between class i c-t ...	1994	7508392
[microbial purine decomposition].	27 microorganisms were tested for their ability to degrade extracellular purines as sole sources of carbon, nitrogen, and energy. beside adenine, guanine, xanthine, hypoxanthine, and urate as free purine bases, this test included 5'-amp, 5'-gmp, 5'-xmp, and 5'-imp, as well as dna and rna as purine compounds. generally, only a limited number of microbial species was capable of metabolizing the substances named above. compared to the other species, paracoccus denitrificans showed the greatest subs ...	1994	7521548
mass spectrometric studies of the effect of ph on the accumulation of intermediates in denitrification by paracoccus denitrificans.	we have used a quadrupole mass spectrometer with a gas-permeable membrane inlet for continuous measurements of the production of n(2)o and n(2) from nitrate or nitrite by cell suspensions of paracoccus denitrificans. the use of nitrate and nitrite labeled with n was shown to simplify the interpretation of the results when these gases were measured. this approach was used to study the effect of ph on the production of denitrification intermediates from nitrate and nitrite under anoxic conditions. ...	1994	16349183
autotrophic, hydrogen-oxidizing, denitrifying bacteria in groundwater, potential agents for bioremediation of nitrate contamination.	addition of hydrogen or formate significantly enhanced the rate of consumption of nitrate in slurried core samples obtained from an active zone of denitrification in a nitrate-contaminated sand and gravel aquifer (cape cod, mass.). hydrogen uptake by the core material was immediate and rapid, with an apparent k(m) of 0.45 to 0.60 mum and a v(max) of 18.7 nmol cm h at 30 degrees c. nine strains of hydrogen-oxidizing denitrifying bacteria were subsequently isolated from the aquifer. eight of the s ...	1994	16349284
a cytochrome cd1-type nitrite reductase isolated from the marine denitrifier pseudomonas nautica 617: purification and characterization.	nitrite reductase (cytochrome cd1) was purified to electrophoretic homogeneity from the soluble extract of the marine denitrifying bacterium pseudomonas nautica strain 617. cells were anaerobically grown with 10 mm nitrate as final electron acceptor. the soluble fraction was purified by four successive chromatographic steps and the purest cytochrome cd1 exhibited an a280 nm(oxidized)/a410nm(oxidized) coefficient of 0.90. in the course of purification, cytochrome cd1 specific activity presented a ...	1995	16887530
involvement of cytochrome c oxidase subunit iii in energy coupling.	the role of the conserved acidic residues of subunit iii of cytochrome c oxidase (coiii) in energy transduction was investigated. using a coiii deletion mutant of paracoccus denitrificans, complemented with a plasmid expressing either the wild type (wt) coiii gene or site-directed mutants of the coiii gene, we measured cytochrome c oxidase-dependent atp synthesis, respiration, and membrane potential. cytochrome c oxidase-dependent atp synthesis was attenuated in nonacidic mutants of either glu98 ...	1995	8845354
engineered fv fragments as a tool for the one-step purification of integral multisubunit membrane protein complexes.	the preparation of pure and homogeneous membrane proteins or membrane protein complexes is time consuming, and the yields are frequently insufficient for structural studies. to circumvent these problems we established an indirect immunoaffinity chromatography method based on engineered fv fragments. cdnas encoding the variable domains of hybridoma-derived antibodies raised against various membrane proteins were cloned and expressed in escherichia coli. the fv fragments were engineered to serve a ...	1995	9634756
paracoccus thiocyanatus sp. nov., a new species of thiocyanate-utilizing facultative chemolithotroph, and transfer of thiobacillus versutus to the genus paracoccus as paracoccus versutus comb. nov. with emendation of the genus.	a facultatively chemolithotrophic thiocyanate-degrading bacterium, strain thi 011t, which was previously isolated from activated sludge and tentatively named thiobacillus sp., was studied taxonomically and phylogenetically. this bacterium utilizes thiocyanate as sole energy source and the specific growth rate for chemolithoautotrophic growth with thiocyanate was 0.059 h-1. molecular phylogenetic relationships of strain thi 011t to thiobacillus versutus and members of the genus paracoccus were el ...	1995	7545513
phylogenetic inferences and taxonomic consequences of 16s ribosomal dna sequence comparison of chromohalobacter marismortui, volcaniella eurihalina, and deleya salina and reclassification of v. eurihalina as halomonas eurihalina comb. nov.	the phylogenetic positions of the moderately halophilic bacteria chromohalobacter marismortui, volcaniella eurihalina, and deleya salina were determined by pcr amplification of rrna genes and direct sequencing. the resulting data were compared with data for other bacteria obtained from 16s rrna sequence databases. c. marismortui, v. eurihalina, and d. salina clustered phylogenetically within the gamma subclass of the proteobacteria and are closely related to other species on the halomonas-deleya ...	1995	7547290
fv fragment-mediated crystallization of the membrane protein bacterial cytochrome c oxidase.	crystallization of membrane proteins, a prerequisite for their x-ray crystallographic analysis, remains difficult. here, we demonstrate that the crystallization of the cytochrome c oxidase from paracoccus denitrificans can be mediated by co-crystallization with an antibody fv fragment. the crystals obtained contain all four subunits of this membrane protein complex and the fv fragment. the approach of co-crystallizing membrane proteins with antibody fragments should be useful in obtaining well-o ...	1995	7552705
reversed electron transfer through the bc1 complex enables a cytochrome c oxidase mutant (delta aa3/cbb3) of paracoccus denitrificans to grow on methylamine.	in paracoccus denitrificans four classes of redox proteins are involved in the electron transfer from methylamine to oxygen:methylamine dehydrogenase (madh), amicyanin, cytochrome c and cytochrome c oxidase. madh and its electron acceptor amicyanin are indispensable for growth on methylamine. at least three different cytochromes c and two types of cytochrome c oxidase, cytochromes aa3 and cbb3, have previously been proposed to participate in the electron transfer pathways from methylamine to oxy ...	1995	7556607
subunit iii of cytochrome c oxidase influences the conformation of subunits i and ii: an infrared study.	the secondary structure of wild-type paracoccus denitrificans cytochrome c oxidase obtained by decomposition of the infrared amide i band contains 44% alpha-helix, 18% beta-sheet, 14% beta-turns, 18% loops, and 6% nonordered segments. the mutant lacking subunit iii presents a small but significant increase (from 18% to 24%) in the percentage of loops and slight differences in the other components. using band/area ratios and tyrosine side chain absorption as an inner standard, it is shown that in ...	1995	7577945
immunoelectron microscopy and epitope mapping with monoclonal antibodies suggest the existence of an additional n-terminal transmembrane helix in the cytochrome b subunit of bacterial ubiquinol:cytochrome-c oxidoreductases.	the topology of the ubiquinol:cytochrome-c oxidoreductase (cytochrome bc1 complex) from paracoccus denitrificans was investigated by immunoelectron microscopy with sequence-specific murine monoclonal antibodies. epitope mapping with synthetic peptides and enzymic proteolytic cleavage of the cytochrome bc1 complex were employed to localize precisely the respective antibody epitopes on the subunits of this membrane protein complex. localization of defined epitopes on the cytochrome bc1 complex by ...	1995	7601123
intermolecular electron transfer from substrate-reduced methylamine dehydrogenase to amicyanin is linked to proton transfer.	within the methylamine dehydrogenase-amicyanin complex, intermolecular electron transfer (et) occurs between tryptophan tryptophylquinone (ttq) and copper. the et reactions from two chemically distinct reduced forms of ttq were studied. the quinol form of ttq was generated by reduction by dithionite. an aminoquinol form of ttq, in which an amino group displaces the carbonyl oxygen, was generated by reduction by the substrate methylamine. thermodynamic analysis of the et reactions suggested that ...	1995	7547947
amperometric detection of histamine at a quinoprotein dehydrogenase enzyme electrode.	methylamine dehydrogenase, a tryptophan tryptophyl quinone (ttq) containing quinoprotein, catalyzes the oxidation of a variety of primary aliphatic monomaines and diamines to their respective aldehydes and ammonia. this paper reports the construction and characterization of an enzyme electrode capable of detecting histamine and methylamine at +200 mv versus a saturated calomel reference electrode. the methylamine dehydrogenase isolated from paracoccus denitrificans was used in conjunction with t ...	1995	7612208
expression and characterization of the 66-kilodalton (nqo3) iron-sulfur subunit of the proton-translocating nadh-quinone oxidoreductase of paracoccus denitrificans.	the proton-translocating nadh-quinone oxidoreductase (ndh-1) of paracoccus denitrificans is composed of at least 14 dissimilar subunits which are designated nqo1-14 and contains one noncovalently bound fmn and at least five epr-visible iron-sulfur clusters (n1a, n1b, n2, n3, and n4) as prosthetic groups. comparison of the deduced primary structures of the subunits with consensus sequences for the cofactor binding sites has predicted that nqo1, nqo2, nqo3, nqo9, and probably nqo6 subunits are cof ...	1995	7629145
dictyostelium discoideum mitochondrial dna encodes a nadh:ubiquinone oxidoreductase subunit which is nuclear encoded in other eukaryotes.	complex i, a key component of the mitochondrial electron transport system, is thought to have evolved from at least two separate enzyme systems prior to the evolution of mitochondria from a bacterial endosymbiont, but the genes for one of the enzyme systems are thought to have subsequently been transferred to the nuclear dna. we demonstrated that the cellular slime mold dictyostelium discoideum retains the ancestral characteristic of having mitochondria encoding at least one gene (80-kda subunit ...	1995	7643412
identification of periplasmic nitrate reductase mo(v) epr signals in intact cells of paracoccus denitrificans.	epr spectroscopy has been successfully used to detect signals due to molybdenum (v) and ferric iron in intact cells of aerobically grown paracoccus denitrificans. the signals are ascribed to the catalytic molybdenum centre and to the haem iron of the periplasmic nitrate reductase. these signals are absent from a mutant strain deficient in this enzyme. the mo(v) signal is due to the high-g split species which has been well characterized in the purified enzyme. this confirms that the high-g split ...	1995	7646461
purification of paracoccus denitrificans cytochrome c552 and sequence analysis of the gene.	unlike mitochondria, many bacteria use a large repertoire of c-type cytochromes in different branches of their electron transport system. among the many cytochromes c present in the soil bacterium paracoccus denitrificans, a membrane-bound cytochrome (c552) has been suggested to mediate the electron transport between the cytochrome bc1 complex and cytochrome-c oxidase [berry, e. a. & trumpower, b. l. (1985) j. biol. chem. 260, 2458-2467]. we have purified this cytochrome from cytoplasmic membran ...	1995	7628479
site-directed mutagenesis of cytochrome c oxidase reveals two acidic residues involved in the binding of cytochrome c.	site-directed mutagenesis in subunit ii of the cytochrome c oxidase (haem aa3) from paracoccus denitrificans reveals that two carboxylic residues, glu-246 and asp-206 (corresponding to 198 and 158 in the bovine subunit ii), are involved in the binding of cytochrome c. spectrophotometric and polarographic measurements with the isolated enzymes of both mutant strains show a strongly reduced activity compared to wild-type oxidase, with the overall catalytic capacity (kcat/km) of both mutants decrea ...	1995	7612644
the napedabc gene cluster encoding the periplasmic nitrate reductase system of thiosphaera pantotropha.	the napedabc locus coding for the periplasmic nitrate reductase of thiosphaera pantotropha has been cloned and sequenced. the large and small subunits of the enzyme are coded by napa and napb. the sequence of napa indicates that this protein binds the gmp-conjugated form of the molybdopterin cofactor. cysteine-181 is proposed to ligate the molybdenum atom. it is inferred that the active site of the periplasmic nitrate reductase is structurally related to those of the molybdenum-dependent formate ...	1995	7639719
integration of heterologous dna into the genome of paracoccus denitrificans is mediated by a family of is1248-related elements and a second type of integrative recombination event.	all members of the is1248 family residing in the genome of paracoccus denitrificans have been isolated by using a set of insertion sequence entrapment vectors. the family consists of five closely related members that integrate the entrapment vectors at distinct sites. one of these, is1248b, was sequenced and, except for a single base change, shown to be identical to the previously isolated is1248a. southern analysis of genomic dna with labeled is1248 revealed different hybridization patterns for ...	1995	7642505
cloning of electron-transferring flavoprotein from megasphaera elsdenii.		1995	7672411