Publications

paracoccus denitrificans ccmg is a periplasmic protein-disulphide oxidoreductase required for c- and aa3-type cytochrome biogenesis; evidence for a reductase role in vivo.	cloning and sequencing of the paracoccus denitrificans ccmg gene indicates that it codes for a periplasmic protein-disulphide oxidoreductase; the presence of the sequence cys-pro-pro-cys at the ccmg active site suggests that it may act in vivo to reduce disulphide bonds rather than to form them. a ccmg-phoa fusion confirmed the periplasmic location. disruption of the ccmg gene resulted in not only the expected phenotype of pleiotropic deficiency in c-type cytochromes, but also loss of spectrosco ...	1997	9220005
amaricoccus gen. nov., a gram-negative coccus occurring in regular packages or tetrads, isolated from activated sludge biomass, and descriptions of amaricoccus veronensis sp. nov., amaricoccus tamworthensis sp. nov., amaricoccus macauensis sp. nov., and amaricoccus kaplicensis sp. nov.	three isolates of gram-negative bacteria, strains ben 102t, ben 103t, and ben 104t, were obtained in pure culture by micromanipulation from activated sludge biomass from wastewater treatment plants in italy, australia, and macau, respectively. these isolates all had a distinctive morphology; the cells were cocci that usually were arranged in tetrads. based on this criterion, they resembled other bacteria from activated sludge previously called "g" bacteria. on the basis of phenotypic characteris ...	1997	9226904
electron paramagnetic resonance studies of succinate:ubiquinone oxidoreductase from paracoccus denitrificans. evidence for a magnetic interaction between the 3fe-4s cluster and cytochrome b.	electron paramagnetic resonance (epr) studies of succinate:ubiquinone oxidoreductase (sqr) from paracoccus denitrificans have been undertaken in the purified and membrane-bound states. spectroscopic "signatures" accounting for the three iron-sulfur clusters (2fe-2s, 3fe-4s, and 4fe-4s), cytochrome b, flavin, and protein-bound ubisemiquinone radicals have been obtained in air-oxidized, succinate-reduced, and dithionite-reduced preparations at 4-10 k. spectra obtained at 170 k in the presence of e ...	1997	9235936
a new non-heme iron environment in paracoccus denitrificans adenylate kinase studied by electron paramagnetic resonance and electron spin echo envelope modulation spectroscopy.	adenylate kinase from the gram-negative bacterium paracoccus denitrificans (akden) has structural features highly similar to those of the enzyme from gram-positive organisms. atomic absorption spectroscopy of the recombinant protein, which is a dimer, revealed the presence of two metals, zinc and iron, each binding most probably to one monomer. under oxidizing conditions, the electron paramagnetic resonance (epr) spectrum of akden at 4.2 k consists of features at g = 9.23, 4.34, 4.21, and 3.68. ...	1997	9235989
the roles of the two proton input channels in cytochrome c oxidase from rhodobacter sphaeroides probed by the effects of site-directed mutations on time-resolved electrogenic intraprotein proton transfer.	the crystal structures of cytochrome c oxidase from both bovine and paracoccus denitrificans reveal two putative proton input channels that connect the heme-copper center, where dioxygen is reduced, to the internal aqueous phase. in this work we have examined the role of these two channels, looking at the effects of site-directed mutations of residues observed in each of the channels of the cytochrome c oxidase from rhodobacter sphaeroides. a photoelectric technique was used to monitor the time- ...	1997	9256439
cloning and characterization of sulfite dehydrogenase, two c-type cytochromes, and a flavoprotein of paracoccus denitrificans gb17: essential role of sulfite dehydrogenase in lithotrophic sulfur oxidation.	a 13-kb genomic region of paracoccus dentrificans gb17 is involved in lithotrophic thiosulfate oxidation. adjacent to the previously reported soxb gene (c. wodara, s. kostka, m. egert, d. p. kelly, and c. g. friedrich, j. bacteriol. 176:6188-6191, 1994), 3.7 kb were sequenced. sequence analysis revealed four additional open reading frames, soxcdef. soxc coded for a 430-amino-acid polypeptide with an mr of 47,339 that included a putative signal peptide of 40 amino acids (mr of 3,599) with a rr mo ...	1997	9260941
complete nucleotide sequence of the replicator region of paracoccus (thiobacillus) versutus ptav1 plasmid and its correlation to several plasmids of agrobacterium and rhizobium species.	the complete nucleotide sequence of the replicator region of ptav1, a cryptic, low copy number plasmid of paracoccus versutus, was determined. the minimal replicon sequence (3149 bp) included in ptav203/18 contains two open reading frames with coding capabilities for putative polypeptides of 23.8 (repx) and 46 kda (repc'). the two genes have the same transcriptional polarity and both seem to be essential for replication of ptav203. the predicted amino acid sequence of repc' shows significant hom ...	1997	9281495
regulation of respiration and energy transduction in cytochrome c oxidase isozymes by allosteric effectors.	the binding of tnp-atp (2' or 3'-o-(2,4,6-trinitrophenyl)-atp) to cytochrome c oxidase (cox) from bovine heart and liver and to the two-subunit cox of paracoccus denitrificans was measured by its change of fluorescence. three binding sites, two with high (dissociation constant kd = 0.2 microm) and one with lower affinity (kd = 0.9 microm), were found at cox from bovine heart and liver, while the paracoccus enzyme showed only one binding site (kd = 3.6 microm). the binding of [35s]atp alpha s was ...	1997	9309677
cloning and analysis of methanol oxidation genes in the methylotroph hyphomicrobium methylovorum gm2.	the gene encoding the alpha-subunit of methanol dehydrogenase (mxaf) and its flanking region was isolated from a methylotrophic bacterium, hyphomicrobium methylovorum gm2. the deduced amino acid sequence of mxaf showed 80, 80, 74 and 66% identity with those of methylobacterium extorquens am1, m. organophilum xx, paracoccus denitrificans and methylophilus methylotrophus, respectively. the putative mxaf promoter sequence (-35 -aaagaca-, -10 -tagaa-) observed in other methylotrophs was not found in ...	1997	9311140
haem-ligand switching during catalysis in crystals of a nitrogen-cycle enzyme.	cytochrome cd1 nitrite reductase catalyses the conversion of nitrite to nitric oxide in the nitrogen cycle. the crystal structure of the oxidized enzyme shows that the d1 haem iron of the active site is ligated by his/tyr side chains, and the c haem iron is ligated by a his/his ligand pair. here we show that both haems undergo re-ligation during catalysis. upon reduction, the tyrosine ligand of the d1 haem is released to allow substrate binding. concomitantly, a refolding of the cytochrome c dom ...	1997	9311786
factors which stabilize the methylamine dehydrogenase-amicyanin electron transfer protein complex revealed by site-directed mutagenesis.	methylamine dehydrogenase (madh) and amicyanin form a physiologic complex within which electrons are transferred from the tryptophan tryptophylquinone (ttq) cofactor of madh to the type 1 copper of amicyanin. interactions responsible for complex formation may be inferred from the crystal structures of complexes of these proteins. site-directed mutagenesis has been performed to probe the roles of specific amino acid residues of amicyanin in stabilizing the madh-amicyanin complex and determining t ...	1997	9335529
iron as a possible mediator of the oxic-to-anoxic transition in paracoccus denitrificans.	expression of the lacz gene from the fnr-regulated ff-melr promoter on a plasmid in iron-deprived paracoccus denitrificans cells required not only a decreased oxygen tension but also supplementation with iron. the levels of beta-galactosidase and 5-aminolevulinate synthase showed comparable responses to changes in iron availability. the presence of soluble and particulate enzymes catalyzing the reduction of fe(iii) by nadh suggests a hypothesis in which the redox state of the cytoplasmic nad-cou ...	1997	9350337
catalytic role of monovalent cations in the mechanism of proton transfer which gates an interprotein electron transfer reaction.	within the methylamine dehydrogenase (madh)-amicyanin protein complex, long range intermolecular electron transfer (et) occurs between tryptophan tryptophylquinone (ttq) of madh and the type i copper of amicyanin. the reoxidations of two chemically distinct reduced forms of ttq were studied, a quinol (o-quinol) generated by reduction by dithionite and the physiologically relevant aminoquinol (n-quinol) generated by reduction by methylamine. the latter contains a substrate-derived amino group whi ...	1997	9354627
isolation and characterization of nitric oxide reductase from paracoccus halodenitrificans.	nitric oxide reductase was isolated from the membrane fraction of a denitrifying bacterium, paracoccus halodenitrificans, in the presence of n-dodecyl beta-d-maltoside. a relatively simple and effective procedure to purify no reductase using deae-toyopearl and hydroxyapatite (ceramic) chromatographies has been developed. the enzyme consisted of two subunits with molecular masses of 20 and 42 kda associated with the c-type heme and two b-type hemes, respectively. the optical and magnetic circular ...	1997	9374857
glutamate 286 in cytochrome aa3 from rhodobacter sphaeroides is involved in proton uptake during the reaction of the fully-reduced enzyme with dioxygen.	the reaction with dioxygen of solubilized fully-reduced wild-type and eq(i-286) (exchange of glutamate 286 of subunit i for glutamine) mutant cytochrome c oxidase from rhodobacter sphaeroides has been studied using the flow-flash technique in combination with optical absorption spectroscopy. proton uptake was measured using a ph-indicator dye. in addition, internal electron-transfer reactions were studied in the absence of oxygen. glutamate 286 is found in a proton pathway proposed to be used fo ...	1997	9374859
structure at 2.7 a resolution of the paracoccus denitrificans two-subunit cytochrome c oxidase complexed with an antibody fv fragment.	the aa3 type cytochrome c oxidase consisting of the core subunits i and ii only was isolated from the soil bacterium paracoccus denitrificans and crystallized as complex with a monoclonal antibody fv fragment. crystals could be grown in the presence of a number of different nonionic detergents. however, only undecyl-beta-d-maltoside and cyclohexyl-hexyl-beta-d-maltoside yielded well-ordered crystals suitable for high resolution x-ray crystallographic studies. the crystals belong to space group p ...	1997	9380672
autotrophic growth on carbon disulfide is a property of novel strains of paracoccus denitrificans.	three distinct strains (kl1, ks1, and ks2) of facultatively chemolitho-autotrophic bacteria able to use carbon disulfide or carbonyl sulfide as sole energy substrates were identified as novel strains of paracoccus denitrificans. evidence for their identity as biovars of p. denitrificans and as close relatives of paracoccus versutus is based on their dna composition, total sequencing of the genes for their 16s rrna, muropeptide profiles, amino acid composition of peptidoglycan, kinetics of murein ...	1997	9382702
inhibition of denitrification activity but not of mrna induction in paracoccus denitrificans by nitrite at a suboptimal ph.	the influence of ph on the denitrification activity of a continuous culture of paracoccus denitrificans was studied in relation to the presence of nitrite. after a transition from aerobic to anaerobic conditions at the suboptimal ph of 6.8, p. denitrificans was not able to build up a functional denitrification pathway. nitrite accumulated in the medium as the predominant denitrification product. although the nitrite reductase gene was induced properly, the enzyme could not be detected at suffici ...	1997	9403103
maue and maud proteins are essential in methylamine metabolism of paracoccus denitrificans.	synthesis of enzymes involved in methylamine oxidation via methylamine dehydrogenase (madh) is encoded by genes present in the mau cluster. here we describe the sequence of the maue and maud genes from paracoccus denitrificans as well as some properties of maue and maud mutants of this organism. the amino acid sequences derived from the maue and maud genes showed high similarity with their counterparts in related methylotrophs. secondary structure analyses of the amino acid sequences predicted t ...	1997	9403107
identification and molecular genetic analysis of multiple loci contributing to high-level tellurite resistance in rhodobacter sphaeroides 2.4.1.	the ability of the facultative photoheterotroph rhodobacter sphaeroides to tolerate and reduce high levels of tellurite in addition to at least 10 other rare earth metal oxides and oxyanions has considerable potential for detoxification and bioremediation of contaminated environments. we report the identification and characterization of two loci involved in high-level tellurite resistance. the first locus contains four genes, two of which, trgab, confer increased tellurite resistance when introd ...	1997	9406390
cell biology and molecular basis of denitrification.	denitrification is a distinct means of energy conservation, making use of n oxides as terminal electron acceptors for cellular bioenergetics under anaerobic, microaerophilic, and occasionally aerobic conditions. the process is an essential branch of the global n cycle, reversing dinitrogen fixation, and is associated with chemolithotrophic, phototrophic, diazotrophic, or organotrophic metabolism but generally not with obligately anaerobic life. discovered more than a century ago and believed to ...	1997	9409151
heterologous expression of heterotrophic nitrification genes.	paracoccus denitrificans is a heterotrophic organism capable of oxidizing ammonia to nitrite during growth on an organic carbon and energy source. this pathway, termed heterotrophic nitrification, requires the concerted action of an ammonia monooxygenase (amo) and hydroxylamine oxidase (hao). the genes required for heterotrophic nitrification have been isolated by introducing a pa. denitrificans genomic library into pseudomonas putida and screening for the accumulation of nitrite. in contrast to ...	1997	9421902
molecular genetic analysis suggesting interactions between appa and ppsr in regulation of photosynthesis gene expression in rhodobacter sphaeroides 2.4.1.	the appa protein plays an essential regulatory role in development of the photosynthetic apparatus in the anoxygenic phototrophic bacterium rhodobacter sphaeroides 2.4.1 (m. gomelsky and s. kaplan, j. bacteriol. 177:4609-4618, 1995). to gain additional insight into both the role and site of action of appa in the regulatory network governing photosynthesis gene expression, we investigated the relationships between appa and other known regulators of photosynthesis gene expression. we determined th ...	1997	8981989
identification of an assimilatory nitrate reductase in mutants of paracoccus denitrificans gb17 deficient in nitrate respiration	a paracoccus denitrificans strain (m6omega) unable to use nitrate as a terminal electron acceptor was constructed by insertional inactivation of the periplasmic and membrane-bound nitrate reductases. the mutant strain was able to grow aerobically with nitrate as the sole nitrogen source. it also grew anaerobically with nitrate as sole nitrogen source when nitrous oxide was provided as a respiratory electron acceptor. these growth characteristics are attributed to the presence of a third, assimil ...	1997	9000343
the proton-translocating nadh-quinone oxidoreductase (ndh-1) of thermophilic bacterium thermus thermophilus hb-8. complete dna sequence of the gene cluster and thermostable properties of the expressed nqo2 subunit.	the genes encoding the proton-translocating nadh-quinone oxidoreductase (ndh-1) of a thermophilic bacterium thermus thermophilus hb-8 were cloned and sequenced. they constitute a cluster that is composed of 14 structural genes and contains no unidentified reading frames. all of the 14 structural genes, which are designated nqo1-14, encode subunits homologous to those of paracoccus denitrificans ndh-1, respectively, and are arranged in the same order as other bacterial ndh-1 genes. t. thermophilu ...	1997	9020134
isolation and characterization of rhodobacter capsulatus mutants affected in cytochrome cbb3 oxidase activity.	the facultative phototrophic bacterium rhodobacter capsulatus contains only one form of cytochrome (cyt) c oxidase, which has recently been identified as a cbb3-type cyt c oxidase. this is unlike other related species, such as rhodobacter sphaeroides and paracoccus denitrificans, which contain an additional mitochondrial-like aa3-type cyt c oxidase. an extensive search for mutants affected in cyt c oxidase activity in r. capsulatus led to the isolation of at least five classes of mutants. plasmi ...	1998	9473054
tryptophan 121 of subunit ii is the electron entry site to cytochrome-c oxidase in paracoccus denitrificans. involvement of a hydrophobic patch in the docking reaction.	to investigate the contribution of hydrophobic residues to the molecular recognition of cytochrome c with cytochrome oxidase, we mutated several hydrophobic amino acids exposed on subunit ii of the paracoccus denitrificans oxidase. km and kcat values and the bimolecular rate constant were determined under steady- or presteady-state conditions, respectively. we present evidence that trp-121 which is surrounded by a hydrophobic patch is the electron entry site to oxidase. mutations in this cluster ...	1998	9478966
genomic dna cloning of the region encoding nitric oxide reductase in paracoccus halodenitrificans and a structure model relevant to cytochrome oxidase.	the structural genes for the no reductase in paracoccus halodenitrificans, norc, norb, and norq were sequenced. the norc and norb encode the cytochrome c (norc) and cytochrome b (norb) subunits, respectively. the matured norc (17,258 da, 148 residues) has a binding motif (cxych) for heme c, which is axially coordinated by his65 and met115. norb (52,337 da, 451 residues) has twelve putative transmembrane helices and the 19% sequence homology with the subunit i of cytochrome oxidase from paracoccu ...	1998	9480821
role of the pathway through k(i-362) in proton transfer in cytochrome c oxidase from r. sphaeroides.	in this study we have combined the use of site-directed mutants with time-resolved optical absorption spectroscopy to investigate the role of the protonatable subunit-i residues lysine-362 (k(i-362)) and threonine-359 (t(i-359)) in cytochrome c oxidase from rhodobacter sphaeroides in electron and proton transfer. these residues have been proposed to be part of a proton-transfer pathway in cytochrome oxidases from paracoccus denitrificans and bovine heart. mutation of k(i-362) and t(i-359) to met ...	1998	9485395
purification and characterization of the hnda subunit of nadp-reducing hydrogenase from desulfovibrio fructosovorans overproduced in escherichia coli.	based on the dna sequence of its structural genes, clustered in the hnd operon, the nadp-reducing hydrogenase of desulfovibrio fructosovorans is thought to be a heterotetrameric complex in which hnda and hndc constitute the nadp-reducing unit and hndd constitutes the hydrogenase unit, respectively. the weak representativity of the enzyme among cell proteins has prevented its purification. this paper discusses the purification and characterization of the hnda subunit of this unique tetrameric iro ...	1998	9485416
cytochrome-c-binding site on cytochrome oxidase in paracoccus denitrificans.	to monitor the docking site for cytochrome c on cytochrome oxidase from paracoccus denitrificans, a series of site-directed mutants in acidic residues exposed on the three largest subunits was constructed, and the purified enzymes were assayed for their steady-state kinetic parameters, their ionic strength dependence, and their fast electron entry kinetics by stopped-flow measurements. increasing the ionic strength, the maximum of the bell-shaped dependence of the steady-state rate observed for ...	1998	9492306
identification of the contiguous paracoccus denitrificans ccmf and ccmh genes: disruption of ccmf, encoding a putative transporter, results in formation of an unstable apocytochrome c and deficiency in siderophore production.	apocytochrome c550 was detected in the periplasm of a new mutant of paracoccus denitrificans, hn48, that is pleiotropically lacking c-type cytochromes, produces reduced levels of siderophores and carries a tn5 insertion in the ccmf gene for which sequence data, along with that for the contiguous ccmh, are reported. a counterpart to the ccmf gene was found in an archaebacterium but could not be located in the yeast genome, whereas mitochondrial haem lyases in the latter were not present in an arc ...	1998	9493384
refined crystal structure of methylamine dehydrogenase from paracoccus denitrificans at 1.75 a resolution.	the three-dimensional structure of the quinoprotein methylamine dehydrogenase from paracoccus denitrificans has been refined at 1.75 a resolution utilizing the dna-based protein sequence. the final model incorporates 8034 atoms per molecule, including 552 molecules of solvent, and gives an r-factor of 0.163. the molecule is an h2l2 hetero-tetramer containing a non-crystallographic 2-fold axis of symmetry. the 373-residue h subunit is folded into seven repeats of a four-stranded antiparallel beta ...	1998	9514722
physiology and genetics of sulfur-oxidizing bacteria.	reduced inorganic sulfur compounds are oxidized by members of the domains archaea and bacteria. these compounds are used as electron donors for anaerobic phototrophic and aerobic chemotrophic growth, and are mostly oxidized to sulfate. different enzymes mediate the conversion of various reduced sulfur compounds. their physiological function in sulfur oxidation is considered (i) mostly from the biochemical characterization of the enzymatic reaction, (ii) rarely from the regulation of their format ...	1998	9328649
carboxin resistance in paracoccus denitrificans conferred by a mutation in the membrane-anchor domain of succinate:quinone reductase.	succinate:quinone reductase is a membrane-bound enzyme of the citric acid cycle and the respiratory chain. carboxin is a potent inhibitor of the enzyme of certain organisms. the bacterium paracoccus denitrificans was found to be sensitive to carboxin in vivo, and mutants that grow in the presence of 3'-methyl carboxin were isolated. membranes of the mutants showed resistant succinate:quinone reductase activity. the mutation conferring carboxin resistance was identified in four mutants. they cont ...	1998	9639600
role of copper during carbon monoxide binding to terminal oxidases.	under fully reduced conditions, reassociation kinetics of co were studied in several terminal oxidases containing copper in their binuclear center. the purified paracoccus denitrificans ba3-type quinol oxidase was found to recombine with co monophasically (tau 25-30 ms) like oxidases of the bo type from escherichia coli, the caa3 type from bacillus halodurans ftu, and the bo type from methylobacillus flagellatum kt. oxidase of the aa3 type from bovine heart recombined with co monophasically at a ...	1998	9650593
cytochrome c oxidase: one enzyme, two mechanisms?		1998	9660711
crystal structures of paracoccus denitrificans aromatic amino acid aminotransferase: a substrate recognition site constructed by rearrangement of hydrogen bond network.	aminotransferase reversibly catalyzes the transamination reaction by a ping-pong bi-bi mechanism with pyridoxal 5'-phosphate (plp) as a cofactor. various kinds of aminotransferases developing into catalysts for particular substrates have been reported. among the aminotransferases, aromatic amino acid aminotransferase (ec 2.6.1. 57) catalyzes the transamination reaction with both acidic substrates and aromatic substrates. to elucidate the multiple substrate recognition mechanism, we determined th ...	1998	9665848
a novel, non-statistical method for predicting breaks in transmembrane helices.	we have developed a novel, non-statistical procedure for predicting possible breaks in transmembrane helices based on energy calculations. the procedure consists of stepwise elongation of the 'core' helical fragment determined by consensus results of several available prediction procedures. at each step, we calculate the conformational energies corresponding to the regular 'frozen' helical conformer of the 'core' fragment elongated by two flanking residues, e(alpha), as well as those to several ...	1998	9680189
occurrence, overexpression and partial purification of the protein (majastridin) corresponding to the urf6 gene of the rhodobacter blasticus atp operon.	antibodies were produced against two antigenic peptides of a protein, which was named majastridin, corresponding to the urf6 gene of the rhodobacter blasticus atp operon [tybulewicz, v. l. j., falk, g. & walker, j. e. (1984) j. mol. biol. 179, 185-214]. a protein band of the expected size is labelled by immunoblotting in western blots containing the cytosolic fractions from rb. blasticus and paracoccus denitrificans but not from escherichia coli or rhodospirillum rubrum. although the protein is ...	1998	9692905
mutational analysis of residues forming hydrogen bonds in the rieske [2fe-2s] cluster of the cytochrome bc1 complex in paracoccus denitrificans.	two mutations (s157a and y159f) in the rieske iron-sulfur subunit of the ubihydroquinone-cytochrome c oxidoreductase from paracoccus denitrificans have been characterized with respect to the protein and [2fe-2s] cluster stability, the enzyme activity and the redox potential of the [2fe-2s] cluster. in the structure of the water-soluble fragment of the rieske iron-sulfur protein of the bovine heart mitochondrial bc1 complex, both residues (s163 and y165 in the bovine sequence) form the following ...	1998	9692907
31p-nmr spectroscopy of human and paracoccus denitrificans electron transfer flavoproteins, and 13c- and 15n-nmr spectroscopy of human electron transfer flavoprotein in the oxidised and reduced states.	human and paracoccus denitrificans wild-type electron transfer flavoproteins have been investigated by 31p-nmr in the oxidised and reduced states. the 31p chemical shifts of the diphosphate moiety of the protein-bound fad were similar in the proteins and were independent of the redox state. the chemical shifts were remarkably similar to those of ferredoxin-nadp+ reductase and, to a lesser degree, with those of nadph-cytochrome p-450 reductase. the wild-type human electron transfer apoprotein was ...	1998	9692910
the primary structure of soluble cytochrome c-551 from the phototrophic green sulfur bacterium chlorobium limicola, strain tassajara, reveals a novel c-type cytochrome.	chlorobium limicola, strain tassajara, cytochrome c-551 is a soluble dimeric protein containing identical subunits of about 30 kda. the amino acid sequence was determined by a combination of automated edman degradation and mass analysis. there are 258 residues with a single heme binding site located at cysteine positions 172 and 175. in addition, there is a disulfide bridge between cys78 and cys109, and a free cysteine at position 219 which was found to occur as cysteic acid. the only homologue ...	1998	9692944
electron transfer from the aminosemiquinone reaction intermediate of methylamine dehydrogenase to amicyanin.	the tryptophan tryptophylquinone (ttq) cofactor of methylamine dehydrogenase (madh) is covalently modified by substrate-derived nitrogen during its two-electron reduction by methylamine to form an aminoquinol (n-quinol). an n-semiquinone, which retains the substrate-derived n, is the intermediate during the two sequential one-electron oxidations of n-quinol madh by its physiologic electron acceptor, amicyanin. electron transfer (et) from n-quinol madh to amicyanin is gated by the deprotonation o ...	1998	9692997
comparison of energization of complex i in membrane particles from paracoccus denitrificans and bovine heart mitochondria.	the results of preliminary studies of the effects of energization on the catalytic and epr properties of complex i in tightly coupled membrane vesicles of paracoccus denitrificans (spp) are presented. they are compared to those observed in submitochondrial particles from bovine heart (smp). all signs of energization of complex i detected by epr in smp (uncoupler-sensitive splitting of the gz lines of the clusters 2 and a broadening of their gxy lines, a fast-relaxing, piericidin-sensitive ubiqui ...	1998	9693721
structure-function studies of iron-sulfur clusters and semiquinones in the nadh-q oxidoreductase segment of the respiratory chain.	our recent experimental data on iron-sulfur clusters and semiquinones in the complex i segment of the respiratory chain is presented, focusing on the paracoccus (p.) denitrificans and bovine heart studies. the iron-sulfur cluster n2 has attracted the attention of investigators in the research field of complex i, since the mid-point redox potential of this cluster is the highest among all clusters in complex i, and is ph dependent (60 mv/ph). it is known that this cluster is located either in the ...	1998	9693742
soxd: an essential mediator of induction of anterior neural tissues in xenopus embryos.	vertebrate neurogenesis is initiated by the organizer factors that inhibit antineuralizing activities of bone morphogenetic proteins (bmps) in the ectoderm. here, we report a candidate mediator of neuralization, soxd. expression of soxd starts at late blastula stages widely in the prospective ectoderm and becomes restricted to the dorsal ectoderm by mid-gastrula stages. soxd expression is enhanced by the neural inducer chordin and is suppressed by bmp4 and its downstream genes. microinjection of ...	1998	9697853
analysis of the pathogenic human mitochondrial mutation nd1/3460, and mutations of strictly conserved residues in its vicinity, using the bacterium paracoccus denitrificans.	the human mitochondrial nd1/3460 mutation changes ala52 to thr in the nd1 subunit of complex i, and causes leber's hereditary optic neuropathy (lhon) [huoponen et al. (1991) am. j. hum. genet. 48, 1147]. we have used a bacterial counterpart of complex i, ndh-1 from paracoccus denitrificans, for studying the effect of mutations in the nd1 subunit on the enzymatic activity. the lhon mutation as well as several other mutations in strictly conserved amino acids in its vicinity were introduced into t ...	1998	9718301
tryptophan-136 in subunit ii of cytochrome bo3 from escherichia coli may participate in the binding of ubiquinol.	in the cytochrome c oxidases, the role of subunit ii is to provide the electron entry site into the enzyme. this subunit contains both the binding site for the substrate, cytochrome c, and the cua redox center, which is initially reduced by cytochrome c. cytochrome bo3 and other quinol oxidases that are members of the heme-copper oxidase superfamily have a homologous subunit ii, but the cua site is absent, as is the docking site for cytochrome c. speculation that subunit ii in the quinol oxidase ...	1998	9718303
expression of the escherichia coli cyo operon in paracoccus denitrificans results in a fully active quinol oxidase of unexpected heme composition.	the cyo operon coding for the membrane-bound bo3-type quinol oxidase of escherichia coli has been expressed in a paracoccus denitrificans strain deleted in its endogenous ba3 quinol oxidase. using the p. denitrificans qox promoter, the his tagged protein complex is synthesized to a level comparable to that in e. coli and the enzyme purified in a single step on a metal-chelating column. whereas the activity of the isolated complex matches that of the oxidase purified directly from e. coli, the he ...	1998	9720906
identification of bacterial isolates from biofilters as paracoccus alkenifer sp. nov. and paracoccus solventivorans with emended description of paracoccus solventivorans.	two groups of strains isolated from biofilters for the treatment of waste gases were assigned to the genus paracoccus by phylogenetic and chemotaxonomic methods. all type strains of the genus paracoccus were compared with these groups using 16s rdna sequence analysis, fatty acid patterns and physiological reaction profiles. for both groups, the nearest related reference species was paracoccus solventivorans based on 16s rdna sequence similarity. however, whereas one group of isolates was identif ...	1998	9731294
paracoccus marcusii sp. nov., an orange gram-negative coccus.	phenotypic, chemotaxonomic and 16s rdna sequence analysis of an orange gram-negative coccus that appeared as a contaminant on a nutrient agar plate delineated a new species of the genus paracoccus. phenotypic features of the strain that differ from all or most of the previously described paracoccus species include its bright orange colour, caused by the synthesis of large amounts of carotenoids (mainly astaxanthin), and its inability to use nitrate as an electron acceptor in respiration. the nam ...	1998	9731296
intrinsic uncoupling of cytochrome c oxidase may cause the maternally inherited mitochondrial diseases melas and lhon.	mutations in the human mtdna gene encoding subunit iii of cytochrome c oxidase (co) have been reported to cause melas and lhon. poracoccus denitrificans cells expressing substitutions homologous to these melas- and lhon-causing mutations had lower growth yield than wild type cells and lower efficiency of proton pumping by co (e.g. lower h+/e ratio and lower deltapsi), but had similar co activity. these results indicate that both substitutions (f263l > a212t) cause intrinsic uncoupling, which may ...	1998	9738940
electron entry in a cua mutant of cytochrome c oxidase from paracoccus denitrificans. conclusive evidence on the initial electron entry metal center.	a cytochrome c oxidase subunit ii c216s mutant from paracoccus denitrificans in which the cua site was changed by site-directed mutagenesis to a mononuclear copper site [zickermann, v., wittershagen, a., kolbesen, b.o. and ludwig, b. biochemistry 36 (1997) 3232-3236] was investigated by stopped-flow spectroscopy. contrary to the behavior of the wild type enzyme, in this mutant cytochrome a cannot be reduced by excess cytochrome c in the millisecond time scale in which cytochrome c oxidation is o ...	1998	9742947
crystallographic and spectroscopic studies of native, aminoquinol, and monovalent cation-bound forms of methylamine dehydrogenase from methylobacterium extorquens am1.	various monovalent cations influence the enzymatic activity and the spectroscopic properties of methylamine dehydrogenase (madh). here, we report the structure determination of this tryptophan tryptophylquinone-containing enzyme from methylobacterium extorquens am1 by high resolution x-ray crystallography (1.75 a). this first madh crystal structure at low ionic strength is compared with the high resolution structure of the related madh from paracoccus denitrificans recently reported. we also des ...	1998	9748238
the active site of the bacterial nitric oxide reductase is a dinuclear iron center.	a novel, improved method for purification of nitric oxide reductase (nor) from membranes of paracoccus denitrificans has been developed. the purified enzyme is a cytochrome bc complex which, according to protein chemical and hydrodynamic data, contains two subunits in a 1:1 stoichiometry. the purified norbc complex binds 0.87 g of dodecyl maltoside/g of protein and forms a dimer in solution. similarly, it is dimeric in two-dimensional crystals. images of these crystals have been processed at 8 a ...	1998	9748316
paracoccus denitrificans cytochrome c oxidase: a kinetic study on the two- and four-subunit complexes.	cytochrome c oxidase from paracoccus denitrificans has been purified in two different forms differing in polypeptide composition. an enzyme containing polypeptides i-iv is obtained when the purification procedure is performed in beta-d-dodecylmaltoside. if, however, triton x-100 is used to purify the enzyme under otherwise identical conditions, an enzyme is obtained containing only subunits i-ii. the two enzymes are undistinguishable by optical spectroscopy but show significant differences in th ...	1998	9757081
development of pcr primer systems for amplification of nitrite reductase genes (nirk and nirs) to detect denitrifying bacteria in environmental samples.	a system was developed for the detection of denitrifying bacteria by the amplification of specific nitrite reductase gene fragments with pcr. primer sequences were found for the amplification of fragments from both nitrite reductase genes (nirk and nirs) after comparative sequence analysis. whenever amplification was tried with these primers, the known nir type of denitrifying laboratory cultures could be confirmed. likewise, the method allowed a determination of the nir type of five laboratory ...	1998	9758798
conformational changes occurring upon reduction and no binding in nitrite reductase from pseudomonas aeruginosa.	nitrite reductase (nir) from pseudomonas aeruginosa (ec 1.9.3.2) (nir-pa) is a soluble enzyme catalyzing the reduction of nitrite (no2-) to nitric oxide (no). the enzyme is a 120 kda homodimer, in which each monomer carries one c and one d1 heme. the oxidized and reduced forms of nir from paracoccus denitrificans gb17 (previously called thiosphaera pantotropha) (nir-pd) have been described [fülop, v., et al. (1995) cell 81, 369-377; williams, p. a., et al. (1997) nature 389, 406-412], and we rec ...	1998	9760233
the diversity of redox proteins involved in bacterial heterotrophic nitrification and aerobic denitrification.		1998	9765887
heterotrophic nitrification in paracoccus denitrificans.		1998	9765927
the periplasmic nitrate reductase of escherichia coli--a comparison with the nap systems of other bacteria.		1998	9765936
chemical modification of histidine residues in human 'electron transferring flavoprotein' (etf).		1998	9765991
pressure and temperature dependence of enantioselective excited-state quenching of chiral tb(iii) and eu(iii) tris(pyridine-2,6-dicarboxylate) chelates by various c-type ferricytochromes.	for mitochondrial ferricytochrome c from horse, cow and tuna and for bacterial cytochrome c-550 from paracoccus versutus, the pressure and temperature dependence of their quenching of racemic tb(dpa)3(3-) and eu(dpa)3(3-) (dpa = pyridine-2,6-dicarboxylate) luminescence in aqueous solution is investigated. of these energy transfer reactions the activation volumes (delta v#) and energies (ea) are determined for the ranges p = 0-3 kbar and t = 15-40 degrees c. for the lambda enantiomers of tb(dpa)3 ...	1998	9783431
second-site reversion analysis is not a reliable method to determine distances in membrane proteins: an assessment using mutations in yeast cytochrome c oxidase subunits i and ii.	we have examined deficiency mutations and reversions in subunits i and ii of yeast cytochrome c oxidase in order to test the reliability of second-site reversion analysis in prediction of tertiary structure of a membrane protein complex. it appears that the method can not provide information on distance between residues, since reversions can be up to 30 a from the primary mutations. however, the reversions are not randomly located in the structure but reveal regions essential for assembly or fun ...	1998	9790835
roles of four iron centers in paracoccus halodenitrificans nitric oxide reductase.	reactions of paracoccus halodenitrificans nitric oxide reductase (nor) containing four iron centers, a low spin hemec, a low spin heme b, a high spin heme b and a non-heme iron, have been studied to show the roles of each iron center. soon after reacting the resting (oxidized) nor with l-ascorbate, the low spin heme c and low spin heme b were reduced to a considerable extent but the high spin heme b was still in the oxidized form and was reduced slowly. when co acted on the reduced nor, the high ...	1998	9790940
ft-ir analysis of membranes of rhodobacter sphaeroides 2.4.3 grown under microaerobic and denitrifying conditions.	fourier transform infrared spectroscopic analysis of co binding proteins in rhodobacter sphaeroides reveals the presence of a membrane-bound nitric oxide reductase (nor). nor has been clearly distinguished from the cytochrome oxidases by the temperature-dependence of relaxation following photodissociation of the co complex at cryogenic temperatures. the center frequency and band shape, 1970 cm-1 and 20-30 cm-1 width at half-peak height, are similar to those reported for resonance raman spectra o ...	1998	9838065
molecular genetics of the genus paracoccus: metabolically versatile bacteria with bioenergetic flexibility.	paracoccus denitrificans and its near relative paracoccus versutus (formerly known as thiobacilllus versutus) have been attracting increasing attention because the aerobic respiratory system of p. denitrificans has long been regarded as a model for that of the mitochondrion, with which there are many components (e.g., cytochrome aa3 oxidase) in common. members of the genus exhibit a great range of metabolic flexibility, particularly with respect to processes involving respiration. prominent exam ...	1998	9841665
molecular and functional analysis of ptav320, a repabc-type replicon of the paracoccus versutus composite plasmid ptav1.	the second replicator region of the native plasmid ptav1 of paracoccus versutus has been identified thus proving the composite nature of this replicon. the minimal replicon designated ptav320 (4.3 kb) was cloned and sequenced. ptav320 encodes three putative proteins--repa, repb and repc. this replicator region shows strong structural and functional similarity to repabc-type replicons found in several agrobacterium and rhizobium plasmids. the origin of replication appears to be localized within t ...	1998	9846751
characterization of cytochrome c-556 from the purple phototrophic bacterium rhodobacter capsulatus as a cytochrome-c peroxidase.	a cytochrome c-556 was purified from rhodobacter capsulatus and the complete amino acid sequence was determined. it contains 328 amino acid residues and two typical heme-binding sites at cysteine residues 54 and 57 and at residues 200 and 203. it is homologous to the family of bacterial cytochrome c peroxidases (bccp) with 69% identity to paracoccus denitrificans bccp and 60% identity to pseudomonas aeruginosa bccp for which there is a three-dimensional structure. there is lesser similarity to t ...	1998	9851688
resonance raman spectroscopic study of the caa3 oxidase from thermus thermophilus.	the terminal caa3 oxidase of thermus thermophilus has been studied by resonance raman spectroscopy. using different excitation wavelengths in the soret band region, it was possible to disentangle the resonance raman spectra of the fully oxidized and fully reduced state in terms of the component spectra of the individual hemes a, a3, and c. for the heme a and a3 groups, the spectra reveal only minor differences compared to those of beef heart cytochrome c oxidase attributable to subtle modificati ...	1998	9851718
molecular basis for interprotein complex-dependent effects on the redox properties of amicyanin.	the quinoprotein methylamine dehydrogenase (madh), type i copper protein amicyanin, and cytochrome c-551i form a complex within which interprotein electron transfer occurs. it was known that complex formation significantly lowered the oxidation-reduction midpoint potential (em) value of amicyanin, which facilitated an otherwise thermodynamically unfavorable electron transfer to cytochrome c-551i. structural, mutagenesis, and potentiometric studies have elucidated the basis for this complex-depen ...	1998	9860825
metal chelating properties of adenylate kinase from paracoccus denitrificans.	zinc, a common element of adenylate kinases from gram-positive bacteria, binds to a structural motif consisting of three or four cysteine residues, cys-x2-cys-x16-cys-x2-cys/asp. the enzyme from paracoccus denitrificans, a gram-negative bacterium, has structural features much similar to those of adenylate kinases from gram-positive organisms [spurgin, p., tomasselli, a.g., and schiltz, e. (1989) eur. j. biochem., 179, 621-628]. however, adenylate kinase isolated from this bacterium was not repor ...	1998	9862211
the surface-charge asymmetry and dimerisation of cytochrome c550 from paracoccus denitrificans--implications for the interaction with cytochrome c peroxidase.	the implications of the dimeric state of cytochrome c550 for its binding to paracoccus cytochrome c peroxidase and its delivery of the two electrons required to restore the active enzyme during catalysis have been investigated. the amino acid sequence of cytochrome c550 of paracoccus denitrificans strain lmd 52.44 was determined and showed 21 differences from that of strain lmd 22.21. based on the x-ray structure of the latter, a structure for the cytochrome c550 monomer from strain 52.44 is pro ...	1998	9874223
extended metal environments of cytochrome c oxidase structures.	the metals of the cytochrome c oxidase structures of the bovine heart mitochondrion (pdb code 1occ) and of the soil bacterium paracoccus denitrificans (1arl) include a dicopper center (cua), magnesium, two proximal hemes, a copper (cub) atom, and a calcium. the mitochondrial structure also possesses a bound distant zinc ion. the extended environments of the metal sites are analyzed emphasizing residues of the second shell in terms of polarity, hydrophobicity, secondary structure, solvent accessi ...	1998	9922138
rhizobium etli cychjkl gene locus involved in c-type cytochrome biogenesis: sequence analysis and characterization of two cych mutants.	the cychjkl gene locus was cloned from rhizobium etli by the rescue of a tn5mob insertion of a mutant (ifc01) which was affected in the production of c-type cytochromes. the cych, cycj, cyck and cycl genes are proposed to code for different subunits of a haem lyase complex involved in the attachment of haem to cytochrome c apoproteins. cych of 365 aa shared 27, 36, 47 and 63% identity with cych from paracoccus denitrificans, bradyrhizobium japonicum, r. meliloti, and r. leguminosarum, respective ...	1998	9524269
genes coding for respiratory complexes map on all three chromosomes of the paracoccus denitrificans genome.	the genome of paracoccus denitrificans (strain pd1222) consists of three distinct dna molecules when separated by standard pulsed-field gel electrophoresis with apparent molecular sizes of approximately 2, 1.1, and 0.64 mb. when the separated chromosomes are digested by restriction enzymes and sizes of resulting fragments are summed up, the three chromosomes are composed of 1.83, 1.16, and 0.67 mb. since their migration behavior relative to size standards is largely independent of electrophoresi ...	1998	9531627
the coupling of electron transfer and proton translocation: electrostatic calculations on paracoccus denitrificans cytochrome c oxidase.	we have calculated the electrostatic potential and interaction energies of ionizable groups and analyzed the response of the protein environment to redox changes in paracoccus denitrificans cytochrome c oxidase by using a continuum dielectric model and finite difference technique. subsequent monte carlo sampling of protonation states enabled us to calculate the titration curves of all protonatable groups in the enzyme complex. inclusion of a model membrane allowed us to restrict the calculations ...	1998	9533684
structure and function of bacterial cytochrome c oxidase.	the crystal structure of cytochrome c oxidase from the soil bacterium paracoccus denitrificans has been reported. this structure has provided a basis for understanding the mechanism of the redox-coupled transmembrane proton pump which is the key component of the respiratory chain in most aerobic organism. over the past ten years, there have been many site-directed mutagenesis studies performed on bacterial oxidases. structural features of paracoccus oxidase have been summarized in the light of t ...	1998	9538216
characterization of the ubiquinone reduction site of mitochondrial complex i using bulky synthetic ubiquinones.	a wide variety of alkyl derivatives of q2 (6-geranyl-2, 3-dimethoxy-5-methyl-1,4-benzoquinone) and db (6-n-decyl-2, 3-dimethoxy-5-methyl-1,4-benzoquinone), in which methoxy groups of the 2- and/or 3-positions of the quinone ring were replaced by other bulky alkoxy groups from ethoxy to butoxy, were prepared by novel synthetic procedures. electron-accepting activities of the bulky quinones were investigated with bovine heart mitochondrial complex i and its counterpart of paracoccus denitrificans( ...	1998	9572861
site-directed mutagenesis of phe 97 to glu in amicyanin alters the electronic coupling for interprotein electron transfer from quinol methylamine dehydrogenase.	conversion by site-directed mutagenesis of phe 97 of amicyanin to glu significantly decreases the rate constant for the electron-transfer reaction from the quinol form of methylamine dehydrogenase to amicyanin. it is shown that the deltag degrees and reorganizational energy (lambda) associated with the electron-transfer reaction are unaffected by the mutation and that the decrease in the electron-transfer rate is attributable completely to a decrease in the electronic coupling matrix element (ha ...	1998	9585551
understanding the electronic properties of the cua site from the soluble domain of cytochrome c oxidase through paramagnetic 1h nmr.	the soluble domain of the subunit ii of cytochrome c oxidase from paracoccus versutus was cloned, expressed, and studied by 1h nmr at 600 mhz. the properties of the redox-active dinuclear cua site in the paramagnetic mixed-valence cu(i)-cu(ii) state were investigated in detail. a group of relatively sharp signals found between 30 and 15 ppm in the 1h nmr spectrum correspond to the imidazole protons of the coordinated histidines (h181 and h224). a second group of broader and farther shifted signa ...	1998	9585552
involvement of glutamic acid 278 in the redox reaction of the cytochrome c oxidase from paracoccus denitrificans investigated by ftir spectroscopy.	the molecular processes concomitant with the redox reactions of wild-type and mutant cytochrome c oxidase from paracoccus denitrificans were analyzed by a combination of protein electrochemistry and fourier transform infrared (ftir) difference spectroscopy. oxidized-minus-reduced ftir difference spectra in the mid-infrared (4000-1000 cm-1) reflecting full or stepwise oxidation and reduction of the respective cofactor(s) were obtained. in the 1800-1000 cm-1 range, these ftir difference spectra re ...	1998	9585553
redox dependent changes at the heme propionates in cytochrome c oxidase from paracoccus denitrificans: direct evidence from ftir difference spectroscopy in combination with heme propionate 13c labeling.	specific isotope labeling at the carboxyl groups of the four heme propionates of cytochrome c oxidase from paracoccus denitrificans was used in order to assign signals observed in electrochemically induced redox fourier transform infrared (ftir) difference spectra of this enzyme. for this purpose, the hema gene of the p. denitrificans strain pd1222, coding for 5-aminolevulinate synthase, was deleted by partial replacement with a kanamycin resistance cartridge, resulting in a stable 5-aminolevuli ...	1998	9585554
iron-sulfur clusters/semiquinones in complex i.	nadh-quinone 1 oxidoreductase (complex i) isolated from bovine heart mitochondria was, until recently, the major source for the study of this most complicated energy transducing device in the mitochondrial respiratory chain. complex i has been shown to contain 43 subunits and possesses a molecular mass of about 1 million. recently, complex i genes have been cloned and sequenced from several bacterial sources including escherichia coli, paracoccus denitrificans, rhodobacter capsulatus and thermus ...	1998	9593887
nitrous oxide reductase (nosz) gene-specific pcr primers for detection of denitrifiers and three nosz genes from marine sediments.	two pcr primer sets for the nitrous oxide reductase gene (nosz) were developed. the initial primers were based on three sequences in genbank and used to amplify nosz from continental shelf sediments and from two denitrifiers in culture, thiosphaera pantotropha and pseudomonas denitrificans. three unique marine sediment nosz genes were identified and sequenced. the marine nosz genes were most closely related to the nosz genes of paracoccus denitrificans or to rhizobium meliloti. alignment of all ...	1998	9595664
redox properties of tryptophan tryptophylquinone enzymes. correlation with structure and reactivity.	the ph dependence of the redox potentials for the oxidized/reduced couples of methylamine dehydrogenase (madh) and aromatic amine dehydrogenase (aadh) were determined. for each enzyme, a change of -30 mv/ph unit was observed, indicating that the two-electron transfer is linked to the transfer of a single proton. this result differs from what was obtained from redox studies of a tryptophan tryptophylquinone (ttq) model compound for which the two-electron couple is linked to the transfer of two pr ...	1998	9603931
molecular characterisation of the 76 kda iron-sulphur protein subunit of potato mitochondrial complex i.	genes encoding subunits of complex i (ec 1.6.5.3) of the mitochondrial respiratory chain vary in their locations between the mitochondrial and nuclear genomes in different organisms, whereas genes for a homologous multisubunit complex in chloroplasts have to date only been found on the plastid genome. in potato (solanum tuberosum l.), the gene coding for the mitochondrial 76 kda iron-sulphur protein is identified in the nuclear genome. the gene is transcribed into polyadenylated mrna which is mo ...	1998	9615461
the role of electrostatic interactions for cytochrome c oxidase function.	in recent years, the enormous increase in high-resolution three-dimensional structures of proteins together with the development of powerful theoretical techniques have provided the basis for a more detailed examination of the role of electrostatics in determining the midpoint potentials of redox-active metal centers and in influencing the protonation behavior of titratable groups in proteins. based on the coordinates of the paracoccus denitrificans cytochrome c oxidase, we have determined the e ...	1998	9623809
cytochrome c oxidase (heme aa3) from paracoccus denitrificans: analysis of mutations in putative proton channels of subunit i.	one of the challenging features of energy-transducing terminal oxidases, like the aa3 cytochrome c oxidase of paracoccus denitrificans, is the translocation of protons across the cytoplasmic membrane, which is coupled to the transfer of electrons to oxygen. as a prerequisite for a more advanced examination of the enzymatic properties, several amino acid residues, selected on the basis of recent three-dimensional structure determinations, were exchanged in subunit i of the paracoccus enzyme by si ...	1998	9623810
gene dosage effects on polyhydroxyalkanoates synthesis from n-alcohols in paracoccus denitrificans.	putative promoters of polyhydroxyalkanoate (pha)-synthetic genes of paracoccus denitrificans were identified. gene dosage effects for pha synthesis were investigated in recombinants of p. denitrificans with increased expression levels of each pha synthetic enzyme. in the cultivation of shake flasks using ethanol or n-pentanol as carbon source, a self-cloning recombinant of the phac-encoding pha synthase showed the highest contents [(g pha). (g total biomass)-1] and the highest rates of pha accum ...	1998	10099406
production of ubiquinone-10 using bacteria.	among the bacterial strains known to contain ubiquinone-10, three strains, agrobacterium tumefaciens ky-3085 (atcc4452), paracoccus denitrificans ky-3940 (atcc19367) and rhodobacter sphaeroides ky-4113 (ferm-p4675), were selected as excellent producers of this ubiquinone. the ubiquinone-10 production by the agrobacterium and rhodobacter strains was affected by aeration. an ethionine-resistant mutant (m-37) derived from a. tumefaciens ky-3085 promoted increased production of ubiquinone-10 (20% hi ...	1998	12501289
pcr detection of genes encoding nitrite reductase in denitrifying bacteria.	using consensus regions in gene sequences encoding the two forms of nitrite reductase (nir), a key enzyme in the denitrification pathway, we designed two sets of pcr primers to amplify cd1- and cu-nir. the primers were evaluated by screening defined denitrifying strains, denitrifying isolates from wastewater treatment plants, and extracts from activated sludge. sequence relationships of nir genes were also established. the cd1 primers were designed to amplify a 778 to 799-bp region of cd1-nir in ...	1999	10103263
the structure of an electron transfer complex containing a cytochrome c and a peroxidase.	efficient biological electron transfer may require a fluid association of redox partners. two noncrystallographic methods (a new molecular docking program and 1h nmr spectroscopy) have been used to study the electron transfer complex formed between the cytochrome c peroxidase (ccp) of paracoccus denitrificans and cytochromes c. for the natural redox partner, cytochrome c550, the results are consistent with a complex in which the heme of a single cytochrome lies above the exposed electron-transfe ...	1999	10196231
the reduction state of the q-pool regulates the electron flux through the branched respiratory network of paracoccus denitrificans.	in this work we demonstrate how the reduction state of the q-pool determines the distribution of electron flow over the two quinol-oxidising branches in paracoccus denitrificans: one to quinol oxidase, the other via the cytochrome bc1 complex to the cytochrome c oxidases. the dependence of the electron-flow rate to oxygen on the fraction of quinol in the q-pool was determined in membrane fractions and in intact cells of the wild-type strain, a bc1-negative mutant and a quinol oxidase-negative mu ...	1999	10215894
heterologous expression of soluble fragments of cytochrome c552 acting as electron donor to the paracoccus denitrificans cytochrome c oxidase.	a membrane-bound c-type cytochrome, c552, acts as the electron mediator between the cytochrome bc1 complex and cytochrome c oxidase in the branched respiratory chain of the bacterium paracoccus denitrificans. unlike in mitochondria where a soluble cytochrome c interacts with both complexes, the bacterial c552, the product of the cycm gene, shows a tripartite structure, with an n-terminal membrane anchor separated from a typical class i cytochrome domain by a highly charged region. two derivative ...	1999	10216157
pseudoazurin mediates periplasmic electron flow in a mutant strain of paracoccus denitrificans lacking cytochrome c550.	a periplasmic protein able to transfer electrons from cytoplasmic membrane to the periplasmic nitrite reductase (cytochrome cd1) has been purified from the anoxically grown cytochrome c550 mutant strain pd2121 and shown to be pseudoazurin by several independent criteria (molecular mass, copper content, visible spectrum, n-terminal amino acid sequence). under our assay conditions, the half-saturation of electron transport occurred at about 10 microm pseudoazurin; the reaction was retarded by incr ...	1999	10217431
determination of the paracoccus denitrificans sos box.	by gel retardation experiments with crude cell extracts of paracoccus denitrificans it was demonstrated that a protein specifically binds to the promoter of the p. denitrificans reca gene. pcr mutagenesis of the reca promoter showed that the gaacn7gaac motif is required for the formation of the dna-protein complex. this protein also binds to the gttcn7gttc motif, which is present in the promoter of the p. denitrificans uvra gene. mutational analysis of the promoter regions of both p. denitrifica ...	1999	10217491
analyses of a polyhydroxyalkanoic acid granule-associated 16-kilodalton protein and its putative regulator in the pha locus of paracoccus denitrificans.	the polyhydroxyalkanoic acid (pha) granule-associated 16-kda protein (ga16 protein) of paracoccus denitrificans was identified, and its corresponding gene was cloned and analyzed at the molecular level. the n-terminal amino acid sequence of ga16 protein revealed that its structural gene is located downstream from the pha synthase gene (phacpd) cloned recently (s. ueda, t. yabutani, a. maehara, and t. yamane, j. bacteriol. 178:774-779, 1996). gene walking around phacpd revealed two new open readi ...	1999	10217786
a re-evaluation of the taxonomy of paracoccus denitrificans and a proposal for the combination paracoccus pantotrophus comb. nov.	comparison of both 16s rrna coding sequences and dna-dna hybridization of ten strains of alpha-subclass of proteobacteria currently classified as strains of paracoccus denitrificans has shown that they fall into two groups which are distinct from each other at the species level. comparison with published data on the cytochrome c profiles and other 16s rrna coding sequences in the literature has confirmed these observations and enabled several other strains also to be assigned to these two groups ...	1999	10319488