Publications

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
crystallization and preliminary x-ray analysis of electron transfer flavoproteins from human and paracoccus denitrificans.	mammalian electron transfer flavoprotein (etf) is a soluble, heterodimeric flavoprotein responsible for the oxidation of at least nine primary matrix flavoprotein dehydrogenases. crystals have been obtained for the recombinant human electron transfer flavoprotein (etfhum) by the sitting-drop vapor diffusion technique using polyethylene glycol (peg) 1500 at ph 7.0 as the precipitating agent. etfhum crystallizes in the monoclinic space group p2(1), with unit cell parameters a = 47.46 angstrum, b = ...	1995	8520493
x-ray studies of quinoproteins.		1995	8524150
the number of nucleotide binding sites in cytochrome c oxidase.	the binding of 2'(3')-o-(2,4,6-trinitrophenyl)-adenosine-5'-triphosphate (tnp-atp), [35s]atp alpha s and 8-azido-[gamma-32p]atp to isolated cytochrome c oxidase of bovine heart and liver and to the two-subunit enzyme of paracoccus dentrificans was studied by measuring the fluorescence change or bound radioactivity, respectively. with tnp-atp three binding sites were determined at cytochrome c oxidase from bovine heart and liver, both with two dissociation constants kd of about 0.2 and 0.9 microm ...	1995	8526931
purification and two-dimensional crystallization of bacterial cytochrome oxidases.	a novel strategy which employes chromatography on an immobilized metal ion has been developed for the purification of bacterial cytochrome c and quinol oxidases. many bacterial oxidase complexes appear to have a natural affinity to bind to the chelated copper ion. a combination of three different chromatographic principles (anion exchange, metal-affinity and gel filtration) makes an effective tool chest for the preparation of homogeneous and protein-chemically pure bacterial oxidases. these prep ...	1995	8536687
perturbation of the cua site in cytochrome-c oxidase of paracoccus denitrificans by replacement of met227 with isoleucine.	subunit ii of cytochrome-c oxidase contains a redox centre, cua, with unusual spectroscopic properties; this site consists of two copper atoms and acts as the entry point for electrons from cytochrome c. we have constructed a site-directed mutant of cytochrome-c oxidase from paracoccus denitrificans in which the cua site has been disturbed by replacement of met227 with isoleucine. the purified, fully assembled enzyme complex has been investigated with various techniques including metal analysis, ...	1995	8536720
molecular analysis of the poly(3-hydroxyalkanoate) synthase gene from a methylotrophic bacterium, paracoccus denitrificans.	a 3.6-kb ecori-sali fragment of paracoccus denitrificans dna hybridized with a dna probe carrying the poly(3-hydroxyalkanoate) (pha) synthase gene (phac) of alcaligenes eutrophus. nucleotide sequence analysis of this region showed the presence of a 1,872-bp open reading frame (orf), which corresponded to a polypeptide with a molecular weight of 69,537. upstream of the orf, a promoter-like sequence was found. escherichia coli carrying the fusion gene between lacz and the orf accumulated a level o ...	1996	8550512
construction and characterization of an azurin analog for the purple copper site in cytochrome c oxidase.	a protein analog of a purple copper center has been constructed from a recombinant blue copper protein (pseudomonas aeruginosa azurin) by replacing the loop containing the three ligands to the blue copper center with the corresponding loop of the cua center in cytochrome c oxidase (cox) from paracoccus denitrificans. the electronic absorption in the uv and visible region (uv-vis) and electron paramagnetic resonance (epr) spectra of this analog are remarkably similar to those of the native cua ce ...	1996	8552661
analysis of beta-ketothiolase and acetoacetyl-coa reductase genes of a methylotrophic bacterium, paracoccus denitrificans, and their expression in escherichia coli.	the beta-ketothiolase gene (phaa) and acetoacetyl-coa reductase gene (phab) were isolated from paracoccus denitrificans. nucleotide sequence analysis showed that they encoded proteins of 391 amino acids with a molecular mass of 40,744 da and of 242 amino acids with a molecular mass of 25,614 da, respectively. the predicted gene products exhibited high amino acid identities with those from other bacteria: 64.4-74.0% for the phaa gene product and 47.6-80.6% for the phab gene product, respectively. ...	1995	8566717
identification of five rhodobacter capsulatus genes encoding the equivalent of nd subunits of the mitochondrial nadh-ubiquinone oxidoreductase.	we previously reported the sequencing of two genes (ndha and ndhi) encoding two of the subunits of the type-i nadh-ubiquinone oxidoreductase from rhodobacter capsulatus (rc). the present paper deals with the cloning and characterization of a chromosomal fragment clustering five new rc genes which encode subunits of this enzyme. this gene cluster is located immediately downstream from ndha and ndhi, and also contains two unidentified open reading frames (urf2, urf3). the five genes, nuoj, nuok, n ...	1995	8566820
the affinity and specificity of ca(2+)-binding sites of cytochrome-c peroxidase from paracoccus denitrificans.	the binding of ca2+ to the dihaem cytochrome-c peroxidase from paracoccus denitrificans was analysed by following perturbations in the visible and 1h-nmr spectra of both haem groups. the enzyme contains at least two types of ca(2+)-binding site. site i is occupied in the isolated enzyme, binds ca2+ with a redox-state-independent kd of 1.2 microm and accommodates neither mg2+ nor mn2+. site ii is unoccupied in dilute solutions of the isolated oxidised enzyme and binds ca2+ cooperatively with a kd ...	1995	8575448
purification, characterization, crystallization, and preliminary x-ray results from paracoccus denitrificans porin.	the porin from paracoccus denitrificans atcc 13543 was purified and crystallized. two crystal forms were obtained from porin solutions with beta-d-octylglucopyranoside as detergent. crystals of form i belong to the monoclinic spacegroup c2 with unit cell dimensions a = 112.2 a, b = 193.8 a, c = 100.5 a and beta = 129.2 degrees. there is 1 trimer per asymmetric unit. crystals of form ii are triclinic with a = 89.7 a, b = 98.8 a, c = 112.5 a, alpha = 112.5 degrees, beta = 101.8 degrees, gamma = 10 ...	1995	8592709
occurrence of polyhydroxyalkanoic acid granule-associated proteins related to the alcaligenes eutrophus h16 ga24 protein in other bacteria.	fifty different polyhydroxyalkanoic acid (pha)-accumulating bacterial strains were investigated for the occurrence of phasin proteins bound to pha granules and related to the ga24 protein of alcaligenes eutrophus h16, by isolating pha granules and western blot analysis of granule-associated proteins employing antibodies raised against the ga24 protein. it could be demonstrated that th pha granules of many poly(3-hydroxybutyrate)-accumulating bacteria exhibited a similar protein pattern, and a pr ...	1996	8598273
bradyrhizobium japonicum possesses two discrete sets of electron transfer flavoprotein genes: fixa, fixb and etfs, etfl.	a group of four co-regulated genes (fixa, fixb, fixc, fixx) essential for symbiotic nitrogen fixation has been described in several rhizobial species, including bradyrhizobium japonicum. the complete nucleotide sequence of the b. japonicum fixa, fixb and fixc, genes is reported here. the derived amino acid sequences confirmed the previously noted sequence similarity between fixa and the beta-subunit and between fixb and the alpha-subunit of mammalian and paracoccus denitrificans electron transfe ...	1996	8599534
cytochrome cb-type nitric oxide reductase with cytochrome c oxidase activity from paracoccus denitrificans atcc 35512.	a highly active nitric oxide reductase was purified from paracoccus denitrificans atcc 35512, formerly named thiosphaera pantotropha, which was anaerobically cultivated in the presence of nitrate. the enzyme was composed of two subunits with molecular masses of 34 and 15 kda and contained two hemes b and one heme c per molecule. copper was not found in the enzyme. the spectral properties suggested that one of the two hemes b and heme c were in six-coordinated low-spin states and another heme b w ...	1996	8606159
the rhodobacter sphaeroides 2.4.1 rho gene: expression and genetic analysis of structure and function.	the gene which encodes transcription termination factor rho from rhodobacter sphaeroides 2.4.1, the gram-negative facultative photosynthetic bacterium, has been cloned and sequenced. the deduced protein shows a high level of sequence similarity to other bacterial rho factors, especially those from proteobacteria. however, several amino acid substitutions in the conserved atp-binding site have been identified. when expressed in escherichia coli, the r. sphaeroides rho gene relieves rho-dependent ...	1996	8606169
crystal structure of the membrane-exposed domain from a respiratory quinol oxidase complex with an engineered dinuclear copper center.	cytochrome oxidase is a membrane protein complex that catalyzes reduction of molecular oxygen to water and utilizes the free energy of this reaction to generate a transmembrane proton gradient during respiration. the electron entry site in subunit ii is a mixed-valence dinuclear copper center in enzymes that oxidize cytochrome c. this center has been lost during the evolution of the quinoloxidizing branch of cytochrome oxidases but can be restored by engineering. herein we describe the crystal s ...	1995	8618822
expression and characterization of the flavoprotein subcomplex composed of 50-kda (nqo1) and 25-kda (nqo2) subunits of the proton-translocating nadh-quinone oxidoreductase of paracoccus denitrificans.	this study reports the expression of the flavoprotein (fp) subcomplex of the proton-translocating nadh-quinone oxidoreductase (ndh-1) from paracoccus denitrificans, which is composed of the nqo1 (50 kda) and the nqo2 (25 kda) subunits. the two subunits are co-expressed in escherichia coli using a double expression plasmid system. the expressed subunits form a water-soluble heterodimer complex with 1:1 stoichiometry. the expressed complex contained one [2fe 2s] cluster but almost no fmn or [4fe 4 ...	1996	8621464
identification and analysis of the dissimilatory nitrous oxide reduction genes, nosrzdfy, of rhizobium meliloti.	the complete nos region essential for dissimilatory nitrous oxide reduction by the endosymbiotic diazotroph rhizobium meliloti was identified in a cosmid (pyc7) carrying a 10.1-kb ecori fragment of the nod megaplasmid. this gene region was localized by southern hybridization and tn5 mutagenesis to within 8 kb downstream from the fixghis cluster. nucleotide sequence determination of a 4.6-kb dna segment including the structural gene nosz and its flanking regions showed sequence homology and simil ...	1996	8626275
a single histidine is required for activity of cytochrome c peroxidase from paracoccus denitrificans.	the diheme cytochrome c peroxidase from paracoccus denitrificans was modified with the histidine-specific reagent diethyl pyrocarbonate. at low excess of reagent, 1 mol of histidine was modified in the oxidized enzyme, and modification was associated with loss of the ability to form the active state. with time, the modification reversed, and the ability to form the active state was recovered. the agreement between the spectrophotometric measurement of histidine modification and radioactive incor ...	1996	8626657
carboxyl group protonation upon reduction of the paracoccus denitrificans cytochrome c oxidase: direct evidence by ftir spectroscopy.	the redox reactions of the cytochrome c oxidase from paracoccus denitrificans were investigated in a thin-layer cell designed for the combination of electrochemistry under anaerobic conditions with uv/vis and ir spectroscopy. quantitative and reversible electrochemical reactions were obtained at a surface-modified electrode for all cofactors as indicated by the optical signals in the 400-700 nm range. fourier transform infrared (ftir) difference spectra of reduction and oxidation (reduced-minus- ...	1996	8641466
use of nanogold- and fluorescent-labeled antibody fv fragments in immunocytochemistry.	recombinant antibody fragments are emerging as a versatile tool in both basic research and medical therapy. we describe the procedures for direct labeling of engineered antibody fragments (fv) with fluorescein or nanogold and their use in fluorescence and immunoelectron microscopy, respectively. the fv fragments were produced in escherichia coli, purified by one-step strep tag affinity chromatography, chemically labeled with the marker, and employed in microscopy to localize epitopes on the memb ...	1996	8648079
the purification of ammonia monooxygenase from paracoccus denitrificans.	the heterotrophic nitrifier paracoccus denitrificans expresses a membrane-associated ammonia monooxygenase. the active enzyme has been solubilized in the detergent dodecyl-beta-d-maltoside and purified by standard chromatographic techniques. this is the first purification of an ammonia monooxygenase. the enzyme consists of two subunits with molecular masses of 38 and 46 kda. the purified enzyme is a quinol oxidase, is inhibited by light and a variety of chelating agents and is activated by cupri ...	1996	8654570
cysteine ligand swapping on a deletable loop of the [2fe-2s] ferredoxin from clostridium pasteurianum.	the [2fe-2s] ferredoxin from clostridium pasteurianum is unique among ferredoxins, both by its sequence and by the distribution of its cysteine residues (in positions 11, 14, 24, 56, and 60). in previous investigations, a combination of site-directed mutagenesis and of spectroscopic techniques showed that cysteines 11, 56, and 60 are ligands of the [2fe-2s] cluster in the wild type protein and that cysteine 14 is not, but the status of cysteine 24 remained unclear. new mutated forms of this ferr ...	1996	8688437
primary structure of a ferredoxin-like iron-sulfur subunit of complex i from neurospora crassa.	we have isolated cdna clones encoding an iron-sulfur polypeptide subunit of the mitochondrial complex i of neurospora crassa. the fungal cdna library was screened by hybridisation with an heterologous probe from paracoccus denitrificans. the dna sequence of relevant isolates was determined and revealed an open reading frame encoding a precursor protein of 219 amino acid residues. the gene product is a ferredoxin-like protein that contains two cysteine-rich motives that may each bind a tetranucle ...	1996	8695631
structural studies of the proton-translocating nadh-quinone oxidoreductase (ndh-1) of paracoccus denitrificans: identity, property, and stoichiometry of the peripheral subunits.	the proton-translocating nadh-quinone oxidoreductase (ndh-1) of paracoccus denitrificans is composed of at least 14 unlike subunits and contains one fmn and at least five epr-detectable iron-sulfur clusters. the 14 subunits are designated nqo1 through nqo14. the expression and partial characterization of the nqo4, -5, and -6 subunits have been performed. the nqo4, -5, and -6 subunits were individually expressed in escherichia coli. the nqo4 subunit was expressed in both the cytoplasmic phase and ...	1996	8703916
regulation of oxidative phosphorylation: the flexible respiratory network of paracoccus denitrificans.	paracoccus denitrificans is a facultative anaerobic bacterium that has the capacity to adjust its metabolic infrastructure, quantitatively and/or qualitatively, to the prevailing growth condition. in this bacterium the relative activity of distinct catabolic pathways is subject to a hierarchical control. in the presence of oxygen the aerobic respiration, the most efficient way of electron transfer-linked phosphorylation, has priority. at high oxygen tensions p. denitrificans synthesizes an oxida ...	1995	8718455
alteration of haem-attachment and signal-cleavage sites for paracoccus denitrificans cytochrome c550 probes pathway of c-type cytochrome biogenesis in escherichia coli.	paracoccus denitrificans cytochrome c550 is expressed as a periplasmic holo-protein in escherichia coli; amino acid substitutions of cysteine residues in the haem-binding motif (cys-x-x-cys-his), either together or singly, prevented covalent attachment of haem but not polypeptide translocation into the periplasm. when the three alanine residues at positions -3 to -1 in the native signal-cleavage site were deleted, or alanine at -1 was changed to glutamine, signal cleavage was at alternative site ...	1996	8730862
phd: predicting one-dimensional protein structure by profile-based neural networks.		1996	8743704
[structure of cytochrome c oxidase from paracoccus denitrificans at 2.8a resolution].		1996	8752885
dynamics of denitrification activity of paracoccus denitrificans in continuous culture during aerobic-anaerobic changes.	induction and repression of denitrification activity were studied in a continuous culture of paracoccus denitrificans during changes from aerobic to anaerobic growth conditions and vice versa. the denitrification activity of the cells was monitored by measuring the formation of denitrification products (nitrite, nitric oxide, nitrous oxide, and dinitrogen), individual mrna levels for the nitrate, nitrite, and nitrous oxide reductases, and the concentration of the nitrite reductase enzyme with po ...	1996	8755862
cytochrome c oxidase.	within the past year, the structures of the cytochrome c oxidase from the soil bacterium paracoccus denitrificans and of the metal centers of the cytochrome c oxidase from bovine heart mitochondria, both determined at 2.8 a resolution by x-ray crystallography, have been reported. the structures form a basis for understanding the mechanism of this redox-coupled transmembrane proton pump, which is the key component of the respiratory chain of most aerobic organisms.	1996	8794157
genetic inactivation of the h(+)-translocating nadh:ubiquinone oxidoreductase of paracoccus denitrificans is facilitated by insertion of the ndh gene from escherichia coli.	the h(+)-translocating nadh:ubiquinone oxidoreductase (ndh1) is probably an obligatory enzyme in paracoccus denitrificans and disruption of its genes may be lethal to this organism. in order to overcome this problem and delete the nqo8 and nqo9 genes of ndh1, it was necessary to render the enzyme non-essential. this was achieved by constructing a deletion plasmid in which most of the coding regions of nqo8 and nqo9 were replaced by the ndh gene of escherichia coli that encodes an alternative nad ...	1996	8804429
structural and functional analysis of aa3-type and cbb3-type cytochrome c oxidases of paracoccus denitrificans reveals significant differences in proton-pump design.	in paracoccus denitrificans the aa3-type cytochrome c oxidase and the bb3-type quinol oxidase have previously been characterized in detail, both biochemically and genetically. here we report on the isolation of a genomic locus that harbours the gene cluster cconoop, and demonstrate that it encodes an alternative cbb3-type cytochrome c oxidase. this oxidase has previously been shown to be specifically induced at low oxygen tensions, suggesting that its expression is controlled by an oxygen-sensin ...	1996	8809776
protein structure: proton-pumping oxidases.	the crystal structures of two cytochrome c oxidases, one bacterial and one mammalian, offer insights into their roles in oxygen chemistry and as proton pumps.	1996	8825522
cytochrome c550 expression in paracoccus denitrificans strongly depends on growth condition: identification of promoter region for cyca by transcription start analysis.	the periplasmic cytochrome c550 content of paracoccus denitrificans has been shown by immunological detection to be strongly dependent on the mode of growth. cells grown under anaerobic, denitrifying conditions or methylotrophically in the presence of oxygen contained substantially more cytochrome c550 than cells grown aerobically on multicarbon substrates. a similar pattern was observed when expression of the cyca gene (encoding cytochrome c550), was monitored using an escherichia coli alkaline ...	1996	8828226
the isolation and some properties of the membrane-bound lactate dehydrogenase of paracoccus denitrificans.	membrane-bound lactate dehydrogenase was isolated from the cells of paracoccus denitrificans by a combination of phase separation and chromatographic methods. it was nad(+)-independent; phenazine methosulphate and 2,6-dichlorophenolindophenol could act as electron acceptors. it preferred d-lactate over the l-form (k(m) = 0.81 and 4.40 mm, respectively). relative molecular weight estimations were 54000 +/- 3000 (electrophoresis) and 50000 +/- 5000 (gel chromatography) it was inhibited by thenoylt ...	1996	8828812
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
site-directed mutagenesis of residues lining a putative proton transfer pathway in cytochrome c oxidase from rhodobacter sphaeroides.	several putative proton transfer pathways have been identified in the recent crystal structures of the cytochrome oxidases from paracoccus denitrificans [iwata et al. (1995) nature 376, 660-669] and bovine [tsukihara (1996) science 272, 1138-1144]. a series of residues along one face of the amphiphilic transmembrane helix iv lie in one of these proton transfer pathways. the possible role of these residues in proton transfer was examined by site-directed mutagenesis. the three conserved residues ...	1996	8855945
isolation and characterization of a new gram-negative, acetone-degrading, nitrate-reducing bacterium from soil, paracoccus solventivorans sp. nov.	an acetone-degrading, nitrate-reducing, coccoid to rod-shaped bacterium, strain l1, was isolated from soil on the site of a natural gas company. cells of the logarithmic growth phase reacted gram positive, while those of the stationary growth phase were gram negative. single organisms were 0.4 to 0.5 by 0.9 to 1.5 microns in size, nonmotile, and non-spore forming and had poly-beta-hydroxybutyrate inclusions. the doubling time of strain l1 on acetone-co2-nitrate at the optimal ph of 7 to 8 and th ...	1996	8863446
s-formylglutathione hydrolase of paracoccus denitrificans is homologous to human esterase d: a universal pathway for formaldehyde detoxification?	downstream of flha, the paracoccus denitrificans gene encoding glutathione-dependent formaldehyde dehydrogenase, an open reading frame was identified and called fgha. the gene product of fgha showed appreciable similarity with human esterase d and with the deduced amino acid sequences of open reading frames found in escherichia coli, haemophilus influenzae, and saccharomyces cerevisiae. mutating fgha strongly reduced s-formylglutathione hydrolase activity. the mutant was unable to grow on methan ...	1996	8892832
nitrogen removal by tubular gel containing nitrosomonas europaea and paracoccus denitrificans.	a new bioreactor for the removal of nitrogen from wastewater is described which consists of a tubular polymeric gel containing nitrosomonas europaea and paracoccus denitrificans. the outer surface of the tube is in aerobic contact with wastewater containing ammonia, while the inside of the tube is in anaerobic contact with ethanol flowing through the tube. n. europaea oxidizes ammonia to nitrite in the gel, and then p. denitrificans reduces the nitrite to nitrogen gas in the same gel. this conce ...	1996	8900015
cytochrome bo from escherichia coli: binding of azide to cub.	azide binds to fast cytochrome bo with a stoichiometry of 1:1, the dissociation constant for this reaction being approximately 2 x 10(-5) m. the changes induced in the electronic absorption are very slight and are consistent with heme o remaining hexacoordinate high-spin, an observation confirmed by room temperature mcd spectroscopy in the region 350-2000 nm. x-band epr spectroscopy of the azide-bound form shows heme o remains coupled to cub, but that the integer spin signal (g = 3.7) that we ha ...	1996	8901520
sequencing of a 17.6 kb segment on the right arm of yeast chromosome vii reveals 12 orfs, including cct, ade3 and tr-i genes, homologues of the yeast pmt and ef1g genes, of the human and bacterial electron-transferring flavoproteins (beta-chain) and of the escherichia coli phosphoserine phosphohydrolase, and five new orfs.	a 17.6 kb dna fragment from the right arm of chromosome vii of saccharomyces cerevisiae has been sequenced and analysed. the sequence contains twelve open reading frames (orfs) longer than 100 amino acids. three genes had already been cloned and sequenced: cct, ade3 and tr-i. two orfs are similar to other yeast genes: g7722 with the yal023 (pmt2) and pmt1 genes, encoding two integral membrane proteins, and g7727 with the first half of the genes encoding elongation factors 1gamma, tef3 and tef4. ...	1996	8904340
tryptophan-derived cofactors functioning in oxidoreductases.		1996	8906320
electron paramagnetic resonance studies of the soluble cua protein from the cytochrome ba3 of thermus thermophilus.	the electron paramagnetic resonance (epr) spectrum of the binuclear cua center in the water-soluble subunit ii fragment from cytochrome ba3 of thermus thermophilus was recorded at 3.93, 9.45, and 34.03 ghz, and the epr parameters were determined by computer simulations. the frequency and m1 dependence of the linewidth was discussed in terms of g strain superimposed on a correlation between the a and g values. the g values were found to be gx = 1.996, gy = 2.011, gz = 2.187, and the two cu ions c ...	1996	8913619
the biochemical characterization of a novel non-haem-iron hydroxylamine oxidase from paracoccus denitrificans gb17.	the characterization of the hydroxylamine oxidase from the heterotrophic nitrifier paracoccus denitrificans gb17 indicates the enzyme to be entirely distinct from the hydroxylamine oxidase from the autotrophic nitrifier nitrosomonas europaea. hydroxylamine oxidase from p. denitrificans contains three to five non-haem, non-iron-sulphur iron atoms as prosthetic groups, predominantly co-ordinated by carboxylate ligands. the interaction of the enzyme with the electron-accepting proteins cytochrome c ...	1996	8920986
biochemical and spectroscopic properties of the four-subunit quinol oxidase (cytochrome ba3) from paracoccus denitrificans.	the ba3 quinol oxidase from paracoccus denitrificans has been purified by a new protocol leading to significantly higher yields than previously reported (richter et al. (1994) j. biol. chem. 269, 23079-23086). in an sds pag an additional protein band compared with the previous preparation appears, which can be identified as the major form of subunit ii. all protein bands can be assigned to genes of the qox operon by n-terminal sequencing, indicating that the oxidase consists of four subunits. in ...	1996	8950374
population analysis in a denitrifying sand filter: conventional and in situ identification of paracoccus spp. in methanol-fed biofilms.	the microbial community of a denitrifying sand filter in a municipal wastewater treatment plant was examined by conventional and molecular techniques to identify the bacteria actively involved in the removal of nitrate. in this system, denitrification is carried out as the last step of water treatment by biofilms growing on quartz grains with methanol as a supplemented carbon source. the biofilms are quite irregular, having a median thickness of 13 to 20 microns. fatty acid analysis of 56 denitr ...	1996	8953706
oxygen increases the steady-state level of nitrate in denitrifying cells of paracoccus denitrificans.	the levels of nitrate in denitrifying cells of paracoccus denitrificans were determined by centrifugation through silicone oil into phosphoric acid and ion-exchange hplc analysis of the cell lysates, using [14c]sucrose to correct for the trapped external medium. introduction of oxygen brought about a significant upward shift in the intracellular nitrate concentration. this result calls into question the current thinking that oxygen blocks nitrate respiration primarily due to the inhibition of ni ...	1996	8961552
nmr assignments and relaxation studies of thiobacillus versutus ferrocytochrome c-550 indicate the presence of a highly mobile 13-residues long c-terminal tail.	cytochrome c-550 of thiobacillus versutus functions as an electron transfer protein in a chain of redox proteins that enables t. versutus to grow on methylamine. it is a single-heme protein of 134 residues, related to mitochondrial cytochrome c. cytochrome c-550, as well as several other bacterial c2-type cytochromes, contain a c-terminal extension of 13-16 amino acids of unknown function, compared to mitochondrial cytochrome c. nmr experiments were performed to obtain structural and dynamic inf ...	1996	8976558
mutants of escherichia coli lacking disulphide oxidoreductases dsba and dsbb cannot synthesise an exogenous monohaem c-type cytochrome except in the presence of disulphide compounds.	absence through mutation of two proteins involved in periplasmic disulphide bond formation, dsba and dsbb, results in failure of anaerobically grown escherichia coli to synthesise the holo forms of either its endogenous c-type cytochrome nitrite reductase or exogenous cytochrome c550 from paracoccus denitrificans. the synthesis of both cytochromes can be restored to the mutants by inclusion in the growth media of compounds containing disulphide bonds, e.g., the oxidised form of glutathione. the ...	1996	8977120
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
mutational analysis of the nor gene cluster which encodes nitric-oxide reductase from paracoccus denitrificans.	the genes that encode the hc-type nitric-oxide reductase from paracoccus denitrificans have been identified. they are part of a cluster of six genes (norcbqdef) and are found near the gene cluster that encodes the cd1-type nitrite reductase, which was identified earlier [de boer, a. p. n., reijnders, w. n. m., kuenen, j. g., stouthamer, a. h. & van spanning, r. j. m. (1994) isolation, sequencing and mutational analysis of a gene cluster involved in nitrite reduction in paracoccus denitrificans, ...	1996	9022686
purification and initial kinetic and spectroscopic characterization of no reductase from paracoccus denitrificans.	a new and relatively simple procedure to purify no reductase from paracoccus denitrificans by using the detergent lauryl maltoside has been developed. the purified enzyme consists of two subunits according to sds polyacrylamide gel electrophoresis. analysis of the content of prosthetic groups indicates the presence of non-haem iron in addition to the presence b and c cytochromes yielding a stoichiometry of haem b/haem c/non-haem iron = 2:1:1. the optical spectrum of reduced no reductase shows ba ...	1997	9030265
the pseudoazurin gene from thiosphaera pantotropha: analysis of upstream putative regulatory sequences and overexpression in escherichia coli.	the pseudoazurin gene from thiosphaera pantotropha has been cloned and sequenced. the deduced amino acid sequence showed that the protein contains an unusually alanine-rich signal peptide, 22 amino acid residues in length, which targets the protein to the periplasm. this pseudoazurin was expressed in large amounts in the periplasm of escherichia coli when the gene with its native ribosome-binding site was placed downstream of the lac promoter. removal of a putative hairpin-forming structure upst ...	1997	9032456
isolation, analysis, and deletion of the gene coding for subunit iv of cytochrome c oxidase in paracoccus denitrificans.	the gene coding for subunit iv of the cytochrome c oxidase in paracoccus denitrificans has been cloned and sequenced. the derived amino acid sequence shows no significant homology to any known protein. gene deletion has no consequences for the integrity of the complex and its spectral and enzymatic properties. complementation of the deletion mutant in trans results in expression of subunit iv; sequence analysis of the 5'-noncoding region leads to the identification of a putative promoter sequenc ...	1997	9038156
distribution of amine oxidases and amine dehydrogenases in bacteria grown on primary amines and characterization of the amine oxidase from klebsiella oxytoca.	the bacteria klebsiella oxytoca lmd 72.65 (atcc 8724), arthrobacter p1 lmd 81.60 (ncib 11625), paracoccus versutus lmd 80.62 (atcc 25364), escherichia coli w lmd 50.28 (atcc 9637), e. coli k12 lmd 93.68, pseudomonas aeruginosa pao1 lmd 89.1 (atcc 17933) and pseudomonas putida lmd 68.20 (atcc 12633) utilized primary amines as a carbon and energy source, although the range of amines accepted varied from organism to organism. the gram-negative bacteria k. oxytoca and e. coli as well as the gram-pos ...	1997	9043125
the paracoccus denitrificans ccma, b and c genes: cloning and sequencing, and analysis of the potential of their products to form a haem or apo- c-type cytochrome transporter.	two c-type cytochrome deficient mutants of paracoccus denitrificans, hn49 and hn53, were isolated by tn5 mutagenesis and screening for failure to oxidize dimethylphenylenediamine (the nadi test). both were completely deficient in c-type cytochromes. genomic dna flanking the site of tn5 insertion in hn53 was cloned by marked rescue and a 3.1 kb region sequenced. three of the genes, designated ccma, ccmb and ccmc, present in this region are proposed to encode the components of a membrane transport ...	1997	9043133
emerging principles of inorganic nitrogen metabolism in paracoccus denitrificans and related bacteria.	the taxonomy of paracoccus denitrificans and related bacteria is discussed. evidence is given which shows that the physiological differences between p. denitrificans and thiosphaera pantotropha are less fundamental than previously thought. a proposal to consider a species p. pantotropha is mentioned. the properties of the denitrifying enzymes and the genes involved in their formation in p. denitrificans is discussed. the synthesis of the membrane-bound-nitrate reductase is regulated by fnr, that ...	1997	9049016
enzyme diversity and mosaic gene organization in denitrification.	denitrification is a main branch of the global nitrogen cycle. in the past ten years unravelling the underlying biochemistry and genetics has proceeded at an increasing pace. fungal denitrification has become a new field. the biochemical investigation of denitrification has culminated in the description of the crystal structures of the two types of nitrite reductases. the n2o reductase shares with cytochrome c oxidase the cua center as a structurally novel metal site. the cytochrome b subunit of ...	1997	9049017
oxidative metabolism of inorganic sulfur compounds by bacteria.	the history of the elucidation of the microbiology and biochemistry of the oxidation of inorganic sulfur compounds in chemolithotrophic bacteria is briefly reviewed, and the contribution of martinus beijerinck to the study of sulfur-oxidizing bacteria highlighted. recent developments in the biochemistry, enzymology and molecular biology of sulfur oxidation in obligately and facultatively lithotrophic bacteria are summarized, and the existence of at least two major pathways of thiosulfate (sulfur ...	1997	9049021
paracoccus denitrificans aromatic amino acid aminotransferase: a model enzyme for the study of dual substrate recognition mechanism.	the gene for aromatic amino acid aminotransferase (arat) from paracoccus denitrificans was cloned, sequenced, and overexpressed in escherichia coli cells. the sequence differed from that reported previously [takagi, t., taniguchi, t., yamamoto, y., and shibatani, t. (1991) biotechnol. appl. biochem. 13, 112-119]. the enzyme (pdarat) was purified to homogeneity, and characterized. it was similar to aspartate aminotransferase (aspat) and arat of e. coli (ecarat) in many respects, including gross p ...	1997	9058208
fnrp and nnr of paracoccus denitrificans are both members of the fnr family of transcriptional activators but have distinct roles in respiratory adaptation in response to oxygen limitation.	the paracoccus denitrificans fnrp gene encoding a homologue of the escherichia coli fnr protein was localized upstream of the gene cluster that encodes the high-affinity cbb3-type oxidase. fnrp harbours the invariant cysteine residues that are supposed to be the ligands of the redox-sensitive [4fe-4s] cluster in fnr. nnr, another fnr-like transcriptional regulator in p. denitrificans, does not. analysis of fnrp and nnr single and double mutants revealed that the two regulators each exert exclusi ...	1997	9076727
the archaeal soxabcd complex is a proton pump in sulfolobus acidocaldarius.	the thermoacidophilic archaeon sulfolobus acidocaldarius expresses a very unusual quinol oxidase, which contains four heme a redox centers and one copper atom. the enzyme was solubilized with dodecyl maltoside and purified to homogeneity by a combination of hydrophobic interaction and anion exchange chromatography. the oxidase complex consists of four polypeptide subunits with apparent molecular masses of 64, 39, 27, and 14 kda that are encoded by the soxabcd operon (lübben, m., kolmerer, b., an ...	1997	9079667
hydroxylamine oxidation in heterotrophic nitrate-reducing soil bacteria and purification of a hydroxylamine-cytochrome c oxidoreductase from a pseudomonas species.	hydroxylamine oxidation was measured in four recently isolated heterotrophic nitrate-reducing bacteria belonging to the genera pseudomonas, moraxella, arthrobacter and aeromonas. a hydroxylamine-cytochrome c oxidoreductase activity was detected in periplasmic fractions of the pseudomonas and aeromonas spp. and in total soluble fractions of the arthrobacter sp. a monomeric 19-kda non-haem iron hydroxylamine-cytochrome c oxidoreductase was purified from the pseudomonas species and shown to be simi ...	1996	9082922
expression of the mau gene cluster of paracoccus denitrificans is controlled by maur and a second transcription regulator.	the mau gene cluster of paracoccus denitrificans constitutes 11 genes (10 are located in the transcriptional order maufbedacjgmn; the 11th, maur, is located upstream and divergently transcribed from these genes) that encode a functional methylamine-oxidizing electron transport branch. the maur gene encodes a lysr-type transcriptional activator essential for induction of the mau operon. in this study, the characteristics of that process were established. by using lacz transcriptional fusions inte ...	1997	9084163
alphat244m mutation affects the redox, kinetic, and in vitro folding properties of paracoccus denitrificans electron transfer flavoprotein.	threonine 244 in the alpha subunit of paracoccus denitrificans transfer flavoprotein (etf) lies seven residues to the amino terminus of a proposed dinucleotide binding motif for the adp moiety of the fad prosthetic group. this residue is highly conserved in the alpha subunits of all known etfs, and the most frequent pathogenic mutation in human etf encodes a methionine substitution at the corresponding position, alphat266. the x-ray crystal structures of human and p. denitrificans etfs are very ...	1997	9100014
transformation of the cua redox site in cytochrome c oxidase into a mononuclear copper center.	subunit ii of the aa3 type cytochrome c oxidase contains a binuclear copper center (cua) which functions as the entry point for electrons donated by cytochrome c. we have introduced site-specific mutations in residues liganding the cua center in the oxidase of the bacterium paracoccus denitrificans; the purified, fully assembled enzyme complexes were analyzed by various techniques, including epr, optical spectroscopy, and total-reflection x-ray fluorescence spectrometry, to determine metal to pr ...	1997	9116000
the structure of porin from paracoccus denitrificans at 3.1 a resolution.	the crystal structure of a non-specific porin from paracoccus denitrificans at 3.1 a resolution has been solved by molecular replacement using the porin from rhodopseudomonas blastica as the search model. paracoccus porin is very similar to other non-specific porins of known structure: a trimer of 16 stranded beta-barrels each with a central pore constricted by a long extracellular loop folding back against the barrel wall. the distinctive distribution of charged residues of this non-specific po ...	1997	9119065
cloning and characterization of the reca of paracoccus denitrificans and construction of a reca-deficient mutant.	the reca gene of paracoccus denitrificans has been isolated from a genomic library by hybridization with the rhodobacter sphaeroides reca gene. its complete nucleotide sequence consists of 1071 bp encoding a polypeptide of 356 amino acids. nucleotide sequence analysis of the p. denitrificans reca gene revealed the closest identities with the r. sphaeroides and the rhodobacter capsulatus reca genes. nevertheless, and surprisingly, reca genes of these two phototrophic bacteria are not dna damage-i ...	1997	9119195
potential nitrosamine formation and its prevention during biological denitrification of red beet juice.	high nitrate intake has been shown to result in an increased risk of endogenous formation of n-nitroso compounds. certain vegetables and vegetable juices contain high concentrations of nitrate. biological denitrification using strains of paracoccus denitrificans (p.d.) has been proposed as effective means to reduce nitrate contents in such vegetable juices. during this bacterial denitrification process, substantial nitrite concentrations are transiently formed. this study investigated whether n- ...	1997	9146735
molecular cloning and functional characterization of the paracoccus denitrificans porin.	bacterial porins facilitate the passive uptake of small solutes across the outer membrane of the cell. the channel properties and the primary structure of the porin from paracoccus denitrificans were investigated. as judged from single-channel conductance experiments, this porin forms trimeric pores that show no ion selectivity in potassium chloride solution, which indicates that the charges within or near the channel are balanced. based on peptide fragment sequence, the gene porg, which codes f ...	1997	9151957
structural characterization of paracoccus denitrificans cytochrome c peroxidase and assignment of the low and high potential heme sites.	the amino acid sequence of the diheme cytochrome c peroxidase from paracoccus denitrificans has been determined as the result of sequence analysis of peptides generated by chemical and enzymatic cleavages of the apoprotein. the sequence shows 60% similarity to the cytochrome c peroxidase from pseudomonas aeruginosa, 39% similarity to an open reading frame encoding a putative triheme c-type cytochrome in escherichia coli, and remote similarity to the maug proteins from two methylotrophic bacteria ...	1997	9201942
asp-193 and glu-218 of subunit ii are involved in the mn2+-binding of paracoccus denitrificans cytochrome c oxidase.	cytochrome c oxidase contains a binding site for a non-redox-active metal at the interface of subunits i and ii, usually a magnesium ion. in paracoccus denitrificans oxidase, typically 20% may be replaced by manganese, using standard growth media. site-directed mutants were constructed in subunit ii (d193n and e218q), and the isolated enzymes analyzed by total-reflection x-ray fluorescence spectrometry and epr. both mutants show a strong reduction of the manganese stoichiometry and a diminished ...	1997	9202131
organization of methylamine utilization genes (mau) in 'methylobacillus flagellatum ' kt and analysis of mau mutants.	the organization of genes involved in utilization of methylamine (mau genes) was studied in the obligate methylotroph 'methylobacillus flagellatum' kt. nine open reading frames were identified as corresponding to the genes maufbedaglmn. in addition, an open reading frame (orf-1 encoding a polypeptide with unknown function was identified upstream of the mau gene cluster. subclones of the 'm. flagellatum' kt gene cluster were used for complementation of a series of chemically induced mau mutants o ...	1997	9202457
expression studies on the ba3 quinol oxidase from paracoccus denitrificans. a bb3 variant is enzymatically inactive.	expression of the quinol oxidase from paracoccus denitrificans has been examined using a polyclonal antibody directed against subunit ii and a promoter probe vector carrying the promoter region of the qox operon. under aerobic conditions nitrate and nitrite act as specific inducers of the expression. to obtain an enzymatically competent quinol oxidase complex, an intact ctab gene is required, which constitutes part of the cta operon coding for the aa3 cytochrome c oxidase of p. denitrificans. de ...	1997	9219517
protein and gene structure of the nadh-binding fragment of rhodobacter capsulatus nadh:ubiquinone oxidoreductase.	membranes of aerobically grown rhodobacter capsulatus contain only one type of nadh:ubiquinone oxidoreductase which is homologous to the proton-translocating complex i. the k(m) value of the enzyme for nadh was determined to be 8 microm. after solubilization of the membranes with an alkylglucoside detergent, two fragments of complex i with molecular masses of 110 kda and 140 kda were isolated by chromatographic steps in the presence of detergent. both fragments contain at least two polypeptides ...	1997	9219542
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
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
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