Publications

eseem and mims endor spectroscopies of cis,trans-(l-n2s2)movo(sch2ph): detection of the two benzylthiolate alpha protons.		2000	11196982
using direct electrochemistry to probe rate limiting events during nitrate reductase turnover.	protein film voltammetry of nargh catalysing nitrate reduction under steady state conditions provides information on events occurring within the enzyme during the catalytic cycle. in this discussion we have focused on exploring the ability of two simple catalytic schemes to reproduce the voltammetric response of nargh; electron transfer to the enzyme's active site being described either by interfacial electron exchange (scheme 1) or intramolecular electron delivery via the operation of an electr ...	2000	11197477
complete 1h, 15n and 13c assignment of the functional domain of paracoccus denitrificans cytochrome c552 in the oxidized state.		2000	11200533
humics as an electron donor for anaerobic respiration.	the possibility that microorganisms might use reduced humic substances (humics) as an electron donor for the reduction of electron acceptors with a more positive redox potential was investigated. all of the fe(iii)- and humics-reducing microorganisms evaluated were capable of oxidizing reduced humics and/or the reduced humics analogue anthrahydroquinone-2,6,-disulphonate (ahods), with nitrate and/or fumarate as the electron acceptor. these included geobacter metallireducens, geobacter sulphurred ...	1999	11207721
the cytochrome c domain of dimeric cytochrome cd(1) of paracoccus pantotrophus can be produced at high levels as a monomeric holoprotein using an improved c-type cytochrome expression system in escherichia coli.	cytochrome cd(1) nitrite reductase from paracoccus pantotrophus is a dimer; within each monomer there is a largely alpha-helical domain that contains the c-type cytochrome centre. the structure of this domain changes significantly upon reduction of the heme iron, for which the ligands change from his17/his69 to met106/his69. overproduction, using an improved escherichia coli expression system, of this c-type cytochrome domain as an independent monomer is reported here. the properties of the inde ...	2001	11237728
map self-validation: a useful discriminator of phase correctness at low resolution.	a new map-validation procedure is based on the correlation-coefficient agreement between the observed structure-factor magnitudes and their extrapolated values from suitably modified electron-density maps from which they have been each in turn systematically excluded. the correlation coefficient tends to a maximum as the phase errors in a map are reduced. this principle was used to resolve the single-wavelength anomalous scattering (sas) and single-derivative isomorphous replacement (sir) phase ...	2001	11264587
identification of the intracellular polyhydroxyalkanoate depolymerase gene of paracoccus denitrificans and some properties of the gene product.	paracoccus denitrificans degraded poly(3-hydroxybutyrate) (phb) in the cells under carbon source starvation. intracellular poly(3-hydroxyalkanoate) (pha) depolymerase gene (phaz) was identified near the pha synthase gene (phac) of p. denitrificans. cell extract of escherichia coli carrying lacz--phaz fusion gene degraded protease-treated phb granules. reaction products were thought to be mainly d(--)-3-hydroxybutyrate (3hb) dimer and 3hb oligomer. diisopropylfluorophosphonate and triton x-100 ex ...	2001	11267773
structure of the bound dioxygen species in the cytochrome oxidase reaction of cytochrome cd1 nitrite reductase.	reduction of dioxygen to water is a key process in aerobic life, but atomic details of this reaction have been elusive because of difficulties in observing active oxygen intermediates by crystallography. cytochrome cd(1) is a bifunctional enzyme, capable of catalyzing the one-electron reduction of nitrite to nitric oxide, and the four-electron reduction of dioxygen to water. the latter is a cytochrome oxidase reaction. here we describe the structure of an active dioxygen species in the enzyme ca ...	2001	11278884
evidence for two pathways of thiosulfate oxidation in starkeya novella (formerly thiobacillus novellus).	the pathway of thiosulfate oxidation in the facultatively chemolithotrophic, sulfur-oxidizing bacterium starkeya novella (formerly thiobacillus novellus) has not been established beyond doubt. recently, isolation of the sorab genes, which encode a soluble sulfite:cytochrome c oxidoreductase, has been reported, indicating that a thiosulfate-oxidizing pathway not involving a multienzyme complex may exist in this organism. here we report the cloning and sequencing of the soxbcd genes from s. novell ...	2001	11285738
functional, biochemical and genetic diversity of prokaryotic nitrate reductases.	prokaryotic nitrate reduction can serve a number of physiological roles and can be catalysed by a number of biochemically distinct nitrate reductases. three distinct nitrate reductase classes can be indentified in prokaryotes, nas, nar and nap. nas is located in the cytoplasmic compartment and participates in nitrogen assimilation. nar is usually a three-subunit complex anchored to the cytoplasmic face of the membrane with its active site located in the cytoplasmic compartment and is involved in ...	2001	11289299
perturbations at the high spin heme b center in the membrane-bound nitric oxide reductase.	the effects of lowering ph from 7 to 5 on the absorption, circular dichroism (mcd) and epr spectra were studied for paracoccus halodenitrificans nitric oxide reductase (nor). intensities of the characteristic bands for the high spin heme b, that at 592 nm in the absorption spectrum and those at 591 (+) and 606 (-) in the mcd spectrum decreased considerably. concomitant cryogenic epr spectrum indicated a drastic increase in the signal intensity due to the high spin heme b at g approximately 6, of ...	2001	11293548
taxonomy of the genus paracoccus.		2000	11293651
plasmid occurrence and diversity in the genus paracoccus.	the results of screening for the occurrence of plasmids in several strains representing 11 out of 13 species of the genus paracoccus are presented. we show that plasmids (ranging in size from 2.7 to above 450 kb) are widely distributed in this genus. only one tested strain (p. alkenifer) appears to be plasmid-free. the majority of the strains harbour at least two plasmids, one of which usually fits into the class of megaplasmids.	2000	11293660
regulation of expression of terminal oxidases in paracoccus denitrificans.	in order to study the induction of terminal oxidases in paracoccus denitrificans, their promoters were fused to the lacz reporter gene and analysed in the wild-type strain, in an fnrp-negative mutant, in a cytochrome bc1-negative mutant, and in six single or double oxidase-negative mutant strains. the strains were grown under aerobic, semi-aerobic, and denitrifying conditions. the oxygen-sensing transcriptional-regulatory protein fnrp negatively regulated the activity of the qox promoter, which ...	2001	11298768
phylogeny and distribution of the soxb gene among thiosulfate-oxidizing bacteria.	a pcr protocol for the detection of sulfur-oxidizing bacteria based on soxb genes that are essential for thiosulfate oxidation by sulfur-oxidizing bacteria of various phylogenetic groups which use the 'paracoccus sulfur oxidation' pathway was developed. five degenerate primers were used to specifically amplify fragments of soxb genes from different sulfur-oxidizing bacteria previously shown to oxidize thiosulfate. the pcr yielded a soxb fragment of approximately 1000 bp from most of the bacteria ...	2001	11313131
[a novel plant-associated thermotolerant alkalophilic methylotroph of the genus paracoccus].	strain gb isolated from the maize rhizosphere is a gram-negative, aerobic, non-spore-forming, nonpigmented, nonmotile, chemolithotrophic, facultatively methylotrophic bacterium. cells are cocci or short rods. the strain does not require vitamins. optimum growth in a medium with methanol occurs at 38-42 degrees c at ph 8.0-9.2. the doubling time is 12 h. in addition to methanol, the bacterium can grow on methylamine, dimethylformamide, acetone, thiosulfate + nahco3, and in an atmosphere of h2 + c ...	2000	11315675
electron and proton transfer in the arginine-54-methionine mutant of cytochrome c oxidase from paracoccus denitrificans.	arginine 54 in subunit i of cytochrome c oxidase from paracoccus denitrificans interacts with the formyl group of heme a. mutation of this arginine to methionine (r54m) dramatically changes the spectral properties of heme a and lowers its midpoint redox potential [kannt et al. (1999) j. biol. chem. 274, 37974-37981; lee et al. (2000) biochemistry 39, 2989-2996; riistama et al. (2000) biochim. biophys. acta 1456, 1-4]. during anaerobic reduction of the mutant enzyme, a small fraction of heme a is ...	2001	11318650
on the routine use of soft x-rays in macromolecular crystallography.	a diffraction data set has been collected from a blood coagulation factor xiii-ca(2+) complex crystal at the x-ray diffraction beamline of the elettra synchrotron (trieste, italy) at a wavelength of 2.6 a. the data collection could be carried out using the beamline as is, without making any time-consuming changes to the apparatus. various data-processing schemes have been employed and it has been observed that local or detector scaling procedures are essential for producing the 'best' anomalous ...	2001	11320309
c-terminal truncation and histidine-tagging of cytochrome c oxidase subunit ii reveals the native processing site, shows involvement of the c-terminus in cytochrome c binding, and improves the assay for proton pumping.	to enable metal affinity purification of cytochrome c oxidase reconstituted into phospholipid vesicles, a histidine-tag was engineered onto the c-terminal end of the rhodobacter sphaeroides cytochrome c oxidase subunit ii. characterization of the natively processed wildtype oxidase and artificially processed forms (truncated with and without a his-tag) reveals km values for cytochrome c that are 6-14-fold higher for the truncated and his-tagged forms than for the wildtype. this lowered ability t ...	2001	11327819
nitrification and denitrification as a source for no and no2 production in high-strength wastewater.	laboratory and half-technical scale experiments were performed to evaluate nitric oxide (no) and nitrogen dioxide (no2) production during biological n-elimination from wastewater with high ammonium concentration (about 700 mg n l-1). in a laboratory scale bioreactor with biomass retention, the ammonia oxidizer nitrosomonas europaea and the denitrifier paracoccus denitrificans were grown as reference organisms in co-culture in order to simulate the nitrifying and denitrifying community of wastewa ...	2001	11337836
[phylogenetic analysis of aerobic methylotrophic bacteria, using dichloromethane].	the phylogenetic relationships of 12 aerobic dichloromethane-degrading bacteria that implement different c1-assimilation pathways was determined based on 16s ribosomal rna sequences and dna-dna hybridization data. the restricted facultative methylotroph "methylophilus leisingerii" dm11 with the ribulose monophosphate pathway was found to belong to the genus methylophilus cluster of the beta subdivision of the phylogenetic kingdom proteobacteria. the facultative methylotroph methylorhabdus multiv ...	2001	11338843
structure of cytochrome c oxidase: a comparison of the bacterial and mitochondrial enzymes.	it has been almost 5 years since the first structures of cytochrome c oxidase, from paracoccus denitrificans and bovine heart mitochondria, were revealed. since then many different proton pumping mechanisms have been proposed for the enzyme; however, no definitive conclusion has been achieved. in this article, we revisit the original structures of bacterial and mitochondrial oxidases and try to clarify similarities as well as differences between the two structures.	2001	11341911
ph-induced conformational transition in the soluble cua domain of paracoccus denitrificans cytochrome oxidase.	the ph-induced conformational transition in the cua domain of subunit ii of cytochrome oxidase of paracoccus denitrificans (pdii) has been investigated using various spectroscopic and stopped-flow kinetic methods. uv-visible absorption and circular dichroism studies showed that an increase in ph from 6 to 10 leads to a conformation change with pk(a) = 8.2 associated with the cua site of the protein. the secondary structure of the protein was, however, shown to remain unchanged in these two confo ...	2001	11352755
isolation and characterization of complex i, rotenone-sensitive nadh: ubiquinone oxidoreductase, from the procyclic forms of trypanosoma brucei.	additional characterization of complex i, rotenone-sensitive nadh:ubiquinone oxidoreductase, in the mitochondria of trypanosoma brucei brucei has been obtained. both proline:cytochrome c reductase and nadh:ubiquinone oxidoreductase of procyclic t. brucei were inhibited by the specific inhibitors of complex i rotenone, piericidin a, and capsaicin. these inhibitors had no effect on succinate: cytochrome c reductase activity. antimycin a, a specific inhibitor of the cytochrome bc1 complex (ubiquino ...	2001	11358527
multivariable control of alcohol concentrations in the production of polyhydroxyalkanoates (phas) by paracoccus denitrificans.	a novel multivariable control strategy is developed for alcohol (ethanol and n-pentanol) concentrations in the production of poly(3-hydroxybutyrate-co-3-hydroxyvalerate), p(hb-co-hv), a biodegradable polymer by paracoccus denitrificans atcc 1774. this controller, which is developed to control the mole fraction of p(hb-co-hv), consists of two parts: one is for ethanol concentration control and the other is for mole fraction control, based on the concept of metabolic flux distribution control. a s ...	2001	11370000
maximal expression of membrane-bound nitrate reductase in paracoccus is induced by nitrate via a third fnr-like regulator named narr.	respiratory reduction of nitrate to nitrite is the first key step in the denitrification process that leads to nitrate loss from soils. in paracoccus pantotrophus, the enzyme system that catalyzes this reaction is encoded by the narkghji gene cluster. expression of this cluster is maximal under anaerobic conditions in the presence of nitrate. upstream from nark is narr, a gene encoding a member of the fnr family of transcriptional activators. narr is transcribed divergently from the other nar ge ...	2001	11371524
the structure of an alternative form of paracoccus pantotrophus cytochrome cd(1) nitrite reductase.	cytochrome cd(1) nitrite reductase is a bifunctional enzyme, which can catalyze the 1-electron reduction of nitrite to nitric oxide and the 4-electron reduction of dioxygen to water. here we describe the structure of reduced nitrite reductase, crystallized under anaerobic conditions. the structure reveals substantial domain rearrangements with the c domain rotated by 60 degrees and shifted by approximately 20 a compared with previously known structures from crystals grown under oxidizing conditi ...	2001	11373294
redox dependent conformational changes in the mixed valence form of the cytochrome c oxidase from p. the reorganization of glutamic acid 278 is coupled to the electron transfer from/to heme a and the binuclear center. denitrificans.	in this work we present the separation of ftir difference signals induced by electron transfer to/from the redox centers of the cytochrome c oxidase from p. denitrificans and compare electrochemically induced ftir difference spectra with those induced by co photolysis. ftir difference spectra of rebinding of co to the half reduced (mixed valence) form of the cytochrome c oxidase after photolysis reflect the conformational changes induced by the rebinding of co and by electron transfer reactions ...	2001	11374571
heme-copper oxidases with modified d- and k-pathways are yet efficient proton pumps.	the cytochrome aa(3)-type quinol oxidase from the archaeon acidianus ambivalens and the ba(3)-type cytochrome c oxidase from thermus thermophilus are divergent members of the heme-copper oxidase superfamily of enzymes. in particular they lack most of the key residues involved in the proposed proton transfer pathways. the pumping capability of the a. ambivalens enzyme was investigated and found to occur with the same efficiency as the canonical enzymes. this is the first demonstration of pumping ...	2001	11377432
calcium-dependent conformation of a heme and fingerprint peptide of the diheme cytochrome c peroxidase from paracoccus pantotrophus.	the structural changes in the heme macrocycle and substituents caused by binding of ca(2+) to the diheme cytochrome c peroxidase from paracoccus pantotrophus were clarified by resonance raman spectroscopy of the inactive fully oxidized form of the enzyme. the changes in the macrocycle vibrational modes are consistent with a ca(2+)-dependent increase in the out-of-plane distortion of the low-potential heme, the proposed peroxidatic heme. most of the increase in out-of-plane distortion occurs when ...	2001	11380251
charge translocation coupled to electron injection into oxidized cytochrome c oxidase from paracoccus denitrificans.	electrons were discretely injected into oxidized cytochrome c oxidase in liposomes by laser flash excitation of bound ruthenium [ii] bispyridyl, and the membrane potential was recorded by time-resolved electrometry. membrane potential is generated in a fast phase when an electron is transferred from the excited dye, via the cua center, to heme a at a relative dielectric depth d inside the membrane [zaslavsky, d., kaulen, a. d., smirnova, i. a., vygodina, t., and konstantinov, a. a. (1993) febs l ...	2001	11401552
characterization and sequence analysis of the replicator region of the novel plasmid palc1 from paracoccus alcaliphilus.	the replicator region of a low-copy-number plasmid, palc1, of paracoccus alcaliphilus jcm 7364 was cloned in a form of the minireplicon palc100 (3.6 kb). the host range of the minireplicon embraces several species of genus paracoccus, as well as agrobacterium tumefaciens, rhizobium leguminosarum, and rhodobacter sphaeroides (all belonging to alpha-proteobacteria), but not escherichia coli. the complete nucleotide sequence of the replicator region (2276 bp) revealed the presence of one complete o ...	2001	11407917
identification and characterization of a periplasmic nitrate reductase in azospirillum brasilense sp245.	the azospirillum brasilense sp245 napabc genes, encoding nitrate reductase activity, were isolated and sequenced. the derived protein sequences are very similar throughout the whole nap segment to the napabc protein sequences of escherichia coli, pseudomonas sp. g-179, ralstonia eutropha, rhodobacter sphaeroides, and paracoccus denitrificans. based on whole-cell nitrate reductase assays with the artificial electron donors benzyl viologen and methyl viologen, and assays with periplasmic cell-free ...	2001	11409544
phar, a protein of unknown function conserved among short-chain-length polyhydroxyalkanoic acids producing bacteria, is a dna-binding protein and represses paracoccus denitrificans phap expression in vitro.	a putative regulatory protein, phar, which was identified in the polyhydroxyalkanoic acid synthetic locus (phazcpr) in paracoccus denitrificans, was investigated. the phar protein purified from a recombinant escherichia coli was estimated to be 22 kda by sodium dodecyl sulfate-polyacrylamide gel electrophoresis, being consistent with the mass calculated from the nucleotide sequence. the molecular mass was determined to be 93 kda by size-exclusion chromatography, suggesting that the protein forme ...	2001	11410342
albibacter methylovorans gen. nov., sp. nov., a novel aerobic, facultatively autotrophic and methylotrophic bacterium that utilizes dichloromethane.	a novel genus, albibacter, with one species, albibacter methylovorans sp. nov., is proposed for a facultatively chemolithotrophic and methylotrophic bacterium (strain dm10t) with the ribulose bisphosphate (rubp) pathway of c1 assimilation. the bacterium is a gram-negative, aerobic, asporogenous, nonmotile, colourless rod that multiplies by binary fission. the organism utilizes dichloromethane, methanol, methylamine, formate and co2/h2, as well as a variety of polycarbon compounds, as carbon and ...	2001	11411673
dynamics of nitric oxide in the active site of reduced cytochrome c oxidase aa3.	nitric oxide (no) is involved in the regulation of respiration by acting as a competitive ligand for molecular oxygen at the binuclear active site of cytochrome c oxidase. the dynamics of no in and near this site are not well understood. we performed flash photolysis studies of no from heme a3 in cytochrome c oxidase from paracoccus denitrificans, using femtosecond transient absorption spectroscopy. the formation of the product state--the unliganded heme a3 ground state--occurs in a similar step ...	2001	11425307
oxidation of reduced inorganic sulfur compounds by bacteria: emergence of a common mechanism?		2001	11425697
protein dynamics enhance electronic coupling in electron transfer complexes.	electron-transferring flavoproteins (etfs) from human and paracoccus denitrificans have been analyzed by small angle x-ray scattering, showing that neither molecule exists in a rigid conformation in solution. both etfs sample a range of conformations corresponding to a large rotation of domain ii with respect to domains i and iii. a model of the human etf.medium chain acyl-coa dehydrogenase complex, consistent with x-ray scattering data, indicates that optimal electron transfer requires domain i ...	2001	11429403
assignment of haem ligands and detection of electronic absorption bands of molybdenum in the di-haem periplasmic nitrate reductase of paracoccus pantotrophus.	the periplasmic nitrate reductase (nap) from paracoccus pantotrophus is a soluble two-subunit enzyme (napab) that binds two c-type haems, a [4fe-4s] cluster and a bis-molybdopterin guanine dinucleotide cofactor that catalyses the reduction of nitrate to nitrite. in the present work the napab complex has been studied by magneto-optical spectroscopy to probe co-ordination of both the napb haems and the napa active site mo. the absorption spectrum of the napab complex is dominated by features from ...	2001	11434929
a novel c1-using denitrifier alcaligenes sp. stc1 and its genes for copper-containing nitrite reductase and azurin.	a novel denitrifier alcaligenes sp. stc1 was identified. the strain efficiently denitrifies under an atmosphere of 10% oxygen (o2) where paracoccus denitrificans, one of the most studied aerobic denitrifiers, had less denitrifying activity, indicating that the strain has an o2-torelant denitrifying system. it denitrified by using c1-carbon sources such as formate and methanol as well as glucose, glycerol, and succinate. the genes for the copper-containing nitrite reductase and azurin of this c1- ...	2001	11440141
novel genes of the sox gene cluster, mutagenesis of the flavoprotein soxf, and evidence for a general sulfur-oxidizing system in paracoccus pantotrophus gb17.	the novel genes soxfgh were identified, completing the sox gene cluster of paracoccus pantotrophus coding for enzymes involved in lithotrophic sulfur oxidation. the periplasmic soxf, soxg, and soxh proteins were induced by thiosulfate and purified to homogeneity from the soluble fraction. soxf coded for a protein of 420 amino acids with a signal peptide containing a twin-arginine motif. soxf was 37% identical to the flavoprotein fccb of flavocytochrome c sulfide dehydrogenase of allochromatium v ...	2001	11443084
significance of asymmetric sites in choosing siderophores as deferration agents.	the syntheses of the microbial iron chelators l-fluviabactin, its unnatural enantiomer, d-fluviabactin, l-homofluviabactin, and l-agrobactin, are described. the key steps involve the selective bis-acylation of the terminal nitrogens of norspermidine, spermidine, or homospermidine with 2,3-bis(benzyloxy)benzoic acid in the presence of 1,1-carbonyldiimidazole, followed by coupling of the n-hydroxysuccinimide ester of cbz-protected l- or d-threonine with the central nitrogen. the effectiveness of e ...	2001	11448229
[microbial decomposition of 3,4-dichloroaniline, adsorbed by activated charcoal].	the accessibility of 3,4-dichloroaniline (dca) sorbed by activated carbon to degradative microorganisms was studied. a paracoccus denitrificans strain capable of growing on medium with dca as the only source of energy, carbon, and nitrogen was used in the experiment. the high sorption capacity of all the carbons studied (powdered rs and skt-6a and granular ag-3) in relation to dca (350 to 360, 480 to 520, and 540 to 580 mg/g, respectively) was demonstrated. the sorption capacity correlated posit ...	2001	11450454
the carboxin-binding site on paracoccus denitrificans succinate:quinone reductase identified by mutations.	succinate:quinone reductase catalyzes electron transfer from succinate to quinone in aerobic respiration. carboxin is a specific inhibitor of this enzyme from several different organisms. we have isolated mutant strains of the bacterium paracoccus denitrificans that are resistant to carboxin due to mutations in the succinate:quinone reductase. the mutations identify two amino acid residues, his228 in sdhb and asp89 in sdhd, that most likely constitute part of a carboxin-binding site. this site i ...	2001	11456223
intramolecular electron transfer from c heme to d1 heme in bacterial cytochrome cd1 nitrite reductase occurs over the same distances at very different rates depending on the source of the enzyme.	intramolecular electron transfer over 12 a from heme c to heme d(1) was investigated in cytochrome cd(1) nitrite reductase from pseudomonas aeruginosa, following reduction of the c heme by pulse radiolysis. the rate constant for the transfer is relatively slow, k = 3 s(-1). the present observations contrast with a corresponding rate of electron transfer, 1.4 x 10(3) s(-1), measured for cytochrome cd(1) from paracoccus pantotrophus, though the relative positions of the two heme groups are the sam ...	2001	11456493
the peroxidase activity of cytochrome c-550 from paracoccus versutus.	next to their natural electron transport capacities, c-type cytochromes possess low peroxidase and cytochrome p-450 activities in the presence of hydrogen peroxide. these catalytic properties, in combination with their structural robustness and covalently bound cofactor make cytochromes c potentially useful peroxidase mimics. this study reports on the peroxidase activity of cytochrome c-550 from paracoccus versutus and the loss of this activity in presence of h2o2. the rate-determining step in t ...	2001	11488914
zn(2+) binding to the cytoplasmic side of paracoccus denitrificans cytochrome c oxidase selectively uncouples electron transfer and proton translocation.	using a combination of stopped-flow spectrophotometric proton pumping measurements and time-resolved potential measurements on black lipid membranes, we have investigated the effect of zn(2+) ions on the proton transfer properties of paracoccus denitrificans cytochrome c oxidase. when zinc was enclosed in the interior of cytochrome c oxidase containing liposomes, the h/e stoichiometry was found to gradually decrease with increasing zn(2+) concentration. half-inhibition of proton pumping was obse ...	2001	11513871
the cysteine residue of the soxy protein as the active site of protein-bound sulfur oxidation of paracoccus pantotrophus gb17.	four proteins of paracoccus pantotrophus are required for hydrogen sulfide-, sulfur-, thiosulfate- and sulfite-dependent horse heart cytochrome c reduction. the lack of free intermediates suggested a protein-bound sulfur oxidation mechanism. the soxy protein has a novel motif containing a cysteine residue. electrospray ionization and matrix-assisted laser desorption ionization mass spectrometry of the soxyz protein revealed one mass for soxz and different masses for soxy, indicating native soxy ...	2001	11513876
the shxvw locus is essential for oxidation of inorganic sulfur and molecular hydrogen by paracoccus pantotrophus gb17: a novel function for lithotrophy.	the shxvw genes of paracoccus pantotrophus were identified to be essential for lithotrophic oxidation of sulfur and hydrogen. shxv predicts a membrane protein which is 42% identical to ccda of p. pantotrophus essential for cytochrome c biogenesis. shxw predicts a periplasmic thioredoxin. disruption of shxv by an omega-kanamycin interposon disabled the resulting mutant gb(omega)v to grow with thiosulfate or molecular hydrogen and to express shxw while cytochrome c formation was not affected. mixo ...	2001	11520617
a direct-method ab initio phasing of a protein, cupredoxin amicyanin, at 1.31 a resolution.	the direct-methods program multan88 has been applied successfully to redetermine the structure of a protein, cupredoxin amicyanin, containing 808 non-h atom sites, one cu atom and 132 ordered water molecules in the asymmetric unit using data at 1.31 a resolution. starting with initially random phases, useful phase sets selected by figures of merit could be obtained from multiple trials. the e maps corresponding to the best eight phase sets in order of combined figures of merit (cfom2) revealed a ...	2001	11526319
the dynamics of the macromolecular composition of biomass.	the biomass composition of microorganisms depends on the growth conditions. this study explores whether a two-component model can explain how the elemental and macromolecular composition of the biomass of bacteria varies with the specific growth rate. the model describes the rates at which microorganisms assimilate substrates into reserves and utilize reserves for maintenance and growth. crucial model assumptions are that biomass consists of reserves and structure and that each of these componen ...	2001	11531388
electron transport in paracoccus halodenitrificans and the role of ubiquinone.	the membrane-bound nadh oxidase of paracoccus halodenitrificans was inhibited by dicoumarol, 2-n-heptyl-4-hydroxy-quinoline-n-oxide (hqno), and exposure to ultraviolet light (at 366 nm). when the membranes were extracted with n-pentane, nadh oxidase activity was lost. partial restoration was achieved by adding the ubiquinone fraction extracted from the membranes. succinate oxidation was not inhibited by dicoumarol or hqno, but was affected by ultraviolet irradiation or n-pentane extraction. ...	1984	11536581
the growth of paracoccus halodenitrificans in a defined medium.	a synthetic medium, consisting of inorganic salts and any of a number of carbon sources, supported the aerobic growth of paracoccus halodenitrificans when supplemented with thiamine. the same medium plus an appropriate nitrogenous oxide supported anaerobic growth when additionally supplemented with methionine. the observation that vitamin b12 or betaine replaced methionine suggested that p. halodenitrificans had a defect in the cobalamin-dependent pathway for methionine biosynthesis, as well a ...	1984	11536589
is the paracoccus halodenitrificans atpase a chimeric enzyme?	membranes from paracoccus halodenitrificans contain an atpase that is most active in the absence of nacl. the most unusual characteristic of the enzyme is its pattern of sensitivity to various inhibitors. azide and rhodamine 6g, inhibitors of f1f0-atpases, inhibit atp hydrolysis as do bafilomycin a1, concanamycin a (folimycin), n-ethylmaleimide, and p-chloromercuriphenylsulfonate which are inhibitors of vacuolar atpases. this indiscriminate sensitivity suggests that this atpase may be a hybrid a ...	1996	11536735
microbial metabolism of tholin.	in this paper, we show that a wide variety of common soil bacteria are able to obtain their carbon and energy needs from tholin (a class of complex organic heteropolymers thought to be widely distributed through the solar system; in this case tholin was produced by passage of electrical discharge through a mixture of methane, ammonia, and water vapor). we have isolated aerobic, anaerobic, and facultatively anaerobic bacteria which are able to use tholin as a sole carbon source. organisms which ...	1990	11538367
the purification and properties of a cd-cytochrome nitrite reductase from paracoccus halodenitrificans.	paracoccus halodenitrificans, grown anaerobically in the presence of nitrite, contained membrane and cytoplasmic nitrite reductases. when assayed in the presence of phenazine methosulfate and ascorbate, the membrane-bound enzyme produced nitrous oxide whereas the cytoplasmic enzyme produced nitric oxide. when both enzymes were assayed in the presence of methyl viologen and dithionite, the cytoplasmic enzyme produced ammonia. following solubilization, the membrane-bound enzyme behaved like the ...	1986	11540874
the phylogeny of purple bacteria: the alpha subdivision.	the technique of oligonucleotide cataloging shows the purple photosynthetic eubacteria to comprise three major subdivisions, temporarily called alpha, beta, and gamma--previously designated groups i-iii by gibson et al. (1979). each subdivision contains a number of non-photosynthetic genera in addition to the photosynthetic ones. the alpha subdivision, the subject of the present report, contains most but not all of the species that fall into the classically defined genera rhodospirillum, rhodo ...	1984	11541974
phylogenetic origins of the plant mitochondrion based on a comparative analysis of 5s ribosomal rna sequences.	the complete nucleotide sequences of 5s ribosomal rnas from rhodocyclus gelatinosa, rhodobacter sphaeroides, and pseudomonas cepacia were determined. comparisons of these 5s rna sequences show that rather than being phylogenetically related to one another, the two photosynthetic bacterial 5s rna sequences show that rather than being phylogenetically related to one another, the two photosynthetic bacterial 5s rnas share more sequence and signature homology with the rnas of two nonphotosynthetic ...	1985	11542018
closed water recirculating system for fish rearing equipped with bioreactor capable of simultaneous nitrification and denitrification.	five crucian carp, carassius auratus langsdorfiicarps had been reared in a closed water recirculating system. the system was equipped with the compact bioreactor using the plate gels capable of both nitrification and denitrification in a single unit. ammonia and nitrite concentrations in the rearing water had been maintained below 0.05 mg-n/l, and nitrate concentration also controlled between 2 and 8 mg-n/l with the bioreactor. as concerns nitrogen budget in the closed system, 95.0% of nitrogen ...	1999	11542800
catalytic protein film voltammetry from a respiratory nitrate reductase provides evidence for complex electrochemical modulation of enzyme activity.	the first step in the respiratory reduction of nitrate to dinitrogen in paracoccus pantotrophus is catalyzed by the quinol-nitrate oxidoreductase narghi. this membrane-anchored protein directs electrons from quinol oxidation at the membrane anchor, nari, to the site of nitrate reduction in the membrane extrinsic [fe-s] cluster and mo-bis-mgd containing dimer, nargh. liberated from the membrane, nargh retains its nitrate reductase activity and forms films on graphite and gold electrodes within wh ...	2001	11560477
crystal structure of chaperonin-60 from paracoccus denitrificans.	the crystal structure of chaperonin-60 from paracoccus denitrificans (p.cpn60) has been determined at 3.2 a resolution by the molecular replacement method. two heptameric rings of identical subunits of p.cpn60 in adjacent asymmetric units are stacked in a back-to-back manner and form a cylinder, as found in groel, cpn60 from escherichia coli. with respect to the unliganded groel structure, each subunit of p.cpn60 tilts 2 degrees outwards and the apical domain twists 4 degrees counter-clockwise i ...	2001	11563912
cytochrome complex essential for photosynthetic oxidation of both thiosulfate and sulfide in rhodovulum sulfidophilum.	many photosynthetic bacteria use inorganic sulfur compounds as electron donors for carbon dioxide fixation. a thiosulfate-induced cytochrome c has been purified from the photosynthetic alpha-proteobacterium rhodovulum sulfidophilum. this cytochrome c(551) is a heterodimer of a diheme 30-kda soxa subunit and a monoheme 15-kda soxx subunit. the cytochrome c(551) structural genes are part of an 11-gene sox locus. sequence analysis suggests that the ligands to the heme iron in soxx are a methionine ...	2001	11567011
re-engineering monovalent cation binding sites of methylamine dehydrogenase: effects on spectral properties and gated electron transfer.	methylamine dehydrogenase (madh) is a tryptophan tryptophylquinone (ttq)-dependent enzyme that catalyzes the oxidative deamination of primary amines. monovalent cations are known to affect the spectral properties of madh and to influence the rate of the gated electron transfer (et) reaction from substrate-reduced madh to amicyanin. two putative monovalent cation binding sites in madh have been identified by x-ray crystallography [labesse, g., ferrari, d., chen, z.-w., rossi, g.-l., kuusk, v., mc ...	2001	11591147
solution structure and dynamics of the functional domain of paracoccus denitrificans cytochrome c(552) in both redox states.	a soluble and fully functional 10.5 kda fragment of the 18.2 kda membrane-bound cytochrome c(552) from paracoccus denitrificans has been heterologously expressed and (13)c/(15)n-labeled to study the structural features of this protein in both redox states. well-resolved solution structures of both the reduced and oxidized states have been determined using high-resolution heteronuclear nmr. the overall protein topology consists of two long terminal helices and three shorter helices surrounding th ...	2001	11591150
identification of the partitioning site within the repabc-type replicon of the composite paracoccus versutus plasmid ptav1.	the replicator region of composite plasmid ptav1 of paracoccus versutus (included in mini-replicon ptav320) belongs to the family of repabc replicons commonly found in plasmids harbored by agrobacterium and rhizobium spp. the repabc replicons encode three genes clustered in an operon, which are involved in partitioning (repa and repb) and replication (repc). in order to localize the partitioning site of ptav320, the two identified incompatibility determinants of this mini-replicon (inc1, located ...	2001	11591666
effect of organics on sulfur-utilizing autotrophic denitrification under mixotrophic conditions.	sulfur-utilizing denitrification can be performed by denitrifying sulfur bacteria under autotrophic and heterotrophic conditions. to investigate the effect of organics (methanol and landfill leachate) on sulfur-utilizing denitrification, six laboratory-scale sulfur packed columns were operated under autotrophic, mixotrophic and heterotrophic conditions for approximately 1 year. the performance of the columns was monitored by measuring the ph, nitrate, nitrite, sulfate, sulfide, alkalinity dissol ...	2001	11604167
characterization of the reduction of selenate and tellurite by nitrate reductases.	preliminary studies showed that the periplasmic nitrate reductase (nap) of rhodobacter sphaeroides and the membrane-bound nitrate reductases of escherichia coli are able to reduce selenate and tellurite in vitro with benzyl viologen as an electron donor. in the present study, we found that this is a general feature of denitrifiers. both the periplasmic and membrane-bound nitrate reductases of ralstonia eutropha, paracoccus denitrificans, and paracoccus pantotrophus can utilize potassium selenate ...	2001	11679335
reaction of carbon monoxide with the reduced active site of bacterial nitric oxide reductase.	bacterial nitric oxide reductase (nor), a member of the superfamily of heme-copper oxidases, catalyzes the two-electron reduction of nitric oxide to nitrous oxide. the key feature that distinguishes nor from the typical heme-copper oxidases is the elemental composition of the dinuclear center, which contains non-heme iron (feb) rather than copper (cub). uv-vis electronic absorption and room-temperature magnetic circular dichroism (rt-mcd) spectroscopies showed that co binds to fe(ii) heme b3 to ...	2001	11683646
a novel denitrifying bacterial isolate that degrades trimethylamine both aerobically and anaerobically via two different pathways.	the aerobic and anaerobic degradation of trimethylamine by a newly isolated denitrifying bacterium from an enrichment culture with trimethylamine inoculated with activated sludge was studied. based on 16s rdna analysis, this strain was identified as a paracoccus sp. the isolate, strain t231, aerobically degraded trimethylamine, dimethylamine and methylamine and released a stoichiometric amount of ammonium ion into the culture fluid as a metabolic product, indicating that these methylated amines ...	2001	11685371
nadh dehydrogenases: from basic science to biomedicine.	this review article is concerned with two on-going research projects in our laboratory, both of which are related to the study of the nadh dehydrogenase enzyme complexes in the respiratory chain. the goal of the first project is to decipher the structure and mechanism of action of the proton-translocating nadh-quinone oxidoreductase (ndh-1) from two bacteria, paracoccus denitrificans and thermus thermophilus hb-8. these microorganisms are of particular interest because of the close resemblance o ...	2001	11695833
active-site residues are critical for the folding and stability of methylamine dehydrogenase.	site-directed mutagenesis was used to alter active-site residues of methylamine dehydrogenase (madh) from paracoccus denitrificans. four residues of the beta subunit of madh which are in close proximity to the tryptophan tryptophylquinone (ttq) prosthetic group were modified. the crystal structure of madh reveals that each of these residues participates in hydrogen bonding interactions with other active-site residues, ttq or water. relatively conservative mutations which removed the potentially ...	2001	11707614
cytochrome cd1, reductive activation and kinetic analysis of a multifunctional respiratory enzyme.	paracoccus pantotrophus cytochrome cd(1) is an enzyme of bacterial respiration, capable of using nitrite in vivo and also hydroxylamine and oxygen in vitro as electron acceptors. we present a comprehensive analysis of the steady state kinetic properties of the enzyme with each electron acceptor and three electron donors, pseudoazurin and cytochrome c(550), both physiological, and the non-physiological horse heart cytochrome c. at ph 5.8, optimal for nitrite reduction, the enzyme has a turnover n ...	2002	11709555
cytochromes c(550), c(552), and c(1) in the electron transport network of paracoccus denitrificans: redundant or subtly different in function?	paracoccus denitrificans strains with mutations in the genes encoding the cytochrome c(550), c(552), or c(1) and in combinations of these genes were constructed, and their growth characteristics were determined. each mutant was able to grow heterotrophically with succinate as the carbon and free-energy source, although their specific growth rates and maximum cell numbers fell variably behind those of the wild type. maximum cell numbers and rates of growth were also reduced when these strains wer ...	2001	11717258
structure of a quinohemoprotein amine dehydrogenase with an uncommon redox cofactor and highly unusual crosslinking.	the crystal structure of the heterotrimeric quinohemoprotein amine dehydrogenase from paracoccus denitrificans has been determined at 2.05-a resolution. within an 82-residue subunit is contained an unusual redox cofactor, cysteine tryptophylquinone (ctq), consisting of an orthoquinone-modified tryptophan side chain covalently linked to a nearby cysteine side chain. the subunit is surrounded on three sides by a 489-residue, four-domain subunit that includes a diheme cytochrome c. both subunits si ...	2001	11717396
direct interaction between a membrane domain subunit and a connector subunit in the h(+)-translocating nadh-quinone oxidoreductase.	when paracoccus denitrificans membranes were treated with a crosslinker, m-maleimidobenzoyl-n-hydroxysuccinimide ester (mbs), a cross-linked product of m(r) approximately 31 kda was found which reacted with antibodies against the hydrophobic subunit nqo7 and the connector subunit nqo6. nai treatment of the paracoccus membranes before, but not after, the crosslinking step prevented the formation of the 31 kda band. when nqo7 and nqo6 were coexpressed in escherichia coli, both subunits were locate ...	2001	11728457
carboxyl residues in the iron-sulfur protein are involved in the proton pumping activity of p. denitrificans bc(1) complex.	a study is presented on chemical modification of the three subunit paracoccus denitrificans bc(1) complex. n-(ethoxycarbonyl)-2-ethoxy-1,2-dihydroquinoline (eedq) treatment caused a loss of the proton pumping activity of liposome-reconstituted bc(1) complex. a similar effect, which is referred to as the decoupling effect, resulted upon reaction of n,n'-dicyclohexylcarbodiimide (dccd) with the complex. direct measurement of the binding of eedq to the complex subunits, performed in the presence of ...	2001	11735423
a glutathione-dependent formaldehyde-activating enzyme (gfa) from paracoccus denitrificans detected and purified via two-dimensional proton exchange nmr spectroscopy.	the formation of s-hydroxymethylglutathione from formaldehyde and glutathione is a central reaction in the consumption of the cytotoxin formaldehyde in some methylotrophic bacteria as well as in many other organisms. we describe here the discovery of an enzyme from paracoccus denitrificans that accelerates this spontaneous condensation reaction. the rates of s-hydroxymethylglutathione formation and cleavage were determined under equilibrium conditions via two-dimensional proton exchange nmr spec ...	2002	11741920
transcription factor fnrp from paracoccus denitrificans contains an iron-sulfur cluster and is activated by anoxia: identification of essential cysteine residues.	the paracoccus denitrificans transcription factor fnrp has been characterized using artificial fnr-dependent promoter-lacz fusion plasmids in escherichia coli. fnrp can activate both class i and class ii fnr-dependent promoters in response to anoxia but shows a marked preference for the class ii promoter, where the fnr binding site is centered at -41.5 with respect to the transcription start site. fnrp was found to be inactive in an iscs mutant in vivo, demonstrating a requirement for cysteine d ...	2002	11751828
respiratory chain supercomplexes.	respiratory chain supercomplexes have been isolated from mammalian and yeast mitochondria, and bacterial membranes. functional roles of respiratory chain supercomplexes are catalytic enhancement, substrate channelling, and stabilization of complex i by complex iii in mammalian cells. bacterial supercomplexes are characterized by their relatively high detergent-stability compared to yeast or mammalian supercomplexes that are stable to sonication. the mobility of substrate cytochrome c increases i ...	2001	11798023
replacement of the methionine axial ligand in cytochrome c(550) by a lysine: effects on the haem electronic structure.	the prosthetic group of low-spin haem proteins is an iron porphyrin with two axial ligands, typically histidine, methionine or lysine. determining the geometry of the axial ligands is an important step in structural characterisation, particularly in the paramagnetic oxidised forms. this work extends earlier studies of the hyperfine nuclear magnetic resonance (nmr) shifts of haem substituents in bis-his and his-met cytochromes to his-lys co-ordination in the m100k mutant of paracoccus versutus cy ...	2002	11801251
succinate:quinone oxidoreductase in the bacteria paracoccus denitrificans and bacillus subtilis.	an overview of the present knowledge about succinate:quinone oxidoreductase in paracoccus denitrificans and bacillus subtilis is presented. p. denitrificans contains a monoheme succinate:ubiquinone oxidoreductase that is similar to that of mammalian mitochondria with respect to composition and sensitivity to carboxin. results obtained with carboxin-resistant p. denitrificans mutants provide information about quinone-binding sites on the enzyme and the molecular basis for the resistance. b. subti ...	2002	11803018
purification and properties of d-(-)-3-hydroxybutyrate oligomer hydrolase of paracoccus denitrificans.	d-(-)-3-hydroxybutyrate (3hb) oligomer hydrolase was purified from paracoccus denitrificans. the enzyme was a monomeric protein with an approximate molecular mass of 31 kda. the isoelectric point of the enzyme was 5.2. optimum temperature and ph were 35-40 degrees c and 8.0, respectively. the enzyme activity was not affected by sulfhydryl reagents but strongly inhibited by serine proteinase inhibitors. both 3hb trimer and 3hb dimer were hydrolyzed by the enzyme, indicating that the enzyme is not ...	2002	11814660
the role of the cross-link his-tyr in the functional properties of the binuclear center in cytochrome c oxidase.	resonance raman and fourier transform infrared spectroscopies have been used to study the aa(3)-type cytochrome c oxidase and the y280h mutant from paracoccus denitrificans. the stability of the binuclear center in the absence of the tyr(280)-his(276) cross-link is not compromised since heme a(3) retains the same proximal environment, spin, and coordination state as in the wild type enzyme in both the oxidized and reduced states. we observe two c-o modes in the y280h mutant at 1966 and 1975 cm(- ...	2002	11825904
proton and electron pathways in the bacterial nitric oxide reductase.	electron- and proton-transfer reactions in bacterial nitric oxide reductase (nor) have been investigated by optical spectroscopy and electrometry. in liposomes, nor does not show any generation of an electric potential during steady-state turnover. this electroneutrality implies that protons are taken up from the same side of the membrane as electrons during catalysis. intramolecular electron redistribution after photolysis of the partially reduced co-bound enzyme shows that the electron transfe ...	2002	11841226
periplasmic nitrate reductase (napabc enzyme) supports anaerobic respiration by escherichia coli k-12.	periplasmic nitrate reductase (napabc enzyme) has been characterized from a variety of proteobacteria, especially paracoccus pantotrophus. whole-genome sequencing of escherichia coli revealed the structural genes napfdaghbc, which encode napabc enzyme and associated electron transfer components. e. coli also expresses two membrane-bound proton-translocating nitrate reductases, encoded by the narghji and narzywv operons. we measured reduced viologen-dependent nitrate reductase activity in a serie ...	2002	11844760
biosynthesis of zeaxanthin via mevalonate in paracoccus species strain pta-3335. a product-based retrobiosynthetic study.	cultures of the zeaxanthin-producing bacterium paracoccus species strain pta-3335 (formerly flavobacterium) were grown with supplements of (13)c-labeled glucose. zeaxanthin was isolated and analyzed by (13)c nmr spectroscopy. the data showed that the isoprenoid precursors of zeaxanthin were biosynthesized via the mevalonate pathway. the microorganism was found to utilize glucose mainly via the entner-doudoroff pathway.	2002	11856031
the ph-dependent redox inactivation of amicyanin from paracoccus versutus as studied by rapid protein-film voltammetry.	the redox properties of the blue copper protein amicyanin have been studied with slow and fast scan protein-film cyclic voltammetry. at slow scan rates, which reveal the thermodynamics of the redox reactions, the reduction potential of amicyanin depends on ph in a sigmoidal manner, and the data can be analysed in terms of electron transfer being coupled to a single protonatable group with pka(red)=6.3 and pka(ox) < or = 3.2 at 22 degrees c. voltammetry at higher scan rates reveals the kinetics a ...	2002	11862545
protein--protein docking of electron transfer complexes: cytochrome c oxidase and cytochrome c.	electron transferring protein complexes form only transiently and the crystal structures of electron transfer protein--protein complexes involving cytochrome c could so far be determined only for the pairs of yeast cytochrome c peroxidase (ccp) with iso-1-cytochrome c (iso-1-cyt c) and with horse heart cytochrome c (cyt c). this article presents models from computational docking for complexes of cytochrome c oxidase (cox) from paracoccus denitrificans with horse heart cytochrome c, and with its ...	2002	11870867
characterization of the replicator region of megaplasmid ptav3 of paracoccus versutus and search for plasmid-encoded traits.	the replicon of the ptav3 megaplasmid (approx. 400 kb) of paracoccus versutus has been localized to a 4center dot3 kb ecori restriction fragment and its entire nucleotide sequence determined. the g+c content of the entire sequence is 66 mol%, which is within the range (62-66 mol%) previously determined for p. versutus total dna. orf1 encodes a replication initiation protein rep (47.2 kda), which shares substantial similarity with putative proteins of the coxiella burnetii plasmids qph1 and qpdv, ...	2002	11882723
semiautomatic sequence-specific assignment of proteins based on the tertiary structure--the program st2nmr.	the sequence-specific assignment of resonances is still the most time-consuming procedure that is necessary as the first step in high-resolution nmr studies of proteins. in many cases a reliable three-dimensional (3d) structure of the protein is available, for example, from x-ray spectroscopy or homology modeling. here we introduce the st2nmr program that uses the 3d structure and nuclear overhauser effect spectroscopy (noesy) peak list(s) to evaluate and optimize trial sequence-specific assignm ...	2002	11908496
a model for the thermal unfolding of amicyanin.	in the present study the thermal unfolding of amicyanin has been addressed using differential scanning calorimetry, fluorescence emission, optical density, circular dichroism and electron paramagnetic resonance. the combined use of these techniques has allowed us to assess, during unfolding of the protein, its global conformational changes in relationship to the local structural modifications occurring in the copper environment and close to the fluorescent chromophore trp46 of the protein. the t ...	2002	11908848
characterization of the membrane domain nqo11 subunit of the proton-translocating nadh-quinone oxidoreductase of paracoccus denitrificans.	the proton-translocating nadh-quinone oxidoreductase (ndh-1) of paracoccus denitrificans consists of at least 14 unlike subunits (designated nqo1-14). the ndh-1 is composed of two segments (the peripheral and membrane segments). the membrane domain segment appears to be made up of seven subunits (nqo7, -8, -10-14). in this report, the characterization of the paracoccus nqo11 subunit has been investigated. an antibody against the c-terminal 12 amino acid residues of the paracoccus nqo11 subunit ( ...	2002	11914084
emended description of paracoccus kondratievae.	an aerobic, facultatively chemolithotrophic and methylotrophic strain, gb, was isolated from a maize rhizosphere. on the basis of comparative analysis of its phenotypic and genotypic properties, it is proposed that strain gb(t) (= vkm b-2222t = ncimb 13773t) be assigned to the genus paracoccus as paracoccus kondratievae sp. nov.	2002	11931183
nitric oxide signaling and no dependent transcriptional control in bacterial denitrification by members of the fnr-crp regulator family.	bacterial denitrification transforms nitrate to dinitrogen. the process is expressed facultatively in response to environmental conditions. around 50 components make up the denitrification apparatus and its assembly pathways. we are beginning to understand how exogenous signals provided by oxygen and n oxides are processed for activating the underlying gene programs. key signals are provided by nitrate, nitric oxide, and a low oxygen tension. in the genus pseudomonas the nitrate signal is proces ...	2002	11931559
nitrite reduction in paracoccus sp. is affected by a novel plasmid pyr1.	two relatively low-copy plasmids of 9 and 16 kb were found to comprise the extrachromosomal dna of a paracoccus strain. reduction of nitrate by plasmid-cured cells resulted in a significant intermediate nitrite accumulation as compared to wild-type cells. by examining nitrate reduction by transformants containing one of the two plasmids, it was found that nitrite accumulation was influenced by the 9.0-kb plasmid, designated as pyr1. subcloning analysis showed that a 1.8-kb fragment of this plasm ...	2002	11934503
nitric oxide reacts with the single-electron reduced active site of cytochrome c oxidase.	the reduction kinetics of the mutants k354m and d124n of the paracoccus denitrificans cytochrome oxidase (heme aa(3)) by ruthenium hexamine was investigated by stopped-flow spectrophotometry in the absence/presence of no. quick heme a reduction precedes the biphasic heme a(3) reduction, which is extremely slow in the k354m mutant (k(1) = 0.09 +/- 0.01 s(-1); k(2) = 0.005 +/- 0.001 s(-1)) but much faster in the d124n aa(3) (k(1) = 21 +/- 6 s(-1); k(2) = 2.2 +/- 0.5 s(-1)). no causes a very large ...	2002	11950842
effect of temperature on biofiltration of nitric oxide.		2001	11963849
mo(v) co-ordination in the periplasmic nitrate reductase from paracoccus pantotrophus probed by electron nuclear double resonance (endor) spectroscopy.	the first electron nuclear double resonance (endor) study of a member of the mo-bis-molybdopterin guanine dinucleotide family of molybdoenzymes is presented, using the periplasmic nitrate reductase from paracoccus pantotrophus. rapid freeze-quenched time-resolved epr revealed that during turnover the intensity of a mo(v) epr signal known as high-g [resting] increases. this signal is split by two interacting protons that are not solvent-exchangeable. x-band proton-endor analysis resolved broad sy ...	2002	11964184
two domains of a dual-function nark protein are required for nitrate uptake, the first step of denitrification in paracoccus pantotrophus.	uptake of nitrate into the cytoplasm is the first but least well understood step of denitrification; no gene has previously been identified to be necessary for this process. upstream from the structural genes of the membrane-bound nitrate reductase (narghji) in paracoccus pantotrophus there is a fusion of two genes, each homologous to members of the nark family. the single open reading frame is predicted to encode 24 transmembrane helices, comprising two domains, nark1 and nark2. analysis of bot ...	2002	11967076
nitric-oxide reductase. structure and properties of the catalytic site from resonance raman scattering.	we have applied resonance raman spectroscopy to investigate the properties of the dinuclear center of oxidized, reduced, and no-bound nitric-oxide reductase from paracoccus denitrificans. the spectra of the oxidized enzyme show two distinct nu(as)(fe-o-fe) modes at 815 and 833 cm(-1) of the heme/non-heme diiron center. the splitting of the fe-o-fe mode suggests that two different conformations (open and closed) are present in the catalytic site of the enzyme. we find evidence from deuterium exch ...	2002	11971903