Publications

the role of the d- and k-pathways of proton transfer in the function of the haem-copper oxidases.	the x-ray structures of several haem-copper oxidases now at hand have given important constraints on how these enzymes function. yet, dynamic data are required to elucidate the mechanisms of electron and proton transfer, the activation of o(2) and its reduction to water, as well as the still enigmatic mechanism by which these enzymes couple the redox reaction to proton translocation. here, some recent observations will be briefly reviewed with special emphasis on the functioning of the so-called ...	2000	11004470
proton-coupled structural changes upon binding of carbon monoxide to cytochrome cd1: a combined flash photolysis and x-ray crystallography study.	we have investigated dynamic events after flash photolysis of co from reduced cytochrome cd(1) nitrite reductase (nir) from paracoccus pantotrophus (formerly thiosphaera pantotropha). upon pulsed illumination of the cytochrome cd(1)-co complex, at 460 nm, a rapid (<50 ns) absorbance change, attributed to dissociation of co, was observed. this was followed by a biphasic rearrangement with rate constants of 1.7 x 10(4) and 2.5 x 10(3) s(-1) at ph 8.0. both parts of the biphasic rearrangement phase ...	2000	10998233
quantum mechanical interpretation of nitrite reduction by cytochrome cd1 nitrite reductase from paracoccus pantotrophus.	the reduction of nitrite to nitric oxide in respiratory denitrification is catalyzed by a cytochrome cd(1) nitrite reductase in paracoccus pantotrophus (formerly known as thiosphaera pantotropha lmd 92.63). high-resolution structures are available for the fully oxidized [fülöp, v., moir, j. w., ferguson, s. j., and hajdu, j. (1995) cell 81, 369-377; baker, s. c., saunders, n. f., willis, a. c., ferguson, s. j., hajdu, j., and fülöp, v. (1997) j. mol. biol. 269, 440-455] and fully reduced forms o ...	2000	10998232
presence of bacterial 16s ribosomal rna gene segments in human intestinal lymph follicles.	there is currently no information regarding microbial agents inside the intestinal lymph follicles.	2000	10994621
conversion of methylamine dehydrogenase to a long-chain amine dehydrogenase by mutagenesis of a single residue.	methylamine dehydrogenase (madh) is a tryptophan tryptophylquinone (ttq) dependent enzyme that catalyzes the oxidative deamination of primary amines. amino acid residues of both the ttq-bearing beta subunit and the noncatalytic alpha subunit line a substrate channel that leads from the protein surface to the enzyme active site. phe55 of the alpha subunit is located at the opening of the active site. conversion of alphaphe55 to alanine dramatically alters the substrate preference of madh. the k(m ...	2000	10985763
characteristics of the aerobic respiratory chains of the microaerophiles campylobacter jejuni and helicobacter pylori.	the respiratory chain enzymes of microaerophilic bacteria should play a major role in their adaptation to growth at low oxygen tensions. the genes encoding the putative nadh:quinone reductases (ndh-1), the ubiquinol:cytochrome c oxidoreductases (bc1 complex) and the terminal oxidases of the microaerophiles campylobacter jejuni and helicobacter pylori were analysed to identify structural elements that may be required for their unique energy metabolism. the gene clusters encoding ndh-1 in both c. ...	2000	10985736
heme o is present in paracoccus denitrificans cells and accumulates under anoxic growth.	in spite of the published claims to the contrary, paracoccus denitrificans was shown to contain a heme derivative, virtually indistinguishable from the escherichia coli heme o on the basis of the reverse-phase high-performance liquid chromatography and maldi-tof mass spectrometry analyses. aeration of the anoxically grown culture resulted in the disappearance of a significant portion of this compound with concomitant build-up of heme a.	2000	10981691
the nosx and nirx proteins of paracoccus denitrificans are functional homologues: their role in maturation of nitrous oxide reductase.	the nos (nitrous oxide reductase) operon of paracoccus denitrificans contains a nosx gene homologous to those found in the nos operons of other denitrifiers. nosx is also homologous to nirx, which is so far unique to p. denitrificans. single mutations of these genes did not result in any apparent phenotype, but a double nosx nirx mutant was unable to reduce nitrous oxide. promoter-lacz assays and immunoblotting against nitrous oxide reductase showed that the defect was not due to failure of expr ...	2000	10960107
purification, crystallization and preliminary crystallographic studies of an integral membrane protein, cytochrome bo3 ubiquinol oxidase from escherichia coli.	cytochrome bo(3) ubiquinol oxidase has been successfully purified for crystallization. single crystals of this integral membrane protein diffract x-rays to 3.5 a resolution and belong to the orthorhombic space group c222(1). from the diffraction data, the unit-cell parameters were determined to be a = 91.3, b = 370.3, c = 232.4 a. the crystals have a solvent content of 59% and contain two molecules per asymmetric unit. a search model generated from the structures of cytochrome c oxidase from par ...	2000	10944359
novel genes coding for lithotrophic sulfur oxidation of paracoccus pantotrophus gb17.	the gene region coding for lithotrophic sulfur oxidation of paracoccus pantotrophus gb17 is located on a 13-kb insert of plasmid peg12. upstream of the previously described six open reading frames (orfs) soxabcdef with a partial sequence of soxa and soxf (c. wodara, f. bardischewsky, and c. g. friedrich, j. bacteriol. 179:5014-5023, 1997), 4,350 bp were sequenced. the sequence completed soxa, and uncovered six new orfs upstream of soxa, designated orf1, orf2, and orf3, and soxxyz. orf1 could enc ...	2000	10940005
expression of prokaryotic and eukaryotic cytochromes c in escherichia coli.	c-type cytochromes from various sources show substantial structural conservation. for the covalent attachment of heme groups to apocytochromes, however, three different enzyme systems have been described so far. we have examined the ability of the heme ligation systems of escherichia coli and of saccharomyces cerevisiae to process cytochromes from s. cerevisiae, paracoccus denitrificans, and synechocystis sp. pcc 6803. e. coli's maturation system with at least eight different proteins accepted a ...	2000	10924906
induction of photochemical auto-reduction of cytochrome-c oxidase by an organic peroxide.	cytochrome-c oxidase aa3 (cco) from paracoccus denitrificans interacts with tertiary butyl hydroperoxide (t-bu-o-o-h, tbhp) by forming an adduct as indicated by an absorption shift at 408/432 nm and the induction of photochemical autoreduction. the adduct was stable at room temperature for several days even under aerobic conditions. upon irradiation (413 nm) of the adduct, a photoproduct, similar to the oxygenated mixed valence species (607 nm form), was formed, as indicated by the 418/442 and 6 ...	2000	10924905
the nadh oxidation domain of complex i: do bacterial and mitochondrial enzymes catalyze ferricyanide reduction similarly?	the hexammineruthenium (har) and ferricyanide reductase activities of complex i (h+-translocating nadh:ubiquinone reductase) from paracoccus denitrificans and bovine heart mitochondria were studied. the rates of har reduction are high, and its steady-state kinetics is similar in both p. denitrificans and bovine complex i. the deamino-nadh:har reductase activity of complex i from both sources is significantly higher than the respective activity in the presence of nadh. the har reductase activity ...	2000	10924899
the met99gln mutant of amicyanin from paracoccus versutus.	the axial copper ligand methionine has been replaced by a glutamine in the cupredoxin amicyanin from paracoccus versutus. dynamic and structural characteristics of the mutant have been studied in detail using uv/vis, epr, nmr, cyclic voltammetry, and isomorphous metal replacement. m99q amicyanin is a blue copper protein with significant spectral and structural similarities to the other cupredoxins umecyanin, stellacyanin, and m121q azurin. in addition, the functional properties of m99q amicyanin ...	2000	10924152
exploring the membrane domain of the reduced nicotinamide adenine dinucleotide-quinone oxidoreductase of paracoccus denitrificans: characterization of the nqo7 subunit.	the proton-translocating reduced nicotinamide adenine dinucleotide- (nadh-) quinone oxidoreductase (ndh-1) of paracoccus denitrificans is composed of at least 14 different subunits (nqo1-14). in addition, this enzyme complex houses one flavin mononucleotide (fmn) and 7-8 iron-sulfur clusters as cofactors. the expression and partial characterization of the nqo7 subunit, one of the seven subunits that constitute the hydrophobic sector of the enzyme complex, have been performed and are reported her ...	2000	10924136
time-resolved infrared spectroscopy reveals a stable ferric heme-no intermediate in the reaction of paracoccus pantotrophus cytochrome cd1 nitrite reductase with nitrite.	cytochrome cd(1) is a respiratory enzyme that catalyzes the physiological one-electron reduction of nitrite to nitric oxide. the enzyme is a dimer, each monomer containing one c-type cytochrome center and one active site d(1) heme. we present stopped-flow fourier transform infrared data showing the formation of a stable ferric heme d(1)-no complex (formally d(1)fe(ii)-no(+)) as a product of the reaction between fully reduced paracoccus pantotrophus cytochrome cd(1) and nitrite, in the absence of ...	2000	10922371
isolation and characterization of diverse halobenzoate-degrading denitrifying bacteria from soils and sediments.	denitrifying bacteria capable of degrading halobenzoates were isolated from various geographical and ecological sites. the strains were isolated after initial enrichment on one of the monofluoro-, monochloro-, or monobromo-benzoate isomers with nitrate as an electron acceptor, yielding a total of 33 strains isolated from the different halobenzoate-utilizing enrichment cultures. each isolate could grow on the selected halobenzoate with nitrate as the terminal electron acceptor. the isolates obtai ...	2000	10919805
a soxa gene, encoding a diheme cytochrome c, and a sox locus, essential for sulfur oxidation in a new sulfur lithotrophic bacterium.	a mobilizable suicide vector, psup5011, was used to introduce tn5-mob in a new facultative sulfur lithotrophic bacterium, kct001, to generate mutants defective in sulfur oxidation (sox(-)). the sox(-) mutants were unable to oxidize thiosulfate while grown mixotrophically in the presence of thiosulfate and succinate. the mutants were also impaired in oxidizing other reduced sulfur compounds and elemental sulfur as evident from the study of substrate oxidation by the whole cells. sulfite oxidase a ...	2000	10894738
proton translocation by cytochrome c oxidase can take place without the conserved glutamic acid in subunit i.	a glutamic acid residue in subunit i of the heme-copper oxidases is highly conserved and has been directly implicated in the o(2) reduction and proton-pumping mechanisms of these respiratory enzymes. its mutation to residues other than aspartic acid dramatically inhibits activity, and proton translocation is lost. however, this glutamic acid is replaced by a nonacidic residue in some structurally distant members of the heme-copper oxidases, which have a tyrosine residue in the vicinity. here, us ...	2000	10891065
solution structure of the functional domain of paracoccus denitrificans cytochrome c552 in the reduced state.	in order to determine the solution structure of paracoccus denitrificans cytochrome c552 by nmr, we cloned and isotopically labeled a 10.5-kda soluble fragment (100 residues) containing the functional domain of the 18.2-kda membrane-bound protein. using uniformly 15n-enriched samples of cytochrome c552 in the reduced state, a variety of two-dimensional and three-dimensional heteronuclear double-resonance nmr experiments was employed to achieve complete 1h and 15n assignments. a total of 1893 dis ...	2000	10866825
specific mutagenesis of the rieske iron-sulfur protein in rhodobacter sphaeroides shows that both the thermodynamic gradient and the pk of the oxidized form determine the rate of quinol oxidation by the bc(1) complex.	in the rieske iron-sulfur protein (isp) of the ubiquinol:cytochrome c(2) oxidoreductase (bc(1) complex) of rhodobacter sphaeroides, residue tyr 156 is located close to the iron-sulfur cluster. previous studies of the equivalent residue in both saccharomyces cerevisiae [denke, e., merbitz-zahradnik, t., hatzfeld, o. m., snyder, c. h., link, t. a., and trumpower, b. l. (1998) j. biol. chem. 273, 9085-9093] and paracoccus denitrificans [schroter, t., hatzfeld, o. m., gemeinhardt, s., korn, m., frie ...	2000	10858292
the structure and dynamics in solution of cu(i) pseudoazurin from paracoccus pantotrophus.	the solution structure and backbone dynamics of cu(i) pseudoazurin, a 123 amino acid electron transfer protein from paracoccus pantotrophus, have been determined using nmr methods. the structure was calculated to high precision, with a backbone rms deviation for secondary structure elements of 0.35+/-0.06 a, using 1,498 distance and 55 torsion angle constraints. the protein has a double-wound greek-key fold with two alpha-helices toward its c-terminus, similar to that of its oxidized counterpart ...	2000	10850794
tracing the d-pathway in reconstituted site-directed mutants of cytochrome c oxidase from paracoccus denitrificans.	heme-copper terminal oxidases use the free energy of oxygen reduction to establish a transmembrane proton gradient. while the molecular mechanism of coupling electron transfer to proton pumping is still under debate, recent structure determinations and mutagenesis studies have provided evidence for two pathways for protons within subunit i of this class of enzymes. here, we probe the d-pathway by mutagenesis of the cytochrome c oxidase of the bacterium paracoccus denitrificans; amino acid replac ...	2000	10841754
reactive oxygen species generated at mitochondrial complex iii stabilize hypoxia-inducible factor-1alpha during hypoxia: a mechanism of o2 sensing.	during hypoxia, hypoxia-inducible factor-1alpha (hif-1alpha) is required for induction of a variety of genes including erythropoietin and vascular endothelial growth factor. hypoxia increases mitochondrial reactive oxygen species (ros) generation at complex iii, which causes accumulation of hif-1alpha protein responsible for initiating expression of a luciferase reporter construct under the control of a hypoxic response element. this response is lost in cells depleted of mitochondrial dna (rho(0 ...	2000	10833514
aerobic denitrifiers isolated from diverse natural and managed ecosystems.	twenty-eight bacterial strains were isolated from an ecosystem adapted to fluctuating oxic-anoxic conditions. this ecosystem comprised a mixture of different natural and wastewater treatment environments. among the 28 strains isolated, 10 exhibited aerobic denitrifying activity, i.e., co-respiration of oxygen and nitrate and simultaneous production of nitrite by 4 of them and of nitrogen gas by the remaining 6. comparisons between the 16s rdna sequences of the 10 strains showed that 3 of them we ...	2000	10833227
binding of o(2) and its reduction are both retarded by replacement of valine 279 by isoleucine in cytochrome c oxidase from paracoccus denitrificans.	the crystal structure of the heme-copper oxidases suggested a putative channel of oxygen entry into the heme-copper site of o(2) reduction. changing a conserved valine near this center in cytochrome bo(3) of escherichia coli to isoleucine caused a significant increase in the apparent k(m) for oxygen with little or no change in v(max), suggesting that oxygen diffusion had been partially blocked [riistama, s., puustinen, a., garcía-horsman, a., iwata, s., michel, h., and wikström, m. (1996) biochi ...	2000	10828950
the caa(3) terminal oxidase of rhodothermus marinus lacking the key glutamate of the d-channel is a proton pump.	the thermohalophilic bacterium rhodothermus marinus expresses a caa(3)-type dioxygen reductase as one of its terminal oxidases. the subunit i amino acid sequence shows the presence of all the essential residues of the d- and k-proton channels, defined in most heme-copper oxidases, with the exception of the key glutamate residue located in the middle of the membrane dielectric (e278 in paracoccus denitrificans). on the basis of homology modeling studies, a tyrosine residue (y256, r. marinus numbe ...	2000	10828946
x-ray crystallographic study of cyanide binding provides insights into the structure-function relationship for cytochrome cd1 nitrite reductase from paracoccus pantotrophus.	we present a 1.59-a resolution crystal structure of reduced paracoccus pantotrophus cytochrome cd(1) with cyanide bound to the d(1) heme and his/met coordination of the c heme. fe-c-n bond angles are 146 degrees for the a subunit and 164 degrees for the b subunit of the dimer. the nitrogen atom of bound cyanide is within hydrogen bonding distance of his(345) and his(388) and either a water molecule in subunit a or tyr(25) in subunit b. the ferrous heme-cyanide complex is unusually stable (k(d) a ...	2000	10827177
complete 1h, 15n and 13c assignment of the functional domain of paracoccus denitrificans cytochrome c552 in the reduced state.		2000	10826890
partially unfolded species populated during equilibrium denaturation of the beta-sheet protein y74w apo-pseudoazurin.	apo-pseudoazurin is a single domain cupredoxin. we have engineered a mutant in which a unique tryptophan replaces the tyrosine residue found in the tyrosine corner of this greek key protein, a region that has been proposed to have an important role in folding. equilibrium denaturation of y74w apo-pseudoazurin demonstrated multistate unfolding in urea (ph 7.0, 0.5 m na(2)so(4) at 15 degrees c), in which one or more partially folded species are populated in 4. 3 m urea. using a variety of biophysi ...	2000	10801317
characterization of a new type of sulfite dehydrogenase from paracoccus pantotrophus gb17.	the periplasmic sulfite dehydrogenase of paracoccus pantotrophus gb17 was purified to homogeneity by a four-step procedure from cells grown lithoautotrophically with thiosulfate. the molecular mass of native sulfite dehydrogenase was 190 kda as determined by native gradient page. sds-page showed sulfite dehydrogenase to comprise two subunits with molecular masses of 47 kda and 50 kda, suggesting an alpha2beta2 structure. the n-terminal amino acid sequence and immunochemical analysis using soxc-s ...	2000	10795683
single-electron reduction of the oxidized state is coupled to proton uptake via the k pathway in paracoccus denitrificans cytochrome c oxidase.	the reductive part of the catalytic cycle of cytochrome c oxidase from paracoccus denitrificans was examined by using time-resolved potential measurements on black lipid membranes. proteoliposomes were adsorbed to the black lipid membranes and ru(ii)(2, 2'-bipyridyl)(3)(2+) was used as photoreductant to measure flash-induced membrane potential generation. single-electron reduction of the oxidized wild-type cytochrome c oxidase reveals two phases of membrane potential generation (tau(1) approxima ...	2000	10781069
crystallization and preliminary x-ray analysis of nitrous oxide reductase from paracoccus pantotrophus.	nitrous oxide reductase is a periplasmic respiratory protein with a novel copper catalytic centre; it catalyses the terminal step, reduction of nitrous oxide to nitrogen, of the bacterial denitrification process. nitrous oxide reductase from paracoccus pantotrophus has been crystallized by the hanging-drop method. a prerequisite for crystallization was the oxidation of the enzyme with potassium ferricyanide in order to obtain homogenous oxidation states of the copper centres. the crystals belong ...	2000	10771440
cytochrome cd(1) from paracoccus pantotrophus exhibits kinetically gated, conformationally dependent, highly cooperative two-electron redox behavior.	each monomer of the dimeric cytochrome cd(1) nitrite reductase from paracoccus pantotrophus contains two hemes: one c-type center and one noncovalently bound d(1) center. potentiometric analysis at 20 degrees c shows substantial cooperativity between the two redox centers in terms of their joint co-reduction (or co-oxidation) at a single apparent potential with an n value of 1.4 +/- 0.1. reproducible hysteresis is demonstrated in the redox titrations. in a reductive titration both centers titrat ...	2000	10757972
oxidase reaction of cytochrome cd(1) from paracoccus pantotrophus.	cytochrome cd(1) (cd(1)nir) from paracoccus pantotrophus, which is both a nitrite reductase and an oxidase, was reduced by ascorbate plus hexaamineruthenium(iii) chloride on a relatively slow time scale (hours required for complete reduction). visible absorption spectroscopy showed that mixing of ascorbate-reduced enzyme with oxygen at ph = 6.0 resulted in the rapid oxidation of both types of heme center in the enzyme with a linear dependence on oxygen concentration. subsequent changes on a long ...	2000	10747791
cloning, characterization, controlled overexpression, and inactivation of the major tributyrin esterase gene of lactococcus lactis.	the gene encoding the major intracellular tributyrin esterase of lactococcus lactis was cloned using degenerate dna probes based on 19 known n-terminal amino acid residues of the purified enzyme. the gene, named esta, was sequenced and found to encode a protein of 258 amino acid residues. the transcription start site was mapped 233 nucleotides upstream of the start codon, and a canonical promoter sequence was identified. the deduced amino acid sequence of the esta product contained the typical g ...	2000	10742212
structure, function, and applications of tryptophan tryptophylquinone enzymes.	tryptophan and tyrosine residues in proteins may be posttranslationally modified to form enzyme cofactors. tryptophan tryptophylquinone (ttq), the cofactor of methylamine dehydrogenase (madh), is formed by covalent cross-linking of two tryptophan residues and incorporation of two oxygen atoms into one of the indole rings to form a quinone. madh converts primary amines to their corresponding aldehydes plus ammonia. during the catalytic cycle, ttq mediates electron transfer from substrate to a cop ...	1999	10721104
mutations in the putative h-channel in the cytochrome c oxidase from rhodobacter sphaeroides show that this channel is not important for proton conduction but reveal modulation of the properties of heme a.	as the final electron acceptor in the respiratory chain of eukaryotic and many prokaryotic organisms, cytochrome c oxidase catalyzes the reduction of oxygen to water, concomitantly generating a proton gradient. x-ray structures of two cytochrome c oxidases have been reported, and in each structure three possible pathways for proton translocation are indicated: the d-, k-, and h-channels. the putative h-channel is most clearly delineated in the bovine heart oxidase and has been proposed to be fun ...	2000	10715119
transcriptional analysis of the nirs gene, encoding cytochrome cd1 nitrite reductase, of paracoccus pantotrophus lmd 92.63.	the gene for cytochrome cd1 nitrite reductase of paracoccus pantotrophus, a protein of known crystal structure, is nirs. this gene is shown to be flanked by genes previously recognized in other organisms to encode proteins involved in the control of its transcription (niri) and the biosynthesis of the d1 cofactor (nire). northern blot analysis has established under anaerobic conditions that a monocistronic transcript is produced from nirs, in contrast to observations with other denitrifying bact ...	2000	10708389
atypical polyphosphate accumulation by the denitrifying bacterium paracoccus denitrificans.	polyphosphate accumulation by paracoccus denitrificans was examined under aerobic, anoxic, and anaerobic conditions. polyphosphate synthesis by this denitrifier took place with either oxygen or nitrate as the electron acceptor and in the presence of an external carbon source. cells were capable of poly-beta-hydroxybutyrate (phb) synthesis, but no polyphosphate was produced when phb-rich cells were incubated under anoxic conditions in the absence of an external carbon source. by comparison of the ...	2000	10698794
tyr(30) of amicyanin is not critical for electron transfer to cytochrome c-551i: implications for predicting electron transfer pathways.	a pathways analysis of the methylamine dehydrogenase-amicyanin-cytochrome c-551i protein electron transfer (et) complex predicts two sets of et pathways of comparable efficiency from the type i copper of amicyanin to the heme of cytochrome c-551i. in one pathway, the electron exits copper via the cys(92) copper ligand, and in the other, it exits via the met(98) copper ligand. if the pathways algorithm is modified to include contributions from the anisotropy of metal-ligand coupling, independent ...	2000	10692547
functional properties of the heme propionates in cytochrome c oxidase from paracoccus denitrificans. evidence from ftir difference spectroscopy and site-directed mutagenesis.	by specific (13)c labeling of the heme propionates, four bands in the reduced-minus-oxidized ftir difference spectrum of cytochrome c oxidase from paracoccus denitrificans have been assigned to the heme propionates [behr, j., hellwig, p., mäntele, w., and michel, h. (1998) biochemistry 37, 7400-7406]. to attribute these signals to the individual propionates, we have constructed seven cytochrome coxidase variants using site-directed mutagenesis of subunit i. the mutant enzymes w87y, w87f, w164f, ...	2000	10684616
sulfite and membrane energization induce two different active states of the paracoccus denitrificans f0f1-atpase.	activation of the latent atpase activity of inside-out vesicles from plasma membranes of paracoccus denitrificans was studied. several factors were found to induce activation: heat, membrane energization by succinate oxidation, methanol, oxyanions (sulfite, phosphate, arsenate, bicarbonate) and limited proteolysis with trypsin. among the oxyanions, sulfite induced the higher increase in atpase activity. sulfite functioned as a nonessential activator that slightly modified the affinity for atp an ...	2000	10672007
protein redox potential measurements based on kinetic analysis with mediated continuous-flow column electrolytic spectroelectrochemical technique. application to ttq-containing methylamine dehydrogenase.	kinetic determination of protein redox potentials with a mediated continuous-flow column electrolytic spectroelectrochemical technique (cfceset) is described. in this method, the redox state of the mediator is completely regulated by the continuous-flow column electrolysis, and the homogeneous redox reaction between the mediator and a protein sample in the column is monitored spectroscopically at the downstream of the column. the protein/mediator reaction is in the pseudo-first-order kinetics, a ...	2000	10655647
distribution of nitrosomonas europaea and paracoccus denitrificans immobilized in tubular polymeric gel for nitrogen removal.	to improve the cooperative removal of nitrogen by nitrosomonas europaea and paracoccus denitrificans, we controlled their distribution in a tubular gel. when ethanol was supplied inside the tubular gel as an electron donor, their distributions overlapped in the external region of the gel. by changing the electron donor from ethanol to gaseous hydrogen, the distribution of p. denitrificans shifted to the inside of the tube and was separated from that of n. europaea. the separation resulted in an ...	2000	10653756
characterization of an azospirillum brasilense tn5 mutant with enhanced n(2) fixation: the effect of orf280 on nifh expression.	disruption of an open reading frame (orf) of 840 bp (280 amino acids; orf280) in an azospirillum brasilense tn5 mutant resulted in a pleiotrophic phenotype. besides an enhanced n(2)-fixing capacity and altered expression pattern of a nifh-gusa fusion, growth on the charged polar amino acids glutamate and arginine was severely affected. orf280, similar to previously identified orfs present in bradyrhizobium japonicum (orf277), paracoccus denitrificans (orf278) and rhodobacter capsulatus (orf277), ...	2000	10650197
structure of the soluble domain of cytochrome c(552) from paracoccus denitrificans in the oxidized and reduced states.	the crystal structure of the soluble domain of the membrane bound cytochrome c(552) (cytochrome c(552)') from paracoccus denitrificans was determined using the multiwavelength anomalous diffraction technique and refined at 1.5 a resolution for the oxidized and at 1. 4 a for the reduced state. this is the first high-resolution crystal structure of a cytochrome c at low ionic strength in both redox states. the atomic model allowed for a detailed assessment of the structural properties including th ...	2000	10623555
sequence conservation from human to prokaryotes of surf1, a protein involved in cytochrome c oxidase assembly, deficient in leigh syndrome.	the human surf1 gene encoding a protein involved in cytochrome c oxidase (cox) assembly, is mutated in most patients presenting leigh syndrome associated with cox deficiency. proteins homologous to the human surf1 have been identified in nine eukaryotes and six prokaryotes using database alignment tools, structure prediction and/or cdna sequencing. their sequence comparison revealed a remarkable surf1 conservation during evolution and put forward at least four highly conserved domains that shoul ...	1999	10622737
interaction between the formyl group of heme a and arginine 54 in cytochrome aa(3) from paracoccus denitrificans.	the optical spectrum of heme a is red-shifted in aa(3)-type cytochrome c oxidases compared to isolated low-spin heme a model compounds. early spectroscopic studies indicated that this may be due to hydrogen-bonding of the formyl group of heme a to an amino acid in the close vicinity. here we show that most of the optical spectral shift of native heme a is due to a hydrogen-bonding interaction between the formyl group and arginine-54 in subunit i of cytochrome aa(3) from paracoccus denitrificans, ...	2000	10611451
mutation of arg-54 strongly influences heme composition and rate and directionality of electron transfer in paracoccus denitrificans cytochrome c oxidase.	the effect of a single site mutation of arg-54 to methionine in paracoccus denitrificans cytochrome c oxidase was studied using a combination of optical spectroscopy, electrochemical and rapid kinetics techniques, and time-resolved measurements of electrical membrane potential. the mutation resulted in a blue-shift of the heme a alpha-band by 15 nm and partial occupation of the low-spin heme site by heme o. additionally, there was a marked decrease in the midpoint potential of the low-spin heme, ...	1999	10608865
mutational analysis of the paracoccus denitrificans c-type cytochrome biosynthetic genes ccmabcdg: disruption of ccmc has distinct effects suggesting a role for ccmc independent of ccmab.	each of the paracoccus denitrificans genes in the c-type cytochrome biogenesis gene cluster ccmabcdg, plus the two flanking genes orf117 and hish, were individually disrupted by omega insertion. resultant phenotypes were restored to the wild-type by complementation from a set of plasmids. all of the ccm genes, but neither orf117 nor hish, were required for c-type cytochrome biogenesis; only ccmg was also implicated in the biosynthesis of cytochrome aa3. disruption of ccmc or ccmg resulted in fai ...	1999	10589712
nitrogen removal reactor using packed gel envelopes containing nitrosomonas europaea and paracoccus denitrificans.	packed gel envelopes were constructed as simple, compact reactors for removing nitrogen from wastewater. each packed gel envelope consisted of two plate gels with a spacer in between. nitrosomonas europaea and paracoccus denitrificans were co-immobilized in the plate gels, and ethanol, serving as an electron donor for denitrification, was injected into the internal spaces of the envelopes. the external surfaces of the envelopes were in contact with ammonia-containing wastewater; the n. europaea ...	2000	10581438
glutamate-89 in subunit ii of cytochrome bo3 from escherichia coli is required for the function of the heme-copper oxidase.	recent electrostatics calculations on the cytochrome c oxidase from paracoccus denitrificans revealed an unexpected coupling between the redox state of the heme-copper center and the state of protonation of a glutamic acid (e78ii) that is 25 a away in subunit ii of the oxidase. examination of more than 300 sequences of the homologous subunit in other heme-copper oxidases shows that this residue is virtually totally conserved and is in a cluster of very highly conserved residues at the "negative" ...	1999	10563797
optical biosensing of nitric oxide using the metalloprotein cytochrome c'.	the metalloprotein cytochrome c' was extracted and purified from the bacterium paracoccus denitrificans in order to develop a specific biosensing system for nitric oxide (no). the metalloprotein was encapsulated in a porous silicate sol-gel glass to enable spectroscopic changes in the haem centre as a function of no ligation to be quantified using absorption measurements. spectroscopic evidence suggested that, between 2 and 4 d after encapsulation, the cytochrome c' protein changed conformation ...	1999	10563051
the cytochrome c oxidase from paracoccus denitrificans does not change the metal center ligation upon reduction.	cytochrome c oxidase catalyzes the reduction of oxygen to water. this process is accompanied by the vectorial transport of protons across the mitochondrial or bacterial membrane ("proton pumping"). the mechanism of proton pumping is still a matter of debate. many proposed mechanisms require structural changes during the reaction cycle of cytochrome c oxidase. therefore, the structure of the cytochrome c oxidase was determined in the completely oxidized and in the completely reduced states at a t ...	1999	10559205
anaerobic growth of paracoccus denitrificans requires cobalamin: characterization of cobk and cobj genes.	a pleiotropic mutant of paracoccus denitrificans, which has a severe defect that affects its anaerobic growth when either nitrate, nitrite, or nitrous oxide is used as the terminal electron acceptor and which is also unable to use ethanolamine as a carbon and energy source for aerobic growth, was isolated. this phenotype of the mutant is expressed only during growth on minimal media and can be reversed by addition of cobalamin (vitamin b(12)) or cobinamide to the media or by growth on rich media ...	1999	10559155
mass spectrometric determination of dioxygen bond splitting in the "peroxy" intermediate of cytochrome c oxidase.	the "peroxy" intermediate (p form) of bovine cytochrome c oxidase was prepared by reaction of the two-electron reduced mixed-valence co complex with (18)o(2) after photolytic removal of co. the water present in the reaction mixture was recovered and analyzed for (18)o enrichment by mass spectrometry. it was found that approximately one oxygen atom ((18)o) per one equivalent of the p form was present in the bulk water. the data show that the oxygen-oxygen dioxygen bond is already broken in the p ...	1999	10557282
transcription regulation of the nir gene cluster encoding nitrite reductase of paracoccus denitrificans involves nnr and niri, a novel type of membrane protein.	the nirix gene cluster of paracoccus denitrificans is located between the nir and nor gene clusters encoding nitrite and nitric oxide reductases respectively. the niri sequence corresponds to that of a membrane-bound protein with six transmembrane helices, a large periplasmic domain and cysteine-rich cytoplasmic domains that resemble the binding sites of [4fe-4s] clusters in many ferredoxin-like proteins. nirx is soluble and apparently located in the periplasm, as judged by the predicted signal ...	1999	10540283
a low-redox potential heme in the dinuclear center of bacterial nitric oxide reductase: implications for the evolution of energy-conserving heme-copper oxidases.	bacterial nitric oxide reductase (nor) catalyzes the two-electron reduction of nitric oxide to nitrous oxide. it is a highly diverged member of the superfamily of heme-copper oxidases. the main feature by which nor is distinguished from the heme-copper oxidases is the elemental composition of the active site, a dinuclear center comprised of heme b(3) and non-heme iron (fe(b)). the visible region electronic absorption spectrum of reduced nor exhibits a maximum at 551 nm with a distinct shoulder a ...	1999	10529222
a cytochrome c peroxidase from pseudomonas nautica 617 active at high ionic strength: expression, purification and characterization.	cytochrome c peroxidase was expressed in cells of pseudomonas nautica strain 617 grown under microaerophilic conditions. the 36.5 kda dihaemic enzyme was purified to electrophoretic homogeneity in three chromatographic steps. n-terminal sequence comparison showed that the ps. nautica enzyme exhibits a high similarity with the corresponding proteins from paracoccus denitrificans and pseudomonas aeruginosa. uv-visible spectra confirm calcium activation of the enzyme through spin state transition o ...	1999	10525144
transmembrane and water-soluble helix bundles display reverse patterns of surface roughness.	amino acid exposure and surface roughness were calculated for 12 helices from three transmembrane alpha-helix bundles and 13 helices from seven water-soluble alpha-helix bundles. transmembrane helix bundles have relatively rough surfaces exposed to the lipid bilayer hydrocarbon chains and relatively smooth surfaces along helix-helix interfaces. this pattern is the reverse of what occurs in water-soluble helix bundles, where relatively rough surfaces are at the helix-helix interfaces and relative ...	1999	10512745
paramagnetic nmr studies of blue and purple copper proteins.	1h- and 13c-nmr spectroscopy is applied to investigate the cu(a) and type 1 active sites of copper proteins in solution. the analysis of hyperfine shifted 1h resonances allows the comparison of the electron spin density delocalization in the cu(a) site of the wild-type soluble domains of various cytochrome c oxidases (thermus thermophilus, paracoccus denitrificans, and paracoccus versutus) and genetically engineered constructs (soluble domain of quinol oxidase from escherichia coli and thiobacil ...	1999	10512535
h(+)-translocating nadh-quinone oxidoreductase (ndh-1) of paracoccus denitrificans. studies on topology and stoichiometry of the peripheral subunits.	the proton-translocating nadh-quinone oxidoreductase (ndh-1) of paracoccus denitrificans is composed of at least 14 subunits (nqo1-14) and is located in the cytoplasmic membrane. in the present study, topological properties and stoichiometry of the 7 subunits (nqo1-6 and nqo9) of the p. denitrificans ndh-1 in the membranes were investigated using immunological techniques. treatments with chaotropic reagents (urea, nai, or nabr) or with alkaline buffer (ph 10-12) resulted in partial or complete e ...	1999	10497227
characterization of the putative 2x[4fe-4s]-binding nqo9 subunit of the proton-translocating nadh-quinone oxidoreductase (ndh-1) of paracoccus denitrificans. expression, reconstitution, and epr characterization.	molecular properties of the nqo9 subunit of paracoccus denitrificans ndh-1, which is predicted to contain 2x[4fe-4s] clusters, were investigated using recombinant expression techniques and epr spectroscopy. the full-length form of nqo9 subunit co-expressed with thioredoxin in escherichia coli at ambient temperature was found dominantly in the cytoplasmic membrane with low amplification. genetic deletion of relatively hydrophobic and less conserved n-terminal stretches (30 or 40 amino acid residu ...	1999	10497226
coherent reaction dynamics in a bacterial cytochrome c oxidase.	biological reactions in protein complexes involve structural dynamics spanning many orders of magnitude in time. in standard descriptions of catalysis by enzymes, the transition state between reactant and product is reached by thermal, stochastic motion. in the ultrashort time domain, however, the protein moiety and cofactor motions leading to altered conformations can be coherent rather than stochastic in nature. such coherent motions may play a key role in controlling the accessibility of the ...	1999	10490029
similarities and dissimilarities in the structure-function relation between the cytochrome c oxidase from bovine heart and from paracoccus denitrificans as revealed by ft-ir difference spectroscopy.	the redox dependent changes in the cytochrome c oxidase from bovine heart were studied with a combined electrochemical and ft-ir spectroscopic approach. a direct comparison to the electrochemically induced ft-ir difference spectra of the cytochrome c oxidase from paracoccus denitrificans reveals differences in the structure and intensity of vibrational modes. these differences are partially attributed to interactions of subunits influencing the heme and protein modes. in the spectral regions cha ...	1999	10481041
the second derivative electronic absorption spectrum of cytochrome c oxidase in the soret region.	the electronic absorption spectrum of solubilized beef heart cytochrome c oxidase was analyzed in the 400-500 nm region to identify the origin of doublet features appearing in the second derivative spectrum associated with ferrocytochrome a. this doublet, centered near 22,600 cm(-1), was observed in the direct absorption spectrum of the a(2+)a(3)(3+).hcoo(-) form of the enzyme at cryogenic temperatures. since evidence for this doublet at room temperature is obtained only on the basis of the seco ...	1999	10465779
kinetic analysis of substrate inhibition in nitric oxide reductase of paracoccus denitrificans.	the current kinetic model for the nitric oxide reductase reaction (girsch, p., and de vries, s. (1997) biochim. biophys. acta 1318, 202-216) does not involve the concentration of an electron donor. here we introduce this variable and show, both theoretically and experimentally, its role in determining the extent of substrate inhibition by the excess of nitric oxide. no is found to inhibit competitively with the electron donor, possibly by binding to the oxidized form of the enzyme. the observed ...	1999	10462514
mutations in the ca2+ binding site of the paracoccus denitrificans cytochrome c oxidase.	recent structure determinations suggested a new binding site for a non-redox active metal ion in subunit i of cytochrome c oxidase both of mitochondrial and of bacterial origin. we analyzed the relevant metal composition of the bovine and the paracoccus denitrificans enzyme and of bacterial site-directed mutants in several residues presumably liganding this ion. unlike the mitochondrial enzyme where a low, substoichiometric content of ca2+ was found, the bacterial wild-type (wt) oxidase showed a ...	1999	10462045
the calcium binding site in cytochrome aa3 from paracoccus denitrificans.	a shift in the spectrum of heme a induced by calcium or proton binding, or by the proton electrochemical gradient, has been attributed to interaction of ca2+ or h+ with the vicinity of the heme propionates in mitochondrial cytochrome c oxidase, and proposed to be associated with the exit path of proton translocation. however, this shift is absent in cytochrome c oxidases from yeast and bacteria [kirichenko et al. (1998) febs lett. 423, 329-333]. here we report that mutations of glu56 or gln63 in ...	1999	10451361
the functions of the flavin contact residues, alphaarg249 and betatyr16, in human electron transfer flavoprotein.	arg249 in the large (alpha) subunit of human electron transfer flavoprotein (etf) heterodimer is absolutely conserved throughout the etf superfamily. the guanidinium group of alphaarg249 is within van der waals contact distance and lies perpendicular to the xylene subnucleus of the flavin ring, near the region proposed to be involved in electron transfer with medium chain acyl-coa dehydrogenase. the backbone amide hydrogen of alphaarg249 is within hydrogen bonding distance of the carbonyl oxygen ...	1999	10446367
anaerobic mineralization of quaternary carbon atoms: isolation of denitrifying bacteria on dimethylmalonate.	the microbial capacity to degrade simple organic compounds with quaternary carbon atoms was demonstrated by enrichment and isolation of five denitrifying strains on dimethylmalonate as the sole electron donor and carbon source. quantitative growth experiments showed a complete mineralization of dimethylmalonate. according to phylogenetic analysis of the complete 16s rrna genes, two strains isolated from activated sewage sludge were related to the genus paracoccus within the alpha-proteobacteria ...	1999	10427013
the intraflavin hydrogen bond in human electron transfer flavoprotein modulates redox potentials and may participate in electron transfer.	electron-transfer flavoprotein (etf) serves as an intermediate electron carrier between primary flavoprotein dehydrogenases and terminal respiratory chains in mitochondria and prokaryotic cells. the three-dimensional structures of human and paracoccus denitrificans etfs determined by x-ray crystallography indicate that the 4'-hydroxyl of the ribityl side chain of fad is hydrogen bonded to n(1) of the flavin ring. we have substituted 4'-deoxy-fad for the native fad and investigated the analog-con ...	1999	10423253
direct evidence for a tyrosine radical in the reaction of cytochrome c oxidase with hydrogen peroxide.	cytochrome c oxidase (cox) catalyzes the reduction of oxygen to water, a process which is accompanied by the pumping of four protons across the membrane. elucidation of the structures of intermediates in these processes is crucial for understanding the mechanism of oxygen reduction. in the work presented here, the reaction of h(2)o(2) with the fully oxidized protein at ph 6.0 has been investigated with electron paramagnetic resonance (epr) spectroscopy. the results reveal an epr signal with part ...	1999	10413492
models for molybdenum coordination during the catalytic cycle of periplasmic nitrate reductase from paracoccus denitrificans derived from epr and exafs spectroscopy.	the periplasmic nitrate reductase from paracoccus denitrificans is a soluble two-subunit enzyme which binds two hemes (c-type), a [4fe-4s] center, and a bis molybdopterin guanine dinucleotide cofactor (bis-mgd). a catalytic cycle for this enzyme is presented based on a study of these redox centers using electron paramagnetic resonance (epr) and extended x-ray absorption fine structure (exafs) spectroscopies. the mo(v) epr signal of resting nap (high g [resting]) has g(av) = 1.9898 is rhombic, ex ...	1999	10413473
mutational analysis of the dimethylsulfoxide respiratory (dor) operon of rhodobacter capsulatus.	four genes, dorc, dord, dorb and dorr of the dmso respiratory gene cluster of rhodobacter capsulatus have been identified and sequenced. dorc encodes a pentahaem c-type cytochrome of the nirt class and the derived dorc protein sequence shows highest similarity to torc from the escherichia coli trimethylamine-n-oxide (tmao) respiratory system. mutagenesis of dorc resulted in the loss of a 46 kda haem-staining polypeptide from membranes of r. capsulatus. dord encodes a protein with highest sequenc ...	1999	10411268
heterologous expression of correctly assembled methylamine dehydrogenase in rhodobacter sphaeroides.	the biosynthesis of methylamine dehydrogenase (madh) from paracoccus denitrificans requires four genes in addition to those that encode the two structural protein subunits, maub and maua. the accessory gene products appear to be required for proper export of the protein to the periplasm, synthesis of the tryptophan tryptophylquinone (ttq) prosthetic group, and formation of several structural disulfide bonds. to accomplish the heterologous expression of correctly assembled madh, eight genes from ...	1999	10400578
expression of plastocyanin and cytochrome f of the cyanobacterium phormidium laminosum in escherichia coli and paracoccus denitrificans and the role of leader peptides.	the gene for plastocyanin from the cyanobacterium phormidium laminosum was successfully expressed in escherichia coli. expression of the gene for cytochrome f resulted in the production of holocytochrome f in the periplasmic space of e. coli, but the yield was low. expression in paracoccus denitrificans yielded no holoprotein. when the region encoding the cytochrome f leader sequence was replaced with more typical bacterial leader sequences (those from the p. laminosum plastocyanin gene and the ...	1999	10395900
nitric oxide is a signal for nnr-mediated transcription activation in paracoccus denitrificans.	by using the 'lacz gene, the activities of the niri, nirs, and norc promoters were assayed in the wild type and in nnr-deficient mutants of paracoccus denitrificans grown under various growth conditions. in addition, induction profiles of the three promoters in response to the presence of various nitrogenous oxides were determined. transcription from the three promoters required the absence of oxygen and the presence both of the transcriptional activator nnr and of nitric oxide. the activity of ...	1999	10383987
anaerobic oxidations of cysteate: degradation via l-cysteate:2-oxoglutarate aminotransferase in paracoccus pantotrophus.	anoxic, fresh-water enrichment cultures to oxidize different organosulfonates were set up with nitrate, ferric iron or sulfate as electron acceptors. pure cultures were easily obtained with two naturally occurring sulfonates, cysteate (2-amino-3-sulfopropionate) and taurine (2-aminoethanesulfonate), under nitrate-reducing conditions. these two sulfonates were also oxidized during reduction of iron(iii), though isolation of pure cultures was not successful. one nitrate-reducing cysteate-oxidizing ...	1999	10376831
time-resolved ft-ir studies on the co adduct of paracoccus denitrificans cytochrome c oxidase: comparison of the fully reduced and the mixed valence form.	the rebinding of co to cytochrome c oxidase from paracoccus denitrificans in the fully reduced and in the half-reduced (mixed valence) form as a function of temperature was investigated using time-resolved rapid-scan ft-ir spectroscopy in the mid-ir (1200-2100 cm-1). for the fully reduced enzyme, rebinding was complete in approximately 2 s at 268 k and showed a biphasic reaction. at 84 k, nonreversible transfer of co from heme a3 to cub was observed. both photolysis at 84 k and photolysis at 268 ...	1999	10360954
biochemical and electrochemical characterization of quinohemoprotein amine dehydrogenase from paracoccus denitrificans.	a new quinohemoprotein amine dehydrogenase from paracoccus denitrificans ifo 12442 was isolated and characterized in views of biochemistry and electrochemistry. this enzyme exists in periplasm and catalyzes the oxidative deamination of primary aliphatic and aromatic amines. n-butylamine or benzylamine as a carbon and energy source strongly induces the expression of the enzyme. carbonyl reagents inhibit the enzyme activity irreversibly. this enzyme is a heterodimer constituted of alpha and beta s ...	1999	10346915
evidence for a copper-coordinated histidine-tyrosine cross-link in the active site of cytochrome oxidase.	following hints from x-ray data (ostermeier c et al., 1997, proc natl acad sci usa 94:10547-10553; yoshikawa s et al., 1998, science 280: 1723-1729), chemical evidence is presented from four distantly related cytochrome-c oxidases for the existence of a copperb-coordinated his240-tyr244) cross-link at the o2-activating heme fea3-cub center in the catalytic subunit 1 of the enzyme. the early evolutionary invention of this unusual structure may have prevented damaging *oh-radical release at e(-)-t ...	1999	10338009
glyceraldehyde-3-phosphate dehydrogenase gene diversity in eubacteria and eukaryotes: evidence for intra- and inter-kingdom gene transfer.	cyanobacteria contain up to three highly divergent glyceraldehyde-3-phosphate dehydrogenase (gapdh) genes: gap1, gap2, and gap3. genes gap1 and gap2 are closely related at the sequence level to the nuclear genes encoding cytosolic and chloroplast gapdh of higher plants and have recently been shown to play distinct key roles in catabolic and anabolic carbon flow, respectively, of the unicellular cyanobacterium synechocystis sp. pcc6803. in the present study, sequences of 10 gapdh genes distribute ...	1999	10331270
does the reduction of c heme trigger the conformational change of crystalline nitrite reductase?	the structures of nitrite reductase from paracoccus denitrificans gb17 (nir-pd) and pseudomonas aeruginosa (nir-pa) have been described for the oxidized and reduced state (fülöp, v., moir, j. w. b., ferguson, s. j., and hajdu, j. (1995) cell 81, 369-377; nurizzo, d., silvestrini, m. c., mathieu, m., cutruzzolà, f., bourgeois, d., fülöp, v., hajdu, j., brunori, m., tegoni, m., and cambillau, c. (1997) structure 5, 1157-1171; nurizzo, d., cutruzzolà, f., arese, m., bourgeois, d., brunori, m., camb ...	1999	10329702
isolated transmembrane helices arranged across a membrane: computational studies.	a computational procedure for predicting the arrangement of an isolated helical fragment across a membrane was developed. the procedure places the transmembrane helical segment into a model triple-phase system 'water-octanol-water'; pulls the segment through the membrane, varying its 'global' position as a rigid body; optimizes the intrahelical and solvation energies in each global position by 'local' coordinates (dihedral angles of side chains); and selects the lowest energy global position for ...	1999	10325400
a re-evaluation of the taxonomy of paracoccus denitrificans and a proposal for the combination paracoccus pantotrophus comb. nov.	comparison of both 16s rrna coding sequences and dna-dna hybridization of ten strains of alpha-subclass of proteobacteria currently classified as strains of paracoccus denitrificans has shown that they fall into two groups which are distinct from each other at the species level. comparison with published data on the cytochrome c profiles and other 16s rrna coding sequences in the literature has confirmed these observations and enabled several other strains also to be assigned to these two groups ...	1999	10319488
analyses of a polyhydroxyalkanoic acid granule-associated 16-kilodalton protein and its putative regulator in the pha locus of paracoccus denitrificans.	the polyhydroxyalkanoic acid (pha) granule-associated 16-kda protein (ga16 protein) of paracoccus denitrificans was identified, and its corresponding gene was cloned and analyzed at the molecular level. the n-terminal amino acid sequence of ga16 protein revealed that its structural gene is located downstream from the pha synthase gene (phacpd) cloned recently (s. ueda, t. yabutani, a. maehara, and t. yamane, j. bacteriol. 178:774-779, 1996). gene walking around phacpd revealed two new open readi ...	1999	10217786
determination of the paracoccus denitrificans sos box.	by gel retardation experiments with crude cell extracts of paracoccus denitrificans it was demonstrated that a protein specifically binds to the promoter of the p. denitrificans reca gene. pcr mutagenesis of the reca promoter showed that the gaacn7gaac motif is required for the formation of the dna-protein complex. this protein also binds to the gttcn7gttc motif, which is present in the promoter of the p. denitrificans uvra gene. mutational analysis of the promoter regions of both p. denitrifica ...	1999	10217491
pseudoazurin mediates periplasmic electron flow in a mutant strain of paracoccus denitrificans lacking cytochrome c550.	a periplasmic protein able to transfer electrons from cytoplasmic membrane to the periplasmic nitrite reductase (cytochrome cd1) has been purified from the anoxically grown cytochrome c550 mutant strain pd2121 and shown to be pseudoazurin by several independent criteria (molecular mass, copper content, visible spectrum, n-terminal amino acid sequence). under our assay conditions, the half-saturation of electron transport occurred at about 10 microm pseudoazurin; the reaction was retarded by incr ...	1999	10217431
heterologous expression of soluble fragments of cytochrome c552 acting as electron donor to the paracoccus denitrificans cytochrome c oxidase.	a membrane-bound c-type cytochrome, c552, acts as the electron mediator between the cytochrome bc1 complex and cytochrome c oxidase in the branched respiratory chain of the bacterium paracoccus denitrificans. unlike in mitochondria where a soluble cytochrome c interacts with both complexes, the bacterial c552, the product of the cycm gene, shows a tripartite structure, with an n-terminal membrane anchor separated from a typical class i cytochrome domain by a highly charged region. two derivative ...	1999	10216157
the reduction state of the q-pool regulates the electron flux through the branched respiratory network of paracoccus denitrificans.	in this work we demonstrate how the reduction state of the q-pool determines the distribution of electron flow over the two quinol-oxidising branches in paracoccus denitrificans: one to quinol oxidase, the other via the cytochrome bc1 complex to the cytochrome c oxidases. the dependence of the electron-flow rate to oxygen on the fraction of quinol in the q-pool was determined in membrane fractions and in intact cells of the wild-type strain, a bc1-negative mutant and a quinol oxidase-negative mu ...	1999	10215894
the structure of an electron transfer complex containing a cytochrome c and a peroxidase.	efficient biological electron transfer may require a fluid association of redox partners. two noncrystallographic methods (a new molecular docking program and 1h nmr spectroscopy) have been used to study the electron transfer complex formed between the cytochrome c peroxidase (ccp) of paracoccus denitrificans and cytochromes c. for the natural redox partner, cytochrome c550, the results are consistent with a complex in which the heme of a single cytochrome lies above the exposed electron-transfe ...	1999	10196231
pcr detection of genes encoding nitrite reductase in denitrifying bacteria.	using consensus regions in gene sequences encoding the two forms of nitrite reductase (nir), a key enzyme in the denitrification pathway, we designed two sets of pcr primers to amplify cd1- and cu-nir. the primers were evaluated by screening defined denitrifying strains, denitrifying isolates from wastewater treatment plants, and extracts from activated sludge. sequence relationships of nir genes were also established. the cd1 primers were designed to amplify a 778 to 799-bp region of cd1-nir in ...	1999	10103263
gene dosage effects on polyhydroxyalkanoates synthesis from n-alcohols in paracoccus denitrificans.	putative promoters of polyhydroxyalkanoate (pha)-synthetic genes of paracoccus denitrificans were identified. gene dosage effects for pha synthesis were investigated in recombinants of p. denitrificans with increased expression levels of each pha synthetic enzyme. in the cultivation of shake flasks using ethanol or n-pentanol as carbon source, a self-cloning recombinant of the phac-encoding pha synthase showed the highest contents [(g pha). (g total biomass)-1] and the highest rates of pha accum ...	1998	10099406
nadh-quinone oxidoreductase: psst subunit couples electron transfer from iron-sulfur cluster n2 to quinone.	the proton-translocating nadh-quinone oxidoreductase (ec 1.6.99.3) is the largest and least understood enzyme complex of the respiratory chain. the mammalian mitochondrial enzyme (also called complex i) contains more than 40 subunits, whereas its structurally simpler bacterial counterpart (ndh-1) in paracoccus denitrificans and thermus thermophilus hb-8 consists of 14 subunits. a major unsolved question is the location and mechanism of the terminal electron transfer step from iron-sulfur cluster ...	1999	10097178
methylamine dehydrogenase: structure and function of electron transfer complexes.		1999	10093734
cytochrome c' from paracoccus denitrificans: spectroscopic studies consistent with a role for the protein in nitric oxide metabolism.	cytochrome c' was purified from the denitrifying bacterium paracoccus denitrificans and the interaction of the protein with nitric oxide was examined spectroscopically. two distinct types of haem-nitrosyl electronic absorption spectrum were observed, which were dependent upon [no]. when cytochrome c' was saturated with no, alpha and beta bands were centred at 562 nm and 530 nm, whereas with sub-saturating concentrations of no the alpha and beta bands were red-shifted to 578 nm and 542 nm respect ...	1999	10082934
evaluation of relative contributions of two enzymes supposed to metabolise hydrogen peroxide in paracoccus denitrificans.	a biosensor exploiting an electrochemically mediated enzyme-catalysed reaction was used to quantify relative contributions of cytoplasmic catalase and periplasmic cytochrome c peroxidase to the overall rate of hydrogen peroxide breakdown in cells of paracoccus denitrificans. the effects of antimycin (an inhibitor of electron flow to cytochrome c peroxidase), the reaction rate versus substrate concentration profiles for the whole cells and subcellular fractions, and the time courses of oxygen con ...	1999	10076016
tyrosine aminotransferase catalyzes the final step of methionine recycling in klebsiella pneumoniae.	an aminotransferase which catalyzes the final step in methionine recycling from methylthioadenosine, the conversion of alpha-ketomethiobutyrate to methionine, has been purified from klebsiella pneumoniae and characterized. the enzyme was found to be a homodimer of 45-kda subunits, and it catalyzed methionine formation primarily using aromatic amino acids and glutamate as the amino donors. histidine, leucine, asparagine, and arginine were also functional amino donors but to a lesser extent. the n ...	1999	10074065