SEARCH · PubMed Health

Results for “Paracoccus”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 127 records · Page 7Linked to original sources

PubMed1987

The genes of the Paracoccus denitrificans bc1 complex. Nucleotide sequence and homologies between bacterial and mitochondrial subunits.

The genes for the three subunits of the cytochrome bc1 complex from the bacterium Paracoccus denitrificans were identified by screening a gene library constructed in pBR 322 for expression using a cytochrome c1-specific antibody. These three genes coding for the FeS subunit, cytochrome b, and cytochrome c1 were located on contiguous sites on the genome in a presumed operon arrangement. The DNA-deduced amino acid sequence shows that all three subunits are homologous to corresponding polypeptides of the mitochondrial cytochrome bc1 complex. Cytochrome c1 of Paracoccus is much larger than its mitochondrial counterpart due to an extra 150 amino acids of unique, highly acidic composition; in addition, it is most likely synthesized as a precursor polypeptide.

Amino Acid Sequence↗

PubMed1988

Stable isotope evidence for the localisation of some metabolic pathways in the bacterium Paracoccus denitrificans.

Paracoccus denitrificans was grown on [6-13C]-glucose as the sole carbon source for growth and the extracts were fractionated and analysed by gas chromatography-mass spectrometry. The 13C-enrichments of some metabolites indicated that the "hydrolysate pools" of these metabolites were not in isotopic equilibrium with the water soluble "free pools". It was concluded that localisation of some metabolic pathways had occurred in Paracoccus during growth on [6-13C]-glucose.

Carbon Isotopes↗

PubMed1983

Turnover of cytochrome c oxidase from Paracoccus denitrificans.

The heme aa3 type cytochrome oxidase from Paracoccus denitrificans incorporated into vesicles with phospholipid reacts during turnover much as the oxidase from mitochondria does. The spectrophotometric changes observed at various wavelengths are closely similar, and the rate is about one-half of that for beef heart oxidase under the same conditions. The rate of appearance of oxidized cytochrome c on initiation of the reaction is also similar and depends on the previous treatment of the oxidase as described by Antonini, E., Brunori, M., Colosimo, A., Greenwood, C. and Wilson, M. T. (1977) Proc. Natl. Acad. Sci. U.S.A. 74, 3128-3132. In terms of their model the resting Paracoccus enzyme is converted to the pulsed form during turnover. The effect is observed with both cytochrome c and hexamine ruthenium as reductants. With the latter a 60-fold increase in rate is observed.

Anaerobiosis↗

PubMed1987

Isolation and analysis of the genes for cytochrome c oxidase in Paracoccus denitrificans.

Synthetic oligonucleotide probes were used to clone two loci from the chromosomal DNA of Paracoccus denitrificans that contain the genes for cytochrome c oxidase (cytochrome aa(3)). One locus seems to contain four or five genes probably forming an operon. Two of these code for the oxidase subunits II and III. Three open reading frames are found between the COII and COIII genes. The other locus codes for the subunit I. A short open reading frame is found upstream of this gene. All three subunits of the Paracoccus enzyme show remarkable homology to the corresponding subunits of the mitochondrial cytochrome oxidase. Possible protein products of the open reading frames have not yet been identified.

Journal Article↗

PubMed1993

Crystal structure analysis of amicyanin and apoamicyanin from Paracoccus denitrificans at 2.0 A and 1.8 A resolution.

The crystal structure of amicyanin, a cupredoxin isolated from Paracoccus denitrificans, has been determined by molecular replacement. The structure has been refined at 2.0 A resolution using energy-restrained least-squares procedures to a crystallographic residual of 15.7%. The copper-free protein, apoamicyanin, has also been refined to 1.8 A resolution with residual 15.5%. The protein is found to have a beta-sandwich topology with nine beta-strands forming two mixed beta-sheets. The secondary structure is very similar to that observed in the other classes of cupredoxins, such as plastocyanin and azurin. Amicyanin has approximately 20 residues at the N-terminus that have no equivalents in the other proteins; a portion of these residues forms the first beta-strand of the structure. The copper atom is located in a pocket between the beta-sheets and is found to have four coordinating ligands: two histidine nitrogens, one cysteine sulfur, and, at a longer distance, one methionine sulfur. The geometry of the copper coordination is very similar to that in the plant plastocyanins. Three of the four copper ligands are located in the loop between beta-strands eight and nine. This loop is shorter than that in the other cupredoxins, having only two residues each between the cysteine and histidine and the histidine and methionine ligands. The amicyanin and apoamicyanin structures are very similar; in particular, there is little difference in the positions of the coordinating ligands with or without copper. One of the copper ligands, a histidine, lies close to the protein surface and is surrounded on that surface by seven hydrophobic residues. This hydrophobic patch is thought to be important as an electron transfer site.

Amino Acid Sequence↗

PubMed2000

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 present in the gels oxidized the ammonia to nitrite aerobically. On the other hand, the internal surfaces of the envelopes were in contact with the ethanol solution, which P. denitrificans used to reduce the nitrite to nitrogen gas anaerobically. In this way, the reactor using the packed gel envelopes removed ammonia from wastewater in a single step. When artificial wastewater containing 200 mg-N/L was treated using the reactor using eight envelopes, the ammonia was removed by the reactor without accumulating nitrite or ethanol. This simple system exhibited high rates of nitrification (ammonia to nitrite; 1.9 kg-N/day for 1m(3) of reactor volume) and nitrogen removal (ammonia to nitrogen gas; 1.6 kg-N/day). It is presumed that these high rates were achieved as a consequence of cooperation between the N. europaea and P. denitrificans present in the gels and the efficient uptake and exhaust of gases leading to the smooth conversion of ammonia to nitrogen gas.

Ammonia↗

PubMedDate not supplied

Investigation of the thermal stability of porin from Paracoccus denitrificans by site-directed mutagenesis and Fourier transform infrared spectroscopy.

The folding of membrane proteins was addressed using outer membrane protein porin from the soil bacterium Paracoccus denitrificans (P. den.). IR spectroscopy and sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) analysis were used to probe the effect of mutagenesis on the thermal stability of the protein. Secondary structure analysis by amide I ir spectroscopy showed that the wild-type protein was predominantly composed of beta-sheet, which supports the x-ray crystal structure information (A. Hirsch, J. Breed, K. Saxena, O.-M. H. Richter, B. Ludwig, K. Diederichs, and W. Welte, FEBS Letters, 1997, Vol. 404, pp. 208-210). The mutants E81Q, W74C, and E81Q/D148N were shown to have similar secondary structure composition as the wild type. Wild-type protein and the mutants in detergent micelles underwent irreversible denaturation as a result of heating. Transition temperature calculated from the amide I analysis revealed that mutant porins were slightly less stable compared to the wild type. The protein in micelles showed complete monomerization of the trimer above 85 degrees C. In native-like conditions (provided by liposomes), no change was observed in the secondary structure of the protein until 95 degrees C. This is supported by SDS-PAGE as no change in quaternary structure was observed, proving that the proteins are structurally thermostable in liposomes as compared to micelles. Our studies demonstrated that porins resistant to detergents and proteases are highly thermostable as well.

Cell Membrane↗

PubMed2006

Structure-function correlation of outer membrane protein porin from Paracoccus denitrificans.

Porins from outer membrane of Gram-negative bacteria have a highly stable structure. Our previous studies on porin from Paracoccus denitrificans showed that the outer membrane protein porin is extremely stable toward heat, pH, and chemical denaturants. The major question we have addressed in this paper is whether the high stability of porin is a consequence of the beta-barrel structure and whether it is required for its function. To explain this we have analyzed two cases: first, we used porin wild-type and mutants and compared their structure and function; second, we compared the activity of porin preheated to different temperatures. Structural changes were monitored by infrared spectroscopy. We observed that the structural stability of porin is not equivalent to functional activity as minor alteration in the structure can result in drastic differences in the activity of porins.

Bacterial Outer Membrane Proteins↗

PubMed2004

Examination of membrane protein expression in Paracoccus denitrificans by two-dimensional gel electrophoresis.

The well-known metabolic versatility of the soil bacterium Paracoccus denitrificans poses a challenge for modern proteomic approaches. We describe here improved preparation conditions that allow good separation and quantitative analyses of hundreds of membrane or periplasmic proteins. To illustrate this optimized procedure, the results of a screening for membrane proteins associated predominantly with aerobic or anaerobic (denitrifying) modes of growth are presented.

Aerobiosis↗

PubMed1990

Formation of a potent respiratory inhibitor at nitrite reduction by nitrite reductase isolated from the bacterium Paracoccus denitrificans.

A new method of dissimilatory nitrite reductase (cytochrome cd1) isolation from the periplasmic fraction of anaerobically grown cells of the bacterium Paracoccus denitrificans was developed, using ionex and gel permeation chromatography with FPLC system (Pharmacia, Sweden). In experiments with isolated enzyme it was shown that through a nitrite reduction, catalysed by this enzyme, a substance (presumably nitric oxide) was formed which at submicromolar concentrations inhibited terminal cytochrome oxidase of the respiratory chain of the same bacterium. These results help to explain formerly observed sensitivity of bacterial oxidase activity to NO2- and the mechanism of switching the electron flow from O2 to nitrogen terminal acceptors.

Chromatography, High Pressure Liquid↗

PubMed2004

Protein composition of Paracoccus denitrificans cells grown on various electron acceptors and in the presence of azide.

Two-dimensional gel electrophoresis (2-DE) with immobilized pH gradients was carried out on total cell lysates and membrane fractions of Paracoccus denitrificans with the aim to characterize differences in protein expression during growth under aerobic and various anaerobic conditions (with nitrate, nitrite or nitrous oxide). Comparative image analysis of the protein pattern revealed several subgroups of the total 800 protein spots resolved that were characteristically induced or repressed in response to individual electron acceptors. The respiratory inhibitor azide also exerted a profound influence upon cellular protein composition. However, since most of the proteins showing an altered expression pattern in cells growing on oxygen differed from those in cells growing on nitrite, we suppose that azide acts mainly indirectly, possibly by influencing other cellular signals. Limited information on the P. denitrificans genome has precluded the identification of more than eight protein spots as yet. A public accessible P. denitrificans 2-DE protein database is currently built up at http://www.mpiib-berlin.mpg.de/2D-PAGE.

Bacterial Proteins↗

PubMed1992

Electronic and vibrational spectroscopy of the cytochrome c:cytochrome c oxidase complexes from bovine and Paracoccus denitrificans.

The 1:1 complex between horse heart cytochrome c and bovine cytochrome c oxidase, and between yeast cytochrome c and Paracoccus denitrificans cytochrome c oxidase have been studied by a combination of second derivative absorption, circular dichroism (CD), and resonance Raman spectroscopy. The second derivative absorption and CD spectra reveal changes in the electronic transitions of cytochrome a upon complex formation. These results could reflect changes in ground state heme structure or changes in the protein environment surrounding the chromophore that affect either the ground or excited electronic states. The resonance Raman spectrum, on the other hand, reflects the heme structure in the ground electronic state only and shows no significant difference between cytochrome a vibrations in the complex or free enzyme. The only major difference between the Raman spectra of the free enzyme and complex is a broadening of the cytochrome a3 formyl band of the complex that is relieved upon complex dissociation at high ionic strength. These data suggest that the differences observed in the second derivative and CD spectra are the result of changes in the protein environment around cytochrome a that affect the electronic excited state. By analogy to other protein-chromophore systems, we suggest that the energy of the Soret pi* state of cytochrome a may be affected by (1) changes in the local dielectric, possibly brought about by movement of a charged amino acid side chain in proximity to the heme group, or (2) pi-pi interactions between the heme and aromatic amino acid residues.

Animals↗

PubMed1995

Crystallization and preliminary X-ray analysis of electron transfer flavoproteins from human and Paracoccus denitrificans.

Mammalian electron transfer flavoprotein (ETF) is a soluble, heterodimeric flavoprotein responsible for the oxidation of at least nine primary matrix flavoprotein dehydrogenases. Crystals have been obtained for the recombinant human electron transfer flavoprotein (ETFhum) by the sitting-drop vapor diffusion technique using polyethylene glycol (PEG) 1500 at pH 7.0 as the precipitating agent. ETFhum crystallizes in the monoclinic space group P2(1), with unit cell parameters a = 47.46 angstrum, b = 104.10 angstrum, c = 63.79 angstrum, and beta = 110.02 degrees. Based on the assumption of one alpha beta dimer per asymmetric unit, the Vm value is 2.69 angstrum 3/Da. A native data set has been collected to 2.1 angstrum resolution. One heavy-atom derivative has also been obtained by soaking a preformed crystal of ETFhum in 2 mM thimerosal solution for 2h at 19 degrees C. Patterson analysis indicates one major site. The analogous electron transfer flavoprotein from Paracoccus denitrificans (ETFpar) has also been crystallized using PEG 8000 at pH 5.5 as the precipitating agent. ETFpar crystallizes in the orthorhombic space group P2(1)2(1)2(1), with unit cell parameters a = 79.98 angstrum, b = 182.90 angstrum, and c = 70.07 angstrum. The Vm value of 2.33 angstrum 3/Da is consistent with two alpha beta dimers per asymmetric unit. A native data set has been collected to 2.5 angstrum resolution.

Bacterial Proteins↗

PubMed1992

Three-dimensional structure of the quinoprotein methylamine dehydrogenase from Paracoccus denitrificans determined by molecular replacement at 2.8 A resolution.

The three-dimensional structure of the quinoprotein methylamine dehydrogenase from Paracoccus dentrificans (PD-MADH) has been determined at 2.8 A resolution by the molecular replacement method combined with map averaging procedures, using data collected from an area detector. The structure of methylamine dehydrogenase from Thio-bacillus versutus, which contains an "X-ray" sequence, was used as the starting search model. MADH consists of 2 heavy (H) and 2 light (L) subunits related by a molecular 2-fold axis. The H subunit is folded into seven four-stranded beta segments, forming a disk-shaped structure, arranged with pseudo-7-fold symmetry. A 31-residue elongated tail exists at the N-terminus of the H subunit in MADH from T. versutus but is partially digested in this crystal form of MADH from P. denitrificans, leaving the H subunit about 18 residues shorter. Each L subunit contains 127 residues arranged into 10 beta-strands connected by turns. The active site of the enzyme is located in the L subunit and is accessible via a hydrophobic channel between the H and L subunits. The redox cofactor of MADH, tryptophan tryptophylquinone is highly unusual. It is formed from two covalently linked tryptophan side chains at positions 57 and 107 of the L subunit, one of which contains an orthoquinone.

Amino Acid Sequence↗

PubMed1995

Purification, characterization, crystallization, and preliminary X-ray results from Paracoccus denitrificans porin.

The porin from Paracoccus denitrificans ATCC 13543 was purified and crystallized. Two crystal forms were obtained from porin solutions with beta-d-octylglucopyranoside as detergent. Crystals of form I belong to the monoclinic spacegroup C2 with unit cell dimensions a = 112.2 A, b = 193.8 A, c = 100.5 A and beta = 129.2 degrees. There is 1 trimer per asymmetric unit. Crystals of form II are triclinic with a = 89.7 A, b = 98.8 A, c = 112.5 A, alpha = 112.5 degrees, beta = 101.8 degrees, gamma = 106.7 degrees (2 trimers per asymmetric unit). Both crystal forms diffract to 3 A.

Crystallization↗

PubMed1994

X-Ray structure of the cytochrome c2 isolated from Paracoccus denitrificans refined to 1.7-A resolution.

The cytochrome c2 (formerly c550) isolated from Paracoccus denitrificans is one of the larger bacterial c-type proteins examined thus far. The molecular structure of this cytochrome has been redetermined and refined to 1.7-A resolution with a crystallographic R-factor of 17.5% for all measured X-ray data. Like other, smaller c-type cytochromes, the molecule consists of five alpha-helices that wrap around the heme group. In addition, this bacterial cytochrome contains two strands of anti-parallel beta-sheet, five Type I turns, and three Type II turns. The present model differs from the originally determined structure in several regions including the N-terminus, the loop delineated by Asp 25 to Lys 31, the region defined by Trp 86 to Val 88, and the C-terminus. A total of 103 water molecules has been positioned into the electron density map. Six of these waters are directly involved in heme binding.

Amino Acid Sequence↗

PubMed1998

Roles of four iron centers in Paracoccus halodenitrificans nitric oxide reductase.

Reactions of Paracoccus halodenitrificans nitric oxide reductase (NOR) containing four iron centers, a low spin hemec, a low spin heme b, a high spin heme b and a non-heme iron, have been studied to show the roles of each iron center. Soon after reacting the resting (oxidized) NOR with L-ascorbate, the low spin heme c and low spin heme b were reduced to a considerable extent but the high spin heme b was still in the oxidized form and was reduced slowly. When CO acted on the reduced NOR, the high spin heme b center changed to a low spin state. On the other hand, when NO acted on the resting NOR, no apparent spectral change was observed. However, when NO acted on the reduced NOR (a steady state condition, excess dithionite is present), both of the low spin centers changed to be partly in the oxidized form. A small but clear new EPR signal with g = 4.1 appeared together with some new signals at the g = 2 region soon after the action of NO on the reduced NOR. During incubation at room temperature the nitrosyl-heme signal typical of 5-coordination developed. These results suggested that both the high spin-heme b center and the non-heme iron are the reaction centers and their reductions are indispensable for the enzyme process in contrast to the reaction mechanism proposed for the P-450 type NOR(P-450nor).

Ascorbic Acid↗

PubMed2000

A novel conformer of oxidized Paracoccus pantotrophus cytochrome cd(1) observed by freeze-quench NIR-MCD spectroscopy.

Paracoccus pantotrophus cytochrome cd(1) is a physiological nitrite reductase and an in vitro hydroxylamine reductase. The oxidised "as isolated" form of the enzyme has bis-histidinyl coordinated c-heme and upon reduction its coordination changes to histidine/methionine. Following treatment of reduced enzyme with hydroxylamine, a novel, oxidised, conformer of the enzyme is obtained. We have devised protocols for freeze-quench near-ir-MCD spectroscopy that have allowed us to establish unequivocally the c-heme coordination of this species as His/Met. Thus it is shown that the catalytically competent, hydroxylamine reoxidised, form of P. pantotrophus cytochrome cd(1) has different axial ligands to the c-heme than "as isolated" enzyme.

Cytochrome c Group↗