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At least 199 records · Page 11Linked to original sources

PubMed1977

Sulphur metabolism in Paracoccus denitrificans. Purification, properties and regulation of cysteinyl-and methionyl-tRNA synthetase.

Cysteinyl- and methionyl-tRNA synthetases (EC 6.11.-) were purified 1200- and 1000-fold, respectively, from sonic extracts of Paracoccus denitrificans strain 8944, and kinetics, substrate specificity and regulatory properties were determined using the ATP-PPi exchange reaction. Both enzymes had pH optima of approx. 8 and were inhibited by sulphydryl-group reagents. Cysteinyl-tRNA synthetase catalysed L-selenocysteine- and alpha-aminobutyric acid-dependent ATP-PPi exchange and methionyl-tRNA synthetase catalysed L-homocysteine-, L-selenomethionine- and norleucine-dependent ATP-PPi exchange. Both enzymes were inhibited by O-acetylserine. Cysteinyl-tRNA synthetase activity was stimulated by methionine and methionyl-tRNA synthetase activity was stimulated by sulphide, cysteine, and cysteic acid.

Adenosine Triphosphate↗

PubMed1979

Comparison of the membrane-bound and detergent-solubilised hydrogenase from paracoccus denitrificans. Isolation of the hydrogenase.

The hydrogenase from Paracoccus denitrificans is an integral membrane protein and has been solubilised by Triton X-100. The membrane-bound and detergent-solubilised forms of the enzyme have been compared. Both forms of the enzyme show a pH optimum for reduction of benzyl viologen at pH 8.5--9.0 and are both inhibited by concentrations of NaCl greater than 30 mM. An Arrhenius plot of the activity of hydrogenase in the membrane shows no 'break'. The form of the Arrhenius plot and the activation energy are not significantly changed on solubilisation of the enzyme. The Km and V values for benzyl viologen, methyl viologen and H2 are unaltered when the enzyme is extracted from the membrane. Therefore, solubilisation of hydrogenase from the membrane by Triton X-400 is unlikely to disrupt the native conformation of the enzyme. The detergent-solubilised hydrogenase has subsequently been purified using ammonium sulphate precipitation, sucrose density gradient centrifugation and chromatography on hydroxyapatite. The overall yield of activity is 23%, with a final purification of over 100-fold.

Cell Membrane↗

PubMed1981

A manganese-containing superoxide dismutase from Paracoccus denitrificans.

A cyanide-insensitive superoxide dismutase (superoxide: superoxide dismutase EC 1.15.1.1) has been isolated from Paracoccus denitrificans, purified to homogeneity and characterized. It is a soluble, manganese-containing protein with an apparent molecular weight of 41 500 +/- 1000. It is composed of two identical subunits (Mr 23 500) not bound by disulfide linkage. It's isoelectric point is 4.5. The amino acid composition shows strong similarities with other dimeric procaryotic and with tetrameric mitochondrial Mn-superoxide dismutases. The fully active enzyme contained from 1.34 to 2 gatom Mn/mol enzyme.

Amino Acids↗

PubMed1983

Saturation behavior of the manganese-containing superoxide dismutase from Paracoccus denitrificans.

A pulse radiolysis study of the Mn-superoxide dismutase from Paracoccus denitrificans has shown that, at concentration of 0(2)-. below 0.8 x 10(-4)M, the catalyzed dismutation of 0(2)-. is a first order reaction with regard to 0(2)-.. At concentration of 0(2)-. above 0.8 x 10(-4)M, the Mn-superoxide dismutase is shown to catalyze superoxide dismutation with a mechanism which exhibits saturation kinetics. This behavior was previously found in the bovine Cu/Zn-superoxide dismutase and in the Fe-superoxide dismutase from Photobacterium leiognathi. Two parameters of catalysis were determined from pH 5 to pH 11: the rate constant k was pH independent at basic pH. The variation of Km with pH indicated that the enzyme possessed an ionizable group with pK 9.8 which participates to the substrate binding.

Hydrogen-Ion Concentration↗

PubMed1983

The effect of uncoupler on the distribution of the electron flow between the terminal acceptors oxygen and nitrite in the cells of Paracoccus denitrificans.

The preferential utilization of oxygen, the terminal acceptor, in anaerobically grown cells of Paracoccus denitrificans was abolished in the presence of uncoupler (3 microM carbonyl cyanide m-chlorophenylhydrazone) which brought about a switch to the reduction of nitrite. It has been proved by measuring the redox state of cytochromes that this effect is due to the inhibition of the electron flow to oxygen caused by nitrite, which attains the site of its inhibitory action when the membrane potential is lowered.

Carbonyl Cyanide m-Chlorophenyl Hydrazone↗

PubMed1991

Inhibitory effects of two structurally related carbocyanine laser dyes on the activity of bovine heart mitochondrial and Paracoccus denitrificans NADH-ubiquinone reductase. Evidence for a rotenone-type mechanism.

Two cationic, lipophilic laser dyes, 1,1',3,3,3',3'-hexamethylindodicarbocyanine iodide (HIDC) and 1,1',3,3,3',3'-hexamethylindotricarbocyanine iodide (HITC), inhibit bovine heart mitochondrial and Paracoccus denitrificans NADH oxidase activities. The mitochondrial I50 values were 0.5 microM (HIDC) and 1.2 microM (HITC), and the P. denitrificans I50 values 1.2 microM (HIDC) and 1.5 microM (HITC). Neither succinate nor cytochrome oxidase (EC 1.9.3.1) activities were inhibited significantly by either compound, localizing the site of inhibition to the segment of each electron transport chain between NADH and ubiquinone. With submitochrondrial particles (SMP), NADH-dependent reduction of menadione, duroquinone and coenzyme Q1 was inhibited markedly (HIDC was the more potent inhibitor). Using purified complex I, only NADH-dependent reduction of duroquinone and coenzyme Q1 was inhibited markedly (HIDC was the more potent inhibitor) and reduction of menadione was inhibited slightly. With P. denitrificans membrane vesicles, NADH-dependent reduction of menadione, juglone, and coenzyme Q1 was inhibited slightly and duroquinone reduction was inhibited markedly. Membrane-dependent interactions appear to be involved, since the compounds were more inhibitory with membrane preparations than with complex I. The mechanism of inhibition (except for the HIDC effect on coenzyme Q1 reduction with P. denitrificans) appeared to be through the interaction of dye with the rotenone site on NADH-ubiquinone reductase (EC 1.6.99.3), since rotenone-insensitive preparations of complex I and P. denitrificans membrane vesicles were also insensitive to HIDC and HITC inhibition.

Animals↗

PubMed1993

Inhibition of mitochondrial and Paracoccus denitrificans NADH-ubiquinone reductase by oxacarbocyanine dyes. A structure-activity study.

In this study, we determined that three structurally related oxacarbocyanine dyes, 3,3'-diethyloxacarbocyanine (DiOC2(3)), 3,3'-dipentyloxacarbocyanine (DiOC5(3)), and 3,3'-dihexyloxacarbocyanine (DiOC6(3)), and one oxadicarbocyanine, 3,3'-diethyloxadicarbocyanine (DiOC2(4)), inhibit bovine heart mitochondrial NADH oxidase activity and one of them, DiOC6(3), inhibits Paracoccus denitrificans NADH oxidase activity. The mitochondrial I50 values were 9 microM (DiOC2(3)), approximately 1 microM (DiOC5(3)) and DiOC6(3)), and approximately 3 microM (DiOC2(4)), whereas the I50 value for P. denitrificans was approximately 2 microM (DiOC6(3)). Neither succinate nor cytochrome oxidase (EC 1.9.3.1) activity was inhibited significantly by any of the compounds in either electron transport chain, localizing the inhibitory site of the oxacarbocyanine dyes to the respiratory chain segment between NADH and ubiquinone. With submitochondrial particles (SMP), NADH-dependent reduction of duroquinone and coenzyme Q1 was inhibited markedly by all four compounds with DiOC6(3) being the most potent inhibitor, and the reduction of menadione was inhibited substantially by DiOC6(3). When purified complex I was used, NADH-dependent reduction of ferricyanide was inhibited by DiOC5(3) and coenzyme Q1 reduction was inhibited by all oxacarbocyanines. With P. denitrificans membrane vesicles, DiOC6(3) substantially inhibited NADH-dependent reduction of coenzyme Q1. All the oxacarbocyanines were more effective inhibitors with membrane preparations than with complex I, suggesting that membrane interactions play a role in inhibition. The mechanism of inhibition of the oxacarbocyanines appears to be similar to that of rotenone since (a) essentially only electron acceptors affected by rotenone were affected by the compounds, (b) inhibition of menadione reduction was diminished drastically with rotenone-saturated SMP, and (c) inhibition of coenzyme Q1 was largely eliminated with rotenone-insensitive complex I, and P. denitrificans membrane vesicles.

Animals↗

PubMed1986

Structural relationships between the NADH dehydrogenases of Paracoccus denitrificans and bovine heart mitochondria as revealed by immunological cross-reactivities.

An antibody raised against two subunits (Mr 48 000 and 25 000) of NADH dehydrogenase from Paracoccus denitrificans cross-reacts with one of more than 20 polypeptides that form the bovine heart mitochondrial NADH dehydrogenase. The cross-reacting subunit has Mr 51 000 and is believed to be the NADH-binding subunit of the enzyme. Antibodies raised against certain subunits of the bovine heart NADH dehydrogenase were tested for cross-reactivity with P. denitrificans cytoplasmic membranes. Of those tested, only one, an antibody specific for the 49 kDa subunit of mitochondrial NADH dehydrogenase, cross-reacted with the bacterial membranes. It recognised a polypeptide of approximate Mr 46 000. This is an indication for a previously undetected third subunit of NADH dehydrogenase from P. denitrificans. The immunological cross-reactions indicate that the NADH dehydrogenases from P. denitrificans and bovine heart mitochondria are related structurally.

Animals↗

PubMed1986

Measurement of the oxidation-reduction potentials of amicyanin and c-type cytochromes from Paracoccus denitrificans.

The oxidation-reduction potentials of four periplasmic electron carrier proteins from Paracoccus denitrificans have been determined. Their midpoint potentials are: amicyanin, 294 +/- 6 mV; cytochrome c-550, 253 +/- 5 mV; cytochrome c-551i, 190 +/- 4 mV; and cytochrome c-553i, 148 +/- 5 mV. Although rapid amicyanin-mediated transfer of electrons from methylamine dehydrogenase to cytochrome c-551i was observed, reduced amicyanin did not reduce oxidized cytochrome c-551i in the absence of methylamine dehydrogenase.

Bacterial Proteins↗

PubMed1988

Proteolysis of Paracoccus denitrificans cytochrome oxidase by trypsin and chymotrypsin.

Paracoccus oxidase containing only two subunits was subjected to proteolysis by trypsin and chymotrypsin. Both subunits of the purified enzyme were cleaved at only a few sites and enzymatic activity was not inhibited. The cleavage sites were identified by protein sequencing. Subunit I was cleaved near the amino-terminus and subunit II in the loop connecting the two predicted trans-membrane helices. In native membrane fragments, but not in intact spheroplasts, this loop was accessible to both proteases. These results provide experimental evidence for the folding of subunit II in the membrane.

Chymotrypsin↗

PubMed1989

Cytochrome c-550 mediates electron transfer from inducible periplasmic c-type cytochromes to the cytoplasmic membrane of Paracoccus denitrificans.

Electron transfer from periplasmic cytochromes c to the membrane-bound respiratory chain has been studied with the isolated cytochromes and membrane preparations from Paracoccus denitrificans. When reduced cytochromes were incubated with spheroplasts only the constitutive cytochrome c-550 was rapidly oxidized. The inducible cytochromes c-551i and c-553i were not oxidized at appreciable rates. Cytochrome c-550 was able to mediate the transfer of electrons from either cytochrome c-551i or cytochrome c-553i to the membrane preparation.

Bacterial Proteins↗

PubMed1990

Are there isoenzymes of cytochrome c oxidase in Paracoccus denitrificans?

We have used a gene replacement strategy to delete the previously isolated gene [(1987) EMBO J. 6, 2825-2833] for the cytochrome c oxidase subunit I from Paracoccus denitrificans. The resulting mutant was still able to synthesize active cytochrome c oxidase. This led us to look for another locus which could completely suppress the mutation. In this study we report the isolation of a second gene encoding subunit I. An open reading frame coding for cytochrome c 550 was found upstream from this gene. We suggest that there are isoenzymes of cytochrome c oxidase (cytochrome aa3) in this bacterium.

Amino Acid Sequence↗

PubMed1990

Mutagenesis of the gene encoding amicyanin of Paracoccus denitrificans and the resultant effect on methylamine oxidation.

The gene encoding the blue-copper protein amicyanin was isolated from a genomic bank of Paracoccus denitrificans by using a synthetic oligonucleotide. It is located directly downstream of the gene encoding the small subunit of methylamine dehydrogenase. Amicyanin is transcribed as a precursor protein with a signal sequence, typical for periplasmic proteins. Specific inactivation of amicyanin by means of gene replacement techniques resulted in the complete loss of the ability to grow on methylamine.

Amino Acid Sequence↗

PubMed1992

Oxidation of methylamine by a Paracoccus denitrificans mutant impaired in the synthesis of the bc1 complex and the aa3-type oxidase. Evidence for the existence of an alternative cytochrome c oxidase in this bacterium.

A Paracoccus denitrificans fbcC-ctaDII double mutant strain impaired in the synthesis of both the bc1 complex and the aa3-type oxidase has been constructed. This mutant strain, which is still able to grow on methylamine as sole carbon and energy source, exhibits unimpaired oxygen consumption with succinate, methylamine and endogenous substrates as electron donors. From kinetic studies of the oxidation and reduction rates of cytochromes c, it can be concluded that P. denitrificans contains a second cytochrome c oxidase, different from the aa3-type.

Electron Transport Complex III↗

PubMed1994

Sulfide dehydrogenase is identical with the SoxB protein of the thiosulfate-oxidizing enzyme system of Paracoccus denitrificans GB17.

Thiosulfate induced cells of Paracoccus denitrificans GB17 oxidize thiosulfate and sulfide to sulfate. A mutant carrying a Tn5-mob insertion in the soxB gene is unable to oxidize thiosulfate or sulfide suggesting a linkage of both activities. To test this assumption we have separated the components of the thiosulfate-oxidizing enzyme system of the wild-type by ion exchange chromatography. The SoxB protein coeluted with a highly active sulfide dehydrogenase. Analysis by polyacrylamide gel electrophoresis revealed one major protein of M(r) 32k. Thus, the SoxB protein appeared to be identical with sulfide dehydrogenase.

Bacterial Proteins↗

PubMed1994

Identification of amino acid residues associated with the [2Fe-2S] cluster of the 25 kDa (NQO2) subunit of the proton-translocating NADH-quinone oxidoreductase of Paracoccus denitrificans.

In order to identify the ligand residues of the [2Fe-2S] cluster of the 25 kDa (NQO2) subunit of the proton-translocating NADH-quinone oxidoreductase of Paracoccus denitrificans, we mutated individually all seven cysteine residues (C61, C96, C101, C104, C113, C137, and C141) and one conserved histidine residue (H92) to Ser or Ala and expressed them in E. coli. After purification of the mutated 25 kDa subunits, the effect of mutations on the iron-sulfur cluster were characterized by chemical analyses and UV-visible and EPR spectroscopy. All mutated subunits, especially mutants of conserved cysteines, contained lower amounts of non-heme iron than wild-type. The subunits of three non-conserved cysteine residues (C61, C104, and C113) mutated to Ser and a histidine residue (H92) mutated to Ala exhibited essentially the same spectroscopic properties as those of the wild-type subunit. In contrast, mutation of the four conserved cysteine residues (C96, C101, C137, and C141) to Ser or Ala considerably altered the UV-visible and EPR spectra from the wild-type subunit. These results indicate that the four conserved cysteine residues coordinate the [2Fe-2S] cluster in the P. denitrificans 25 kDa subunit.

Amino Acids↗

PubMed1994

Synthesis of holo Paracoccus denitrificans cytochrome c550 requires targeting to the periplasm whereas that of holo Hydrogenobacter thermophilus cytochrome c552 does not. Implications for c-type cytochrome biogenesis.

Expression from a plasmid of the complete gene, including the codons for the N-terminal periplasmic targeting signal, for cytochrome c550 of Paracoccus denitrificans led to the formation of the holo protein in the periplasms of both P. denitrificans and Escherichia coli. Expression of the gene from which the region coding for the targeting signal had been specifically deleted resulted in formation of apo-protein in the cytoplasms of both organisms. These findings are consistent with haem attachment occurring in the periplasm. In contrast, the formation of holo cytochrome c552 from Hydrogenobacter thermophilus following expression of the gene lacking the periplasmic targeting sequence in either P. denitrificans or E. coli is attributed to spontaneous cytoplasmic attachment of haem to the thermostable protein.

Bacteria, Aerobic↗

PubMed1995

Nitrite and nitric oxide reduction in Paracoccus denitrificans is under the control of NNR, a regulatory protein that belongs to the FNR family of transcriptional activators.

The nir and nor genes, which encode nitrite and nitric oxide reductase, lie close together on the DNA of Paracoccus denitrificans. We here identify an adjacent gene, nnr, which is involved in the expression of nir and nor under anaerobic conditions. The corresponding protein of 224 amino acids is homologous with the family of FNR proteins, although it lacks the N-terminal cysteines. A mutation in the nnr gene had a negative effect on the expression of nitrite and nitric oxide reductase. Synthesis of membrane bound nitrate reductase, of nitrous oxide reductase, and of the cbb3-type cytochrome c oxidase were not affected by mutation of this gene. These results suggest that denitrification in P. denitrificans may be governed by a signal transduction network that is similar to that involved in oxygen regulation of nitrogen metabolism in other organisms.

Amino Acid Sequence↗