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the kinetic and isotopic competence of nitric oxide as an intermediate in denitrification.rates of no uptake by five denitrifying bacteria were estimated by no-electrode and gas chromatography methods under conditions of rather low cell densities and [noaq]. the rates so measured, vmaxno, represent lower limits for the true value of that parameter, but nevertheless exceed vmax for nitrite uptake, vmaxni, by a factor of two typically. previous estimates under suboptimal conditions had placed vmaxno at 0.3-0.5 of vmaxni (st. john, r. t., and hollocher, t. c. (1977) j. biol. chem. 252, ...19902295624
inhibition by trimethylamine of methylamine oxidation by paracoccus denitrificans and bacterium w3a1.trimethylamine, a common substrate for methylotrophic growth, specifically inhibited methylamine-dependent respiration by paracoccus denitrificans and bacterium w3a1. these effects were caused by the specific inhibition by trimethylamine of the periplasmic quinoprotein methylamine dehydrogenase. steady-state kinetic analysis of the effect of trimethylamine on methylamine oxidation by methylamine dehydrogenase indicated that the inhibition was a mixed type. apparent ki values for trimethylamine o ...19902331476
spectral and electrochemical properties of glutaryl-coa dehydrogenase from paracoccus denitrificans.studies of the spectral (uv/vis and resonance raman) and electrochemical properties of the fad-containing enzyme glutaryl-coa dehydrogenase (gcd) from paracoccus denitrificans reveal that the properties of the oxidized enzyme (gcdox) appear to be invariant from those properties known for other acyl-coa dehydrogenases such as mammalian general acyl-coa dehydrogenase (gacd) and butyryl-coa dehydrogenase (bcd) from megasphaera elsdenii. however, when either free or complexed gcd is reduced, its spe ...19902340266
periplasmic and membrane-bound respiratory nitrate reductases in thiosphaera pantotropha. the periplasmic enzyme catalyzes the first step in aerobic denitrification.the unusual ability of thiosphaera pantotropha to catalyze respiratory nitrate reduction under aerobic conditions is shown to correlate with the activity of a periplasmic nitrate reductase that is expressed under both aerobic and anaerobic growth conditions. the organism also synthesizes, but only under anaerobic conditions, a membrane-bound nitrate reductase which resembles the corresponding enzyme in paracoccus denitrificans in respect of both catalytic properties and inhibition of activity in ...19902365057
steady-state nitric oxide concentrations during denitrification.three species of denitrifying bacteria, paracoccus denitrificans, pseudomonas stutzeri strain jm300, and achromobacter cycloclastes, were allowed to reduce nitrate or nitrite in anaerobic, closed vials while the equilibration of gases between aqueous and gas phases was facilitated by vigorous stirring. the gas phase was sampled and analyzed for no with use of a chemiluminescence detector calibrated against bottled no standards or against no produced by the nitrite-iodide reaction. [noaq] was inf ...19902365685
chemical cross-linking study of complex formation between methylamine dehydrogenase and amicyanin from paracoccus denitrificans.two soluble periplasmic redox proteins from paracoccus denitrificans, the quinoprotein methylamine dehydrogenase and the copper protein amicyanin, form a weakly associated complex that is critical to their physiological function in electron transport [gray, k. a., davidson, v. l., & knaff, d. b. (1988) j. biol. chem. 263, 13987-13990]. the specific interactions between methylamine dehydrogenase and amicyanin have been studied by using the water-soluble cross-linking agent 1-ethyl-3-[3-(dimethyla ...19902383547
paracoccus aminophilus sp. nov. and paracoccus aminovorans sp. nov., which utilize n,n-dimethylformamide.two methylamine- and n,n-dimethylformamide-utilizing paracoccus spp. are described. these bacteria are gram-negative, nonsporeforming, nonmotile, coccoid or short rod-shaped organisms. their dna base composition is 62 to 68 mol% g + c. their cellular fatty acids include large amounts of c18:1 acid. their major hydroxy acids are 3-oh c10:0 and 3-oh c14:0 acids. the major ubiquinone is q-10. these bacteria are distinguished from paracoccus denitrificans and paracoccus alcaliphilus by physiological ...19902397196
paracoccus kocurii sp. nov., a tetramethylammonium-assimilating bacterium.a new species of tetramethylammonium-assimilating bacteria was isolated from an activated sludge which was used for the treatment of tetramethylammonium hydroxide contained in the wastewater from semiconductor manufacturing processes. cells of the bacteria were gram-negative, nonmotile, short rods (0.5 to 0.8 micron by 0.7 to 1.1 microns). the major respiratory quinone component of the bacteria was q-10. the g + c content was 71 mol%. isolates are mesophilic and assimilate methylated amines such ...19902397197
rapid purification of cytochrome c oxidase from paracoccus denitrificans.two methods are described for the purification of cytochrome c oxidase from triton x-100 extracts of the periplasma membrane of paracoccus denitrificans. the first is a large-scale procedure for the preparation of 100-250 nmol of cytochrome c oxidase (10-20 mg) in 1 week. the second is a rapid procedure for isolating up to 25 nmol in 2-3 days. owing to the high yields given by fast protein liquid chromatography (fplc) on mono q columns, the overall yield is about 20%, whereas the yield in many o ...19901962788
review article: structural and functional properties of cytochrome aa3 from bacteria.the aa3 oxidases from bacteria form a group of related enzymes that resemble the far more complex mitochondrial cytochrome c oxidase, both functionally and structurally. these enzymes catalyze electron transfer from ferrocytochrome c to oxygen to produce water. this transfer is coupled to proton translocation. several oxidases of this type have been purified from cytoplasmic membranes of bacteria. this review summarizes the present knowledge on purified bacterial aa3 oxidases and correlates thes ...19901963305
nucleotide sequence of the gene coding for four subunits of cytochrome c oxidase from the thermophilic bacterium ps3.the gene coding for four subunits of cytochrome aa3-type oxidase was isolated from a genomic dna library of the thermophilic bacterium ps3 and sequenced. the n-terminus of each subunit was also sequenced to verify the initiation site of the reading frame. the deduced amino acid sequences contained 615 amino acid residues for subunit i (co1/caab product), 333 residues for subunit ii (co2/caaa product), 207 residues for subunit iii (co3/caac product), and 109 residues for subunit iv (co4/caad prod ...19901964459
microbial metabolism of tholin.in this paper, we show that a wide variety of common soil bacteria are able to obtain their carbon and energy needs from tholin (a class of complex organic heteropolymers thought to be widely distributed through the solar system; in this case tholin was produced by passage of electrical discharge through a mixture of methane, ammonia, and water vapor). we have isolated aerobic, anaerobic, and facultatively anaerobic bacteria which are able to use tholin as a sole carbon source. organisms which ...199011538367
inhibition by cyclopropylamine of the quinoprotein methylamine dehydrogenase is mechanism-based and causes covalent cross-linking of alpha and beta subunits.cyclopropylamine acted as a mechanism-based inhibitor of the quinoprotein methylamine dehydrogenase from paracoccus denitrificans. the protein-bound quinone cofactor of this enzyme was rapidly reduced by addition of a stoichiometric amount of cyclopropylamine, but this compound did not serve as a substrate for the enzyme in the steady-state kinetic assay. time-dependent inactivation of the enzyme by cyclopropylamine was observed only in the presence of a reoxidant. saturation behavior was observ ...19911993204
paracoccus denitrificans. 19912050652
metabolic regulation including anaerobic metabolism in paracoccus denitrificans.under anaerobic circumstances in the presence of nitrate paracoccus denitrificans is able to denitrify. the properties of the reductases involved in nitrate reductase, nitrite reductase, nitric oxide reductase, and nitrous oxide reductase are described. for that purpose not only the properties of the enzymes of p. denitrificans are considered but also those from escherichia coli, pseudomonas aeruginosa, and pseudomonas stutzeri. nitrate reductase consists of three subunits: the alpha subunit con ...19912050653
c1 metabolism in paracoccus denitrificans: genetics of paracoccus denitrificans.paracoccus denitrificans is able to grow on the c1 compounds methanol and methylamine. these compounds are oxidized to formaldehyde which is subsequently oxidized via formate to carbon dioxide. biomass is produced by carbon dioxide fixation via the ribulose biphosphate pathway. the first oxidation reaction is catalyzed by the enzymes methanol dehydrogenase and methylamine dehydrogenase, respectively. both enzymes contain two different subunits in an alpha 2 beta 2 configuration. the genes encodi ...19912050654
bacterial nadh-quinone oxidoreductases.the nadh-quinone oxidoreductases of the bacterial respiratory chain could be divided in two groups depending on whether they bear an energy-coupling site. those enzymes that bear the coupling site are designated as nadh dehydrogenase 1 (ndh-1) and those that do not as nadh dehydrogenase 2 (ndh-2). all members of the ndh-1 group analyzed to date are multiple polypeptide enzymes and contain noncovalently bound fmn and iron-sulfur clusters as prosthetic groups. the nadh-ubiquinone-1 reductase activ ...19912050655
molecular cloning of the l-phenylalanine transaminase gene from paracoccus denitrificans in escherichia coli k-12.the l-phenylalanine transaminase gene of paracoccus denitrificans was cloned by a shotgun method using the escherichia coli k-12 mutant dg30, which lacks three distinct transaminase genes. plasmid ppap142 was constructed by inserting a 2.2-kb fragment carrying the transaminase gene into puc18. strain e. coli k-12 hb101 cells harboring the plasmid produced 20-fold to 30-fold more transaminase than wild type p. denitrificans cells. the nucleotide sequence of the 2.2-kb fragment was determined, rev ...19912054101
nitric oxide reductase. purification from paracoccus denitrificans with use of a single column and some characteristics.nitric oxide reductase was purified from paracoccus denitrificans very nearly to homogeneity by a simple method that involved the use of octyl glucoside to solubilize the enzyme from membranes and required a single hydroxyapatite column. the enzyme had specific activities of about 10 mumol no reduced x min-1 x mg-1 at ph 6.5 in an amperometric assay system using phenazine methosulfate/ascorbate as the reducing agent and about 22 mumol no reduced x min-1 x mg-1 at ph 5.0, which is the optimum ph. ...19911645715
the functions and synthesis of bacterial c-type cytochromes with particular reference to paracoccus denitrificans and rhodobacter capsulatus. 19911646010
the cytochrome c peroxidase of paracoccus denitrificans.the size, visible absorption spectra, nature of haem and haem content suggest that the cytochrome c peroxidase of paracoccus denitrificans is related to that of pseudomonas aeruginosa. however, the paracoccus enzyme shows a preference for cytochrome c donors with a positively charged 'front surface' and in this respect resembles the cytochrome c peroxidase from saccharomyces cerevisiae. paracoccus cytochrome c-550 is the best electron donor tested and, in spite of an acidic isoelectric point, ha ...19911646012
evidence for the role of soluble cytochrome c in the dissimilatory reduction of nitrite and nitrous oxide by cells of paracoccus denitrificans.the role of periplasmic cytochrome c in the denitrification pathway has been investigated using a wild-type and/or a cytochrome c deficient strain of paracoccus denitrificans. the reconstitution experiments with the isolated proteins showed that bacterial cytochrome c-550 restored the electron transport from the cytoplasmic membrane to soluble nitrite reductase (cytochrome cd1). in response to decreased aeration lasting 3 h, the huug25 strain synthesized nitrous-oxide reductase significantly sta ...19911646632
the cytochrome c reductase/oxidase respiratory pathway of paracoccus denitrificans: genetic and functional studies.data are presented on three components of the quinol oxidation branch of the paracoccus respiratory chain: cytochrome c reductase, cytochrome c552, and the a-type terminal oxidase. deletion mutants in the bc1 and the aa3 complex give insight into electron pathways, assembly processes, and stability of both redox complexes, and, moreover, are an important prerequisite for future site-directed mutagenesis experiments. in addition, evidence for a role of cytochrome c552 in electron transport betwee ...19911646794
the three-subunit cytochrome bc1 complex of paracoccus denitrificans. its physiological function, structure, and mechanism of electron transfer and energy transduction.the cytochrome bc1 complex purified from p. denitrificans has the same electron-transfer and energy-transducing activities, is sensitive to the same electron-transfer inhibitors, and contains cytochromes b, c1, iron-sulfur protein, and thermodynamically stable ubisemiquinone identical to the counterpart complexes from mitochondria. however, the bacterial bc1 complex consists of only three proteins, the obligate electron-transfer proteins, while the mitochondrial complexes contain six or more sup ...19911646795
genes coding for cytochrome c oxidase in paracoccus denitrificans.several loci on the paracoccus denitrificans chromosome are involved in the synthesis of cytochrome c oxidase. so far three genetic loci have been isolated. one of them contains the structural genes of subunits ii and iii, as well as two regulatory genes which probably code for oxidase-specific assembly factors. in addition, two distinct genes for subunit i have been cloned, one of which is located adjacent to the cytochrome c550 gene. an alignment of six promoter regions reveals only short comm ...19911646796
cytochrome c oxidase in paracoccus denitrificans. protein, chemical, structural, and evolutionary aspects.preparations and protein chemical characterizations performed with cytochrome c oxidase (e.c. 1.9.3.1) from the purple bacterium paracoccus denitrificans are reviewed. the simplest catalytically competent complex of the enzyme consists of two subunits of 62012 and 2799 da. the theoretical heme a/protein ratio of the purified enzyme is 22.0 nmol/mg. the amino acid sequences of both proteins are compared with examples of subunits i and ii of mitochondrial terminal oxidases from the main kingdoms o ...19911646797
cytochrome c oxidase metal centers: location and function.cytochrome c oxidase of paracoccus denitrificans is spectroscopically and functionally very similar to the mammalian enzyme. however, it has a very much simpler quaternary structure, consisting of only three subunits instead of the 13 of the bovine enzyme. the known primary structure of the paracoccus denitrificans subunits, the knowledge of a large number of sequences from other species, and data on the controlled proteolytic digestion of the enzyme allow structural restrictions to be placed on ...19911646798
the reactions of the oxidase and reductases of paracoccus denitrificans with cytochromes c.electron transport in the paracoccus denitrificans respiratory chain system is considerably more rapid when it includes the membrane-bound cytochrome c552 than with either soluble paracoccus c550 or bovine cytochrome c; a pool function for cytochrome c is not necessary. low concentrations of paracoccus or bovine cytochrome c stimulate the oxidase activity. this observation could explain the multiphasic scatchard plots which are obtained. a negatively charged area on the "back side" of paracoccus ...19911646799
evolutionary aspects of cytochrome c oxidase.the presence of additional subunits in cytochrome oxidase distinguish the multicellular eukaryotic enzyme from that of a simple unicellular bacterial enzyme. the number of these additional subunits increases with increasing evolutionary stage of the organism. subunits i-iii of the eukaryotic enzyme are related to the three bacterial subunits, and they are encoded on mitochondrial dna. the additional subunits are nuclear encoded. experimental evidences are presented here to indicate that the lowe ...19911646800
the gene encoding cytochrome c oxidase subunit ii from rhodobacter sphaeroides; comparison of the deduced amino acid sequence with sequences of corresponding peptides from other species.the gene (coxii) encoding subunit ii of rhodobacter sphaeroides cytochrome c oxidase (cytochrome aa3) has been isolated by screening a genomic dna library in phage lambda with a probe derived from coxii of paracoccus denitrificans. a 2-kb fragment containing coxii dna was subcloned into the phage m13mp18 and the sequence determined. the 2-kb insert contains the entire coding region for coxii gene, including the atg start codon and a tga stop codon. the deduced amino acid (aa) sequence of subunit ...19911648008
subunit iii of cytochrome c oxidase is not involved in proton translocation: a site-directed mutagenesis study.subunit iii (coiii) is one of the three core subunits of the aa3-type cytochrome c oxidase. coiii does not contain any of the redox centres and can be removed from the purified enzyme but has a function during biosynthesis of the enzyme. dicyclohexyl carbodiimide (dccd) modifies a conserved glutamic acid residue in coiii and abolishes the proton translocation activity of the enzyme. in this study, the invariant carboxylic acids e98 (the dccd-binding glutamic acid) and d259 of coiii were changed ...19911648477
cytochrome c2 is essential for electron transfer to nitrous oxide reductase from physiological substrates in rhodobacter capsulatus and can act as an electron donor to the reductase in vitro. correlation with photoinhibition studies.1. addition of nitrous oxide to a periplasmic fraction released from rhodobacter capsulatus strains mt1131, n22dnar+ or ad2 caused oxidation of c-type cytochrome, as judged by the decrease in absorbance at 550 nm. the periplasmic fraction catalysed reduction of nitrous oxide in the presence of either isoascorbate plus phenazine ethosulphate or reduced methyl viologen. the rates with these two electron donors were similar and were comparable to the activity observed with a quantity of cells equiv ...19911651241
cytochrome c' of paracoccus denitrificans.cytochrome c' was identified in periplasmic extracts of the paracoccus denitrificans strains lmd 22.21 and lmd 52.44. the cytochrome c' was purified from the latter using the device of sequential molecular exclusion chromatography in the dimeric and monomeric states. although showing the overall spectroscopic features of the cytochrome c' family, the paracoccus cytochrome c' is unusual in having a red-shifted oxidised soret band at 407 nm. also unusual is the midpoint potential of 202 mv, well a ...19911653018
potentiometric and spectral studies with the two-subunit cytochrome aa3 from paracoccus denitrificans. comparison with the 13-subunit beef heart enzyme.previous work from this laboratory has revealed a complex and interactive redox behavior for the active metal centers in beef heart cytochrome aa3. all of these centers are contained in two of the 13 subunits which make up the enzyme. the isolated cytochrome aa3 of paracoccus denitrificans contains only two subunits. the purpose of the current investigation was to see if the complex redox behavior is dependent on the presence of the additional 11 peptides that are present in the mammalian enzyme ...19911655082
comparison of energy-transducing capabilities of the two- and three-subunit cytochromes aa3 from paracoccus denitrificans and the 13-subunit beef heart enzyme.in the accompanying paper, we have shown that the two-subunit cytochrome aa3 isolated from paracoccus denitrificans displays the same kind of complex and interactive redox behavior as the 13-subunit cytochrome aa3 from beef heart. therefore, the redox characteristics are not dependent on the additional 11 subunits. in the current work, we have examined the energy-transducing capabilities of both the two- and three-subunit enzymes obtained from paracoccus denitrificans in relation to that of the ...19911655083
isolation and characterization of the moxj, moxg, moxi, and moxr genes of paracoccus denitrificans: inactivation of moxj, moxg, and moxr and the resultant effect on methylotrophic growth.by using the moxf gene encoding the large fragment of methanol dehydrogenase as a probe, a downstream linked chromosomal fragment was isolated from a genomic bank of paracoccus denitrificans. the nucleotide sequence of the fragment was determined and revealed the 3' part of moxf, four additional open reading frames, and the 5' part of a sixth one. the organization and deduced amino acid sequences of the first three frames downstream from moxf were found to be largely homologous to the moxj, moxg ...19911657871
a method for introduction of unmarked mutations in the genome of paracoccus denitrificans: construction of strains with multiple mutations in the genes encoding periplasmic cytochromes c550, c551i, and c553i.a new suicide vector, prvs1, was constructed to facilitate the site-directed introduction of unmarked mutations in the chromosome of paracoccus denitrificans. the vector was derived from suicide vector pgrpd1, which was equipped with the lacz gene encoding beta-galactosidase. the reporter gene was found to be a successful screening marker for the discrimination between plasmid integrant strains and mutant strains which had lost the plasmid after homologous recombination. suicide vectors pgrpd1 a ...19911657872
isolation, sequencing, and mutagenesis of the gene encoding cytochrome c553i of paracoccus denitrificans and characterization of the mutant strain.the periplasmically located cytochrome c553i of paracoccus denitrificans was purified from cells grown aerobically on choline as the carbon source. the purified protein was digested with trypsin to obtain several protein fragments. the n-terminal regions of these fragments were sequenced. on the basis of one of these sequences, a mix of 17-mer oligonucleotides was synthesized. by using this mix as a probe, the structural gene encoding cytochrome c553i (cycb) was isolated. the nucleotide sequence ...19911657873
molecular cloning of the cytochrome aa3 gene from the archaeon (archaebacterium) halobacterium halobium.a novel aa3-type cytochrome oxidase from the extremely halophilic archaeon, halobacterium halobium, differs significantly from those of other prokaryotic and eukaryotic cytochrome oxidases (fujiwara, t., fukumori, y., and yamanaka, t. (1989) j. biochem. 105, 287-292). in the present study, we cloned and sequenced the gene which encodes the cytochrome aa3 by using the polymerase chain reaction methods. the deduced amino acid sequence of subunit i of h. halobium cytochrome aa3 was more similar to ...19911659810
the periplasmic modifier protein for methanol dehydrogenase in the methylotrophs methylophilus methylotrophus and paracoccus denitrificans.a modifier protein (m-protein), which increases the affinity of methanol dehydrogenase (mdh) for alcohols but decreases its affinity for formaldehyde, has been partially purified from methylophilus methylotrophus and paracoccus denitrificans. analysis was complicated by non-protein factors in bacterial extracts that are able to mimic m-protein in one of its functions-that of increasing the activity of mdh with butane-1,3-diol in the dye-linked assay system. the 67 kda polypeptide, previously ide ...19911663153
removal of nitrate from water by cells of paracoccus denitrificans in a membrane flow reactor.a new type of flow bioreactor designed to remove nitrate from water was developed. denitrification activity of native paracoccus denitrificans cells was used, the cells being separated from the refined medium by a semipermeable membrane. relationships between the degree of nitrate conversion and the denitrification rate, on the one hand, and the volume flow rate and the amount of biomass, on the other, together with the results concerning denitrification during closed-circuit recirculation of th ...19911668747
assimilation of ammonia in paracoccus denitrificans.two pathways serve for assimilation of ammonia in paracoccus denitrificans. glutamate dehydrogenase (nadp+) catalyzes the assimilation at a high nh4+ concentration. if nitrate serves as the nitrogen source, glutamate is synthesized by glutamate-ammonia ligase and glutamate synthase (nadph). at a very low nh4+ concentration, all three enzymes are synthesized simultaneously. no direct relationship exists between glutamate dehydrogenase (nadp+) and glutamate-ammonia ligase in p. denitrificans, whil ...19911688163
the production and utilization of nitric oxide by a new, denitrifying strain of pseudomonas aeruginosa.when a new strain of pseudomonas aeruginosa was grown aerobically and then transferred to anaerobic conditions, cells reduced no3- quantitatively to no2- in no3(-)-respiration. in the absence of nitrate, no2- was immediately reduced to no or n2o but not to n2 indicating that no2(-)-reductase but not n2o-reductase was active. the formation of the products no or n2o depended on the ph in the medium and the concentration of no2- present. when p. aeruginosa was grown anaerobically for at least three ...19911772347
using the bacterium, paracoccus denitrificans and other 'runaway mitochondria' as classroom models for respiratory electron transport studies.our suggestions for experiments demonstrating electron-transport-chain composition and reactions all exploit bacteria which can be prepared quickly, easily and cheaply from cells grown in erlenmeyer flasks. while they have been designed from a cytochrome oxidase point of view using organisms of our own prejudice, strains containing mutations in other sites could be just as educational. most bacteria that can grow aerobically have features in common with the mitochondrial respiratory chain. becau ...19911794596
determination of nitrate by conversion to nitrite using paracoccus denitrificans.a new method of determination of nitrate was developed, utilizing the nitrate reductase activity of paracoccus denitrificans in which a further reduction of nitrate is blocked either by a mutation affecting formation of cytochromes c or by inhibition of the electron flow to nitrite reductase by mucidin. after deproteinization of the sample with zinc acetate the nitrite produced is determined colorimetrically.19911823647
the f0 subunits of bovine mitochondrial atp synthase complex: purification, antibody production, and interspecies cross-immunoreactivity.the known subunits of the membrane sector f0 of the bovine mitochondrial atp synthase complex are subunits b, d, 6, f6, oscp (oligomycin sensitivity-conferring protein), the dccd (dicyclohexylcarbodiimide) binding proteolipid, and a6l. the first six subunits were purified from smp or preparations of the atp synthase complex, and monospecific antibodies were raised against each. the antisera were shown to be competent for immuno-blotting, and each antiserum recognized a single polypeptide of the ...19911824914
increase in spermine content coordinated with siderophore production in paracoccus denitrificans.spermine is present in relatively low amounts in paracoccus denitrificans cultured aerobically in an ammonium succinate minimal salts medium supplemented with 50 microm iron(iii). however, in iron-deprived cultures [minimal salts medium containing 0.5 microm iron(iii)], spermine content increases by an order of magnitude in coordination with the well-known responses to iron derivation, e.g., derepression of siderophore synthesis and siderophore excretion. when iron-deprived cultures exhibiting b ...19911826103
the bacillus subtilis cytochrome-c oxidase. variations on a conserved protein theme.the structural genes of cytochrome-c oxidase in bacillus subtilis have been isolated and sequenced. five genes, ctab-f, are closely spaced. ctac, ctad, ctae and ctaf are the genes for subunits ii, i, iii and ivb, respectively, ctab, which may encode an assembly factor, is separated and upstream from the others. in comparison to its mitochondrial counterparts, subunit i has an extended c-terminus with two additional transmembrane segments, whereas subunit iii has lost two such segments from its n ...19911847686
paracoccus denitrificans mutants deleted in the gene for subunit ii of cytochrome c oxidase also lack subunit i.as a prerequisite to site-directed mutagenesis on cytochrome c oxidase, two different mutants are constructed by inactivating the cta gene locus encoding subunits ii and iii (ctac and ctae) of the paracoccus denitrificans oxidase. either a short fragment encoding part of the putative copper binding site near the c terminus of subunit ii, or a substantial fragment, comprising parts of the coding region for both subunits and all of the intervening three open reading frames, are removed and replace ...19911850416
resolution of the electronic transitions of cytochrome c oxidase: evidence for two conformational states of ferrous cytochrome alpha.second-derivative absorption spectra are reported for a variety of oxidation and ligation states of bovine cytochrome c oxidase (ferrocytochrome-c:oxygen oxidoreductase, ec 1.9.3.1). the high resolving power of the second-derivative method allows us to assign the individual electronic transitions of cytochrome alpha and cytochrome alpha 3 in many of these states. in the fully reduced enzyme, one observes a single electronic transition at 444 nm, corresponding to the soret transition for both fer ...19911852001
crystallographic investigations of the tryptophan-derived cofactor in the quinoprotein methylamine dehydrogenase.a model of tryptophan tryptophylquinone (ttq), recently proposed by mcintire et al. (science (1991) 252, 817-824) to be the prosthetic group of the quinoprotein methylamine dehydrogenase, has been compared with electron density maps of this dehydrogenase from thiobacillus versutus and paracoccus denitrificans. the comparison shows that the ttq model can be neatly accommodated, providing strong supportive evidence that ttq is indeed the cofactor for this group of quinoproteins.19911879526
characterization of the tryptophan-derived quinone cofactor of methylamine dehydrogenase by resonance raman spectroscopy.the resonance raman (rr) spectrum of oxidized methylamine dehydrogenase (madhox) exhibits a set of c-h, c-c, c = c, and c = o vibrational modes between 900 and 1700 cm-1 that are characteristic of the quinone moiety of the tryptophan tryptophlyquinone (ttq) cofactor. the close similarity of the rr spectra for madhs from paracoccus denitrificans (pd), thiobacillus versutus (tv), and bacterium w3a1 proves that the same cofactor is present in all three proteins. the madhs from pd and tv have a v(c ...19911892829
identification of the nadh-binding subunit of energy-transducing nadh-quinone oxidoreductase (ndh-1) of thermus thermophilus hb-8.the energy-transducing nadh--quinone oxidoreductase (ndh-1) isolated from thermus thermophilus hb-8 is composed of approximately 10 unlike polypeptides and contains noncovalently bound fmn and at least three iron-sulfur clusters [yagi, t., hon-nami, k., and ohnishi, t. (1988) biochemistry 27, 2008-2013]. when ndh-1 of t. thermophilus hb-8 was irradiated by short uv light in the presence of [adenylate-32p]nadh or [adenylate-32p]nad, radioactivity was incorporated into a single polypeptide of mr 4 ...19911899572
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 eit ...19911900156
anaerobic degradation of cresols by denitrifying bacteria.the initial reactions in anaerobic metabolism of methylphenols (cresols) and dimethylphenols were studied with denitrifying bacteria. a newly isolated strain, possibly a paracoccus sp., was able to grow on o- or p-cresol as sole organic substrate with a generation time of 11 h; o- or p-cresol was completely oxidized to co2 with nitrate being reduced to n2. a denitrifying pseudomonas-like strain oxidized m- or -p-cresol as the sole organic growth substrate completely to co2 with a generation time ...19911904702
the nadh-binding subunit of the energy-transducing nadh-ubiquinone oxidoreductase of paracoccus denitrificans: gene cloning and deduced primary structure.the nadh dehydrogenase complex isolated from paracoccus denitrificans is composed of approximately 10 unlike polypeptides and contains noncovalently bound fmn, non-heme iron, and acid-labile sulfide [yagi, t. (1986) arch. biochem. biophys. 250, 302-311]. the nadh-binding subunit (mr = 50,000) of this enzyme complex was identified by direct photoaffinity labeling with [32p]nadh [yagi, t., & dinh, t.m. (1990) biochemistry 29, 5515-5520]. primers were synthesized on the basis of the n-terminal amin ...19911905152
characterization of the 25-kilodalton subunit of the energy-transducing nadh-ubiquinone oxidoreductase of paracoccus denitrificans: sequence similarity to the 24-kilodalton subunit of the flavoprotein fraction of mammalian complex i.the nadh dehydrogenase complex isolated from paracoccus denitrificans is composed of approximately 10 unlike polypeptides [yagi, t. (1986) arch. biochem. biophys. 250, 302-311]. structural genes encoding the subunits of this enzyme complex constitute at least one gene cluster [xu, x., matsuno-yagi, a., & yagi, t. (1991) biochemistry 30, 6422-6428]. the 25-kda subunit (nqo2), which has been isolated from sodium dodecyl sulfate-polyacrylamide gels, is a polypeptide of this enzyme complex. the part ...19911909571
identification of the dna region responsible for sulfur-oxidizing ability of thiosphaera pantotropha.for the identification of the dna region responsible for the sulfur-oxidizing ability (sox) of thiosphaera pantotropha, we used previously isolated tn5-mob insertional sox- mutants. for seven mutants, the tn5-mob insertion was localized on the chromosome rather than on the megaplasmids phg41 or phg42 by using the tn5-mob-harboring vehicle psup5011 as probe. the specific insertion of tn5-mob into a sox gene was determined for one sox- mutant, strain tp19. an 18-kb ecori fragment was cloned in esc ...19911938925
comparison of dentrification by paracoccus denitrificans, pseudomonas stutzeri and pseudomonas aeruginosa.the course of denitrification of nitrate, nitrite and both compounds together by static cultures of paracoccus denitrificans, pseudomonas stutzeri and pseudomonas aeruginosa was studied. these strains represent three different types of denitrification: 1. reduction of nitrate to gaseous nitrogen without accumulation of nitrite (p. denitrificans); 2. partial accumulation of nitrite in growing cultures during reduction of nitrate to gaseous nitrogen (p. aeruginosa) and 3. two-phase denitrification ...19921284849
reduction of cua induces a conformational change in cytochrome c oxidase from paracoccus denitrificans.cytochrome c oxidase (cytochrome aa3) from paracoccus denitrificans contains a tightly bound manganese(ii) ion, which responds to reduction of the enzyme by a change in its epr signal (seelig et al. (1981) biochim. biophys. acta 636, 162-167). in this paper, the nature of this phenomenon is studied and the bound manganese is used as a reporter group to monitor a redox-linked conformational change in the protein. a reductive titration of the cyanide-inhibited enzyme shows that the change in the m ...19921310624
cloning, sequencing and deletion from the chromosome of the gene encoding subunit i of the aa3-type cytochrome c oxidase of rhodobacter sphaeroides.the ctad gene encoding subunit i of the aa3-type cytochrome c oxidase from rhodobacter sphaeroides has been cloned. the gene encodes a polypeptide of 565 residues which is highly homologous to the sequences of subunit i from other prokaryotic and eukaryotic sources, e.g. 51% identity with that from bovine, and 75% identity with that from paracoccus denitrificans. the ctad gene was deleted from the chromosome of r. sphaeroides, resulting in a strain that spectroscopically lacks cytochrome a. this ...19921313140
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 seco ...19921321057
terminal oxidases in paracoccus denitrificans. 19921321668
oscillations of nitric oxide concentration in the perturbed denitrification pathway of paracoccus denitrificans.the metabolism of nitric oxide in paracoccus denitrificans has been studied using a clark-type electrode. the uncoupler carbonyl cyanide m-chlorophenylhydrazone (cccp) and the sh reagent n-ethylmaleimide, both of which released nitric oxide from cells respiring nitrite, were found to be efficient inhibitors of nitric oxide reductase activity. control experiments with another uncoupler, pentachlorophenol, showed that the inhibitory effect of cccp was not the result of a decrease in membrane poten ...19921325776
factors affecting the stability of methanol dehydrogenase from paracoccus denitrificans.methanol dehydrogenase from paracoccus denitrificans was purified to homogeneity in two steps from the periplasmic fraction of methanol-grown cells. the enzyme was composed of subunits of m(r) 67,000 and 12,000, and non-covalently bound pyrroloquinoline quinone. it exhibited a ph optimum at ph values of 9.0 and above. it was not stable at ph greater than 9.0, but exhibited little loss of activity after prolonged incubation at ph values as low as 4.5. methyl dehydrogenase was relatively stable to ...19921325939
purification of cytochrome c oxidase by lysine-affinity chromatography.a method for the purification of cytochrome c oxidase that is based on the affinity of this enzyme for polycations such as poly-l-lysine is described. when detergent extracts of bovine cardiac mitochondria were applied to either a poly-l-lysine-agarose or a lysine-sepharose column at low ionic strength, cytochrome c oxidase was found to adhere tightly, whereas the bulk of the proteins were eluted by washing with the same buffer. the cytochrome c oxidase was eluted by application of a linear pota ...19921330132
a comparative epr investigation of the multicopper proteins nitrous-oxide reductase and cytochrome c oxidase.the multicopper proteins, nitrous-oxide reductase (n2or) and cytochrome c oxidase (cox), were investigated by epr spectroscopy at microwave frequencies 2.4-35 ghz. our results support a cu-cu interaction in cox and n2or. at least 10 lines in the 2.7-ghz, 12 lines in the 4.6-ghz and 14 lines in the 9.2 ghz spectra were resolved for n2or. eight copper lines at 2.7 ghz, about nine lines at 4.6 ghz and about six lines at 9.2 ghz were resolved for cox. simulations of the epr spectra were consistent w ...19921330560
the three-dimensional structures of methanol dehydrogenase from two methylotrophic bacteria at 2.6-a resolution.the structures of methanol dehydrogenase (medh) from two closely related methylotrophic bacteria, methylophilus methylotrophus and w3a1, have been determined at 2.6-a resolution. the molecule, a quinoprotein of molecular mass of about 138 kda, contains two heavy (h) and two light (l) subunits of unknown sequence and two molecules of noncovalently associated pyrroloquinoline quinone. the two enzymes crystallize isomorphously in space group p2(1) with one h2l2 heterotetramer in the asymmetric unit ...19921331050
characterization of mutant forms of the quinoprotein methanol dehydrogenase lacking an essential calcium ion.methanol dehydrogenase (mdh) from methylobacterium extorquens, methylophilus methylotrophus, paracoccus denitrificans and hyphomicrobium x all contained a single atom of ca2+ per alpha 2 beta 2 tetramer. the role of ca2+ was investigated using the mdh from methylobacterium extorquens. this was shown to be similar to the mdh from hyphomicrobium x in having 2 mol of prosthetic group (pyrroloquinoline quinine; pqq) per mol of tetramer, the pqq being predominantly in the semiquinone form. mdh isolat ...19921332681
relationship between cardiolipin content and cytochrome c oxidase activity of cytochrome aa3 in paracoccus denitrificans.using cultivation at different oxygen tensions, the molar ratio of cardiolipin to haem a in cells of paracoccus denitrificans was varied systematically from 30 to 300. the molecular activity of cytochrome aa3 (with n, n, n', n'-tetramethyl-p-phenylenediamine as substrate) remained unchanged in this interval, this ruling out any regulatory effect of physiological cardiolipin levels on the terminal oxidase. titration of anaerobically grown cells with cyanide indicated the presence of cytochrome aa ...19921332723
epr studies of cytochrome aa3 from sulfolobus acidocaldarius. evidence for a binuclear center in archaebacterial terminal oxidase.the purified cytochrome aa3-type oxidase from sulfolobus acidocaldarius (dsm 639) consists of a single subunit, containing one low-spin and one high-spin a-type hemes and copper [anemüller, s. and schäfer, g. (1990) eur. j. biochem. 191, 297-305]. the enzyme metal centers were investigated by electron paramagnetic resonance spectroscopy (epr), coupled to redox potentiometry. the low-spin heme epr signal has the following g-values: gz = 3.02, gy = 2.23 and gx = 1.45 and the high-spin heme exhibit ...19921332857
cytochrome aa3 of rhodobacter sphaeroides as a model for mitochondrial cytochrome c oxidase. the coxii/coxiii operon codes for structural and assembly proteins homologous to those in yeast.the coxii/coxiii operon of rhodobacter sphaeroides cytochrome c oxidase has been sequenced and characterized by insertional inactivation/complementation analysis. the organization of the genes in this locus (coxii.orf1.orf3.coxiii) is the same as that of the equivalent operon of paracoccus denitrificans (ctac.ctab.ctag.ctae), but unlike that of other bacteria whose cytochrome oxidase genes have been characterized so far. the predicted amino acid sequence homology with eukaryotic oxidases is also ...19921332950
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 ...19921338946
cytochrome c550 from thiobacillus versutus: cloning, expression in escherichia coli, and purification of the heterologous holoprotein.the gene coding for cytochrome c550 from thiobacillus versutus, cyca, has been cloned and sequenced. it codes for a protein of 134 amino acids plus a 19-amino-acid-long signal peptide. both coding and noncoding dna sequences of the clone are homologous to the paracoccus denitrificans dna sequence. an expression vector was constructed by cloning the cyca gene directly behind the lac promoter of puc. the cyca gene was expressed in escherichia coli under semianaerobic conditions, and mature holo-cy ...19921339423
structure of holo-chaperonin studied with electron microscopy. oligomeric cpn10 on top of two layers of cpn60 rings with two stripes each.a structural model of holo-chaperonin, known as a protein-folding control protein comprising 60 kda (cpn60) and 10 kda polypeptides (cpn10), is proposed based on the electron microscopic images of holo-chaperonin from thermus thermophilus and cpn60 from paracoccus denitrificans. isolated paracoccus cpn60 shows very similar images to those of escherichia coli tetradecameric cpn60, a seven-membered ring in the top view and a rectangular shape with four stripes in the side view. however, a small nu ...19921347504
purification and some properties of glutamate dehydrogenase and glutamine synthetase from paracoccus denitrificans.the purification and some properties of nadp-dependent glutamate dehydrogenase (gdh) and glutamine synthetase (gs) from the facultatively anaerobic gram-negative bacterium paracoccus denitrificans were investigated. the enzymes were purified to homogeneity using a procedure which involved affinity chromatography on blue sepharose cl-6b as the major purification step. the recoveries in the purification of gdh and gs were 28% and 64%, respectively. the specific activity of purified gdh was 183 nka ...19921356141
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 ...19921409575
genes for a second terminal oxidase in bradyrhizobium japonicum.bradyrhizobium japonicum possesses a mitochondria-like respiratory chain terminating with an aa3-type cytochrome c oxidase. the gene for subunit i of this enzyme (coxa) had been identified and cloned previously via heterologous hybridization using a paracoccus denitrificans dna probe. in the course of these studies, another b. japonicum dna region was discovered which apparently encoded a second terminal oxidase that was different from cytochrome aa3 but also belonged to the superfamily of heme/ ...19921444719
an fnr-dependent promoter from escherichia coli is active and anaerobically inducible in paracoccus denitrificans.a transcriptional fusion of a synthetic fnr-dependent promoter derived from escherichia coli has been introduced into paracoccus denitrificans on a broad-host-range plasmid. the patterns of expression of beta-galactosidase from this fusion and from a control which is not regulated by fnr have been studied. the results indicate that p. denitrificans expresses a transcriptional regulator which has a very similar dna-binding specificity to fnr, and responds to a similar physiological signal.19921459402
coordinate expression of the enzymes of nitric oxide metabolism in paracoccus denitrificans.cellular activities of nitric oxide producing nitrite reductase (nir) and nitric oxide reductase (nor) in paracoccus denitrificans increased in parallel upon anaerobic adaptation of aerobically grown cells. in addition, both activities exhibited comparable dependences on oxygen supply into the growing culture. the results suggest that the maintenance of a sufficiently high nor/nir activity ratio plays an important role in preventing nitric oxide accumulation and its toxic effects on the cells du ...19921482406
reactions of benzylamines with methylamine dehydrogenase. evidence for a carbanionic reaction intermediate and reaction mechanism similar to eukaryotic quinoproteins.it had been previously reported that aromatic amines were not substrates for the bacterial quinoprotein methylamine dehydrogenase. in this study, benzylamine-dependent activity was also not observed in the steady-state assay of this enzyme with the artificial electron acceptor phenazine ethosulfate (pes). benzylamines did, however, stoichiometrically reduce the protein-bound tryptophan tryptophylquinone (ttq) prosthetic group and acted as reversible competitive inhibitors of methylamine oxidatio ...19921554720
oxidation of dithiothreitol during turnover of nitric oxide reductase: evidence for generation of nitroxyl with the enzyme from paracoccus denitrificans.the stoichiometric relationship between thiol oxidized and no reduced was studied for the reaction catalyzed by nitric oxide reductase from paracoccus denitrificans. the reaction systems consisted of dithiothreitol, ascorbate, phenazine methosulfate, enzyme and no, or that system minus ascorbate. the mole ratio of thiol groups oxidized to no reduced was observed to be 2.3 to 1.5 over a range of no from 0.09 to 0.35 mumol. a ratio of 1.0 was expected for the simple reduction of no by 1-electron t ...19921567412
metabolic pathways in paracoccus denitrificans and closely related bacteria in relation to the phylogeny of prokaryotes.denitrification and methylotrophy in paracoccus denitrificans are discussed. the properties of the enzymes of denitrification: the nitrate-nitrite antiporter, nitrate reductase, nitrite reductase, nitric oxide reductase and nitrous oxide reductase are described. the genes for none of these proteins have yet been cloned and sequenced from p. denitrificans. a number of sequences are available for enzymes from escherichia coli, pseudomonas stutzeri and pseudomonas aeruginosa. it is concluded that p ...19921575465
structural and redox relationships between paracoccus denitrificans, porcine and human electron-transferring flavoproteins.electron-transferring flavoprotein (etf) was purified from the bacterium paracoccus denitrificans and the structural and redox relationships to the porcine and human etfs were investigated. the three proteins have essentially identical subunit masses and the alpha-helix content of the bacterial and porcine etfs are very similar, indicating global structural similarity. an anti-(porcine etf) polyclonal antibody that crossreacts with the human large and small subunits also crossreacts strongly wit ...19921576992
the genetic organization of the mau gene cluster of the facultative autotroph paracoccus denitrificans.the mau gene cluster from paracoccus denitrificans was cloned. the regions of a cloned fragment carrying genes for the small and the large subunit of the methylamine dehydrogenase were identified and sequenced. open reading frames for the madh small subunit gene and the madh large subunit gene were identified. three other open reading frames coding polypeptides with unknown function were found in the sequence. the small subunit gene sequence data reveal that the madh small subunit polypeptide fr ...19921590782
crystal structure of an electron-transfer complex between methylamine dehydrogenase and amicyanin.the crystal structure of the complex between the quinoprotein methylamine dehydrogenase (madh) and the type i blue copper protein amicyanin, both from paracoccus denitrificans, has been determined at 2.5-a resolution using molecular replacement. the search model was madh from thiobacillus versutus. the amicyanin could be located in an averaged electron density difference map and the model improved by refinement and model building procedures. nine beta-strands are observed within the amicyanin mo ...19921599920
cofactor-directed inactivation by nucleophilic amines of the quinoprotein methylamine dehydrogenase from paracoccus denitrificans.phenylhydrazine, semicarbazide, aminoguanidine, hydrazine, and hydroxylamine each irreversibly inactivated methylamine dehydrogenase from paracoccus denitrificans and caused changes in the absorbance spectrum of the protein-bound tryptophan tryptophylquinone [ttq] prosthetic group. different spectral perturbations were observed on reaction with each of these inactivators. in each case a stoichiometry of 2 mol per mol of enzyme (1:1 per cofactor) was required to observe complete modification of t ...19921599932
structural features of the 66-kda subunit of the energy-transducing nadh-ubiquinone oxidoreductase (ndh-1) of paracoccus denitrificans.the structural gene of the paracoccus denitrificans nadh-ubiquinone oxidoreductase encoding a homologue of the 75-kda subunit of bovine complex i (nqo3) has been located and sequenced. it is located approximately 1 kbp downstream of the gene coding for the nadh-binding subunit (nqo1) [xu, x., matsuno-yagi, a., and yagi, t. (1991) biochemistry 30, 6422-6428] and is composed of 2019 base pairs and codes for 673 amino acid residues with a calculated molecular weight of 73,159. the m(r) 66,000 polyp ...19921605643
the energy-transducing nadh-quinone oxidoreductase (ndh-1) of paracoccus denitrificans. 19921633184
gene cluster of the energy-transducing nadh-quinone oxidoreductase of paracoccus denitrificans: characterization of four structural gene products.in previous reports from our laboratory, the three structural genes (nqo1, nqo2, and nqo3) of the energy-transducing nadh-quinone oxidoreductase of paracoccus denitrificans were characterized [xu, x., matsuno-yagi, a., & yagi, t. (1991) biochemistry 30, 6422-6428; (1991) biochemistry 30, 8678-8684; (1992) arch. biochem. biophys. 296, 40-48]. in this report, the four structural genes nqo4, nqo5, nqo6, and nqo7 of the same paracoccus denitrificans oxidoreductase were cloned and sequenced. on the b ...19921637825
synthesis of poly(3-hydroxybutyrate-co-3-hydroxyvalerate) from methanol and n-amyl alcohol by the methylotrophic bacteria paracoccus denitrificans and methylobacterium extorquens.strains of two types of methylotrophic bacteria, paracoccus denitrificans and methylobacterium extorquens, synthesized the copolyester poly(3-hydroxybutyrate-co-3-hydroxyvalerate) when methanol and n-amyl alcohol were added together to nitrogen-limited medium. the composition of the copolyester differed considerably between the two strains: the copolyester from p. denitrificans was comparatively rich in 3-hydroxyvalerate (3hv). the 3hv content of the copolyester synthesized by this strain increa ...199216348804
effect of medium composition on the denitrification of nitrate by paracoccus denitrificans.the course of denitrification of nitrate in static cultures of paracoccus denitrificans was studied. reduction of nitrate to gaseous nitrogen without accumulation of nitrite because of parallel and balanced activities of nitrate and nitrite reductases was observed in nutrient broth. in minimal liquid cultures supplemented with either methanol, acetate, or ethanol as a sole carbon source, substantial amounts of nitrite (up to 70%) accumulated. the reduction in nitrite concentration began just aft ...199316349097
reduction of nitric oxide by denitrifying bacteria.two heterotrophic denitrifying bacteria, paracoccus denitrificans and pseudomonas denitrificans, have been shown to utilize nitric oxide (no) as a terminal electron acceptor and succinate, yeast extract, and heat/alkali pretreated municipal sewage sludge as carbon and energy sources. complete removal of no (0.50%) from a feed gas sparged into the cultures was observed. it is suggested that reduction of no may be a common feature of denitrifying bacteria and that a microbial process to dispose of ...19938323271
binding constants for a physiologic electron-transfer protein complex between methylamine dehydrogenase and amicyanin. effects of ionic strength and bound copper on binding.two soluble proteins, methylamine dehydrogenase and amicyanin, form a physiologically relevant complex in which intermolecular electron transfer occurs. to characterize and quantitate the binding of these two weakly-associating proteins, an ultrafiltration binding assay has been developed which involves brief centrifugation of mixtures of proteins in centrifuge concentrators followed by quantitation of proteins on each side of the filtration membrane by hplc. under low ionic strength conditions ...19938347660
purification and properties of malate dehydrogenase from paracoccus denitrificans.affinity chromatography on immobilized cibacron blue (matrex gel blue a) gel permeation chromatography on ultropac tsk g 3000 swg column and ion-exchange chromatography on "mono q" column were used to purify the malate dehydrogenase (mdh) from p. denitrificans to electrophoretic homogeneity. the last two purification steps were performed in fplc system. the enzyme having a specific activity of about 2300 nkat/mg protein was obtained with an approximate 70% yield. mdh is a dimer with a molecular ...19938361952
a method for extracting rate constants from initial rates of stopped-flow kinetic data: application to a physiological electron-transfer reaction.the most commonly used methods for analysis of stopped-flow kinetic data require performing a series of measurements in which one reactant is varied at concentrations significantly greater than the concentration of the other reactant. for enzyme-catalysed reactions this may not be possible, because the dissociation constants for the enzyme-substrate complex are often of the same order of magnitude as the high concentrations of enzyme that must frequently be used in stopped-flow studies. an alter ...19938363574
isolation and characterization of the nd2 polypeptide of the bovine energy-transducing nadh-ubiquinone oxidoreductase (complex i).the m(r) 30,000 polypeptide of the hydrophobic protein fraction of the energy-transducing nadh-ubiquinone oxidoreductase (complex i) of bovine heart mitochondria was identified as the nd2 gene product based on a comparison of amino acid analysis and partial n-terminal sequencing results with the known dna sequence of nd2 (anderson, s. et al. (1982) j. mol. biol. 156, 683-717). a simple purification procedure was devised for this nd2 gene product. the procedure, which is described, involves treat ...19938364407
cloning, sequencing, and expression of the genes encoding subunits of paracoccus denitrificans electron transfer flavoprotein.the genes encoding the two subunits of paracoccus denitrificans electron transfer flavoprotein (etf) were identified by screening a genomic library constructed in pbluescript ii sk+ with probes generated by amplification of genomic sequences by the polymerase chain reaction. primers for the polymerase chain reaction were designed based on peptide sequences from purified paracoccus etf subunits. the genes are arranged in tandem in the genomic dna with the deoxyadenylic acid residue in the tga ter ...19938376381
preliminary crystal structure studies of a ternary electron transfer complex between a quinoprotein, a blue copper protein, and a c-type cytochrome.a ternary electron transfer protein complex has been crystallized and a preliminary structure investigation has been carried out. the complex is composed of a quinoprotein, methylamine dehydrogenase (madh), a blue copper protein, amicyanin, and a c-type cytochrome (c551i). all three proteins were isolated from paracoccus denitrificans. the crystals of the complex are orthorhombic, space group c222(1) with cell dimensions a = 148.81 a, b = 68.85 a, and c = 187.18 a. two types of isomorphous cryst ...19938382992
identification and characterization of the ctac (coxb) gene as part of an operon encoding subunits i, ii, and iii of the cytochrome c oxidase (cytochrome aa3) in the cyanobacterium synechocystis pcc 6803.the gene (coxii = coxb = ctac) encoding subunit ii of synechocystis pcc 6803 cytochrome c oxidase has been isolated by screening a genomic dna library in puc18 with a 17-bp oligonucleotide probe (probe c) derived from coxi of paracoccus denitrificans after southern blots with a 19-kb oligonucleotide (probe a) derived from coxii of p. denitrificans had given equivocal results. a 2.2 kb psti-kpni restriction fragment was subcloned into puc 18 and the resulting plasmid pdauv26, which contained the ...19938383492
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