Publications
| Title | Abstract | Year Filter | PMID(sorted ascending) Filter |
|---|
| reduction of cytochrome c oxidase by a second electron leads to proton translocation. | cytochrome c oxidase, the terminal enzyme of cellular respiration in mitochondria and many bacteria, reduces o(2) to water. this four-electron reduction process is coupled to translocation (pumping) of four protons across the mitochondrial or bacterial membrane; however, proton pumping is poorly understood. proton pumping was thought to be linked exclusively to the oxidative phase, that is, to the transfer of the third and fourth electron. upon re-evaluation of these data, however, this proposal ... | 2002 | 11986672 |
| mitochondria recycle nitrite back to the bioregulator nitric monoxide. | nitric monoxide (no) exerts a great variety of physiological functions. l-arginine supplies amino groups which are transformed to no in various no-synthase-active isoenzyme complexes. no-synthesis is stimulated under various conditions increasing the tissue of stable no-metabolites. the major oxidation product found is nitrite. elevated nitrite levels were reported to exist in a variety of diseases including hiv, reperfusion injury and hypovolemic shock. denitrifying bacteria such as paracoccus ... | 2000 | 11996114 |
| cloning, nucleotide sequencing, and expression in escherichia coli of the gene for formate dehydrogenase of paracoccus sp. 12-a, a formate-assimilating bacterium. | the gene for the nad-dependent formate dehydrogenase (fdh) of paracoccus sp. 12-a, a formate-assimilating bacterium, was cloned through screening of the genomic library with activity staining. the fdh gene included an open reading frame of 1,200 base pairs, and encoded a protein of 43,757 da, which had high amino acid sequence identity with known fdhs, in particular, with bacterial enzymes such as those of moraxella sp. (86.5%) and pseudomonas sp. 101 (83.5%). the gene was highly expressed in es ... | 2002 | 11999398 |
| reduction of perchlorate and nitrate by salt tolerant bacteria. | spent regenerant brine from ion-exchange technology for the removal of perchlorate and nitrate produces a high salt waste stream, which requires remediation before disposal. bioremediation is an attractive treatment option. in this study, we enriched for salt tolerant bacteria from sediments from cargill salt evaporation facility (california, usa), the salton sea (california, usa), and a high density hydrocarbon oxidizing bacterial cocktail. the bacterial cocktail enrichment culture reduced clo4 ... | 2002 | 12009133 |
| enzyme-catalysed nitrate reduction-themes and variations as revealed by protein film voltammetry. | protein film voltammetry has been used to define the catalytic performance of two nitrate reductases: the respiratory nitrate reductase, nargh, from paracoccus pantotrophus and the assimilatory nitrate reductase, narb, from synechococcus sp. pcc 7942. nargh and narb present distinct "fingerprints" of catalytic activity when viewed in this way. potentials that provide insufficient driving force for significant rates of nitrate reduction by narb result in appreciable rates of nitrate reduction by ... | 2002 | 12009435 |
| the vbs genes that direct synthesis of the siderophore vicibactin in rhizobium leguminosarum: their expression in other genera requires ecf sigma factor rpoi. | a cluster of eight genes, vbsgso, vbsadl, vbsc and vbsp, are involved in the synthesis of vicibactin, a cyclic, trihydroxamate siderophore made by the symbiotic bacterium rhizobium leguminosarum. none of these vbs genes was required for symbiotic n2 fixation on peas or vicia. transcription of vbsc, vbsgso and vbsadl (but not vbsp) was enhanced by growth in low levels of fe. transcription of vbsgso and vbsadl, but not vbsp or vbsc, required the closely linked gene rpoi, which encodes an ecf sigma ... | 2002 | 12028377 |
| expression of human electron transfer flavoprotein-ubiquinone oxidoreductase from a baculovirus vector: kinetic and spectral characterization of the human protein. | electron transfer flavoprotein-ubiquinone oxidoreductase (etf-qo) is an iron-sulphur flavoprotein and a component of an electron-transfer system that links 10 different mitochondrial flavoprotein dehydrogenases to the mitochondrial bc1 complex via electron transfer flavoprotein (etf) and ubiquinone. etf-qo is an integral membrane protein, and the primary sequences of human and porcine etf-qo were deduced from the sequences of the cloned cdnas. we have expressed human etf-qo in sf9 insect cells u ... | 2002 | 12049629 |
| multiple forms of the catalytic centre, cuz, in the enzyme nitrous oxide reductase from paracoccus pantotrophus. | nitrous oxide reductase catalyses the reduction of nitrous oxide to dinitrogen at a unique tetranuclear copper site, called cu(z), which has a central inorganic sulphide ligand. limited incubation with oxygen during the preparation of nitrous oxide reductase from paracoccus pantotrophus results in changed redox properties of the catalytic centre by comparison with anaerobic preparations. while the anaerobically purified enzyme has a catalytic centre which performs a single electron step at a mid ... | 2002 | 12049645 |
| inter-subunit cross-linking of methylamine dehydrogenase by cyclopropylamine requires residue alphaphe55. | cyclopropylamine is a mechanism-based inhibitor of the quinoprotein methylamine dehydrogenase (madh) from paracoccus denitrificans. the resulting inactivation is accompanied by the formation of a covalent cross-link between the alpha and beta subunits of madh. the results of site-directed mutagenesis studies indicate that phe55 on the alpha subunit is required for this process. no cross-linking is seen with alphaf55a or alphaf55i madh mutants. in contrast, with alphaf55e madh cross-linking of su ... | 2002 | 12062431 |
| detection, with a ph indicator, of bacterial mutants unable to denitrify. | in order to facilitate isolation of mutants with alterations in the denitrification pathway, a new screening procedure using phenol red incorporated into agar overlay has been defined. alkalinization in the neighbourhood of denitrifying colonies respiring nitrate or nitrite gives rise to a red circular halo. antimycin blocked these colour changes, which suggests their association with the periplasmic reduction of nitrite. inhibition of nitrous oxide reductase by acetylene had no significant effe ... | 2002 | 12069895 |
| mutations in the docking site for cytochrome c on the paracoccus heme aa3 oxidase. electron entry and kinetic phases of the reaction. | introducing site-directed mutations in surface-exposed residues of subunit ii of the heme aa3 cytochrome c oxidase of paracoccus denitrificans, we analyze the kinetic parameters of electron transfer from reduced horse heart cytochrome c. specifically we address the following issues: (a) which residues on oxidase contribute to the docking site for cytochrome c, (b) is an aromatic side chain required for electron entry from cytochrome c, and (c) what is the molecular basis for the previously obser ... | 2002 | 12071962 |
| inhibition of bacterial alpha-glucosidases by castanospermine in pure cultures and activated sludge. | castanospermine (cast) is a known and potent inhibitor of various alpha-glucosidases in eukaryotes. in this work, we elucidated whether cast could also be used for determining bacterial alpha-glucosidase activity, when measured with 4-methylumbelliferyl-alpha- d-glucoside as a substrate, both in a complex bacterial community, in activated sludge and in pure cultures of bacterial isolates. we found that 140 microm cast inhibited alpha-glucosidase activity by 30% in a pure culture of pseudomonas s ... | 2002 | 12073134 |
| a repressor protein, phar, regulates polyhydroxyalkanoate (pha) synthesis via its direct interaction with pha. | phasins (phap) are predominantly polyhydroxyalkanoate (pha) granule-associated proteins that positively affect pha synthesis. recently, we reported that the phar gene, which is located downstream of phap in paracoccus denitrificans, codes for a negative regulator involved in phap expression. in this study, dnase i footprinting revealed that phar specifically binds to two regions located upstream of phap and phar, suggesting that phar plays a role in the regulation of phap expression as well as a ... | 2002 | 12081972 |
| a novel, kinetically stable, catalytically active, all-ferric, nitrite-bound complex of paracoccus pantotrophus cytochrome cd1. | the oxidized form of paracoccus pantotrophus cytochrome cd(1) nitrite reductase, as isolated, has bis-histidinyl co-ordination of the c haem and his/tyr co-ordination of the d(1) haem. on reduction, the haem co-ordinations change to his/met and his/vacant respectively. if the latter form of the enzyme is reoxidized, a conformer is generated in which the ferric c haem is his/met co-ordinated; this can revert to the 'as isolated' state of the enzyme over approx. 20 min at room temperature. however ... | 2002 | 12086580 |
| a novel type of nitric-oxide reductase. escherichia coli flavorubredoxin. | escherichia coli flavorubredoxin is a member of the family of the a-type flavoproteins, which are built by two core domains: a metallo-beta-lactamase-like domain, at the n-terminal region, harboring a non-heme di-iron site, and a flavodoxin-like domain, containing one fmn moiety. the enzyme from e. coli has an extra module at the c terminus, containing a rubredoxin-like center. the a-type flavoproteins are widespread among strict and facultative anaerobes, as deduced from the analysis of the com ... | 2002 | 12101220 |
| ca(2+)-binding site in rhodobacter sphaeroides cytochrome c oxidase. | cytochrome c oxidase (cox) from r. sphaeroides contains one ca(2+) ion per enzyme that is not removed by dialysis versus egta. this is similar to cox from paracoccus denitrificans [pfitzner, u., kirichenko, a., konstantinov, a. a., mertens, m., wittershagen, a., kolbesen, b. o., steffens, g. c. m., harrenga, a., michel, h., and ludwig, b. (1999) febs lett. 456, 365-369] and is in contrast to the bovine oxidase, which binds ca(2+) reversibly. a series of r. sphaeroides mutants with replacements o ... | 2002 | 12102631 |
| vibrational modes of tyrosines in cytochrome c oxidase from paracoccus denitrificans: ftir and electrochemical studies on tyr-d4-labeled and on tyr280his and tyr35phe mutant enzymes. | a combined electrochemical and ftir spectroscopic approach was used to identify the vibrational modes of tyrosines in cytochrome c oxidase from paracoccus denitrificans which change upon electron transfer and coupled proton transfer. electrochemically induced ftir difference spectra of the tyr-d4-labeled cytochrome c oxidase reveal that only small contributions arise from the tyrosines. contributions between 1600 and 1560 cm(-1) are attributed to nu8a/8b(cc) ring modes. the nu19(cc) ring mode fo ... | 2002 | 12119026 |
| redox properties of an engineered purple cu(a) azurin. | purple cu(a) centers are a class of binuclear, mixed-valence copper complexes found in cytochrome c oxidase and nitrous oxide reductase. an engineered cu(a) protein was formed by replacing a portion of the amino acid sequence that contains three of the ligands to the native type i copper center of pseudomonas aeruginosa azurin with the corresponding portion of sequence from the cu(a) center of cytochrome c oxidase from paracoccus denitrificans [proc. natl. acad. sci. usa 93 (1996) 461]. oxidatio ... | 2002 | 12127080 |
| the cytochrome complex soxxa of paracoccus pantotrophus is produced in escherichia coli and functional in the reconstituted sulfur-oxidizing enzyme system. | the heterodimeric c-type cytochrome complex soxxa of paracoccus pantotrophus was produced in escherichia coli. the soxx and soxa genes, separated by two genes in the sox gene cluster of p. pantotrophus, were fused with ribosome binding sites optimal for e. coli and combined to give soxxa in prd133.27. the cytochrome complex soxxa was produced in e. coli m15 containing prd133.27, prep4 encoding the lac repressor and plasmid pec86, carrying essential cytochrome c maturation genes. soxx and soxa we ... | 2002 | 12147345 |
| crystallisation of membrane proteins mediated by antibody fragments. | x-ray structures of three different membrane proteins in complex with antibody fragments have been published. the binding of fv or fab fragments enlarges the hydrophilic part of integral membrane proteins, thereby providing additional surface for crystal contacts and space for the detergent micelle. in all reported cases, antibody binding was either essential for the crystallisation of the membrane protein or it substantially improved the diffraction quality of the crystals. antibody-fragment-me ... | 2002 | 12163074 |
| hierarchy of carbon source selection in paracoccus pantotrophus: strict correlation between reduction state of the carbon substrate and aerobic expression of the nap operon. | paracoccus pantotrophus can express a periplasmic nitrate reductase (nap) during aerobic growth. a proposed role for this enzyme is the dissipation of excess redox energy during oxidative metabolism of reduced carbon substrates. to investigate the regulation of nap expression, a transcriptional fusion between the nap promoter region of p. pantotrophus and the lacz gene was constructed. when this fusion was used, analyses showed that transcription from the nap promoter increases as the average re ... | 2002 | 12169601 |
| effects of chaotropic anions on the distribution of conformational substates of amicyanin, wild type and cys3ala/cys26ala azurin mutant. | the effect of azide and thiocyanate on the structure and dynamics of wild type and disulfide bond depleted azurin and of amicyanin has been investigated by electron paramagnetic resonance (epr) spectroscopy at low temperature. the analysis of the epr spectra, which can be described in terms of gaussian distributions of the components of the axial symmetric <--> g and <--> a tensors of the spin-hamiltonian, has shown that the two small exogenous ligands, known as chaotropic agents, are effective ... | 2002 | 12175938 |
| nadh oxidation and nad+ reduction catalysed by tightly coupled inside-out vesicles from paracoccus denitrificans. | tightly coupled inside-out vesicles were prepared from paracoccus denitrificans cells (spp, sub-paracoccus particles) and characterized kinetically. the rate of nadh oxidation, catalysed by spp, increases 6-8 times on addition of gramicidin. the vesicles are capable of catalysing delta micro h+-dependent reverse electron transfer from quinol to nad+. the kinetic parameters of the nadh-oxidase and the reverse electron transfer carried out by membrane-bound p. denitrificans complex i were estimate ... | 2002 | 12180978 |
| specificity of the interaction between the paracoccus denitrificans oxidase and its substrate cytochrome c: comparing the mitochondrial to the homologous bacterial cytochrome c(552), and its truncated and site-directed mutants. | under in vitro conditions, bacterial cytochrome c oxidases may accept several nonhomologous c-type electron donors, including the evolutionarily related mitochondrial cytochrome c. several lines of evidence suggest that in intact membranes the heme aa(3) oxidase from paracoccus denitrificans receives its electrons from the membrane-bound cytochrome c(552). both the structures of the oxidase and of a heterologously expressed, soluble fragment of the c(552) have been determined recently, but no di ... | 2002 | 12186548 |
| identification of two domains and distal histidine ligands to the four haems in the bacterial c-type cytochrome napc; the prototype connector between quinol/quinone and periplasmic oxido-reductases. | napc is a tetra-haem member of a family of bacterial membrane-anchored multi-haem c -type cytochromes implicated in electron transfer between membrane quinols and periplasmic enzymes. the water-soluble tetra-haem fragment of paracoccus pantotrophus napc has been expressed as a periplasmic protein (napc(sol)) in paracoccus denitrificans, p. pantotrophus and escherichia coli. site-specific mutagenesis of napc(sol), combined with spectroscopic studies, suggests that each haem iron centre has bis -h ... | 2002 | 12186631 |
| properties of a soluble domain of subunit c of a bacterial nitric oxide reductase. | bacterial nitric oxide reductases are integral membrane proteins that catalyze the reduction of two molecules of nitric oxide to nitrous oxide and water. they are diverged members of the superfamily of heme/copper oxidases. the enzyme from paracoccus denitrificans (norbc) contains two subunits; norb comprises the membrane-integrated active site, which harbors a heme iron/non-heme iron dinuclear center. norc is a membrane-anchored c-type cytochrome and presumably the site of electron uptake. a dn ... | 2002 | 12196025 |
| a turbo engine with automatic transmission? how to marry chemicomotion to the subtleties and robustness of life. | most genomes are much more complex than required for the minimum chemistry of life. evolution has selected sophistication more than life itself. could this also apply to bioenergetics? we first examine mechanisms through which bioenergetics could deliver sophistication. we illustrate possible benefits of the turbo-charging of catabolic pathways, of loose coupling, low-gear catabolism, automatic transmission in energy coupling, and of homeostasis. mechanisms for such phenomena may reside at the l ... | 2002 | 12206895 |
| respiratory chain supercomplexes of mitochondria and bacteria. | respiratory chain complexes are fragments of larger structural and functional units, the respiratory chain supercomplexes or "respirasomes", which exist in bacterial and mitochondrial membranes. supercomplexes of mitochondria and bacteria contain complexes iii, iv, and complex i, with the notable exception of saccharomyces cerevisiae, which does not possess complex i. these supercomplexes often are stable to sonication but sensitive to most detergents except digitonin. in s. cerevisiae, a major ... | 2002 | 12206908 |
| recovery and separation of cell lysate proteins using hydrogels guided by aqueous two-phase extraction principles. | the addition of poly(ethylene glycol) and salts to clarified cell lysates of thiosphaera pantotropha increases sorption of microbial proteins into dextran hydrogels, consistent with the thermodynamics of aqueous two-phase extraction. addition of 12 wt% peg-10,000 to the lysate increased total sorption of protein by the dextran gel from 5.2 mg/g dextran to 37 mg/g; addition of either 0.1 m potassium iodide or tetrabutylammonium fluoride along with peg to the lysate increased protein sorption to m ... | 2002 | 12209769 |
| molecular characterization of functional modules of plasmid pwks1 of paracoccus pantotrophus dsm 11072. | the complete nucleotide sequence of the small, cryptic plasmid pwks1 (2697 bp) of paracoccus pantotrophus dsm 11072 was determined. the g+c content of the sequence of this plasmid was 62 mol%. analysis revealed that over 80% of the plasmid genome was covered by two orfs, orf1 and orf2, which were capable of encoding putative peptides of 44.1 and 37.8 kda, respectively. mutational analysis showed that orf2 was crucial for plasmid replication. the translational product of orf2 shared local homolog ... | 2002 | 12213930 |
| crystal structure of nitrous oxide reductase from paracoccus denitrificans at 1.6 a resolution. | n2o is generated by denitrifying bacteria as a product of no reduction. in denitrification, n2o is metabolized further by the enzyme n2o reductase (n2or), a multicopper protein which converts n2o into dinitrogen and water. the structure of n2or remained unknown until the recent elucidation of the structure of the enzyme isolated from pseudomonas nautica. in the present paper, we report the crystal structure of a blue form of the enzyme that was purified under aerobic conditions from paracoccus d ... | 2003 | 12356332 |
| the transition between active and de-activated forms of nadh:ubiquinone oxidoreductase (complex i) in the mitochondrial membrane of neurospora crassa. | the mammalian mitochondrial nadh:ubiquinone oxidoreductase (complex i) has been shown to exist in two kinetically and structurally distinct slowly interconvertible forms, active (a) and de-activated (d) [vinogradov and grivennikova (2001) iubmb life 52, 129-134]. this work was undertaken to investigate the putative complex i a-d transition in the mitochondrial membrane of the lower eukaryote neurospora crassa and in plasma membrane of the prokaryote paracoccus denitrificans, organisms that are e ... | 2003 | 12379145 |
| comparative characterization of repabc-type replicons of paracoccus pantotrophus composite plasmids. | the repabc replicons have an unusual structure, since they carry genes coding for partitioning (repa, repb) and replication (repc) proteins, which are organized in an operon. so far, the presence of these compact bi-functional modules has been reported only in the megaplasmids of the rhizobiaceae and within the plasmid ptav1 (107kb) of paracoccus versutus. we studied the distribution of repabc-type replicons within bacteria belonging to the genus paracoccus. we found that repabc replicons occur ... | 2002 | 12383730 |
| genetics of isoprenoid biosynthesis in paracoccus zeaxanthinifaciens. | the genes coding for all the enzymes involved in the conversion of acetyl-coa to farnesyl diphosphate (fpp) in the zeaxanthin-producing bacterium paracoccus zeaxanthinifaciens were cloned and characterized. two genes encoding enzymes catalysing the condensation of two acetyl-coa molecules to acetoacetyl-coa were found. the six enzymes involved in the conversion of acetyl-coa and acetoacetyl-coa to isopentenyl diphosphate (ipp) and dimethylallyl diphosphate (dmapp) are grouped in an operon, desig ... | 2002 | 12384294 |
| peroxidase activity as a tool for studying the folding of c-type cytochromes. | the peroxidase activity of c-type cytochromes increases substantially by unfolding. this phenomenon was used to study the equilibrium unfolding of ferricytochrome c. the peroxidase activity is already enhanced at low denaturant concentrations. the lowest free energy folding intermediate is easily detected by this method, while it is invisible using fluorescence or optical spectroscopy. the free energy difference between this folding intermediate and the native state depends on the strength of th ... | 2002 | 12390035 |
| sulfite inhibits the f1f0-atp synthase and activates the f1f0-atpase of paracoccus denitrificans. | the f1f0 complex of paracoccus denitrificans (pdf1f0) is the fastest atp synthase but the slowest atpase. sulfite exerts maximal activation of the pdf1f0-atpase (pacheco-moisés, f., garcía, j. j., rodríguez-zavala, j. s., and moreno-sánchez, r. (2000). eur j. biochem. 267, 993-1000) but its effect on the pdf1f0-atp synthase activity remains unknown. therefore, we studied the effect of sulfite on atp synthesis and 32pi <--> atp exchange reactions of inside-out membrane vesicles of p. denitrifican ... | 2002 | 12392190 |
| microbial population in a hydrogen-dependent denitrification reactor. | the bacterial population in an h2-dependent denitrification system was studied. the laboratory set-up was designed for the treatment of potable water and consisted of an electrochemical cell, where the water to be treated was enriched with h2 prior to entering a bioreactor. bioreactors (columns packed with granulated active carbon) were inoculated with denitrifying bacterial strains isolated from a previous reactor, then sampled immediately after inoculation, or after 1 or 3 months of continuous ... | 2002 | 12405417 |
| long-chain acyl-homoserine lactone quorum-sensing regulation of rhodobacter capsulatus gene transfer agent production. | many proteobacteria use acyl-homoserine lactones as quorum-sensing signals. traditionally, biological detection systems have been used to identify bacteria that produce acyl-homoserine lactones, although the specificities of these detection systems can limit discovery. we used a sensitive approach that did not require a bioassay to detect production of long-acyl-chain homoserine lactone production by rhodobacter capsulatus and paracoccus denitrificans. these long-chain acyl-homoserine lactones a ... | 2002 | 12426339 |
| spectroelectrochemical evaluation of redox potentials of cysteine tryptophylquinone and two hemes c in quinohemoprotein amine dehydrogenase from paracoccus denitrificans. | quinohemoprotein amine dehydrogenase (qh-amdh) from paracoccus denitrificans has a novel cofactor cysteine tryptophylquinone (ctq) in the smallest gamma subunit and two hemes c in the largest alpha subunit [datta, s., mori, y., takagi, k., kawaguchi, k., chen, z., okajima, t., kuroda, s., ikeda, t., kano, k., tanizawa, k., and mathews, f. s. (2001) proc. natl. acad. sci. u.s.a. 98, 14268-14273]. the spectral change of qh-amdh was assigned to the redox reaction of the hemes c alone. the redox pot ... | 2002 | 12427036 |
| mutation of alphaphe55 of methylamine dehydrogenase alters the reorganization energy and electronic coupling for its electron transfer reaction with amicyanin. | methylamine dehydrogenase (madh) possesses an alpha(2)beta(2) structure with each smaller beta subunit possessing a tryptophan tryptophylquinone (ttq) prosthetic group. phe55 of the alpha subunit is located where the substrate channel from the enzyme surface opens into the active site. site-directed mutagenesis of alphaphe55 has revealed roles for this residue in determining substrate specificity and binding monovalent cations at the active site. it is now shown that the alphaf55a mutation also ... | 2002 | 12437349 |
| thermodynamics of the acid transition in blue copper proteins. | the thermodynamic parameters of the conformational transition occurring at low ph (acid transition, at) in blue copper proteins, involving protonation and detachment from the cu(i) ion of one histidine ligand, have been determined electrochemically for spinach and cucumber plastocyanins, rhus vernicifera stellacyanin, cucumber basic protein (cbp), and paracoccus versutus amicyanin. these data were obtained from direct protein electrochemistry experiments carried out at varying ph and temperature ... | 2002 | 12450394 |
| cytochrome c maturation. the in vitro reactions of horse heart apocytochrome c and paracoccus dentrificans apocytochrome c550 with heme. | c-type cytochromes are characterized by having the heme moiety covalently attached via thioether bonds between the heme vinyl groups and the thiols of conserved cysteine residues of the polypeptide chain. previously, we have shown the in vitro formation of hydrogenobacter thermophilus cytochrome c(552) (daltrop, o., allen, j. w. a., willis, a. c., and ferguson, s. j. (2002) proc. natl. acad. sci. u. s. a. 99, 7872-7876). in this work we report that thioether bonds can form spontaneously in vitro ... | 2003 | 12458205 |
| ca2+ and the bacterial peroxidases: the cytochrome c peroxidase from pseudomonas stutzeri. | the production of cytochrome c peroxidase (ccp) from pseudomonas ( ps.) stutzeri (atcc 11607) was optimized by adjusting the composition of the growth medium and aeration of the culture. the protein was isolated and characterized biochemically and spectroscopically in the oxidized and mixed valence forms. the activity of ps. stutzeri ccp was studied using two different ferrocytochromes as electron donors: ps. stutzeri cytochrome c(551) (the physiological electron donor) and horse heart cytochrom ... | 2003 | 12459896 |
| production of ubiquinone-10 using bacteria. | among the bacterial strains known to contain ubiquinone-10, three strains, agrobacterium tumefaciens ky-3085 (atcc4452), paracoccus denitrificans ky-3940 (atcc19367) and rhodobacter sphaeroides ky-4113 (ferm-p4675), were selected as excellent producers of this ubiquinone. the ubiquinone-10 production by the agrobacterium and rhodobacter strains was affected by aeration. an ethionine-resistant mutant (m-37) derived from a. tumefaciens ky-3085 promoted increased production of ubiquinone-10 (20% hi ... | 1998 | 12501289 |
| inhibition by phenylglyoxal of nitrate transport in paracoccus denitrificans: a comparison with the effect of a protonophorous uncoupler. | the amino acid modifier phenylglyoxal (pg) gradually inactivated the methyl viologen-coupled nitrate reductase activity of the anoxically grown whole cells of paracoccus denitrificans. a double log plot of the pseudo-first-order inactivation rate constant versus pg concentration was linear with a mean slope of 1.4 (0.1m sodium phosphate) or 0.87 (0.1m sodium borate). phenylglyoxalation of cells lowered the limiting velocity (v), while hardly affecting the apparent half-saturation concentration ( ... | 2003 | 12504899 |
| structure and dynamics of reduced bacillus pasteurii cytochrome c: oxidation state dependent properties and implications for electron transfer processes. | the solution structure of reduced bacillus pasteurii cytochrome c, which has only 71 amino acids, has been determined by nmr to an rmsd of 0.46 +/- 0.08 a for all backbone atoms and 0.79 +/- 0.08 a for all heavy atoms and refined through restrained energy minimization. the target function out of 1645 constraints is 0.52 +/- 0.11 a(2), and the penalty function is 66 +/- 12 kj mol(-)(1). the structure appears very similar to that in the oxidized state, only trp87 and the propionates showing signif ... | 2003 | 12534286 |
| structure and kinetic properties of paracoccus pantotrophus cytochrome cd1 nitrite reductase with the d1 heme active site ligand tyrosine 25 replaced by serine. | the 1.4-a crystal structure of the oxidized state of a y25s variant of cytochrome cd(1) nitrite reductase from paracoccus pantotrophus is described. it shows that loss of tyr(25), a ligand via its hydroxy group to the iron of the d(1) heme in the oxidized (as prepared) wild-type enzyme, does not result in a switch at the c heme of the unusual bishistidinyl coordination to the histidine/methionine coordination seen in other conformations of the enzyme. the ser(25) side chain is seen in two positi ... | 2003 | 12556530 |
| characterization of the interaction of rhodobacter capsulatus cytochrome c peroxidase with charge reversal mutants of cytochrome c(2). | steady-state kinetics for the reaction of rhodobacter capsulatus bacterial cytochrome c peroxidase (bccp) with its substrate cytochrome c(2) were investigated. the rb. capsulatus bccp is dependent on calcium for activation as previously shown for the pseudomonas aeruginosa bccp and paracoccus denitrificans enzymes. furthermore, the activity shows a bell-shaped ph dependence with optimum at ph 7.0. enzyme activity is greatest at low ionic strength and drops off steeply as ionic strength increases ... | 2003 | 12573282 |
| effects of engineering uphill electron transfer into the methylamine dehydrogenase-amicyanin-cytochrome c-551i complex. | within the methylamine dehydrogenase-amicyanin-cytochrome c-551i complex, electrons are transferred from tryptophan tryptophylquinone (ttq) to heme via the type i copper center of amicyanin. mutation of pro94 of amicyanin to phe increases the redox potential of the copper center within the protein complex by approximately 195 mv. this introduces a large energy barrier for the second electron transfer (et) step in this three-protein et chain. as a consequence of this mutation, the et rate from tt ... | 2003 | 12578392 |
| the electron transfer complexes of cytochrome c peroxidase from paracoccus denitrificans. | we have used microcalorimetry and analytical ultracentrifugation to test the model proposed in pettigrew et al. [(1999) j. biol. chem. 274, 11383-11389] for the binding of small cytochromes to the cytochrome c peroxidase of paracoccus denitrificans. both methods reveal complexity in behavior due to the presence of a monomer/dimer equilibrium in the peroxidase. in the presence of either ca(2+), or higher ionic strength, this equilibrium is shifted to the dimer. experiments to study complex format ... | 2003 | 12590592 |
| characterization of cluster n5 as a fast-relaxing [4fe-4s] cluster in the nqo3 subunit of the proton-translocating nadh-ubiquinone oxidoreductase from paracoccus denitrificans. | the nadh-quinone oxidoreductase from paracoccus denitrificans consists of 14 subunits (nqo1-14) and contains one fmn and eight iron-sulfur clusters. the nqo3 subunit possesses fully conserved 11 cys and 1 his in its n-terminal region and is considered to harbor three iron-sulfur clusters; however, only one binuclear (n1b) and one tetranuclear (n4) were previously identified. in this study, the nqo3 subunit containing 1x[2fe-2s] and 2x[4fe-4s] clusters was expressed in escherichia coli. the secon ... | 2003 | 12600982 |
| passive penetration of nitrate through the plasma membrane of paracoccus denitrificans and its potentiation by the lipophilic tetraphenylphosphonium cation. | previously, it has been shown that treatment of paracoccus denitrificans cells with phenylglyoxal inhibits the methyl-viologen-linked nitrate reductase activity by blocking the nitrate transporter. this inhibition disappears if tetraphenylphosphonium cation (tpp(+)) is added to the assay medium. in the present paper, the following evidence suggests that the effect of tpp(+) results from an increased transmembrane anion permeability and not from transporter reactivation or cell lysis. (1) beside ... | 2003 | 12615355 |
| paracoccus yeeii sp. nov. (formerly cdc group eo-2), a novel bacterial species associated with human infection. | cdc eugonic oxidizer group 2 (eo-2) is a group of unclassified gram-negative bacterial strains isolated from various human sources. as determined by biochemical tests and analyses of fatty acid compositions, these organisms form a homogeneous group that appears to be distinct from but related to other paracoccus species. molecular studies were performed on a set of 13 eo-2 strains from various clinical sources and geographic locations in the united states and canada to determine their relationsh ... | 2003 | 12624070 |
| direct detection of fe(iv)[double bond]o intermediates in the cytochrome aa3 oxidase from paracoccus denitrificans/h2o2 reaction. | we report the first evidence for the formation of the "607- and 580-nm forms" in the cytochrome oxidase aa3/h2o2 reaction without the involvement of tyrosine 280. the pka of the 607-580-nm transition is 7.5. the 607-nm form is also formed in the mixed valence cytochrome oxidase/o2 reaction in the absence of tyrosine 280. steady-state resonance raman characterization of the reaction products of both the wild-type and y280h cytochrome aa3 from paracoccus denitrificans indicate the formation of six ... | 2003 | 12637529 |
| understanding quinone cofactor biogenesis in methylamine dehydrogenase through novel cofactor generation. | cofactors made from constitutive amino acids in proteins are now known to be relatively common. a number of these involve the generation of quinone cofactors, such as topaquinone in the copper-containing amine oxidases, and lysine tyrosylquinone in lysyl oxidase. the biogenesis of the quinone cofactor tryptophan tryptophylquinone (ttq) in methylamine dehydrogenase (madh) involves the post-translational modification of two constitutive trp residues (trp(beta)(57) and trp(beta)(108) in paracoccus ... | 2003 | 12641453 |
| paracoccus zeaxanthinifaciens sp. nov., a zeaxanthin-producing bacterium. | a comprehensive taxonomic re-evaluation was performed on the marine, zeaxanthin-producing bacterium formerly classified as [favobacterium] sp. strain r-1 512 (atcc 21588). this strain, together with two other previously described marine isolates, [flavobacterium] strain r-1506 and paracoccus sp. strain mbic 3966, were found to comprise a new species of the genus paracoccus. the name paracoccus zeaxanthinifaciens sp. nov. is proposed, with atcc 21588t (= r-1512t =lmg 21293t) designated as the typ ... | 2003 | 12656178 |
| 1.3 a x-ray structure of an antibody fv fragment used for induced membrane-protein crystallization. | the antibody fv fragment 7e2 has previously been employed in the induced crystallization of the integral membrane protein cytochrome c oxidase from paracoccus denitrificans. the 1.3 a x-ray structure of the uncomplexed antibody fragment reveals conserved water networks on the surfaces of the framework regions. a novel consensus motif for water coordination, xx(s/t), is found along the edges of the beta-sandwich, where a water molecule forms hydrogen bonds to the carbonyl o atom of a residue at p ... | 2003 | 12657787 |
| effects of multiple ligand binding on kinetic isotope effects in pqq-dependent methanol dehydrogenase. | the reaction of pqq-dependent methanol dehydrogenase (mdh) from methylophilus methylotrophus has been studied by steady-state and stopped-flow kinetic methods, with particular reference to multiple ligand binding and the kinetic isotope effect (kie) for pqq reduction. phenazine ethosulfate (pes; an artificial electron acceptor) and cyanide (a suppressant of endogenous activity), but not ammonium (an activator of mdh), compete for binding at the catalytic methanol-binding site. cyanide does not a ... | 2003 | 12667088 |
| properties of the periplasmic nitrate reductases from paracoccus pantotrophus and escherichia coli after growth in tungsten-supplemented media. | paracoccus pantotrophus grown anaerobically under denitrifying conditions expressed similar levels of the periplasmic nitrate reductase (nap) when cultured in molybdate- or tungstate-containing media. a native page gel stained for nitrate reductase activity revealed that only napa from molybdate-grown cells displayed readily detectable nitrate reductase activity. further kinetic analysis showed that the periplasmic fraction from cells grown on molybdate (3 microm) reduced nitrate at a rate of v( ... | 2003 | 12670690 |
| redox properties of quinohemoprotein amine dehydrogenase from paracoccus denitrificans. | paracoccus denitrificans produces two primary enzymes for the amine oxidation, tryptophan-tryptophylquinone (ttq)-containing methylamine dehydrogenase (madh) and quinohemoprotein amine dehydrogenase (qh-amdh). qh-amdh has a novel cofactor, cysteine tryptophylquinone (ctq) and two hemes c. in this work, the redox potentials of three redox centers in qh-amdh were determined by a mediator-assisted continuous-flow column electrolytic spectroelectrochemical technique. kinetics of the electron transfe ... | 2003 | 12686147 |
| catalysis and electron transfer in protein crystals: the binary and ternary complexes of methylamine dehydrogenase with electron acceptors. | polarized absorption microspectrophotometry has been used to detect catalysis and intermolecular electron transfer in single crystals of two multiprotein complexes: (1) the binary complex between paracoccus denitrificans methylamine dehydrogenase, which contains tryptophan-tryptophylquinone (ttq) as a cofactor, and its redox partner, the blue copper protein amicyanin; (2) the ternary complex between the same two proteins and cytochrome c-551i. continuous wave electron paramagnetic resonance has ... | 2003 | 12686155 |
| catching catalysis in the act: using single crystal kinetics to trap methylamine dehydrogenase reaction intermediates. | methylamine dehydrogenase (madh) is produced by a range of gram-negative methylotrophic and autotrophic bacteria, and allows the organisms to utilise methylamine as the sole source of carbon. the enzyme catalyses the oxidation of methylamine to formaldehyde and ammonia, leaving it in a two-electron reduced state. to complete the catalytic cycle, madh is reoxidised via an electron transfer (et) chain. the redox center in the enzyme is the organic cofactor tryptophan tryptophylquinone (ttq) derive ... | 2003 | 12686162 |
| characterization and topology of the membrane domain nqo10 subunit of the proton-translocating nadh-quinone oxidoreductase of paracoccus denitrificans. | the proton-translocating nadh-quinone oxidoreductase (ndh-1) of paracoccus denitrificans is composed of 14 different subunits (nqo1-nqo14). of these, seven subunits (nqo7, nqo8, and nqo10-14) which are equivalent to the mitochondrial dna-encoded subunits of complex i constitute the membrane segment of the enzyme complex; the remaining subunits make up the peripheral part of the enzyme. we report here on the biochemical characterization and heterologus expression of the nqo10 subunit. the nqo10 s ... | 2003 | 12693950 |
| loop-contraction mutagenesis of a type 1 copper site. | loop-contraction mutagenesis has been applied to the cupredoxin pseudoazurin to introduce the active-site loop of amicyanin. the mutation has a limited effect on the spectroscopic properties, and therefore structure, of the cupric protein. the loop contraction results in the increase of the pka for the detachable his ligand of pseudoazurin by two ph units, similar to the value as found in amicyanin. | 2003 | 12708836 |
| paracoccus seriniphilus sp. nov., an l-serine-dehydratase-producing coccus isolated from the marine bryozoan bugula plumosa. | a novel marine gram-negative, non-motile, non-spore-forming, aerobic bacterium, associated with the bryozoan bugula plumosa, was isolated in a screening programme for strains containing enzymes able to convert the amino acid l-serine. strain mbt-a4t produced l-serine dehydratase and was able to grow on l-serine as the sole carbon and nitrogen source. the nearest phylogenetic neighbour was paracoccus marcusii, as determined by 16s rdna sequence analysis (97.8% similarity). the dna-dna reassociati ... | 2003 | 12710610 |
| bacterial diversity in a marine methanol-fed denitrification reactor at the montreal biodome, canada. | the bacterial biota of a methanol-fed denitrification reactor used to treat seawater at the montreal biodome were investigated using culture-dependent and molecular biology methods. the microbiota extracted from the reactor carriers were cultivated on three media. three isolate types were recovered and their 16s ribosomal dna (rdna) genes were determined. the analysis showed that the isolate types were related to alpha-proteobacteria. they are members of the hyphomicrobium and paracoccus genera ... | 2003 | 12739074 |
| interaction of cytochrome c with cytochrome c oxidase: an nmr study on two soluble fragments derived from paracoccus denitrificans. | the functional interactions between the various components of the respiratory chain are relatively short-lived, thus allowing high turnover numbers but at the same time complicating the structural analysis of the complexes. chemical shift mapping by nmr spectroscopy is a useful tool to investigate such transient contacts, since it can monitor changes in the electron-shielding properties of a protein as the result of temporary contacts with a reaction partner. in this study, we investigated the m ... | 2003 | 12755602 |
| initial investigations into the ultrasonic lysis of microbial cells for the release of adenosine triphosphate. | 2003 | 12758267 | |
| characterization of the expression and activity of the periplasmic nitrate reductase of paracoccus pantotrophus in chemostat cultures. | the periplasmic nitrate reductase (nap) from paracoccus pantotrophus has a role in cellular redox balancing. previously, transcription from the nap promoter in p. pantotrophus was shown to be responsive to the oxidation state of the carbon substrate. during batch culture, expression was higher during growth on reduced substrates such as butyrate compared to more oxidized substrates such as succinate. in the present study the effect of growth rate on nap expression in succinate-, acetate- and but ... | 2003 | 12777493 |
| cytochrome c oxidase--structure, function, and physiology of a redox-driven molecular machine. | cytochome c oxidase is the terminal member of the electron transport chains of mitochondria and many bacteria. providing an efficient mechanism for dioxygen reduction on the one hand, it also acts as a redox-linked proton pump, coupling the free energy of water formation to the generation of a transmembrane electrochemical gradient to eventually drive atp synthesis. the overall complexity of the mitochondrial enzyme is also reflected by its subunit structure and assembly pathway, whereas the div ... | 2003 | 12783267 |
| purification and characterization of formate dehydrogenase from ancylobacter aquaticus strain knk607m, and cloning of the gene. | ancylobacter aquaticus strain knk607m, which had high nad-dependent formate dehydrogenase (fdh) activity, was newly isolated. the enzyme, purified to homogeneity, was a dimer composed of identical subunits with a molecular mass of 44 kda. the specific activity was 9.5 u/mg, and the enzyme was optimum at ph 6.3 and 50 degrees c, most stable at ph 7.0, and stable at 50 degrees c or lower. the apparent km values for formate and nad+ were 2.4 and 0.057 mm, respectively. the enzyme was specific to fo ... | 2003 | 12784610 |
| aerobic denitrifying bacteria that produce low levels of nitrous oxide. | most denitrifiers produce nitrous oxide (n(2)o) instead of dinitrogen (n(2)) under aerobic conditions. we isolated and characterized novel aerobic denitrifiers that produce low levels of n(2)o under aerobic conditions. we monitored the denitrification activities of two of the isolates, strains tr2 and k50, in batch and continuous cultures. both strains reduced nitrate (no(3)(-)) to n(2) at rates of 0.9 and 0.03 micro mol min(-1) unit of optical density at 540 nm(-1) at dissolved oxygen (o(2)) (d ... | 2003 | 12788710 |
| [study on denitrification using different carbon sources]. | in this study, bench scale tests were conducted to study the potentials of immobilized denitrifier to reduce nitrate in the presence of 4 different carbon sources: glucose, cane sugar, methanol and acetic acid. the results showed that the carbon sources can be used by the immobilized bacteria as exogenous carbon sources. while using methanol, the average denitrifying velocity was lower than the others. dissimilatory reduction to ammonium was not significant and accounted for less than 5% of redu ... | 2003 | 12792992 |
| nitrate reductase from the magnetotactic bacterium magnetospirillum magnetotacticum ms-1: purification and sequence analyses. | we purified the nitrate reductase from the soluble fraction of magnetospirillum magnetotacticum ms-1. the enzyme was composed of 86- and 17-kda subunits and contained molybdenum, non-heme iron, and heme c. these properties are very similar to those of the periplasmic nitrate reductase found in paracoccus pantotrophus. the m. magnetotacticum nap locus was clustered in seven open reading frames, napfdaghbc. the phylogenetic analyses of napa, napb, and napc suggested a close relationship between m. ... | 2003 | 12795406 |
| maug, a novel diheme protein required for tryptophan tryptophylquinone biogenesis. | the biosynthesis of methylamine dehydrogenase (madh) from paracoccus denitrificans requires four genes in addition to those that encode the two structural protein subunits. none of these gene products have been previously isolated. one of these, maug, exhibits sequence similarity to diheme cytochrome c peroxidases and is required for the synthesis of the tryptophan tryptophylquinone (ttq) prosthetic group of madh. a system was developed for the homologous expression of maug in p. denitrificans. ... | 2003 | 12809487 |
| identification and characterization of transposable elements of paracoccus pantotrophus. | we studied diversity and distribution of transposable elements residing in different strains (dsm 11072, dsm 11073, dsm 65, and lmd 82.5) of a soil bacterium paracoccus pantotrophus (alpha-proteobacteria). with application of a shuttle entrapment vector pmec1, several novel insertion sequences (iss) and transposons (tns) have been identified. they were sequenced and subjected to detailed comparative analysis, which allowed their characterization (i.e., identification of transposase genes, termin ... | 2003 | 12813068 |
| electron transport to periplasmic nitrate reductase (napa) of wolinella succinogenes is independent of a napc protein. | the rumen bacterium wolinella succinogenes grows by respiratory nitrate ammonification with formate as electron donor. whereas the enzymology and coupling mechanism of nitrite respiration is well known, nitrate reduction to nitrite has not yet been examined. we report here that intact cells and cell fractions catalyse nitrate and chlorate reduction by reduced viologen dyes with high specific activities. a gene cluster encoding components of a putative periplasmic nitrate reductase system (napa, ... | 2003 | 12823811 |
| the proton pump of the mitochondrial bc1 complex. | the molecular mechanism of the proton pump activity by the respiratory chain bc1 complex is still unknown. this group has proposed since long time that protonation/deprotonation events in the apoproteins of the complex are cooperatively linked to the oxido-reduction reactions at the quinone catalytic centre. protolytic residues in the apoproteins can thus provide proton transfer pathways between the bulk aqueons phases and the redox centre. a series of experiments has been carried out aimed at d ... | 2003 | 12833636 |
| a novel enzyme, d-3-hydroxyaspartate aldolase from paracoccus denitrificans ifo 13301: purification, characterization, and gene cloning. | a novel enzyme, d-3-hydroxyaspartate aldolase (d-haa), catalyzing the conversion of d-3-hydroxyaspartate to glyoxylate plus glycine, was purified to homogeneity from paracoccus denitrificans ifo 13301. d-haa is strictly d-specific as to the alpha-position, whereas the enzyme does not distinguish between threo and erythro forms at the beta-position. in addition to d-3-hydroxyaspartate, the enzyme also acts on d-threonine, d-3-3,4-dihydroxyphenylserine, d-3-3,4-methylenedioxyphenylserine, and d-3- ... | 2003 | 12835921 |
| sequence analysis of a gene product synthesized by xanthomonas sp. during growth on natural rubber latex. | xanthomonas sp. secretes an extracellular protein (mr approximately 70+/-5 kda) during growth on purified natural rubber [poly(1,4-cis-isoprene)] but not during growth on water-soluble carbon sources such as glucose or gluconate. a 1.3 kbp dna fragment coding for an internal part of the structural gene of the 70 kda protein was amplified by nested polymerase chain reaction (pcr) using amino acid sequence information obtained after edman degradation of selected trypsin-generated peptides of the p ... | 2003 | 12855168 |
| atr-ftir spectroscopy of the p(m) and f intermediates of bovine and paracoccus denitrificans cytochrome c oxidase. | the structures of p(m) and f intermediates of bovine and paracoccus denitrificans cytochrome c oxidase were investigated by perfusion-induced attenuated total reflection-fourier transform infrared (atr-ftir) spectroscopy. transitions from the "fast" oxidized state to the p(m) or f states were initiated by perfusion with buffer containing either co/oxygen or h(2)o(2). intermediates were quantitated by simultaneous monitoring of visible absorption changes in the protein film. for both bovine and p ... | 2003 | 12873142 |
| role of tryptophan 121 in the soluble cua domain of cytochrome c oxidase: structure and electron transfer studies. | to investigate the contribution of tryptophan-121 (trp121) residue to the structure and function of soluble cua domain of cytochrome c oxidase, three mutant proteins, trp121tyr, trp121leu and trp121-deleted mutant of the soluble domain of paracoccus versutus cytochrome c oxidase, were constructed and expressed in escherichia coli bl21 (de3). optical spectral studies showed that both the coordination structure of the cua center and the secondary structure of the protein were changed significantly ... | 2003 | 12874377 |
| control of metalloprotein reduction potential: compensation phenomena in the reduction thermodynamics of blue copper proteins. | the reduction thermodynamics (delta h degrees '(rc) and delta s degrees '(rc)) for native paracoccus versutus amicyanin, for alcaligenes faecalis s-6 pseudoazurin, and for the g45p, m64e, and k27c variants of pseudomonas aeruginosa azurin were measured electrochemically. comparison with the data available for other native and mutated blue copper proteins indicates that the features of metal coordination and the electrostatic potential due to the protein matrix and the solvent control the reducti ... | 2003 | 12885256 |
| chloride dependence of growth in bacteria. | chloride is an abundant anion on earth but studies analyzing a possible function of chloride in prokaryotes are scarce. to address the question, we have tested 44 different gram-negative and gram-positive bacteria for a chloride dependence or chloride stimulation of growth. none required chloride for growth at their optimal growth (salt) conditions. however, in hyperosmotic media containing high concentrations of na+, 11 bacteria (aeromonas hydrophila, bacillus megaterium, bacillus subtilis, cor ... | 2003 | 12900036 |
| physiological role of s-formylglutathione hydrolase in c(1) metabolism of the methylotrophic yeast candida boidinii. | the methylotrophic yeast candida boidinii exhibits s-formylglutathione hydrolase activity (fgh, ec 3.1.2.12), which is involved in the glutathione-dependent formaldehyde oxidation pathway during growth on methanol as the sole carbon source. the structural gene, fgh1, was cloned from c. boidinii, and its predicted amino acid sequence showed more than 60 % similarity to those of fghs from paracoccus denitrificans and saccharomyces cerevisiae, and human esterase d. fgh from c. boidinii contained a ... | 2003 | 12904537 |
| steady-state kinetic analysis of substrate pair cycling between two enzymes: application to a mediated electron transport between the cytoplasmic membrane and the periplasmic nitrite reductase of paracoccus denitrificans. | an extended kinetic model is presented for the process catalysed by two enzymes mutually connected by the cycling of two reversibly interconvertible chemically relative species. expressions are derived for the steady-state velocity, limiting velocity (v) and the half-saturation concentration of the cycling substrate (a(0.5)). it is shown that the velocity depends on the total concentration of cycling substrate hyperbolically if both enzymes have equal activities. based on these theoretical consi ... | 2003 | 12914907 |
| unidirectional effect of lauryl sulfate on the reversible nadh:ubiquinone oxidoreductase (complex i). | lauryl sulfate inhibits the deltamu;(h)(+)-dependent reverse electron transfer reactions catalyzed by nadh:ubiquinone oxidoreductase (complex i) in coupled bovine heart submitochondrial particles and in vesicles derived from paracoccus denitrificans. the inhibitor affects neither nadh oxidase (coupled or uncoupled) nor nadh:ferricyanide reductase and succinate oxidase activities at the concentrations that selectively prevent the succinate-supported, rotenone-sensitive nad(+) or ferricyanide redu ... | 2003 | 12914921 |
| structure of the phenylhydrazine adduct of the quinohemoprotein amine dehydrogenase from paracoccus denitrificans at 1.7 a resolution. | the 109 kda quinohemoprotein amine dehydrogenase (qhndh) from paracoccus denitrificans contains a novel redox cofactor, cysteine tryptophylquinone (ctq). this cofactor is derived from a pair of gene-encoded amino acids by post-translational modification and was previously identified and characterized within an 82-residue subunit by chemical methods and crystallographic analysis at 2.05 a resolution. it contains an orthoquinone moiety bound to the indole ring and catalyzes the oxidation of alipha ... | 2003 | 12925784 |
| different interaction modes of two cytochrome-c oxidase soluble cua fragments with their substrates. | cytochrome-c oxidase is the terminal enzyme in the respiratory chains of mitochondria and many bacteria and catalyzes the formation of water by reduction of dioxygen. the first step in the cytochrome oxidase reaction is the bimolecular electron transfer from cytochrome c to the homobinuclear mixed-valence cua center of subunit ii. in thermus thermophilus a soluble cytochrome c552 acts as the electron donor to ba3 cytochrome-c oxidase, an interaction believed to be mainly hydrophobic. in paracocc ... | 2003 | 12937163 |
| isolation and characterization of novel halotolerant and/or halophilic denitrifying bacteria with versatile metabolic pathways for the degradation of trimethylamine. | four denitrifying bacteria capable of degrading trimethylamine under both aerobic and denitrifying conditions were newly isolated from coastal sediments and wastewater contaminated by marine water. all strains were in alpha-proteobacteria. strain gp43 was classified as a member of genus paracoccus, and strain ph32, ph34 and grp21 were novel organisms with remote phylogenetic position from other genus alpha-proteobacteria. among these four strains were the halophilic strains ph32, ph34 and grp21, ... | 2003 | 12951251 |
| growth and nitrite and nitrous oxide accumulation of paracoccus denitrificans atcc 19367 in the presence of selected pesticides. | the effects of the application of eight pesticides (aldrin, lindane, dimetoate, methylparathion, methidation, atrazine, simazine, and captan) on growth, respiratory activity (as co2 production), denitrifying activity (as n2o released), and nitrite accumulation in the culture medium by paracoccus denitrificans strain atcc 19367 were studied. the fungicide captan totally inhibited growth and biological activity of p. denitrificans, while the rest of the tested pesticides delayed the growth and co2 ... | 2003 | 12959522 |
| an engineered cua amicyanin capable of intermolecular electron transfer reactions. | the type i copper center of amicyanin was replaced with a binuclear cua center. to create this model cua protein, a portion of the amino acid sequence that contains three of the ligands to the native type i copper center of paracoccus denitrificans amicyanin was replaced with the corresponding portion of sequence that provides five ligands for the cua center of cytochrome c oxidase from p. denitrificans. uv-visible and electron paramagnetic resonance spectroscopy confirm that the engineered prot ... | 2003 | 12970350 |
| chemical and kinetic reaction mechanisms of quinohemoprotein amine dehydrogenase from paracoccus denitrificans. | quinohemoprotein amine dehydrogenase (qhndh) possesses a cysteine tryptophylquinone (ctq) prosthetic group that catalyzes the oxidative deamination of primary amines. in addition to ctq, two heme c cofactors are present in qhndh that mediate the transfer of the substrate-derived electrons from ctq to an external electron acceptor. steady-state kinetic assays yielded relatively small k(cat) values (<6 s(-1)), and the rate-limiting step appears to be the interprotein electron transfer from heme in ... | 2003 | 12974623 |
| x-ray structure of methanol dehydrogenase from paracoccus denitrificans and molecular modeling of its interactions with cytochrome c-551i. | the x-ray structure of methanol dehydrogenase (medh) from paracoccus denitrificans (medh-pd) was determined at 2.5 a resolution using molecular replacement based on the structure of medh from methylophilus methylotrophus w3a1 (medh-wa). the overall structures from the two bacteria are similar to each other except that the former has a longer c-terminal tail in each subunit and shows local differences in several insertion regions. the "x-ray sequence" of the segment alphagly444-alphaleu452 was es ... | 2003 | 14505072 |
| active/de-active transition of respiratory complex i in bacteria, fungi, and animals. | mammalian complex i (nadh:ubiquinone oxidoreductase) exists as a mixture of interconvertible active (a) and de-activated (d) forms. the a-form is capable of nadh:quinone-reductase catalysis, but not the d-form. complex i from the bacterium paracoccus denitrificans, by contrast, exists only in the a-form. this bacterial complex contains 32 fewer subunits than the mammalian complex. the question arises therefore if the structural complexity of complex i from higher organisms correlates with its ab ... | 2003 | 14507430 |
| electron transfer complexes of cytochrome c peroxidase from paracoccus denitrificans containing more than one cytochrome. | according to the model proposed in previous papers [pettigrew, g. w., prazeres, s., costa, c., palma, n., krippahl, l., and moura, j. j. (1999) the structure of an electron-transfer complex containing a cytochrome c and a peroxidase, j. biol. chem. 274, 11383-11389; pettigrew, g. w., goodhew, c. f., cooper, a., nutley, m., jumel, k., and harding, s. e. (2003) electron transfer complexes of cytochrome c peroxidase from paracoccus denitrificans, biochemistry 42, 2046-2055], cytochrome c peroxidase ... | 2003 | 14556628 |
| a mutant of paracoccus denitrificans with disrupted genes coding for cytochrome c550 and pseudoazurin establishes these two proteins as the in vivo electron donors to cytochrome cd1 nitrite reductase. | in paracoccus denitrificans, electrons pass from the membrane-bound cytochrome bc(1) complex to the periplasmic nitrite reductase, cytochrome cd(1). the periplasmic protein cytochrome c(550) has often been implicated in this electron transfer, but its absence, as a consequence of mutation, has previously been shown to result in almost no attenuation in the ability of the nitrite reductase to function in intact cells. here, the hypothesis that cytochrome c(550) and pseudoazurin are alternative el ... | 2003 | 14563865 |
| electrochemical and ftir spectroscopic characterization of the cytochrome bc1 complex from paracoccus denitrificans: evidence for protonation reactions coupled to quinone binding. | the cytochrome bc(1) complex from paracoccus denitrificans and soluble fragments of its cytochrome c(1) and rieske isp subunits are characterized by a combined approach of protein electrochemistry and ftir difference spectroscopy. the ftir difference spectra provide information about alterations in the protein upon redox reactions: signals from the polypeptide backbone, from the cofactors, and from amino acid side chains. we describe typical modes for conformational changes in the polypeptide an ... | 2003 | 14567700 |
| kinetic stability of the peroxidase activity of unfolded cytochrome c: heme degradation and catalyst inactivation by hydrogen peroxide. | unfolding converts paracoccus versutus cytochrome c-550 into a potent peroxidase (diederix, r. e. m.; ubbink, m.; canters, g. w. chembiochem 2002, 3, 110-112). the catalytic activity is accompanied by peroxide-driven inactivation that is prevented, in part, by reducing substrate. here, the kinetics of inactivation are described, and evidence is presented for the occurrence of a labile intermediate on the catalytic peroxidase pathway of unfolded cytochrome c-550. this intermediate represents a br ... | 2003 | 14577794 |
| amicyanin metal-site structure and interaction with madh: pac and nmr spectroscopy of ag-, cd-, and cu-amicyanin. | to investigate the structural control mechanisms in the metal site of amicyanin when interacting with madh, redox-inactive ag(+)- and cd(2+)-substituted amicyanins were studied with perturbed angular correlations of gamma-rays (pac) spectroscopy. pac experiments on (111m)cd-substituted amicyanin revealed two different metal-site structures, which are very likely in dynamic exchange on a ~5 ns timescale. only one structure binds to madh. the dissociation constants, k(d), are 9+/-2 microm with mad ... | 2004 | 14605949 |