| identification and molecular genetic analysis of multiple loci contributing to high-level tellurite resistance in rhodobacter sphaeroides 2.4.1. | the ability of the facultative photoheterotroph rhodobacter sphaeroides to tolerate and reduce high levels of tellurite in addition to at least 10 other rare earth metal oxides and oxyanions has considerable potential for detoxification and bioremediation of contaminated environments. we report the identification and characterization of two loci involved in high-level tellurite resistance. the first locus contains four genes, two of which, trgab, confer increased tellurite resistance when introd ... | 1997 | 9406390 |
| cell biology and molecular basis of denitrification. | denitrification is a distinct means of energy conservation, making use of n oxides as terminal electron acceptors for cellular bioenergetics under anaerobic, microaerophilic, and occasionally aerobic conditions. the process is an essential branch of the global n cycle, reversing dinitrogen fixation, and is associated with chemolithotrophic, phototrophic, diazotrophic, or organotrophic metabolism but generally not with obligately anaerobic life. discovered more than a century ago and believed to ... | 1997 | 9409151 |
| heterologous expression of heterotrophic nitrification genes. | paracoccus denitrificans is a heterotrophic organism capable of oxidizing ammonia to nitrite during growth on an organic carbon and energy source. this pathway, termed heterotrophic nitrification, requires the concerted action of an ammonia monooxygenase (amo) and hydroxylamine oxidase (hao). the genes required for heterotrophic nitrification have been isolated by introducing a pa. denitrificans genomic library into pseudomonas putida and screening for the accumulation of nitrite. in contrast to ... | 1997 | 9421902 |
| isolation and characterization of rhodobacter capsulatus mutants affected in cytochrome cbb3 oxidase activity. | the facultative phototrophic bacterium rhodobacter capsulatus contains only one form of cytochrome (cyt) c oxidase, which has recently been identified as a cbb3-type cyt c oxidase. this is unlike other related species, such as rhodobacter sphaeroides and paracoccus denitrificans, which contain an additional mitochondrial-like aa3-type cyt c oxidase. an extensive search for mutants affected in cyt c oxidase activity in r. capsulatus led to the isolation of at least five classes of mutants. plasmi ... | 1998 | 9473054 |
| tryptophan 121 of subunit ii is the electron entry site to cytochrome-c oxidase in paracoccus denitrificans. involvement of a hydrophobic patch in the docking reaction. | to investigate the contribution of hydrophobic residues to the molecular recognition of cytochrome c with cytochrome oxidase, we mutated several hydrophobic amino acids exposed on subunit ii of the paracoccus denitrificans oxidase. km and kcat values and the bimolecular rate constant were determined under steady- or presteady-state conditions, respectively. we present evidence that trp-121 which is surrounded by a hydrophobic patch is the electron entry site to oxidase. mutations in this cluster ... | 1998 | 9478966 |
| genomic dna cloning of the region encoding nitric oxide reductase in paracoccus halodenitrificans and a structure model relevant to cytochrome oxidase. | the structural genes for the no reductase in paracoccus halodenitrificans, norc, norb, and norq were sequenced. the norc and norb encode the cytochrome c (norc) and cytochrome b (norb) subunits, respectively. the matured norc (17,258 da, 148 residues) has a binding motif (cxych) for heme c, which is axially coordinated by his65 and met115. norb (52,337 da, 451 residues) has twelve putative transmembrane helices and the 19% sequence homology with the subunit i of cytochrome oxidase from paracoccu ... | 1998 | 9480821 |
| role of the pathway through k(i-362) in proton transfer in cytochrome c oxidase from r. sphaeroides. | in this study we have combined the use of site-directed mutants with time-resolved optical absorption spectroscopy to investigate the role of the protonatable subunit-i residues lysine-362 (k(i-362)) and threonine-359 (t(i-359)) in cytochrome c oxidase from rhodobacter sphaeroides in electron and proton transfer. these residues have been proposed to be part of a proton-transfer pathway in cytochrome oxidases from paracoccus denitrificans and bovine heart. mutation of k(i-362) and t(i-359) to met ... | 1998 | 9485395 |
| purification and characterization of the hnda subunit of nadp-reducing hydrogenase from desulfovibrio fructosovorans overproduced in escherichia coli. | based on the dna sequence of its structural genes, clustered in the hnd operon, the nadp-reducing hydrogenase of desulfovibrio fructosovorans is thought to be a heterotetrameric complex in which hnda and hndc constitute the nadp-reducing unit and hndd constitutes the hydrogenase unit, respectively. the weak representativity of the enzyme among cell proteins has prevented its purification. this paper discusses the purification and characterization of the hnda subunit of this unique tetrameric iro ... | 1998 | 9485416 |
| cytochrome-c-binding site on cytochrome oxidase in paracoccus denitrificans. | to monitor the docking site for cytochrome c on cytochrome oxidase from paracoccus denitrificans, a series of site-directed mutants in acidic residues exposed on the three largest subunits was constructed, and the purified enzymes were assayed for their steady-state kinetic parameters, their ionic strength dependence, and their fast electron entry kinetics by stopped-flow measurements. increasing the ionic strength, the maximum of the bell-shaped dependence of the steady-state rate observed for ... | 1998 | 9492306 |
| identification of the contiguous paracoccus denitrificans ccmf and ccmh genes: disruption of ccmf, encoding a putative transporter, results in formation of an unstable apocytochrome c and deficiency in siderophore production. | apocytochrome c550 was detected in the periplasm of a new mutant of paracoccus denitrificans, hn48, that is pleiotropically lacking c-type cytochromes, produces reduced levels of siderophores and carries a tn5 insertion in the ccmf gene for which sequence data, along with that for the contiguous ccmh, are reported. a counterpart to the ccmf gene was found in an archaebacterium but could not be located in the yeast genome, whereas mitochondrial haem lyases in the latter were not present in an arc ... | 1998 | 9493384 |
| refined crystal structure of methylamine dehydrogenase from paracoccus denitrificans at 1.75 a resolution. | the three-dimensional structure of the quinoprotein methylamine dehydrogenase from paracoccus denitrificans has been refined at 1.75 a resolution utilizing the dna-based protein sequence. the final model incorporates 8034 atoms per molecule, including 552 molecules of solvent, and gives an r-factor of 0.163. the molecule is an h2l2 hetero-tetramer containing a non-crystallographic 2-fold axis of symmetry. the 373-residue h subunit is folded into seven repeats of a four-stranded antiparallel beta ... | 1998 | 9514722 |
| construction of mobilizable cloning vectors derived from pbgs18 and their application for analysis of replicator region of a ptav202 mini-derivative of paracoccus versutus ptav1 plasmid. | two mobilizable cloning vectors, designated pabw1 and pawb2, were constructed basing on the e. coli vector pbgs18 and orit originating from rk2. in pabw2 the kanamycin resistance gene was replaced by a novel tetracycline resistance cassette derived from tn1721. both vectors, specific for e. coli, allow to perform the cloning steps in e. coli and then to efficiently transfer the constructs by conjugation to the host of choice. a vector which cannot propagate in the given host can be applied for i ... | 1997 | 9516985 |
| rhizobium etli cychjkl gene locus involved in c-type cytochrome biogenesis: sequence analysis and characterization of two cych mutants. | the cychjkl gene locus was cloned from rhizobium etli by the rescue of a tn5mob insertion of a mutant (ifc01) which was affected in the production of c-type cytochromes. the cych, cycj, cyck and cycl genes are proposed to code for different subunits of a haem lyase complex involved in the attachment of haem to cytochrome c apoproteins. cych of 365 aa shared 27, 36, 47 and 63% identity with cych from paracoccus denitrificans, bradyrhizobium japonicum, r. meliloti, and r. leguminosarum, respective ... | 1998 | 9524269 |
| genes coding for respiratory complexes map on all three chromosomes of the paracoccus denitrificans genome. | the genome of paracoccus denitrificans (strain pd1222) consists of three distinct dna molecules when separated by standard pulsed-field gel electrophoresis with apparent molecular sizes of approximately 2, 1.1, and 0.64 mb. when the separated chromosomes are digested by restriction enzymes and sizes of resulting fragments are summed up, the three chromosomes are composed of 1.83, 1.16, and 0.67 mb. since their migration behavior relative to size standards is largely independent of electrophoresi ... | 1998 | 9531627 |
| the coupling of electron transfer and proton translocation: electrostatic calculations on paracoccus denitrificans cytochrome c oxidase. | we have calculated the electrostatic potential and interaction energies of ionizable groups and analyzed the response of the protein environment to redox changes in paracoccus denitrificans cytochrome c oxidase by using a continuum dielectric model and finite difference technique. subsequent monte carlo sampling of protonation states enabled us to calculate the titration curves of all protonatable groups in the enzyme complex. inclusion of a model membrane allowed us to restrict the calculations ... | 1998 | 9533684 |
| structure and function of bacterial cytochrome c oxidase. | the crystal structure of cytochrome c oxidase from the soil bacterium paracoccus denitrificans has been reported. this structure has provided a basis for understanding the mechanism of the redox-coupled transmembrane proton pump which is the key component of the respiratory chain in most aerobic organism. over the past ten years, there have been many site-directed mutagenesis studies performed on bacterial oxidases. structural features of paracoccus oxidase have been summarized in the light of t ... | 1998 | 9538216 |
| characterization of the ubiquinone reduction site of mitochondrial complex i using bulky synthetic ubiquinones. | a wide variety of alkyl derivatives of q2 (6-geranyl-2, 3-dimethoxy-5-methyl-1,4-benzoquinone) and db (6-n-decyl-2, 3-dimethoxy-5-methyl-1,4-benzoquinone), in which methoxy groups of the 2- and/or 3-positions of the quinone ring were replaced by other bulky alkoxy groups from ethoxy to butoxy, were prepared by novel synthetic procedures. electron-accepting activities of the bulky quinones were investigated with bovine heart mitochondrial complex i and its counterpart of paracoccus denitrificans( ... | 1998 | 9572861 |
| site-directed mutagenesis of phe 97 to glu in amicyanin alters the electronic coupling for interprotein electron transfer from quinol methylamine dehydrogenase. | conversion by site-directed mutagenesis of phe 97 of amicyanin to glu significantly decreases the rate constant for the electron-transfer reaction from the quinol form of methylamine dehydrogenase to amicyanin. it is shown that the deltag degrees and reorganizational energy (lambda) associated with the electron-transfer reaction are unaffected by the mutation and that the decrease in the electron-transfer rate is attributable completely to a decrease in the electronic coupling matrix element (ha ... | 1998 | 9585551 |
| understanding the electronic properties of the cua site from the soluble domain of cytochrome c oxidase through paramagnetic 1h nmr. | the soluble domain of the subunit ii of cytochrome c oxidase from paracoccus versutus was cloned, expressed, and studied by 1h nmr at 600 mhz. the properties of the redox-active dinuclear cua site in the paramagnetic mixed-valence cu(i)-cu(ii) state were investigated in detail. a group of relatively sharp signals found between 30 and 15 ppm in the 1h nmr spectrum correspond to the imidazole protons of the coordinated histidines (h181 and h224). a second group of broader and farther shifted signa ... | 1998 | 9585552 |
| involvement of glutamic acid 278 in the redox reaction of the cytochrome c oxidase from paracoccus denitrificans investigated by ftir spectroscopy. | the molecular processes concomitant with the redox reactions of wild-type and mutant cytochrome c oxidase from paracoccus denitrificans were analyzed by a combination of protein electrochemistry and fourier transform infrared (ftir) difference spectroscopy. oxidized-minus-reduced ftir difference spectra in the mid-infrared (4000-1000 cm-1) reflecting full or stepwise oxidation and reduction of the respective cofactor(s) were obtained. in the 1800-1000 cm-1 range, these ftir difference spectra re ... | 1998 | 9585553 |
| redox dependent changes at the heme propionates in cytochrome c oxidase from paracoccus denitrificans: direct evidence from ftir difference spectroscopy in combination with heme propionate 13c labeling. | specific isotope labeling at the carboxyl groups of the four heme propionates of cytochrome c oxidase from paracoccus denitrificans was used in order to assign signals observed in electrochemically induced redox fourier transform infrared (ftir) difference spectra of this enzyme. for this purpose, the hema gene of the p. denitrificans strain pd1222, coding for 5-aminolevulinate synthase, was deleted by partial replacement with a kanamycin resistance cartridge, resulting in a stable 5-aminolevuli ... | 1998 | 9585554 |
| iron-sulfur clusters/semiquinones in complex i. | nadh-quinone 1 oxidoreductase (complex i) isolated from bovine heart mitochondria was, until recently, the major source for the study of this most complicated energy transducing device in the mitochondrial respiratory chain. complex i has been shown to contain 43 subunits and possesses a molecular mass of about 1 million. recently, complex i genes have been cloned and sequenced from several bacterial sources including escherichia coli, paracoccus denitrificans, rhodobacter capsulatus and thermus ... | 1998 | 9593887 |
| nitrous oxide reductase (nosz) gene-specific pcr primers for detection of denitrifiers and three nosz genes from marine sediments. | two pcr primer sets for the nitrous oxide reductase gene (nosz) were developed. the initial primers were based on three sequences in genbank and used to amplify nosz from continental shelf sediments and from two denitrifiers in culture, thiosphaera pantotropha and pseudomonas denitrificans. three unique marine sediment nosz genes were identified and sequenced. the marine nosz genes were most closely related to the nosz genes of paracoccus denitrificans or to rhizobium meliloti. alignment of all ... | 1998 | 9595664 |
| redox properties of tryptophan tryptophylquinone enzymes. correlation with structure and reactivity. | the ph dependence of the redox potentials for the oxidized/reduced couples of methylamine dehydrogenase (madh) and aromatic amine dehydrogenase (aadh) were determined. for each enzyme, a change of -30 mv/ph unit was observed, indicating that the two-electron transfer is linked to the transfer of a single proton. this result differs from what was obtained from redox studies of a tryptophan tryptophylquinone (ttq) model compound for which the two-electron couple is linked to the transfer of two pr ... | 1998 | 9603931 |
| molecular characterisation of the 76 kda iron-sulphur protein subunit of potato mitochondrial complex i. | genes encoding subunits of complex i (ec 1.6.5.3) of the mitochondrial respiratory chain vary in their locations between the mitochondrial and nuclear genomes in different organisms, whereas genes for a homologous multisubunit complex in chloroplasts have to date only been found on the plastid genome. in potato (solanum tuberosum l.), the gene coding for the mitochondrial 76 kda iron-sulphur protein is identified in the nuclear genome. the gene is transcribed into polyadenylated mrna which is mo ... | 1998 | 9615461 |
| the role of electrostatic interactions for cytochrome c oxidase function. | in recent years, the enormous increase in high-resolution three-dimensional structures of proteins together with the development of powerful theoretical techniques have provided the basis for a more detailed examination of the role of electrostatics in determining the midpoint potentials of redox-active metal centers and in influencing the protonation behavior of titratable groups in proteins. based on the coordinates of the paracoccus denitrificans cytochrome c oxidase, we have determined the e ... | 1998 | 9623809 |
| cytochrome c oxidase (heme aa3) from paracoccus denitrificans: analysis of mutations in putative proton channels of subunit i. | one of the challenging features of energy-transducing terminal oxidases, like the aa3 cytochrome c oxidase of paracoccus denitrificans, is the translocation of protons across the cytoplasmic membrane, which is coupled to the transfer of electrons to oxygen. as a prerequisite for a more advanced examination of the enzymatic properties, several amino acid residues, selected on the basis of recent three-dimensional structure determinations, were exchanged in subunit i of the paracoccus enzyme by si ... | 1998 | 9623810 |
| engineered fv fragments as a tool for the one-step purification of integral multisubunit membrane protein complexes. | the preparation of pure and homogeneous membrane proteins or membrane protein complexes is time consuming, and the yields are frequently insufficient for structural studies. to circumvent these problems we established an indirect immunoaffinity chromatography method based on engineered fv fragments. cdnas encoding the variable domains of hybridoma-derived antibodies raised against various membrane proteins were cloned and expressed in escherichia coli. the fv fragments were engineered to serve a ... | 1995 | 9634756 |
| carboxin resistance in paracoccus denitrificans conferred by a mutation in the membrane-anchor domain of succinate:quinone reductase. | succinate:quinone reductase is a membrane-bound enzyme of the citric acid cycle and the respiratory chain. carboxin is a potent inhibitor of the enzyme of certain organisms. the bacterium paracoccus denitrificans was found to be sensitive to carboxin in vivo, and mutants that grow in the presence of 3'-methyl carboxin were isolated. membranes of the mutants showed resistant succinate:quinone reductase activity. the mutation conferring carboxin resistance was identified in four mutants. they cont ... | 1998 | 9639600 |
| role of copper during carbon monoxide binding to terminal oxidases. | under fully reduced conditions, reassociation kinetics of co were studied in several terminal oxidases containing copper in their binuclear center. the purified paracoccus denitrificans ba3-type quinol oxidase was found to recombine with co monophasically (tau 25-30 ms) like oxidases of the bo type from escherichia coli, the caa3 type from bacillus halodurans ftu, and the bo type from methylobacillus flagellatum kt. oxidase of the aa3 type from bovine heart recombined with co monophasically at a ... | 1998 | 9650593 |
| cytochrome c oxidase: one enzyme, two mechanisms? | | 1998 | 9660711 |
| crystal structures of paracoccus denitrificans aromatic amino acid aminotransferase: a substrate recognition site constructed by rearrangement of hydrogen bond network. | aminotransferase reversibly catalyzes the transamination reaction by a ping-pong bi-bi mechanism with pyridoxal 5'-phosphate (plp) as a cofactor. various kinds of aminotransferases developing into catalysts for particular substrates have been reported. among the aminotransferases, aromatic amino acid aminotransferase (ec 2.6.1. 57) catalyzes the transamination reaction with both acidic substrates and aromatic substrates. to elucidate the multiple substrate recognition mechanism, we determined th ... | 1998 | 9665848 |
| a novel, non-statistical method for predicting breaks in transmembrane helices. | we have developed a novel, non-statistical procedure for predicting possible breaks in transmembrane helices based on energy calculations. the procedure consists of stepwise elongation of the 'core' helical fragment determined by consensus results of several available prediction procedures. at each step, we calculate the conformational energies corresponding to the regular 'frozen' helical conformer of the 'core' fragment elongated by two flanking residues, e(alpha), as well as those to several ... | 1998 | 9680189 |
| occurrence, overexpression and partial purification of the protein (majastridin) corresponding to the urf6 gene of the rhodobacter blasticus atp operon. | antibodies were produced against two antigenic peptides of a protein, which was named majastridin, corresponding to the urf6 gene of the rhodobacter blasticus atp operon [tybulewicz, v. l. j., falk, g. & walker, j. e. (1984) j. mol. biol. 179, 185-214]. a protein band of the expected size is labelled by immunoblotting in western blots containing the cytosolic fractions from rb. blasticus and paracoccus denitrificans but not from escherichia coli or rhodospirillum rubrum. although the protein is ... | 1998 | 9692905 |
| mutational analysis of residues forming hydrogen bonds in the rieske [2fe-2s] cluster of the cytochrome bc1 complex in paracoccus denitrificans. | two mutations (s157a and y159f) in the rieske iron-sulfur subunit of the ubihydroquinone-cytochrome c oxidoreductase from paracoccus denitrificans have been characterized with respect to the protein and [2fe-2s] cluster stability, the enzyme activity and the redox potential of the [2fe-2s] cluster. in the structure of the water-soluble fragment of the rieske iron-sulfur protein of the bovine heart mitochondrial bc1 complex, both residues (s163 and y165 in the bovine sequence) form the following ... | 1998 | 9692907 |
| 31p-nmr spectroscopy of human and paracoccus denitrificans electron transfer flavoproteins, and 13c- and 15n-nmr spectroscopy of human electron transfer flavoprotein in the oxidised and reduced states. | human and paracoccus denitrificans wild-type electron transfer flavoproteins have been investigated by 31p-nmr in the oxidised and reduced states. the 31p chemical shifts of the diphosphate moiety of the protein-bound fad were similar in the proteins and were independent of the redox state. the chemical shifts were remarkably similar to those of ferredoxin-nadp+ reductase and, to a lesser degree, with those of nadph-cytochrome p-450 reductase. the wild-type human electron transfer apoprotein was ... | 1998 | 9692910 |
| the primary structure of soluble cytochrome c-551 from the phototrophic green sulfur bacterium chlorobium limicola, strain tassajara, reveals a novel c-type cytochrome. | chlorobium limicola, strain tassajara, cytochrome c-551 is a soluble dimeric protein containing identical subunits of about 30 kda. the amino acid sequence was determined by a combination of automated edman degradation and mass analysis. there are 258 residues with a single heme binding site located at cysteine positions 172 and 175. in addition, there is a disulfide bridge between cys78 and cys109, and a free cysteine at position 219 which was found to occur as cysteic acid. the only homologue ... | 1998 | 9692944 |
| electron transfer from the aminosemiquinone reaction intermediate of methylamine dehydrogenase to amicyanin. | the tryptophan tryptophylquinone (ttq) cofactor of methylamine dehydrogenase (madh) is covalently modified by substrate-derived nitrogen during its two-electron reduction by methylamine to form an aminoquinol (n-quinol). an n-semiquinone, which retains the substrate-derived n, is the intermediate during the two sequential one-electron oxidations of n-quinol madh by its physiologic electron acceptor, amicyanin. electron transfer (et) from n-quinol madh to amicyanin is gated by the deprotonation o ... | 1998 | 9692997 |
| comparison of energization of complex i in membrane particles from paracoccus denitrificans and bovine heart mitochondria. | the results of preliminary studies of the effects of energization on the catalytic and epr properties of complex i in tightly coupled membrane vesicles of paracoccus denitrificans (spp) are presented. they are compared to those observed in submitochondrial particles from bovine heart (smp). all signs of energization of complex i detected by epr in smp (uncoupler-sensitive splitting of the gz lines of the clusters 2 and a broadening of their gxy lines, a fast-relaxing, piericidin-sensitive ubiqui ... | 1998 | 9693721 |
| structure-function studies of iron-sulfur clusters and semiquinones in the nadh-q oxidoreductase segment of the respiratory chain. | our recent experimental data on iron-sulfur clusters and semiquinones in the complex i segment of the respiratory chain is presented, focusing on the paracoccus (p.) denitrificans and bovine heart studies. the iron-sulfur cluster n2 has attracted the attention of investigators in the research field of complex i, since the mid-point redox potential of this cluster is the highest among all clusters in complex i, and is ph dependent (60 mv/ph). it is known that this cluster is located either in the ... | 1998 | 9693742 |
| soxd: an essential mediator of induction of anterior neural tissues in xenopus embryos. | vertebrate neurogenesis is initiated by the organizer factors that inhibit antineuralizing activities of bone morphogenetic proteins (bmps) in the ectoderm. here, we report a candidate mediator of neuralization, soxd. expression of soxd starts at late blastula stages widely in the prospective ectoderm and becomes restricted to the dorsal ectoderm by mid-gastrula stages. soxd expression is enhanced by the neural inducer chordin and is suppressed by bmp4 and its downstream genes. microinjection of ... | 1998 | 9697853 |
| analysis of the pathogenic human mitochondrial mutation nd1/3460, and mutations of strictly conserved residues in its vicinity, using the bacterium paracoccus denitrificans. | the human mitochondrial nd1/3460 mutation changes ala52 to thr in the nd1 subunit of complex i, and causes leber's hereditary optic neuropathy (lhon) [huoponen et al. (1991) am. j. hum. genet. 48, 1147]. we have used a bacterial counterpart of complex i, ndh-1 from paracoccus denitrificans, for studying the effect of mutations in the nd1 subunit on the enzymatic activity. the lhon mutation as well as several other mutations in strictly conserved amino acids in its vicinity were introduced into t ... | 1998 | 9718301 |
| tryptophan-136 in subunit ii of cytochrome bo3 from escherichia coli may participate in the binding of ubiquinol. | in the cytochrome c oxidases, the role of subunit ii is to provide the electron entry site into the enzyme. this subunit contains both the binding site for the substrate, cytochrome c, and the cua redox center, which is initially reduced by cytochrome c. cytochrome bo3 and other quinol oxidases that are members of the heme-copper oxidase superfamily have a homologous subunit ii, but the cua site is absent, as is the docking site for cytochrome c. speculation that subunit ii in the quinol oxidase ... | 1998 | 9718303 |
| expression of the escherichia coli cyo operon in paracoccus denitrificans results in a fully active quinol oxidase of unexpected heme composition. | the cyo operon coding for the membrane-bound bo3-type quinol oxidase of escherichia coli has been expressed in a paracoccus denitrificans strain deleted in its endogenous ba3 quinol oxidase. using the p. denitrificans qox promoter, the his tagged protein complex is synthesized to a level comparable to that in e. coli and the enzyme purified in a single step on a metal-chelating column. whereas the activity of the isolated complex matches that of the oxidase purified directly from e. coli, the he ... | 1998 | 9720906 |
| identification of bacterial isolates from biofilters as paracoccus alkenifer sp. nov. and paracoccus solventivorans with emended description of paracoccus solventivorans. | two groups of strains isolated from biofilters for the treatment of waste gases were assigned to the genus paracoccus by phylogenetic and chemotaxonomic methods. all type strains of the genus paracoccus were compared with these groups using 16s rdna sequence analysis, fatty acid patterns and physiological reaction profiles. for both groups, the nearest related reference species was paracoccus solventivorans based on 16s rdna sequence similarity. however, whereas one group of isolates was identif ... | 1998 | 9731294 |
| paracoccus marcusii sp. nov., an orange gram-negative coccus. | phenotypic, chemotaxonomic and 16s rdna sequence analysis of an orange gram-negative coccus that appeared as a contaminant on a nutrient agar plate delineated a new species of the genus paracoccus. phenotypic features of the strain that differ from all or most of the previously described paracoccus species include its bright orange colour, caused by the synthesis of large amounts of carotenoids (mainly astaxanthin), and its inability to use nitrate as an electron acceptor in respiration. the nam ... | 1998 | 9731296 |
| intrinsic uncoupling of cytochrome c oxidase may cause the maternally inherited mitochondrial diseases melas and lhon. | mutations in the human mtdna gene encoding subunit iii of cytochrome c oxidase (co) have been reported to cause melas and lhon. poracoccus denitrificans cells expressing substitutions homologous to these melas- and lhon-causing mutations had lower growth yield than wild type cells and lower efficiency of proton pumping by co (e.g. lower h+/e ratio and lower deltapsi), but had similar co activity. these results indicate that both substitutions (f263l > a212t) cause intrinsic uncoupling, which may ... | 1998 | 9738940 |
| electron entry in a cua mutant of cytochrome c oxidase from paracoccus denitrificans. conclusive evidence on the initial electron entry metal center. | a cytochrome c oxidase subunit ii c216s mutant from paracoccus denitrificans in which the cua site was changed by site-directed mutagenesis to a mononuclear copper site [zickermann, v., wittershagen, a., kolbesen, b.o. and ludwig, b. biochemistry 36 (1997) 3232-3236] was investigated by stopped-flow spectroscopy. contrary to the behavior of the wild type enzyme, in this mutant cytochrome a cannot be reduced by excess cytochrome c in the millisecond time scale in which cytochrome c oxidation is o ... | 1998 | 9742947 |
| crystallographic and spectroscopic studies of native, aminoquinol, and monovalent cation-bound forms of methylamine dehydrogenase from methylobacterium extorquens am1. | various monovalent cations influence the enzymatic activity and the spectroscopic properties of methylamine dehydrogenase (madh). here, we report the structure determination of this tryptophan tryptophylquinone-containing enzyme from methylobacterium extorquens am1 by high resolution x-ray crystallography (1.75 a). this first madh crystal structure at low ionic strength is compared with the high resolution structure of the related madh from paracoccus denitrificans recently reported. we also des ... | 1998 | 9748238 |
| the active site of the bacterial nitric oxide reductase is a dinuclear iron center. | a novel, improved method for purification of nitric oxide reductase (nor) from membranes of paracoccus denitrificans has been developed. the purified enzyme is a cytochrome bc complex which, according to protein chemical and hydrodynamic data, contains two subunits in a 1:1 stoichiometry. the purified norbc complex binds 0.87 g of dodecyl maltoside/g of protein and forms a dimer in solution. similarly, it is dimeric in two-dimensional crystals. images of these crystals have been processed at 8 a ... | 1998 | 9748316 |
| paracoccus denitrificans cytochrome c oxidase: a kinetic study on the two- and four-subunit complexes. | cytochrome c oxidase from paracoccus denitrificans has been purified in two different forms differing in polypeptide composition. an enzyme containing polypeptides i-iv is obtained when the purification procedure is performed in beta-d-dodecylmaltoside. if, however, triton x-100 is used to purify the enzyme under otherwise identical conditions, an enzyme is obtained containing only subunits i-ii. the two enzymes are undistinguishable by optical spectroscopy but show significant differences in th ... | 1998 | 9757081 |
| development of pcr primer systems for amplification of nitrite reductase genes (nirk and nirs) to detect denitrifying bacteria in environmental samples. | a system was developed for the detection of denitrifying bacteria by the amplification of specific nitrite reductase gene fragments with pcr. primer sequences were found for the amplification of fragments from both nitrite reductase genes (nirk and nirs) after comparative sequence analysis. whenever amplification was tried with these primers, the known nir type of denitrifying laboratory cultures could be confirmed. likewise, the method allowed a determination of the nir type of five laboratory ... | 1998 | 9758798 |
| conformational changes occurring upon reduction and no binding in nitrite reductase from pseudomonas aeruginosa. | nitrite reductase (nir) from pseudomonas aeruginosa (ec 1.9.3.2) (nir-pa) is a soluble enzyme catalyzing the reduction of nitrite (no2-) to nitric oxide (no). the enzyme is a 120 kda homodimer, in which each monomer carries one c and one d1 heme. the oxidized and reduced forms of nir from paracoccus denitrificans gb17 (previously called thiosphaera pantotropha) (nir-pd) have been described [fülop, v., et al. (1995) cell 81, 369-377; williams, p. a., et al. (1997) nature 389, 406-412], and we rec ... | 1998 | 9760233 |
| the diversity of redox proteins involved in bacterial heterotrophic nitrification and aerobic denitrification. | | 1998 | 9765887 |
| heterotrophic nitrification in paracoccus denitrificans. | | 1998 | 9765927 |
| the periplasmic nitrate reductase of escherichia coli--a comparison with the nap systems of other bacteria. | | 1998 | 9765936 |
| chemical modification of histidine residues in human 'electron transferring flavoprotein' (etf). | | 1998 | 9765991 |
| pressure and temperature dependence of enantioselective excited-state quenching of chiral tb(iii) and eu(iii) tris(pyridine-2,6-dicarboxylate) chelates by various c-type ferricytochromes. | for mitochondrial ferricytochrome c from horse, cow and tuna and for bacterial cytochrome c-550 from paracoccus versutus, the pressure and temperature dependence of their quenching of racemic tb(dpa)3(3-) and eu(dpa)3(3-) (dpa = pyridine-2,6-dicarboxylate) luminescence in aqueous solution is investigated. of these energy transfer reactions the activation volumes (delta v#) and energies (ea) are determined for the ranges p = 0-3 kbar and t = 15-40 degrees c. for the lambda enantiomers of tb(dpa)3 ... | 1998 | 9783431 |
| second-site reversion analysis is not a reliable method to determine distances in membrane proteins: an assessment using mutations in yeast cytochrome c oxidase subunits i and ii. | we have examined deficiency mutations and reversions in subunits i and ii of yeast cytochrome c oxidase in order to test the reliability of second-site reversion analysis in prediction of tertiary structure of a membrane protein complex. it appears that the method can not provide information on distance between residues, since reversions can be up to 30 a from the primary mutations. however, the reversions are not randomly located in the structure but reveal regions essential for assembly or fun ... | 1998 | 9790835 |
| roles of four iron centers in paracoccus halodenitrificans nitric oxide reductase. | reactions of paracoccus halodenitrificans nitric oxide reductase (nor) containing four iron centers, a low spin hemec, a low spin heme b, a high spin heme b and a non-heme iron, have been studied to show the roles of each iron center. soon after reacting the resting (oxidized) nor with l-ascorbate, the low spin heme c and low spin heme b were reduced to a considerable extent but the high spin heme b was still in the oxidized form and was reduced slowly. when co acted on the reduced nor, the high ... | 1998 | 9790940 |
| ft-ir analysis of membranes of rhodobacter sphaeroides 2.4.3 grown under microaerobic and denitrifying conditions. | fourier transform infrared spectroscopic analysis of co binding proteins in rhodobacter sphaeroides reveals the presence of a membrane-bound nitric oxide reductase (nor). nor has been clearly distinguished from the cytochrome oxidases by the temperature-dependence of relaxation following photodissociation of the co complex at cryogenic temperatures. the center frequency and band shape, 1970 cm-1 and 20-30 cm-1 width at half-peak height, are similar to those reported for resonance raman spectra o ... | 1998 | 9838065 |
| molecular genetics of the genus paracoccus: metabolically versatile bacteria with bioenergetic flexibility. | paracoccus denitrificans and its near relative paracoccus versutus (formerly known as thiobacilllus versutus) have been attracting increasing attention because the aerobic respiratory system of p. denitrificans has long been regarded as a model for that of the mitochondrion, with which there are many components (e.g., cytochrome aa3 oxidase) in common. members of the genus exhibit a great range of metabolic flexibility, particularly with respect to processes involving respiration. prominent exam ... | 1998 | 9841665 |
| molecular and functional analysis of ptav320, a repabc-type replicon of the paracoccus versutus composite plasmid ptav1. | the second replicator region of the native plasmid ptav1 of paracoccus versutus has been identified thus proving the composite nature of this replicon. the minimal replicon designated ptav320 (4.3 kb) was cloned and sequenced. ptav320 encodes three putative proteins--repa, repb and repc. this replicator region shows strong structural and functional similarity to repabc-type replicons found in several agrobacterium and rhizobium plasmids. the origin of replication appears to be localized within t ... | 1998 | 9846751 |
| characterization of cytochrome c-556 from the purple phototrophic bacterium rhodobacter capsulatus as a cytochrome-c peroxidase. | a cytochrome c-556 was purified from rhodobacter capsulatus and the complete amino acid sequence was determined. it contains 328 amino acid residues and two typical heme-binding sites at cysteine residues 54 and 57 and at residues 200 and 203. it is homologous to the family of bacterial cytochrome c peroxidases (bccp) with 69% identity to paracoccus denitrificans bccp and 60% identity to pseudomonas aeruginosa bccp for which there is a three-dimensional structure. there is lesser similarity to t ... | 1998 | 9851688 |
| resonance raman spectroscopic study of the caa3 oxidase from thermus thermophilus. | the terminal caa3 oxidase of thermus thermophilus has been studied by resonance raman spectroscopy. using different excitation wavelengths in the soret band region, it was possible to disentangle the resonance raman spectra of the fully oxidized and fully reduced state in terms of the component spectra of the individual hemes a, a3, and c. for the heme a and a3 groups, the spectra reveal only minor differences compared to those of beef heart cytochrome c oxidase attributable to subtle modificati ... | 1998 | 9851718 |
| molecular basis for interprotein complex-dependent effects on the redox properties of amicyanin. | the quinoprotein methylamine dehydrogenase (madh), type i copper protein amicyanin, and cytochrome c-551i form a complex within which interprotein electron transfer occurs. it was known that complex formation significantly lowered the oxidation-reduction midpoint potential (em) value of amicyanin, which facilitated an otherwise thermodynamically unfavorable electron transfer to cytochrome c-551i. structural, mutagenesis, and potentiometric studies have elucidated the basis for this complex-depen ... | 1998 | 9860825 |
| metal chelating properties of adenylate kinase from paracoccus denitrificans. | zinc, a common element of adenylate kinases from gram-positive bacteria, binds to a structural motif consisting of three or four cysteine residues, cys-x2-cys-x16-cys-x2-cys/asp. the enzyme from paracoccus denitrificans, a gram-negative bacterium, has structural features much similar to those of adenylate kinases from gram-positive organisms [spurgin, p., tomasselli, a.g., and schiltz, e. (1989) eur. j. biochem., 179, 621-628]. however, adenylate kinase isolated from this bacterium was not repor ... | 1998 | 9862211 |
| the surface-charge asymmetry and dimerisation of cytochrome c550 from paracoccus denitrificans--implications for the interaction with cytochrome c peroxidase. | the implications of the dimeric state of cytochrome c550 for its binding to paracoccus cytochrome c peroxidase and its delivery of the two electrons required to restore the active enzyme during catalysis have been investigated. the amino acid sequence of cytochrome c550 of paracoccus denitrificans strain lmd 52.44 was determined and showed 21 differences from that of strain lmd 22.21. based on the x-ray structure of the latter, a structure for the cytochrome c550 monomer from strain 52.44 is pro ... | 1998 | 9874223 |
| extended metal environments of cytochrome c oxidase structures. | the metals of the cytochrome c oxidase structures of the bovine heart mitochondrion (pdb code 1occ) and of the soil bacterium paracoccus denitrificans (1arl) include a dicopper center (cua), magnesium, two proximal hemes, a copper (cub) atom, and a calcium. the mitochondrial structure also possesses a bound distant zinc ion. the extended environments of the metal sites are analyzed emphasizing residues of the second shell in terms of polarity, hydrophobicity, secondary structure, solvent accessi ... | 1998 | 9922138 |
| enhanced rate of intramolecular electron transfer in an engineered purple cua azurin. | the recent expression of an azurin mutant where the blue type 1 copper site is replaced by the purple cua site of paracoccus denitrificans cytochrome c oxidase has yielded an optimal system for examining the unique electron mediation properties of the binuclear cua center, because both type 1 and cua centers are placed in the same location in the protein while all other structural elements remain the same. long-range electron transfer is induced between the disulfide radical anion, produced puls ... | 1999 | 9927665 |
| the active site of paracoccus denitrificans aromatic amino acid aminotransferase has contrary properties: flexibility and rigidity. | paracoccus denitrificans aromatic amino acid aminotransferase (ec 2. 6.1.57; pdaroat) binds with a series of aliphatic monocarboxylates attached to the bulky hydrophobic groups. to analyze the properties of the active site in this enzyme, we determined the tertiary structures of pdaroat complexed with nine different inhibitors. comparison of these active site structures showed that the active site of pdaroat consists of two parts with contrary properties: rigidity and flexibility. the regions th ... | 1999 | 9930977 |
| electrochemical and ultraviolet/visible/infrared spectroscopic analysis of heme a and a3 redox reactions in the cytochrome c oxidase from paracoccus denitrificans: separation of heme a and a3 contributions and assignment of vibrational modes. | cytochrome c oxidase from paracoccus denitrificans was studied with a combined electrochemical and ultraviolet/visible/infrared (uv/vis/ir) spectroscopic approach. global fit analysis of oxidative electrochemical redox titrations was used to separate the spectral contributions coupled to heme a and a3 redox transitions, respectively. simultaneous adjustment of the midpoint potentials and of the amplitudes for a user-defined number of redox components (here heme a and a3) at all wavelengths in th ... | 1999 | 10026246 |
| crystal structure of paracoccus denitrificans electron transfer flavoprotein: structural and electrostatic analysis of a conserved flavin binding domain. | the crystal structure of electron transfer flavoprotein (etf) from paracoccus denitrificans was determined and refined to an r-factor of 19.3% at 2.6 a resolution. the overall fold is identical to that of the human enzyme, with the exception of a single loop region. like the human structure, the structure of the p. denitrificans etf is comprised of three distinct domains, two contributed by the alpha-subunit and the third from the beta-subunit. close analysis of the structure reveals that the lo ... | 1999 | 10026281 |
| ion selectivity reversal and induction of voltage-gating by site-directed mutations in the paracoccus denitrificans porin. | the porin from paracoccus denitrificans, a slightly anion specific outer membrane pore protein, was expressed in escherichia coli, isolated from inclusion bodies, and refolded in the presence of urea and detergents. the purified recombinant protein was reconstituted into black lipid bilayer membranes and showed no difference in its functional properties in comparison to the native porin isolated from p.denitrificans membranes. to investigate the molecular basis of its ion selectivity and voltage ... | 1999 | 10026305 |
| paracoccus carotinifaciens sp. nov., a new aerobic gram-negative astaxanthin-producing bacterium. | the strain e-396t, isolated from soil, was gram-negative, aerobic, orange-pigmented, rod-shaped, motile by peritrichous flagella and astaxanthin-producing. this organism produced carotenoids, mainly astaxanthin, and did not produce bacteriochlorophyll. the ubiquinone system was q-10. analysis of the 16s rrna sequence of strain e-396t showed it to be a member of the alpha-3 subclass of the proteobacteria, forming a cluster with the species of the genus paracoccus. on the basis of the production o ... | 1999 | 10028273 |
| steady-state nitrogen isotope effects of n2 and n2o production in paracoccus denitrificans. | nitrogen stable-isotope compositions (delta15n) can help track denitrification and n2o production in the environment, as can knowledge of the isotopic discrimination, or isotope effect, inherent to denitrification. however, the isotope effects associated with denitrification as a function of dissolved-oxygen concentration and their influence on the isotopic composition of n2o are not known. we developed a simple steady-state reactor to allow the measurement of denitrification isotope effects in ... | 1999 | 10049852 |
| the greek key protein apo-pseudoazurin folds through an obligate on-pathway intermediate. | folding of the 123 amino acid residue greek key protein apo-pseudo azurin from thiosphaera pantotropha has been examined using stopped-flow circular dichroism in 0.5 m na2so4 at ph 7.0 and 15 degrees c. the data show that the protein folds from the unfolded state with all eight proline residues in their native isomers (seven trans and one cis) to an intermediate within the dead-time of the stopped-flow mixing (50 ms). the urea dependence of the rates of folding and unfolding of the protein were ... | 1999 | 10064719 |
| tyrosine aminotransferase catalyzes the final step of methionine recycling in klebsiella pneumoniae. | an aminotransferase which catalyzes the final step in methionine recycling from methylthioadenosine, the conversion of alpha-ketomethiobutyrate to methionine, has been purified from klebsiella pneumoniae and characterized. the enzyme was found to be a homodimer of 45-kda subunits, and it catalyzed methionine formation primarily using aromatic amino acids and glutamate as the amino donors. histidine, leucine, asparagine, and arginine were also functional amino donors but to a lesser extent. the n ... | 1999 | 10074065 |
| evaluation of relative contributions of two enzymes supposed to metabolise hydrogen peroxide in paracoccus denitrificans. | a biosensor exploiting an electrochemically mediated enzyme-catalysed reaction was used to quantify relative contributions of cytoplasmic catalase and periplasmic cytochrome c peroxidase to the overall rate of hydrogen peroxide breakdown in cells of paracoccus denitrificans. the effects of antimycin (an inhibitor of electron flow to cytochrome c peroxidase), the reaction rate versus substrate concentration profiles for the whole cells and subcellular fractions, and the time courses of oxygen con ... | 1999 | 10076016 |
| cytochrome c' from paracoccus denitrificans: spectroscopic studies consistent with a role for the protein in nitric oxide metabolism. | cytochrome c' was purified from the denitrifying bacterium paracoccus denitrificans and the interaction of the protein with nitric oxide was examined spectroscopically. two distinct types of haem-nitrosyl electronic absorption spectrum were observed, which were dependent upon [no]. when cytochrome c' was saturated with no, alpha and beta bands were centred at 562 nm and 530 nm, whereas with sub-saturating concentrations of no the alpha and beta bands were red-shifted to 578 nm and 542 nm respect ... | 1999 | 10082934 |
| methylamine dehydrogenase: structure and function of electron transfer complexes. | | 1999 | 10093734 |
| nadh-quinone oxidoreductase: psst subunit couples electron transfer from iron-sulfur cluster n2 to quinone. | the proton-translocating nadh-quinone oxidoreductase (ec 1.6.99.3) is the largest and least understood enzyme complex of the respiratory chain. the mammalian mitochondrial enzyme (also called complex i) contains more than 40 subunits, whereas its structurally simpler bacterial counterpart (ndh-1) in paracoccus denitrificans and thermus thermophilus hb-8 consists of 14 subunits. a major unsolved question is the location and mechanism of the terminal electron transfer step from iron-sulfur cluster ... | 1999 | 10097178 |
| gene dosage effects on polyhydroxyalkanoates synthesis from n-alcohols in paracoccus denitrificans. | putative promoters of polyhydroxyalkanoate (pha)-synthetic genes of paracoccus denitrificans were identified. gene dosage effects for pha synthesis were investigated in recombinants of p. denitrificans with increased expression levels of each pha synthetic enzyme. in the cultivation of shake flasks using ethanol or n-pentanol as carbon source, a self-cloning recombinant of the phac-encoding pha synthase showed the highest contents [(g pha). (g total biomass)-1] and the highest rates of pha accum ... | 1998 | 10099406 |
| pcr detection of genes encoding nitrite reductase in denitrifying bacteria. | using consensus regions in gene sequences encoding the two forms of nitrite reductase (nir), a key enzyme in the denitrification pathway, we designed two sets of pcr primers to amplify cd1- and cu-nir. the primers were evaluated by screening defined denitrifying strains, denitrifying isolates from wastewater treatment plants, and extracts from activated sludge. sequence relationships of nir genes were also established. the cd1 primers were designed to amplify a 778 to 799-bp region of cd1-nir in ... | 1999 | 10103263 |
| the structure of an electron transfer complex containing a cytochrome c and a peroxidase. | efficient biological electron transfer may require a fluid association of redox partners. two noncrystallographic methods (a new molecular docking program and 1h nmr spectroscopy) have been used to study the electron transfer complex formed between the cytochrome c peroxidase (ccp) of paracoccus denitrificans and cytochromes c. for the natural redox partner, cytochrome c550, the results are consistent with a complex in which the heme of a single cytochrome lies above the exposed electron-transfe ... | 1999 | 10196231 |
| the reduction state of the q-pool regulates the electron flux through the branched respiratory network of paracoccus denitrificans. | in this work we demonstrate how the reduction state of the q-pool determines the distribution of electron flow over the two quinol-oxidising branches in paracoccus denitrificans: one to quinol oxidase, the other via the cytochrome bc1 complex to the cytochrome c oxidases. the dependence of the electron-flow rate to oxygen on the fraction of quinol in the q-pool was determined in membrane fractions and in intact cells of the wild-type strain, a bc1-negative mutant and a quinol oxidase-negative mu ... | 1999 | 10215894 |
| heterologous expression of soluble fragments of cytochrome c552 acting as electron donor to the paracoccus denitrificans cytochrome c oxidase. | a membrane-bound c-type cytochrome, c552, acts as the electron mediator between the cytochrome bc1 complex and cytochrome c oxidase in the branched respiratory chain of the bacterium paracoccus denitrificans. unlike in mitochondria where a soluble cytochrome c interacts with both complexes, the bacterial c552, the product of the cycm gene, shows a tripartite structure, with an n-terminal membrane anchor separated from a typical class i cytochrome domain by a highly charged region. two derivative ... | 1999 | 10216157 |
| pseudoazurin mediates periplasmic electron flow in a mutant strain of paracoccus denitrificans lacking cytochrome c550. | a periplasmic protein able to transfer electrons from cytoplasmic membrane to the periplasmic nitrite reductase (cytochrome cd1) has been purified from the anoxically grown cytochrome c550 mutant strain pd2121 and shown to be pseudoazurin by several independent criteria (molecular mass, copper content, visible spectrum, n-terminal amino acid sequence). under our assay conditions, the half-saturation of electron transport occurred at about 10 microm pseudoazurin; the reaction was retarded by incr ... | 1999 | 10217431 |
| determination of the paracoccus denitrificans sos box. | by gel retardation experiments with crude cell extracts of paracoccus denitrificans it was demonstrated that a protein specifically binds to the promoter of the p. denitrificans reca gene. pcr mutagenesis of the reca promoter showed that the gaacn7gaac motif is required for the formation of the dna-protein complex. this protein also binds to the gttcn7gttc motif, which is present in the promoter of the p. denitrificans uvra gene. mutational analysis of the promoter regions of both p. denitrifica ... | 1999 | 10217491 |
| analyses of a polyhydroxyalkanoic acid granule-associated 16-kilodalton protein and its putative regulator in the pha locus of paracoccus denitrificans. | the polyhydroxyalkanoic acid (pha) granule-associated 16-kda protein (ga16 protein) of paracoccus denitrificans was identified, and its corresponding gene was cloned and analyzed at the molecular level. the n-terminal amino acid sequence of ga16 protein revealed that its structural gene is located downstream from the pha synthase gene (phacpd) cloned recently (s. ueda, t. yabutani, a. maehara, and t. yamane, j. bacteriol. 178:774-779, 1996). gene walking around phacpd revealed two new open readi ... | 1999 | 10217786 |
| a re-evaluation of the taxonomy of paracoccus denitrificans and a proposal for the combination paracoccus pantotrophus comb. nov. | comparison of both 16s rrna coding sequences and dna-dna hybridization of ten strains of alpha-subclass of proteobacteria currently classified as strains of paracoccus denitrificans has shown that they fall into two groups which are distinct from each other at the species level. comparison with published data on the cytochrome c profiles and other 16s rrna coding sequences in the literature has confirmed these observations and enabled several other strains also to be assigned to these two groups ... | 1999 | 10319488 |
| isolated transmembrane helices arranged across a membrane: computational studies. | a computational procedure for predicting the arrangement of an isolated helical fragment across a membrane was developed. the procedure places the transmembrane helical segment into a model triple-phase system 'water-octanol-water'; pulls the segment through the membrane, varying its 'global' position as a rigid body; optimizes the intrahelical and solvation energies in each global position by 'local' coordinates (dihedral angles of side chains); and selects the lowest energy global position for ... | 1999 | 10325400 |
| does the reduction of c heme trigger the conformational change of crystalline nitrite reductase? | the structures of nitrite reductase from paracoccus denitrificans gb17 (nir-pd) and pseudomonas aeruginosa (nir-pa) have been described for the oxidized and reduced state (fülöp, v., moir, j. w. b., ferguson, s. j., and hajdu, j. (1995) cell 81, 369-377; nurizzo, d., silvestrini, m. c., mathieu, m., cutruzzolà, f., bourgeois, d., fülöp, v., hajdu, j., brunori, m., tegoni, m., and cambillau, c. (1997) structure 5, 1157-1171; nurizzo, d., cutruzzolà, f., arese, m., bourgeois, d., brunori, m., camb ... | 1999 | 10329702 |
| glyceraldehyde-3-phosphate dehydrogenase gene diversity in eubacteria and eukaryotes: evidence for intra- and inter-kingdom gene transfer. | cyanobacteria contain up to three highly divergent glyceraldehyde-3-phosphate dehydrogenase (gapdh) genes: gap1, gap2, and gap3. genes gap1 and gap2 are closely related at the sequence level to the nuclear genes encoding cytosolic and chloroplast gapdh of higher plants and have recently been shown to play distinct key roles in catabolic and anabolic carbon flow, respectively, of the unicellular cyanobacterium synechocystis sp. pcc6803. in the present study, sequences of 10 gapdh genes distribute ... | 1999 | 10331270 |
| evidence for a copper-coordinated histidine-tyrosine cross-link in the active site of cytochrome oxidase. | following hints from x-ray data (ostermeier c et al., 1997, proc natl acad sci usa 94:10547-10553; yoshikawa s et al., 1998, science 280: 1723-1729), chemical evidence is presented from four distantly related cytochrome-c oxidases for the existence of a copperb-coordinated his240-tyr244) cross-link at the o2-activating heme fea3-cub center in the catalytic subunit 1 of the enzyme. the early evolutionary invention of this unusual structure may have prevented damaging *oh-radical release at e(-)-t ... | 1999 | 10338009 |
| biochemical and electrochemical characterization of quinohemoprotein amine dehydrogenase from paracoccus denitrificans. | a new quinohemoprotein amine dehydrogenase from paracoccus denitrificans ifo 12442 was isolated and characterized in views of biochemistry and electrochemistry. this enzyme exists in periplasm and catalyzes the oxidative deamination of primary aliphatic and aromatic amines. n-butylamine or benzylamine as a carbon and energy source strongly induces the expression of the enzyme. carbonyl reagents inhibit the enzyme activity irreversibly. this enzyme is a heterodimer constituted of alpha and beta s ... | 1999 | 10346915 |
| time-resolved ft-ir studies on the co adduct of paracoccus denitrificans cytochrome c oxidase: comparison of the fully reduced and the mixed valence form. | the rebinding of co to cytochrome c oxidase from paracoccus denitrificans in the fully reduced and in the half-reduced (mixed valence) form as a function of temperature was investigated using time-resolved rapid-scan ft-ir spectroscopy in the mid-ir (1200-2100 cm-1). for the fully reduced enzyme, rebinding was complete in approximately 2 s at 268 k and showed a biphasic reaction. at 84 k, nonreversible transfer of co from heme a3 to cub was observed. both photolysis at 84 k and photolysis at 268 ... | 1999 | 10360954 |
| anaerobic oxidations of cysteate: degradation via l-cysteate:2-oxoglutarate aminotransferase in paracoccus pantotrophus. | anoxic, fresh-water enrichment cultures to oxidize different organosulfonates were set up with nitrate, ferric iron or sulfate as electron acceptors. pure cultures were easily obtained with two naturally occurring sulfonates, cysteate (2-amino-3-sulfopropionate) and taurine (2-aminoethanesulfonate), under nitrate-reducing conditions. these two sulfonates were also oxidized during reduction of iron(iii), though isolation of pure cultures was not successful. one nitrate-reducing cysteate-oxidizing ... | 1999 | 10376831 |
| nitric oxide is a signal for nnr-mediated transcription activation in paracoccus denitrificans. | by using the 'lacz gene, the activities of the niri, nirs, and norc promoters were assayed in the wild type and in nnr-deficient mutants of paracoccus denitrificans grown under various growth conditions. in addition, induction profiles of the three promoters in response to the presence of various nitrogenous oxides were determined. transcription from the three promoters required the absence of oxygen and the presence both of the transcriptional activator nnr and of nitric oxide. the activity of ... | 1999 | 10383987 |
| expression of plastocyanin and cytochrome f of the cyanobacterium phormidium laminosum in escherichia coli and paracoccus denitrificans and the role of leader peptides. | the gene for plastocyanin from the cyanobacterium phormidium laminosum was successfully expressed in escherichia coli. expression of the gene for cytochrome f resulted in the production of holocytochrome f in the periplasmic space of e. coli, but the yield was low. expression in paracoccus denitrificans yielded no holoprotein. when the region encoding the cytochrome f leader sequence was replaced with more typical bacterial leader sequences (those from the p. laminosum plastocyanin gene and the ... | 1999 | 10395900 |