Publications

expression of prokaryotic and eukaryotic cytochromes c in escherichia coli.	c-type cytochromes from various sources show substantial structural conservation. for the covalent attachment of heme groups to apocytochromes, however, three different enzyme systems have been described so far. we have examined the ability of the heme ligation systems of escherichia coli and of saccharomyces cerevisiae to process cytochromes from s. cerevisiae, paracoccus denitrificans, and synechocystis sp. pcc 6803. e. coli's maturation system with at least eight different proteins accepted a ...	2000	10924906
novel genes coding for lithotrophic sulfur oxidation of paracoccus pantotrophus gb17.	the gene region coding for lithotrophic sulfur oxidation of paracoccus pantotrophus gb17 is located on a 13-kb insert of plasmid peg12. upstream of the previously described six open reading frames (orfs) soxabcdef with a partial sequence of soxa and soxf (c. wodara, f. bardischewsky, and c. g. friedrich, j. bacteriol. 179:5014-5023, 1997), 4,350 bp were sequenced. the sequence completed soxa, and uncovered six new orfs upstream of soxa, designated orf1, orf2, and orf3, and soxxyz. orf1 could enc ...	2000	10940005
purification, crystallization and preliminary crystallographic studies of an integral membrane protein, cytochrome bo3 ubiquinol oxidase from escherichia coli.	cytochrome bo(3) ubiquinol oxidase has been successfully purified for crystallization. single crystals of this integral membrane protein diffract x-rays to 3.5 a resolution and belong to the orthorhombic space group c222(1). from the diffraction data, the unit-cell parameters were determined to be a = 91.3, b = 370.3, c = 232.4 a. the crystals have a solvent content of 59% and contain two molecules per asymmetric unit. a search model generated from the structures of cytochrome c oxidase from par ...	2000	10944359
the nosx and nirx proteins of paracoccus denitrificans are functional homologues: their role in maturation of nitrous oxide reductase.	the nos (nitrous oxide reductase) operon of paracoccus denitrificans contains a nosx gene homologous to those found in the nos operons of other denitrifiers. nosx is also homologous to nirx, which is so far unique to p. denitrificans. single mutations of these genes did not result in any apparent phenotype, but a double nosx nirx mutant was unable to reduce nitrous oxide. promoter-lacz assays and immunoblotting against nitrous oxide reductase showed that the defect was not due to failure of expr ...	2000	10960107
heme o is present in paracoccus denitrificans cells and accumulates under anoxic growth.	in spite of the published claims to the contrary, paracoccus denitrificans was shown to contain a heme derivative, virtually indistinguishable from the escherichia coli heme o on the basis of the reverse-phase high-performance liquid chromatography and maldi-tof mass spectrometry analyses. aeration of the anoxically grown culture resulted in the disappearance of a significant portion of this compound with concomitant build-up of heme a.	2000	10981691
characteristics of the aerobic respiratory chains of the microaerophiles campylobacter jejuni and helicobacter pylori.	the respiratory chain enzymes of microaerophilic bacteria should play a major role in their adaptation to growth at low oxygen tensions. the genes encoding the putative nadh:quinone reductases (ndh-1), the ubiquinol:cytochrome c oxidoreductases (bc1 complex) and the terminal oxidases of the microaerophiles campylobacter jejuni and helicobacter pylori were analysed to identify structural elements that may be required for their unique energy metabolism. the gene clusters encoding ndh-1 in both c. ...	2000	10985736
conversion of methylamine dehydrogenase to a long-chain amine dehydrogenase by mutagenesis of a single residue.	methylamine dehydrogenase (madh) is a tryptophan tryptophylquinone (ttq) dependent enzyme that catalyzes the oxidative deamination of primary amines. amino acid residues of both the ttq-bearing beta subunit and the noncatalytic alpha subunit line a substrate channel that leads from the protein surface to the enzyme active site. phe55 of the alpha subunit is located at the opening of the active site. conversion of alphaphe55 to alanine dramatically alters the substrate preference of madh. the k(m ...	2000	10985763
presence of bacterial 16s ribosomal rna gene segments in human intestinal lymph follicles.	there is currently no information regarding microbial agents inside the intestinal lymph follicles.	2000	10994621
quantum mechanical interpretation of nitrite reduction by cytochrome cd1 nitrite reductase from paracoccus pantotrophus.	the reduction of nitrite to nitric oxide in respiratory denitrification is catalyzed by a cytochrome cd(1) nitrite reductase in paracoccus pantotrophus (formerly known as thiosphaera pantotropha lmd 92.63). high-resolution structures are available for the fully oxidized [fülöp, v., moir, j. w., ferguson, s. j., and hajdu, j. (1995) cell 81, 369-377; baker, s. c., saunders, n. f., willis, a. c., ferguson, s. j., hajdu, j., and fülöp, v. (1997) j. mol. biol. 269, 440-455] and fully reduced forms o ...	2000	10998232
proton-coupled structural changes upon binding of carbon monoxide to cytochrome cd1: a combined flash photolysis and x-ray crystallography study.	we have investigated dynamic events after flash photolysis of co from reduced cytochrome cd(1) nitrite reductase (nir) from paracoccus pantotrophus (formerly thiosphaera pantotropha). upon pulsed illumination of the cytochrome cd(1)-co complex, at 460 nm, a rapid (<50 ns) absorbance change, attributed to dissociation of co, was observed. this was followed by a biphasic rearrangement with rate constants of 1.7 x 10(4) and 2.5 x 10(3) s(-1) at ph 8.0. both parts of the biphasic rearrangement phase ...	2000	10998233
the role of the d- and k-pathways of proton transfer in the function of the haem-copper oxidases.	the x-ray structures of several haem-copper oxidases now at hand have given important constraints on how these enzymes function. yet, dynamic data are required to elucidate the mechanisms of electron and proton transfer, the activation of o(2) and its reduction to water, as well as the still enigmatic mechanism by which these enzymes couple the redox reaction to proton translocation. here, some recent observations will be briefly reviewed with special emphasis on the functioning of the so-called ...	2000	11004470
structural changes in cytochrome c oxidase induced by cytochrome c binding. a resonance raman study.	electrostatically stabilized complexes of fully oxidized cytochrome c oxidase from paracoccus denitrificans and horse heart cytochrome c were studied by resonance raman spectroscopy. the experiments were carried out with the wild-type oxidase and a variant in which a negatively charged amino acid in the binding domain (d257) is replaced by an asparagine. it is shown that cytochrome c induces structural changes at heme a and heme a(3) which are reminiscent to those found in mammalian cytochrome c ...	2000	11004555
a switch in heme axial ligation prepares paracoccus pantotrophus cytochrome cd1 for catalysis.	cytochrome cd1 nitrite reductase (cd1) from paracoccus pantotrophus is a respiratory enzyme capable of using nitrite, hydroxylamine and oxygen as electron accepting substrates. structural studies have shown that when the enzyme is reduced there is a change in the axial ligation of both hemes, which has been proposed to form part of the catalytic cycle. here we report the use of a physiological electron donor, pseudoazurin, to investigate the relationship between heme ligation and catalysis. a co ...	2000	11017198
the nitric oxide regulated nor promoter of paracoccus denitrificans.	the promoter of the paracoccus denitrificans nitric oxide reductase operon (norcbqdef) has been characterized by primer extension and deletion analysis. a major transcript that is detectable only in anaerobically grown cells initiates 43.5 bp downstream of the centre of a putative binding site for the transcription factor nnr (nitrite and nitric oxide reductase regulator, which is known to regulate nor expression). a minor transcript initiates 121 bp upstream of the major transcript and is detec ...	2000	11021938
revisiting the catalytic cuz cluster of nitrous oxide (n2o) reductase. evidence of a bridging inorganic sulfur.	nitrous-oxide reductases (n2or) catalyze the two-electron reduction of n(2)o to n(2). the crystal structure of n2ors from pseudomonas nautica (pn) and paracoccus denitrificans (pd) were solved at resolutions of 2.4 and 1.6 a, respectively. the pn n2or structure revealed that the catalytic cuz center belongs to a new type of metal cluster in which four copper ions are liganded by seven histidine residues. a bridging oxygen moiety and two other hydroxide ligands were proposed to complete the ligat ...	2000	11024061
proposal for the reclassification of thiobacillus novellus as starkeya novella gen. nov., comb. nov., in the alpha-subclass of the proteobacteria.	thiobacillus novellus is a facultatively chemolithoautotrophic and methylotrophic, gram-negative, rod-shaped sulfur bacterium, shown by 16s rrna gene sequence analysis to be a member of the alpha-2 subclass of the proteobacteria. as such, it must be excluded from the genus thiobacillus, whose species are members of the beta-proteobacteria. it closest phylogenetic neighbour appears to be ancylobacter, from which it is distinct morphologically and in some physiological characteristics. it is disti ...	2000	11034489
[a novel plant-associated thermotolerant alkalophilic methylotroph of the genus paracoccus].	strain gb isolated from the maize rhizosphere is a gram-negative, aerobic, non-spore-forming, nonpigmented, nonmotile, chemolithotrophic, facultatively methylotrophic bacterium. cells are cocci or short rods. the strain does not require vitamins. optimum growth in a medium with methanol occurs at 38-42 degrees c at ph 8.0-9.2. the doubling time is 12 h. in addition to methanol, the bacterium can grow on methylamine, dimethylformamide, acetone, thiosulfate + nahco3, and in an atmosphere of h2 + c ...	2000	11315675
interaction between the formyl group of heme a and arginine 54 in cytochrome aa(3) from paracoccus denitrificans.	the optical spectrum of heme a is red-shifted in aa(3)-type cytochrome c oxidases compared to isolated low-spin heme a model compounds. early spectroscopic studies indicated that this may be due to hydrogen-bonding of the formyl group of heme a to an amino acid in the close vicinity. here we show that most of the optical spectral shift of native heme a is due to a hydrogen-bonding interaction between the formyl group and arginine-54 in subunit i of cytochrome aa(3) from paracoccus denitrificans, ...	2000	10611451
nitrogen removal reactor using packed gel envelopes containing nitrosomonas europaea and paracoccus denitrificans.	packed gel envelopes were constructed as simple, compact reactors for removing nitrogen from wastewater. each packed gel envelope consisted of two plate gels with a spacer in between. nitrosomonas europaea and paracoccus denitrificans were co-immobilized in the plate gels, and ethanol, serving as an electron donor for denitrification, was injected into the internal spaces of the envelopes. the external surfaces of the envelopes were in contact with ammonia-containing wastewater; the n. europaea ...	2000	10581438
a novel conformer of oxidized paracoccus pantotrophus cytochrome cd(1) observed by freeze-quench nir-mcd spectroscopy.	paracoccus pantotrophus cytochrome cd(1) is a physiological nitrite reductase and an in vitro hydroxylamine reductase. the oxidised "as isolated" form of the enzyme has bis-histidinyl coordinated c-heme and upon reduction its coordination changes to histidine/methionine. following treatment of reduced enzyme with hydroxylamine, a novel, oxidised, conformer of the enzyme is obtained. we have devised protocols for freeze-quench near-ir-mcd spectroscopy that have allowed us to establish unequivocal ...	2000	11118344
taxonomy of the genus paracoccus.		2000	11293651
plasmid occurrence and diversity in the genus paracoccus.	the results of screening for the occurrence of plasmids in several strains representing 11 out of 13 species of the genus paracoccus are presented. we show that plasmids (ranging in size from 2.7 to above 450 kb) are widely distributed in this genus. only one tested strain (p. alkenifer) appears to be plasmid-free. the majority of the strains harbour at least two plasmids, one of which usually fits into the class of megaplasmids.	2000	11293660
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
transcriptional regulation of nir and nor operons of paracoccus denitrificans.	transcripts of nitrite reductase (nir) and nitric oxide reductase (nor) operons of paracoccus denitrificans were expressed only under anaerobic conditions in the presence of potassium nitrite. the nir and nor operons produced at least two transcription products. large transcripts seemed to contain whole operons and small ones seemed to contain the genes encoding denitrifying enzymes. all transcription start sites were detected 41.5 or 42.5 bp downstream from the center of fnr boxes.	2000	16232764
development of chitosan-magnetite aggregates containing nitrosomonas europaea cells for nitrification enhancement.	a cell suspension of the nitrifying bacterium nitrosomonas europaea obtained after 96-h cultivation was subjected to magnetic separation using chitosan-conjugated magnetite particles (chitosan-magnetite), which have the ability to form aggregates with microbial cells. an equilibrium condition was obtained at room temperature after 30 min and over 90% of the cells were recovered when the chitosan-magnetite concentration was 200 mg/l. the relationship between the cell concentration in the supernat ...	2000	16232771
effect of oxygen concentration on nitrogen removal by nitrosomonas europaea and paracoccus denitrificans immobilized within tubular polymeric gel.	tubular gel reactors containing nitrosomonas europaea and paracoccus denitrificans, which remove nitrogen from solutions through a process of nitrification and denitrification, require oxygen for ammonia oxidation, the first and rate-limiting step in the process. to accelerate ammonia oxidation, high concentrations of oxygen were applied to the reactors instead of air. although a 50% o2:n2 gas mixture and pure oxygen were both toxic to free n. europaea cells, they actually accelerated ammonia ox ...	2000	16232927
asymmetric reduction of ethyl acetoacetate to ethyl (r)-3-hydroxybutyrate coupled with nitrate reduction by paracoccus denitrificans.	we found that the asymmetric reduction of ethyl acetoacetate (eaa) to ethyl (r)-3-hydroxybutyrate (ehb) by paracoccus denitrificans could be induced by nitrate addition under anaerobic conditions. however, the addition of electron donors such as glucose, ethanol, and methanol together with nitrate did not stimulate ehb production from eaa. when the reaction was carried out under optimum conditions (cell concentration, 10 g-d.w.l(-1); eaa, 150 mm; no3-, 100 mm), after 8 h of reaction 49 mm of ehb ...	2001	16233006
regulation of expression of terminal oxidases in paracoccus denitrificans.	in order to study the induction of terminal oxidases in paracoccus denitrificans, their promoters were fused to the lacz reporter gene and analysed in the wild-type strain, in an fnrp-negative mutant, in a cytochrome bc1-negative mutant, and in six single or double oxidase-negative mutant strains. the strains were grown under aerobic, semi-aerobic, and denitrifying conditions. the oxygen-sensing transcriptional-regulatory protein fnrp negatively regulated the activity of the qox promoter, which ...	2001	11298768
phylogeny and distribution of the soxb gene among thiosulfate-oxidizing bacteria.	a pcr protocol for the detection of sulfur-oxidizing bacteria based on soxb genes that are essential for thiosulfate oxidation by sulfur-oxidizing bacteria of various phylogenetic groups which use the 'paracoccus sulfur oxidation' pathway was developed. five degenerate primers were used to specifically amplify fragments of soxb genes from different sulfur-oxidizing bacteria previously shown to oxidize thiosulfate. the pcr yielded a soxb fragment of approximately 1000 bp from most of the bacteria ...	2001	11313131
two-component system that regulates methanol and formaldehyde oxidation in paracoccus denitrificans.	a chromosomal region encoding a two-component regulatory system, flhrs, has been isolated from paracoccus denitrificans. flhrs-deficient mutants were unable to grow on methanol, methylamine, or choline as the carbon and energy source. expression of the gene encoding glutathione-dependent formaldehyde dehydrogenase (fhla) was undetectable in the mutant, and expression of the s-formylglutathione hydrolase gene (fgha) was reduced in the mutant background. in addition, methanol dehydrogenase was imm ...	2001	11133961
gene cluster of rhodothermus marinus high-potential iron-sulfur protein: oxygen oxidoreductase, a caa(3)-type oxidase belonging to the superfamily of heme-copper oxidases.	the respiratory chain of the thermohalophilic bacterium rhodothermus marinus contains an oxygen reductase, which uses hipip (high potential iron-sulfur protein) as an electron donor. the structural genes encoding the four subunits of this hipip:oxygen oxidoreductase were cloned and sequenced. the genes for subunits ii, i, iii, and iv (named rcoxa to rcoxd) are found in this order and seemed to be organized in an operon of at least five genes with a terminator structure a few nucleotides downstre ...	2001	11133964
cytochromes c(550), c(552), and c(1) in the electron transport network of paracoccus denitrificans: redundant or subtly different in function?	paracoccus denitrificans strains with mutations in the genes encoding the cytochrome c(550), c(552), or c(1) and in combinations of these genes were constructed, and their growth characteristics were determined. each mutant was able to grow heterotrophically with succinate as the carbon and free-energy source, although their specific growth rates and maximum cell numbers fell variably behind those of the wild type. maximum cell numbers and rates of growth were also reduced when these strains wer ...	2001	11717258
structure of a quinohemoprotein amine dehydrogenase with an uncommon redox cofactor and highly unusual crosslinking.	the crystal structure of the heterotrimeric quinohemoprotein amine dehydrogenase from paracoccus denitrificans has been determined at 2.05-a resolution. within an 82-residue subunit is contained an unusual redox cofactor, cysteine tryptophylquinone (ctq), consisting of an orthoquinone-modified tryptophan side chain covalently linked to a nearby cysteine side chain. the subunit is surrounded on three sides by a 489-residue, four-domain subunit that includes a diheme cytochrome c. both subunits si ...	2001	11717396
direct interaction between a membrane domain subunit and a connector subunit in the h(+)-translocating nadh-quinone oxidoreductase.	when paracoccus denitrificans membranes were treated with a crosslinker, m-maleimidobenzoyl-n-hydroxysuccinimide ester (mbs), a cross-linked product of m(r) approximately 31 kda was found which reacted with antibodies against the hydrophobic subunit nqo7 and the connector subunit nqo6. nai treatment of the paracoccus membranes before, but not after, the crosslinking step prevented the formation of the 31 kda band. when nqo7 and nqo6 were coexpressed in escherichia coli, both subunits were locate ...	2001	11728457
carboxyl residues in the iron-sulfur protein are involved in the proton pumping activity of p. denitrificans bc(1) complex.	a study is presented on chemical modification of the three subunit paracoccus denitrificans bc(1) complex. n-(ethoxycarbonyl)-2-ethoxy-1,2-dihydroquinoline (eedq) treatment caused a loss of the proton pumping activity of liposome-reconstituted bc(1) complex. a similar effect, which is referred to as the decoupling effect, resulted upon reaction of n,n'-dicyclohexylcarbodiimide (dccd) with the complex. direct measurement of the binding of eedq to the complex subunits, performed in the presence of ...	2001	11735423
effect of temperature on biofiltration of nitric oxide.		2001	11963849
electron and proton transfer in the arginine-54-methionine mutant of cytochrome c oxidase from paracoccus denitrificans.	arginine 54 in subunit i of cytochrome c oxidase from paracoccus denitrificans interacts with the formyl group of heme a. mutation of this arginine to methionine (r54m) dramatically changes the spectral properties of heme a and lowers its midpoint redox potential [kannt et al. (1999) j. biol. chem. 274, 37974-37981; lee et al. (2000) biochemistry 39, 2989-2996; riistama et al. (2000) biochim. biophys. acta 1456, 1-4]. during anaerobic reduction of the mutant enzyme, a small fraction of heme a is ...	2001	11318650
on the routine use of soft x-rays in macromolecular crystallography.	a diffraction data set has been collected from a blood coagulation factor xiii-ca(2+) complex crystal at the x-ray diffraction beamline of the elettra synchrotron (trieste, italy) at a wavelength of 2.6 a. the data collection could be carried out using the beamline as is, without making any time-consuming changes to the apparatus. various data-processing schemes have been employed and it has been observed that local or detector scaling procedures are essential for producing the 'best' anomalous ...	2001	11320309
c-terminal truncation and histidine-tagging of cytochrome c oxidase subunit ii reveals the native processing site, shows involvement of the c-terminus in cytochrome c binding, and improves the assay for proton pumping.	to enable metal affinity purification of cytochrome c oxidase reconstituted into phospholipid vesicles, a histidine-tag was engineered onto the c-terminal end of the rhodobacter sphaeroides cytochrome c oxidase subunit ii. characterization of the natively processed wildtype oxidase and artificially processed forms (truncated with and without a his-tag) reveals km values for cytochrome c that are 6-14-fold higher for the truncated and his-tagged forms than for the wildtype. this lowered ability t ...	2001	11327819
nitrification and denitrification as a source for no and no2 production in high-strength wastewater.	laboratory and half-technical scale experiments were performed to evaluate nitric oxide (no) and nitrogen dioxide (no2) production during biological n-elimination from wastewater with high ammonium concentration (about 700 mg n l-1). in a laboratory scale bioreactor with biomass retention, the ammonia oxidizer nitrosomonas europaea and the denitrifier paracoccus denitrificans were grown as reference organisms in co-culture in order to simulate the nitrifying and denitrifying community of wastewa ...	2001	11337836
[phylogenetic analysis of aerobic methylotrophic bacteria, using dichloromethane].	the phylogenetic relationships of 12 aerobic dichloromethane-degrading bacteria that implement different c1-assimilation pathways was determined based on 16s ribosomal rna sequences and dna-dna hybridization data. the restricted facultative methylotroph "methylophilus leisingerii" dm11 with the ribulose monophosphate pathway was found to belong to the genus methylophilus cluster of the beta subdivision of the phylogenetic kingdom proteobacteria. the facultative methylotroph methylorhabdus multiv ...	2001	11338843
structure of cytochrome c oxidase: a comparison of the bacterial and mitochondrial enzymes.	it has been almost 5 years since the first structures of cytochrome c oxidase, from paracoccus denitrificans and bovine heart mitochondria, were revealed. since then many different proton pumping mechanisms have been proposed for the enzyme; however, no definitive conclusion has been achieved. in this article, we revisit the original structures of bacterial and mitochondrial oxidases and try to clarify similarities as well as differences between the two structures.	2001	11341911
ph-induced conformational transition in the soluble cua domain of paracoccus denitrificans cytochrome oxidase.	the ph-induced conformational transition in the cua domain of subunit ii of cytochrome oxidase of paracoccus denitrificans (pdii) has been investigated using various spectroscopic and stopped-flow kinetic methods. uv-visible absorption and circular dichroism studies showed that an increase in ph from 6 to 10 leads to a conformation change with pk(a) = 8.2 associated with the cua site of the protein. the secondary structure of the protein was, however, shown to remain unchanged in these two confo ...	2001	11352755
isolation and characterization of complex i, rotenone-sensitive nadh: ubiquinone oxidoreductase, from the procyclic forms of trypanosoma brucei.	additional characterization of complex i, rotenone-sensitive nadh:ubiquinone oxidoreductase, in the mitochondria of trypanosoma brucei brucei has been obtained. both proline:cytochrome c reductase and nadh:ubiquinone oxidoreductase of procyclic t. brucei were inhibited by the specific inhibitors of complex i rotenone, piericidin a, and capsaicin. these inhibitors had no effect on succinate: cytochrome c reductase activity. antimycin a, a specific inhibitor of the cytochrome bc1 complex (ubiquino ...	2001	11358527
multivariable control of alcohol concentrations in the production of polyhydroxyalkanoates (phas) by paracoccus denitrificans.	a novel multivariable control strategy is developed for alcohol (ethanol and n-pentanol) concentrations in the production of poly(3-hydroxybutyrate-co-3-hydroxyvalerate), p(hb-co-hv), a biodegradable polymer by paracoccus denitrificans atcc 1774. this controller, which is developed to control the mole fraction of p(hb-co-hv), consists of two parts: one is for ethanol concentration control and the other is for mole fraction control, based on the concept of metabolic flux distribution control. a s ...	2001	11370000
maximal expression of membrane-bound nitrate reductase in paracoccus is induced by nitrate via a third fnr-like regulator named narr.	respiratory reduction of nitrate to nitrite is the first key step in the denitrification process that leads to nitrate loss from soils. in paracoccus pantotrophus, the enzyme system that catalyzes this reaction is encoded by the narkghji gene cluster. expression of this cluster is maximal under anaerobic conditions in the presence of nitrate. upstream from nark is narr, a gene encoding a member of the fnr family of transcriptional activators. narr is transcribed divergently from the other nar ge ...	2001	11371524
the structure of an alternative form of paracoccus pantotrophus cytochrome cd(1) nitrite reductase.	cytochrome cd(1) nitrite reductase is a bifunctional enzyme, which can catalyze the 1-electron reduction of nitrite to nitric oxide and the 4-electron reduction of dioxygen to water. here we describe the structure of reduced nitrite reductase, crystallized under anaerobic conditions. the structure reveals substantial domain rearrangements with the c domain rotated by 60 degrees and shifted by approximately 20 a compared with previously known structures from crystals grown under oxidizing conditi ...	2001	11373294
redox dependent conformational changes in the mixed valence form of the cytochrome c oxidase from p. the reorganization of glutamic acid 278 is coupled to the electron transfer from/to heme a and the binuclear center. denitrificans.	in this work we present the separation of ftir difference signals induced by electron transfer to/from the redox centers of the cytochrome c oxidase from p. denitrificans and compare electrochemically induced ftir difference spectra with those induced by co photolysis. ftir difference spectra of rebinding of co to the half reduced (mixed valence) form of the cytochrome c oxidase after photolysis reflect the conformational changes induced by the rebinding of co and by electron transfer reactions ...	2001	11374571
heme-copper oxidases with modified d- and k-pathways are yet efficient proton pumps.	the cytochrome aa(3)-type quinol oxidase from the archaeon acidianus ambivalens and the ba(3)-type cytochrome c oxidase from thermus thermophilus are divergent members of the heme-copper oxidase superfamily of enzymes. in particular they lack most of the key residues involved in the proposed proton transfer pathways. the pumping capability of the a. ambivalens enzyme was investigated and found to occur with the same efficiency as the canonical enzymes. this is the first demonstration of pumping ...	2001	11377432
calcium-dependent conformation of a heme and fingerprint peptide of the diheme cytochrome c peroxidase from paracoccus pantotrophus.	the structural changes in the heme macrocycle and substituents caused by binding of ca(2+) to the diheme cytochrome c peroxidase from paracoccus pantotrophus were clarified by resonance raman spectroscopy of the inactive fully oxidized form of the enzyme. the changes in the macrocycle vibrational modes are consistent with a ca(2+)-dependent increase in the out-of-plane distortion of the low-potential heme, the proposed peroxidatic heme. most of the increase in out-of-plane distortion occurs when ...	2001	11380251
charge translocation coupled to electron injection into oxidized cytochrome c oxidase from paracoccus denitrificans.	electrons were discretely injected into oxidized cytochrome c oxidase in liposomes by laser flash excitation of bound ruthenium [ii] bispyridyl, and the membrane potential was recorded by time-resolved electrometry. membrane potential is generated in a fast phase when an electron is transferred from the excited dye, via the cua center, to heme a at a relative dielectric depth d inside the membrane [zaslavsky, d., kaulen, a. d., smirnova, i. a., vygodina, t., and konstantinov, a. a. (1993) febs l ...	2001	11401552
characterization and sequence analysis of the replicator region of the novel plasmid palc1 from paracoccus alcaliphilus.	the replicator region of a low-copy-number plasmid, palc1, of paracoccus alcaliphilus jcm 7364 was cloned in a form of the minireplicon palc100 (3.6 kb). the host range of the minireplicon embraces several species of genus paracoccus, as well as agrobacterium tumefaciens, rhizobium leguminosarum, and rhodobacter sphaeroides (all belonging to alpha-proteobacteria), but not escherichia coli. the complete nucleotide sequence of the replicator region (2276 bp) revealed the presence of one complete o ...	2001	11407917
identification and characterization of a periplasmic nitrate reductase in azospirillum brasilense sp245.	the azospirillum brasilense sp245 napabc genes, encoding nitrate reductase activity, were isolated and sequenced. the derived protein sequences are very similar throughout the whole nap segment to the napabc protein sequences of escherichia coli, pseudomonas sp. g-179, ralstonia eutropha, rhodobacter sphaeroides, and paracoccus denitrificans. based on whole-cell nitrate reductase assays with the artificial electron donors benzyl viologen and methyl viologen, and assays with periplasmic cell-free ...	2001	11409544
phar, a protein of unknown function conserved among short-chain-length polyhydroxyalkanoic acids producing bacteria, is a dna-binding protein and represses paracoccus denitrificans phap expression in vitro.	a putative regulatory protein, phar, which was identified in the polyhydroxyalkanoic acid synthetic locus (phazcpr) in paracoccus denitrificans, was investigated. the phar protein purified from a recombinant escherichia coli was estimated to be 22 kda by sodium dodecyl sulfate-polyacrylamide gel electrophoresis, being consistent with the mass calculated from the nucleotide sequence. the molecular mass was determined to be 93 kda by size-exclusion chromatography, suggesting that the protein forme ...	2001	11410342
albibacter methylovorans gen. nov., sp. nov., a novel aerobic, facultatively autotrophic and methylotrophic bacterium that utilizes dichloromethane.	a novel genus, albibacter, with one species, albibacter methylovorans sp. nov., is proposed for a facultatively chemolithotrophic and methylotrophic bacterium (strain dm10t) with the ribulose bisphosphate (rubp) pathway of c1 assimilation. the bacterium is a gram-negative, aerobic, asporogenous, nonmotile, colourless rod that multiplies by binary fission. the organism utilizes dichloromethane, methanol, methylamine, formate and co2/h2, as well as a variety of polycarbon compounds, as carbon and ...	2001	11411673
dynamics of nitric oxide in the active site of reduced cytochrome c oxidase aa3.	nitric oxide (no) is involved in the regulation of respiration by acting as a competitive ligand for molecular oxygen at the binuclear active site of cytochrome c oxidase. the dynamics of no in and near this site are not well understood. we performed flash photolysis studies of no from heme a3 in cytochrome c oxidase from paracoccus denitrificans, using femtosecond transient absorption spectroscopy. the formation of the product state--the unliganded heme a3 ground state--occurs in a similar step ...	2001	11425307
oxidation of reduced inorganic sulfur compounds by bacteria: emergence of a common mechanism?		2001	11425697
protein dynamics enhance electronic coupling in electron transfer complexes.	electron-transferring flavoproteins (etfs) from human and paracoccus denitrificans have been analyzed by small angle x-ray scattering, showing that neither molecule exists in a rigid conformation in solution. both etfs sample a range of conformations corresponding to a large rotation of domain ii with respect to domains i and iii. a model of the human etf.medium chain acyl-coa dehydrogenase complex, consistent with x-ray scattering data, indicates that optimal electron transfer requires domain i ...	2001	11429403
assignment of haem ligands and detection of electronic absorption bands of molybdenum in the di-haem periplasmic nitrate reductase of paracoccus pantotrophus.	the periplasmic nitrate reductase (nap) from paracoccus pantotrophus is a soluble two-subunit enzyme (napab) that binds two c-type haems, a [4fe-4s] cluster and a bis-molybdopterin guanine dinucleotide cofactor that catalyses the reduction of nitrate to nitrite. in the present work the napab complex has been studied by magneto-optical spectroscopy to probe co-ordination of both the napb haems and the napa active site mo. the absorption spectrum of the napab complex is dominated by features from ...	2001	11434929
a novel c1-using denitrifier alcaligenes sp. stc1 and its genes for copper-containing nitrite reductase and azurin.	a novel denitrifier alcaligenes sp. stc1 was identified. the strain efficiently denitrifies under an atmosphere of 10% oxygen (o2) where paracoccus denitrificans, one of the most studied aerobic denitrifiers, had less denitrifying activity, indicating that the strain has an o2-torelant denitrifying system. it denitrified by using c1-carbon sources such as formate and methanol as well as glucose, glycerol, and succinate. the genes for the copper-containing nitrite reductase and azurin of this c1- ...	2001	11440141
novel genes of the sox gene cluster, mutagenesis of the flavoprotein soxf, and evidence for a general sulfur-oxidizing system in paracoccus pantotrophus gb17.	the novel genes soxfgh were identified, completing the sox gene cluster of paracoccus pantotrophus coding for enzymes involved in lithotrophic sulfur oxidation. the periplasmic soxf, soxg, and soxh proteins were induced by thiosulfate and purified to homogeneity from the soluble fraction. soxf coded for a protein of 420 amino acids with a signal peptide containing a twin-arginine motif. soxf was 37% identical to the flavoprotein fccb of flavocytochrome c sulfide dehydrogenase of allochromatium v ...	2001	11443084
significance of asymmetric sites in choosing siderophores as deferration agents.	the syntheses of the microbial iron chelators l-fluviabactin, its unnatural enantiomer, d-fluviabactin, l-homofluviabactin, and l-agrobactin, are described. the key steps involve the selective bis-acylation of the terminal nitrogens of norspermidine, spermidine, or homospermidine with 2,3-bis(benzyloxy)benzoic acid in the presence of 1,1-carbonyldiimidazole, followed by coupling of the n-hydroxysuccinimide ester of cbz-protected l- or d-threonine with the central nitrogen. the effectiveness of e ...	2001	11448229
[microbial decomposition of 3,4-dichloroaniline, adsorbed by activated charcoal].	the accessibility of 3,4-dichloroaniline (dca) sorbed by activated carbon to degradative microorganisms was studied. a paracoccus denitrificans strain capable of growing on medium with dca as the only source of energy, carbon, and nitrogen was used in the experiment. the high sorption capacity of all the carbons studied (powdered rs and skt-6a and granular ag-3) in relation to dca (350 to 360, 480 to 520, and 540 to 580 mg/g, respectively) was demonstrated. the sorption capacity correlated posit ...	2001	11450454
the carboxin-binding site on paracoccus denitrificans succinate:quinone reductase identified by mutations.	succinate:quinone reductase catalyzes electron transfer from succinate to quinone in aerobic respiration. carboxin is a specific inhibitor of this enzyme from several different organisms. we have isolated mutant strains of the bacterium paracoccus denitrificans that are resistant to carboxin due to mutations in the succinate:quinone reductase. the mutations identify two amino acid residues, his228 in sdhb and asp89 in sdhd, that most likely constitute part of a carboxin-binding site. this site i ...	2001	11456223
intramolecular electron transfer from c heme to d1 heme in bacterial cytochrome cd1 nitrite reductase occurs over the same distances at very different rates depending on the source of the enzyme.	intramolecular electron transfer over 12 a from heme c to heme d(1) was investigated in cytochrome cd(1) nitrite reductase from pseudomonas aeruginosa, following reduction of the c heme by pulse radiolysis. the rate constant for the transfer is relatively slow, k = 3 s(-1). the present observations contrast with a corresponding rate of electron transfer, 1.4 x 10(3) s(-1), measured for cytochrome cd(1) from paracoccus pantotrophus, though the relative positions of the two heme groups are the sam ...	2001	11456493
the peroxidase activity of cytochrome c-550 from paracoccus versutus.	next to their natural electron transport capacities, c-type cytochromes possess low peroxidase and cytochrome p-450 activities in the presence of hydrogen peroxide. these catalytic properties, in combination with their structural robustness and covalently bound cofactor make cytochromes c potentially useful peroxidase mimics. this study reports on the peroxidase activity of cytochrome c-550 from paracoccus versutus and the loss of this activity in presence of h2o2. the rate-determining step in t ...	2001	11488914
zn(2+) binding to the cytoplasmic side of paracoccus denitrificans cytochrome c oxidase selectively uncouples electron transfer and proton translocation.	using a combination of stopped-flow spectrophotometric proton pumping measurements and time-resolved potential measurements on black lipid membranes, we have investigated the effect of zn(2+) ions on the proton transfer properties of paracoccus denitrificans cytochrome c oxidase. when zinc was enclosed in the interior of cytochrome c oxidase containing liposomes, the h/e stoichiometry was found to gradually decrease with increasing zn(2+) concentration. half-inhibition of proton pumping was obse ...	2001	11513871
the cysteine residue of the soxy protein as the active site of protein-bound sulfur oxidation of paracoccus pantotrophus gb17.	four proteins of paracoccus pantotrophus are required for hydrogen sulfide-, sulfur-, thiosulfate- and sulfite-dependent horse heart cytochrome c reduction. the lack of free intermediates suggested a protein-bound sulfur oxidation mechanism. the soxy protein has a novel motif containing a cysteine residue. electrospray ionization and matrix-assisted laser desorption ionization mass spectrometry of the soxyz protein revealed one mass for soxz and different masses for soxy, indicating native soxy ...	2001	11513876
the shxvw locus is essential for oxidation of inorganic sulfur and molecular hydrogen by paracoccus pantotrophus gb17: a novel function for lithotrophy.	the shxvw genes of paracoccus pantotrophus were identified to be essential for lithotrophic oxidation of sulfur and hydrogen. shxv predicts a membrane protein which is 42% identical to ccda of p. pantotrophus essential for cytochrome c biogenesis. shxw predicts a periplasmic thioredoxin. disruption of shxv by an omega-kanamycin interposon disabled the resulting mutant gb(omega)v to grow with thiosulfate or molecular hydrogen and to express shxw while cytochrome c formation was not affected. mixo ...	2001	11520617
a direct-method ab initio phasing of a protein, cupredoxin amicyanin, at 1.31 a resolution.	the direct-methods program multan88 has been applied successfully to redetermine the structure of a protein, cupredoxin amicyanin, containing 808 non-h atom sites, one cu atom and 132 ordered water molecules in the asymmetric unit using data at 1.31 a resolution. starting with initially random phases, useful phase sets selected by figures of merit could be obtained from multiple trials. the e maps corresponding to the best eight phase sets in order of combined figures of merit (cfom2) revealed a ...	2001	11526319
the dynamics of the macromolecular composition of biomass.	the biomass composition of microorganisms depends on the growth conditions. this study explores whether a two-component model can explain how the elemental and macromolecular composition of the biomass of bacteria varies with the specific growth rate. the model describes the rates at which microorganisms assimilate substrates into reserves and utilize reserves for maintenance and growth. crucial model assumptions are that biomass consists of reserves and structure and that each of these componen ...	2001	11531388
catalytic protein film voltammetry from a respiratory nitrate reductase provides evidence for complex electrochemical modulation of enzyme activity.	the first step in the respiratory reduction of nitrate to dinitrogen in paracoccus pantotrophus is catalyzed by the quinol-nitrate oxidoreductase narghi. this membrane-anchored protein directs electrons from quinol oxidation at the membrane anchor, nari, to the site of nitrate reduction in the membrane extrinsic [fe-s] cluster and mo-bis-mgd containing dimer, nargh. liberated from the membrane, nargh retains its nitrate reductase activity and forms films on graphite and gold electrodes within wh ...	2001	11560477
crystal structure of chaperonin-60 from paracoccus denitrificans.	the crystal structure of chaperonin-60 from paracoccus denitrificans (p.cpn60) has been determined at 3.2 a resolution by the molecular replacement method. two heptameric rings of identical subunits of p.cpn60 in adjacent asymmetric units are stacked in a back-to-back manner and form a cylinder, as found in groel, cpn60 from escherichia coli. with respect to the unliganded groel structure, each subunit of p.cpn60 tilts 2 degrees outwards and the apical domain twists 4 degrees counter-clockwise i ...	2001	11563912
cytochrome complex essential for photosynthetic oxidation of both thiosulfate and sulfide in rhodovulum sulfidophilum.	many photosynthetic bacteria use inorganic sulfur compounds as electron donors for carbon dioxide fixation. a thiosulfate-induced cytochrome c has been purified from the photosynthetic alpha-proteobacterium rhodovulum sulfidophilum. this cytochrome c(551) is a heterodimer of a diheme 30-kda soxa subunit and a monoheme 15-kda soxx subunit. the cytochrome c(551) structural genes are part of an 11-gene sox locus. sequence analysis suggests that the ligands to the heme iron in soxx are a methionine ...	2001	11567011
re-engineering monovalent cation binding sites of methylamine dehydrogenase: effects on spectral properties and gated electron transfer.	methylamine dehydrogenase (madh) is a tryptophan tryptophylquinone (ttq)-dependent enzyme that catalyzes the oxidative deamination of primary amines. monovalent cations are known to affect the spectral properties of madh and to influence the rate of the gated electron transfer (et) reaction from substrate-reduced madh to amicyanin. two putative monovalent cation binding sites in madh have been identified by x-ray crystallography [labesse, g., ferrari, d., chen, z.-w., rossi, g.-l., kuusk, v., mc ...	2001	11591147
solution structure and dynamics of the functional domain of paracoccus denitrificans cytochrome c(552) in both redox states.	a soluble and fully functional 10.5 kda fragment of the 18.2 kda membrane-bound cytochrome c(552) from paracoccus denitrificans has been heterologously expressed and (13)c/(15)n-labeled to study the structural features of this protein in both redox states. well-resolved solution structures of both the reduced and oxidized states have been determined using high-resolution heteronuclear nmr. the overall protein topology consists of two long terminal helices and three shorter helices surrounding th ...	2001	11591150
identification of the partitioning site within the repabc-type replicon of the composite paracoccus versutus plasmid ptav1.	the replicator region of composite plasmid ptav1 of paracoccus versutus (included in mini-replicon ptav320) belongs to the family of repabc replicons commonly found in plasmids harbored by agrobacterium and rhizobium spp. the repabc replicons encode three genes clustered in an operon, which are involved in partitioning (repa and repb) and replication (repc). in order to localize the partitioning site of ptav320, the two identified incompatibility determinants of this mini-replicon (inc1, located ...	2001	11591666
effect of organics on sulfur-utilizing autotrophic denitrification under mixotrophic conditions.	sulfur-utilizing denitrification can be performed by denitrifying sulfur bacteria under autotrophic and heterotrophic conditions. to investigate the effect of organics (methanol and landfill leachate) on sulfur-utilizing denitrification, six laboratory-scale sulfur packed columns were operated under autotrophic, mixotrophic and heterotrophic conditions for approximately 1 year. the performance of the columns was monitored by measuring the ph, nitrate, nitrite, sulfate, sulfide, alkalinity dissol ...	2001	11604167
characterization of the reduction of selenate and tellurite by nitrate reductases.	preliminary studies showed that the periplasmic nitrate reductase (nap) of rhodobacter sphaeroides and the membrane-bound nitrate reductases of escherichia coli are able to reduce selenate and tellurite in vitro with benzyl viologen as an electron donor. in the present study, we found that this is a general feature of denitrifiers. both the periplasmic and membrane-bound nitrate reductases of ralstonia eutropha, paracoccus denitrificans, and paracoccus pantotrophus can utilize potassium selenate ...	2001	11679335
reaction of carbon monoxide with the reduced active site of bacterial nitric oxide reductase.	bacterial nitric oxide reductase (nor), a member of the superfamily of heme-copper oxidases, catalyzes the two-electron reduction of nitric oxide to nitrous oxide. the key feature that distinguishes nor from the typical heme-copper oxidases is the elemental composition of the dinuclear center, which contains non-heme iron (feb) rather than copper (cub). uv-vis electronic absorption and room-temperature magnetic circular dichroism (rt-mcd) spectroscopies showed that co binds to fe(ii) heme b3 to ...	2001	11683646
a novel denitrifying bacterial isolate that degrades trimethylamine both aerobically and anaerobically via two different pathways.	the aerobic and anaerobic degradation of trimethylamine by a newly isolated denitrifying bacterium from an enrichment culture with trimethylamine inoculated with activated sludge was studied. based on 16s rdna analysis, this strain was identified as a paracoccus sp. the isolate, strain t231, aerobically degraded trimethylamine, dimethylamine and methylamine and released a stoichiometric amount of ammonium ion into the culture fluid as a metabolic product, indicating that these methylated amines ...	2001	11685371
nadh dehydrogenases: from basic science to biomedicine.	this review article is concerned with two on-going research projects in our laboratory, both of which are related to the study of the nadh dehydrogenase enzyme complexes in the respiratory chain. the goal of the first project is to decipher the structure and mechanism of action of the proton-translocating nadh-quinone oxidoreductase (ndh-1) from two bacteria, paracoccus denitrificans and thermus thermophilus hb-8. these microorganisms are of particular interest because of the close resemblance o ...	2001	11695833
active-site residues are critical for the folding and stability of methylamine dehydrogenase.	site-directed mutagenesis was used to alter active-site residues of methylamine dehydrogenase (madh) from paracoccus denitrificans. four residues of the beta subunit of madh which are in close proximity to the tryptophan tryptophylquinone (ttq) prosthetic group were modified. the crystal structure of madh reveals that each of these residues participates in hydrogen bonding interactions with other active-site residues, ttq or water. relatively conservative mutations which removed the potentially ...	2001	11707614
respiratory chain supercomplexes.	respiratory chain supercomplexes have been isolated from mammalian and yeast mitochondria, and bacterial membranes. functional roles of respiratory chain supercomplexes are catalytic enhancement, substrate channelling, and stabilization of complex i by complex iii in mammalian cells. bacterial supercomplexes are characterized by their relatively high detergent-stability compared to yeast or mammalian supercomplexes that are stable to sonication. the mobility of substrate cytochrome c increases i ...	2001	11798023
heme ligation and conformational plasticity in the isolated c domain of cytochrome cd1 nitrite reductase.	the heme ligation in the isolated c domain of paracoccus pantotrophus cytochrome cd(1) nitrite reductase has been characterized in both oxidation states in solution by nmr spectroscopy. in the reduced form, the heme ligands are his69-met106, and the tertiary structure around the c heme is similar to that found in reduced crystals of intact cytochrome cd1 nitrite reductase. in the oxidized state, however, the structure of the isolated c domain is different from the structure seen in oxidized crys ...	2001	11035020
two conserved glutamates in the bacterial nitric oxide reductase are essential for activity but not assembly of the enzyme.	the bacterial nitric oxide reductase (nor) is a divergent member of the family of respiratory heme-copper oxidases. it differs from other family members in that it contains an fe(b)-heme-fe dinuclear catalytic center rather than a cu(b)-heme-fe center and in that it does not pump protons. several glutamate residues are conserved in nors but are absent in other heme-copper oxidases. to facilitate mutagenesis-based studies of these residues in paracoccus denitrificans nor, we developed two express ...	2001	11114916
identification of ccda in paracoccus pantotrophus gb17: disruption of ccda causes complete deficiency in c-type cytochromes.	a transposon tn5-mob insertional mutant of paracoccus pantotrophus gb17, strain tp43, was unable to oxidize thiosulfate aerobically or to reduce nitrite anaerobically, and the cellular yields were generally decreased by 11 to 20%. strain tp43 was unable to form functional c-type cytochromes, as determined by difference spectroscopy and heme staining. however, formation of apocytochromes and their transport to the periplasm were not affected, as seen with soxd, a c-type cytochrome associated with ...	2001	11114924
sulfocyanin and subunit ii, two copper proteins with novel features, provide new insight into the archaeal soxm oxidase supercomplex.	the isolation of a fully functional soxm terminal oxidase supercomplex from the archaeon sulfolobus acidocaldarius has failed thus far and several of its constituents have only been predicted genetically, such as the small cu protein sulfocyanin and the subunit ii bearing a cu(a) center. here we report the recombinant expression of sulfocyanin and prove its transcription in sulfolobus as well as its presence in the enriched complex. it reveals a redox potential of +300 mv and spectroscopic featu ...	2001	11163357
new pathway of amine oxidation respiratory chain of paracoccus denitrificans ifo 12442.	the physiological electron acceptor of quinohemoprotein amine dehydrogenase (qh-amdh) from paracoccus denitrificans ifo 12442 was identified by biochemical and electrochemical methods. of three types of heme c-containing proteins purified together with qh-amdh from the periplasm of n-butylamine-grown cells, only constitutive cytochrome c-550 was reduced by the addition of qh-amdh and n-butylamine. reconstitution of the respiratory chain revealed that cytochrome c-550 mediates the electron transf ...	2001	11168384
an amicyanin c-terminal loop mutant where the active-site histidine donor cannot be protonated.	a novel blue copper protein was constructed by replacing the c-terminal loop of amicyanin (paracoccus versutus) by the homologous loop of rusticyanin. the c-terminal loop of both amicyanin and rusticyanin contains three (his, cys, met) of the four copper ligands. the amicyanin mutant exhibits all spectroscopic properties normally encountered for blue copper sites. the midpoint potential (369 mv) is the highest reported value for an amicyanin mutant. cyclic voltammetry and nmr studies of the redu ...	2001	11191220
the cytochrome c domain of dimeric cytochrome cd(1) of paracoccus pantotrophus can be produced at high levels as a monomeric holoprotein using an improved c-type cytochrome expression system in escherichia coli.	cytochrome cd(1) nitrite reductase from paracoccus pantotrophus is a dimer; within each monomer there is a largely alpha-helical domain that contains the c-type cytochrome centre. the structure of this domain changes significantly upon reduction of the heme iron, for which the ligands change from his17/his69 to met106/his69. overproduction, using an improved escherichia coli expression system, of this c-type cytochrome domain as an independent monomer is reported here. the properties of the inde ...	2001	11237728
map self-validation: a useful discriminator of phase correctness at low resolution.	a new map-validation procedure is based on the correlation-coefficient agreement between the observed structure-factor magnitudes and their extrapolated values from suitably modified electron-density maps from which they have been each in turn systematically excluded. the correlation coefficient tends to a maximum as the phase errors in a map are reduced. this principle was used to resolve the single-wavelength anomalous scattering (sas) and single-derivative isomorphous replacement (sir) phase ...	2001	11264587
identification of the intracellular polyhydroxyalkanoate depolymerase gene of paracoccus denitrificans and some properties of the gene product.	paracoccus denitrificans degraded poly(3-hydroxybutyrate) (phb) in the cells under carbon source starvation. intracellular poly(3-hydroxyalkanoate) (pha) depolymerase gene (phaz) was identified near the pha synthase gene (phac) of p. denitrificans. cell extract of escherichia coli carrying lacz--phaz fusion gene degraded protease-treated phb granules. reaction products were thought to be mainly d(--)-3-hydroxybutyrate (3hb) dimer and 3hb oligomer. diisopropylfluorophosphonate and triton x-100 ex ...	2001	11267773
structure of the bound dioxygen species in the cytochrome oxidase reaction of cytochrome cd1 nitrite reductase.	reduction of dioxygen to water is a key process in aerobic life, but atomic details of this reaction have been elusive because of difficulties in observing active oxygen intermediates by crystallography. cytochrome cd(1) is a bifunctional enzyme, capable of catalyzing the one-electron reduction of nitrite to nitric oxide, and the four-electron reduction of dioxygen to water. the latter is a cytochrome oxidase reaction. here we describe the structure of an active dioxygen species in the enzyme ca ...	2001	11278884
evidence for two pathways of thiosulfate oxidation in starkeya novella (formerly thiobacillus novellus).	the pathway of thiosulfate oxidation in the facultatively chemolithotrophic, sulfur-oxidizing bacterium starkeya novella (formerly thiobacillus novellus) has not been established beyond doubt. recently, isolation of the sorab genes, which encode a soluble sulfite:cytochrome c oxidoreductase, has been reported, indicating that a thiosulfate-oxidizing pathway not involving a multienzyme complex may exist in this organism. here we report the cloning and sequencing of the soxbcd genes from s. novell ...	2001	11285738
functional, biochemical and genetic diversity of prokaryotic nitrate reductases.	prokaryotic nitrate reduction can serve a number of physiological roles and can be catalysed by a number of biochemically distinct nitrate reductases. three distinct nitrate reductase classes can be indentified in prokaryotes, nas, nar and nap. nas is located in the cytoplasmic compartment and participates in nitrogen assimilation. nar is usually a three-subunit complex anchored to the cytoplasmic face of the membrane with its active site located in the cytoplasmic compartment and is involved in ...	2001	11289299
perturbations at the high spin heme b center in the membrane-bound nitric oxide reductase.	the effects of lowering ph from 7 to 5 on the absorption, circular dichroism (mcd) and epr spectra were studied for paracoccus halodenitrificans nitric oxide reductase (nor). intensities of the characteristic bands for the high spin heme b, that at 592 nm in the absorption spectrum and those at 591 (+) and 606 (-) in the mcd spectrum decreased considerably. concomitant cryogenic epr spectrum indicated a drastic increase in the signal intensity due to the high spin heme b at g approximately 6, of ...	2001	11293548
replacement of the methionine axial ligand in cytochrome c(550) by a lysine: effects on the haem electronic structure.	the prosthetic group of low-spin haem proteins is an iron porphyrin with two axial ligands, typically histidine, methionine or lysine. determining the geometry of the axial ligands is an important step in structural characterisation, particularly in the paramagnetic oxidised forms. this work extends earlier studies of the hyperfine nuclear magnetic resonance (nmr) shifts of haem substituents in bis-his and his-met cytochromes to his-lys co-ordination in the m100k mutant of paracoccus versutus cy ...	2002	11801251
succinate:quinone oxidoreductase in the bacteria paracoccus denitrificans and bacillus subtilis.	an overview of the present knowledge about succinate:quinone oxidoreductase in paracoccus denitrificans and bacillus subtilis is presented. p. denitrificans contains a monoheme succinate:ubiquinone oxidoreductase that is similar to that of mammalian mitochondria with respect to composition and sensitivity to carboxin. results obtained with carboxin-resistant p. denitrificans mutants provide information about quinone-binding sites on the enzyme and the molecular basis for the resistance. b. subti ...	2002	11803018
purification and properties of d-(-)-3-hydroxybutyrate oligomer hydrolase of paracoccus denitrificans.	d-(-)-3-hydroxybutyrate (3hb) oligomer hydrolase was purified from paracoccus denitrificans. the enzyme was a monomeric protein with an approximate molecular mass of 31 kda. the isoelectric point of the enzyme was 5.2. optimum temperature and ph were 35-40 degrees c and 8.0, respectively. the enzyme activity was not affected by sulfhydryl reagents but strongly inhibited by serine proteinase inhibitors. both 3hb trimer and 3hb dimer were hydrolyzed by the enzyme, indicating that the enzyme is not ...	2002	11814660