| an additional simple denitrification bioreactor using packed gel envelopes applicable to industrial wastewater treatment. | a simple denitrification bioreactor for nitrate-containing wastewater without organic compounds was developed. this bioreactor consisted of packed gel envelopes in a single tank. each envelope comprised two plates of gels containing paracoccus denitrificans cells with an internal space between the plates. as an electron donor for denitrification, ethanol was injected into the internal space and not directly into the wastewater. p. denitrificans cells in the gel reduced nitrate to nitrogen gas by ... | 2007 | 17252606 |
| exploring the proton pump mechanism of cytochrome c oxidase in real time. | cytochrome c oxidase catalyzes most of the biological oxygen consumption on earth, a process responsible for energy supply in aerobic organisms. this remarkable membrane-bound enzyme also converts free energy from o(2) reduction to an electrochemical proton gradient by functioning as a redox-linked proton pump. although the structures of several oxidases are known, the molecular mechanism of redox-linked proton translocation has remained elusive. here, correlated internal electron and proton tra ... | 2007 | 17293458 |
| generation of novel copper sites by mutation of the axial ligand of amicyanin. atomic resolution structures and spectroscopic properties. | amicyanin from paracoccus denitrificans is a type 1 copper protein with three strong equatorial copper ligands provided by nitrogens of his53 and his95 and the sulfur of cys92, with an additional weak axial ligand provided by the sulfur of met98. met98 was replaced with either gln or ala. as isolated, the m98a and m98q mutant proteins contain zinc in the active site. the zinc is then removed and replaced with copper so that the copper-containing proteins may be studied. each of the mutant amicya ... | 2007 | 17295442 |
| effect of carbon substrate on electron acceptor diauxic lag and anoxic maximum specific growth rate in species with and without periplasmic enzyme. | the effect of oxidation state of carbon substrate on the diauxic lag of facultative anaerobic denitrifying bacteria growing aerobically upon switching to anoxic growth was studied. also studied was the effect on the anoxic maximum specific growth rate. two pure bacteria cultures were used, paracoccus pantotrophus, denitrifying bacteria containing a periplasmic nitrate reductase (nap), and pseudomonas denitrificans, denitrifying bacteria lacking the periplasmic nitrate reductase. the anoxic maxim ... | 2007 | 17129955 |
| spectropotentiometric and structural analysis of the periplasmic nitrate reductase from escherichia coli. | the escherichia coli napa (periplasmic nitrate reductase) contains a [4fe-4s] cluster and a mo-bis-molybdopterin guanine dinucleotide cofactor. the napa holoenzyme associates with a di-heme c-type cytochrome redox partner (napb). these proteins have been purified and studied by spectropotentiometry, and the structure of napa has been determined. in contrast to the well characterized heterodimeric napab systems ofalpha-proteobacteria, such as rhodobacter sphaeroides and paracoccus pantotrophus, t ... | 2007 | 17130127 |
| growth yields in bacterial denitrification and nitrate ammonification. | denitrification and nitrate ammonification are considered the highest-energy-yielding respiration systems in anoxic environments after oxygen has been consumed. the corresponding free energy changes are 7 and 35% lower than that of aerobic respiration, respectively. growth yield determinations with pure cultures of paracoccus denitrificans and pseudomonas stutzeri revealed that far less energy is converted via atp into cell mass than expected from the above calculations. denitrification with for ... | 2007 | 17209072 |
| rna microarray for estimating relative abundance of 16s rrna in microbial communities. | we developed an rna microarray protocol in which total rna from a microbial community was attached to a slide glass, and rrna was detected by fluorescently labeled oligonucleotide probes. the rna microarray requires only 4 h for hybridization and enables double staining and estimating relative abundance of rrna. | 2007 | 17320226 |
| a highly specific glyoxylate reductase derived from a formate dehydrogenase. | a glu141asn mutant paracoccus sp. 12-a formate dehydrogenase catalyzes marked glyoxylate reduction. additional replacement of the his332-gln313 pair with his-glu, which is a consensus acid/base catalyst in d-hydroxyacid dehydrogenases, further improved the catalytic activity of the enzyme as to glyoxylate reduction through enhancement of the hydrogen transfer step in the catalytic process, slightly shifting the optimal ph for the reaction. on the other hand, the replacement induced no marked act ... | 2007 | 17320818 |
| protolytic reactions on reduction of cytochrome c oxidase studied by atr-ftir spectroscopy. | reduction of cytochrome c oxidase is coupled to proton uptake, and the reduced-minus-oxidized ftir spectrum should include signatures of protonation of protolytic centers. the major part of the spectrum shows only small differences between acidic and alkaline conditions, which is consistent with the rather weak ph dependence of the proton uptake stoichiometry. here we aim at revealing redox state-dependent protonatable sites and present a comprehensive investigation over a wide ph range. the red ... | 2007 | 17341097 |
| mediated catalysis of paracoccus pantotrophus cytochrome c peroxidase by p. pantotrophus pseudoazurin: kinetics of intermolecular electron transfer. | this work reports the direct electrochemistry of paracoccus pantotrophus pseudoazurin and the mediated catalysis of cytochrome c peroxidase from the same organism. the voltammetric behaviour was examined at a gold membrane electrode, and the studies were performed in the presence of calcium to enable the peroxidase activation. a formal reduction potential, e (0)', of 230 +/- 5 mv was determined for pseudoazurin at ph 7.0. its voltammetric signal presented a ph dependence, defined by pk values of ... | 2007 | 17361419 |
| toward iron sensors: bioinspired tripods based on fluorescent phenol-oxazoline coordination sites. | in the quest for fast throughput metal biosensors, it would be of interest to prepare fluorophoric ligands with surface-adhesive moieties. biomimetic analogues to microbial siderophores possessing such ligands offer attractive model compounds and new opportunities to meet this challenge. the design, synthesis, and physicochemical characterization of biomimetic analogues of microbial siderophores from paracoccus denitrificans and from the vibrio genus are described. the (4s,5s)-2-(2-hydroxyphenyl ... | 2007 | 17326624 |
| chemolithoautotrophic oxidation of thiosulfate, tetrathionate and thiocyanate by a novel rhizobacterium belonging to the genus paracoccus. | two tropical leguminous-rhizospheric strains, sst and jt 001, phylogenetically closest to paracoccus thiocyanatus and paracoccus pantotrophus, respectively, were isolated on reduced sulfur compounds as sole energy and electron sources. while sst had versatile chemolithotrophic abilities to oxidize thiosulfate, tetrathionate, thiocyanate, sulfide and elemental sulfur, jt 001 could oxidize thiosulfate, soluble sulfide, elemental sulfur and a relatively lesser amount of tetrathionate. positive hybr ... | 2007 | 17326754 |
| protein-protein interactions studied by epr relaxation measurements: cytochrome c and cytochrome c oxidase. | the complex formed between cytochrome c oxidase from paracoccus denitrificans and its electron-transfer partner cytochrome c has been studied by multi-frequency pulse electron paramagnetic resonance spectroscopy. the dipolar relaxation of a fast-relaxing paramagnetic center induced on a more slowly relaxing center can be used to measure their distance in the range of 1-4 nm. this method has been used here for the first time to study transient protein-protein complex formation, employing soluble ... | 2007 | 17388530 |
| replication system of plasmid pmth4 of paracoccus methylutens dm12 contains an enhancer. | the replication system of plasmid pmth4 (22 kb) of dichloromethane-degrading paracoccus methylutens dm12 (alphaproteobacteria) has been cloned within a mini-replicon pmth100 (4.7 kb) and preliminarily characterized. functional analysis, performed with a series of mutated plasmid mini-derivatives, showed that the replicator region consists of three elements: (i) gene repa coding for a replication initiation protein repa, (ii) origin of replication (oriv), placed in the promoter region of repa and ... | 2006 | 17416062 |
| accommodation of no in the active site of mammalian and bacterial cytochrome c oxidase aa3. | following different reports on the stoichiometry and configuration of no binding to mammalian and bacterial reduced cytochrome c oxidase aa(3) (cco), we investigated no binding and dynamics in the active site of beef heart cco as a function of no concentration, using ultrafast transient absorption and epr spectroscopy. we find that in the physiological range only one no molecule binds to heme a(3), and time-resolved experiments indicate that even transient binding to cu(b) does not occur. only a ... | 2007 | 17434442 |
| structures and physiological roles of 13 integral lipids of bovine heart cytochrome c oxidase. | all 13 lipids, including two cardiolipins, one phosphatidylcholine, three phosphatidylethanolamines, four phosphatidylglycerols and three triglycerides, were identified in a crystalline bovine heart cytochrome c oxidase (cco) preparation. the chain lengths and unsaturated bond positions of the fatty acid moieties determined by mass spectrometry suggest that each lipid head group identifies its specific binding site within ccos. the x-ray structure demonstrates that the flexibility of the fatty a ... | 2007 | 17332748 |
| the soxyz complex carries sulfur cycle intermediates on a peptide swinging arm. | the bacterial sox (sulfur oxidizing) system allows the utilization of inorganic sulfur compounds in energy metabolism. central to this process is the soxyz complex that carries the pathway intermediates on a cysteine residue near the c terminus of soxy. crystal structures have been determined for paracoccus pantotrophus soxyz with the carrier cysteine in the underivatized state, conjugated to the polysulfide mimic beta-mercaptoethanol, and as the sulfonate adduct pathway intermediate. the carrie ... | 2007 | 17522046 |
| a novel approach to analyze membrane proteins by laser mass spectrometry: from protein subunits to the integral complex. | a novel laser-based mass spectrometry method termed lilbid (laser-induced liquid bead ion desorption) is applied to analyze large integral membrane protein complexes and their subunits. in this method the ions are ir-laser desorbed from aqueous microdroplets containing the hydrophobic protein complexes solubilized by detergent. the method is highly sensitive, very efficient in sample handling, relatively tolerant to various buffers, and detects the ions in narrow, mainly low-charge state distrib ... | 2007 | 17544294 |
| the unusal redox centers of soxxa, a novel c-type heme-enzyme essential for chemotrophic sulfur-oxidation of paracoccus pantotrophus. | the heterodimeric hemoprotein soxxa, essential for lithotrophic sulfur oxidation of the aerobic bacterium paracoccus pantotrophus, was examined by a combination of spectroelectrochemistry and epr spectroscopy. the epr spectra for soxxa showed contributions from three paramagnetic heme iron centers. one highly anisotropic low-spin (hals) species (gmax = 3.45) and two "standard" cytochrome-like low-spin heme species with closely spaced g-tensor values were identified, ls1 (gz = 2.54, gy = 2.30, an ... | 2007 | 17547421 |
| [screening and characterization of marine bacteria with antibacterial and cytotoxic activities, and existence of pks i and nrps genes in bioactive strains]. | antibacterial and cytotoxic activities were screened for marine bacteria which have been isolated from organism, sediments and seawater in china coastal area. the results showed that 42 isolates had antimicrobial activity and 12 isolates had cytotoxicity. molecular phylogenetic analysis of marine bacteria with cytotoxicity based on 16s rrna sequences indicated that they were belong to the genera aerococcus, agrobacterium, alteromona, bacillus, exiguobacterium, paracoccus, pseudoalteromons, rhein ... | 2007 | 17552225 |
| asymmetric binding of stigmatellin to the dimeric paracoccus denitrificans bc1 complex: evidence for anti-cooperative ubiquinol oxidation and communication between center p ubiquinol oxidation sites. | we have investigated the mechanism responsible for half-of-the-sites activity in the dimeric cytochrome bc(1) complex from paracoccus denitrificans by characterizing the kinetics of inhibitor binding to the ubiquinol oxidation site at center p. both myxothiazol and stigmatellin induced a 2-3 nm shift of the visible absorbance spectrum of the b(l) heme. the shift generated by myxothiazol was symmetric, with monophasic kinetics that indicate equal binding of this inhibitor to both center p sites. ... | 2007 | 17561507 |
| morphological change in cellular granule formation of poly[(r)-3-hydroxybutyrate] caused by dna-binding-related mutations of an autoregulated repressor phar. | phap is a major poly[(r)-3-hydroxybutyrate] [p(3hb)]-granule-associated protein. its gene expression is controlled by an autoregulated repressor, phar, in paracoccus denitrificans. the packing force of the p(3hb) granule by phap is greatly influenced by the number of phap molecules. in this study, the effects of dna-binding-ability-reduced mutations of phar on morphological change in the cellular granule formation of p(3hb) were examined under a transmission electron microscope using an escheric ... | 2007 | 17587694 |
| correlation of rhombic distortion of the type 1 copper site of m98q amicyanin with increased electron transfer reorganization energy. | mutation of the axial met ligand of the type 1 copper site of amicyanin to ala or gln yielded m98a amicyanin, which exhibits typical axial type 1 ligation geometry but with a water molecule providing the axial ligand, and m98q amicyanin, which exhibits significant rhombic distortion of the type 1 site (carrell, c. j., ma, j. k., antholine, w. e., hosler, j. p., mathews, f. s., and davidson, v. l. (2007) biochemistry 46, 1900-1912). despite the change of the axial ligand, the m98q and m98a mutati ... | 2007 | 17602663 |
| cultivable bacterial diversity of alkaline lonar lake, india. | aerobic, alkaliphilic bacteria were isolated and characterized from water and sediment samples collected in the winter season, january 2002 from alkaline lonar lake, india, having ph 10.5. the total number of microorganisms in the sediment and water samples was found to be 10(2)-10(6) cfu g(-1) and 10(2)-10(4) cfu ml(-1), respectively. one hundred and ninety-six strains were isolated using different enrichment media. to study the bacterial diversity of lonar lake and to select the bacterial stra ... | 2008 | 17604989 |
| characterization of a tir-like protein from paracoccus denitrificans. | based on protein sequence homology searches, we found a conserved open reading frame within the genome of several human pathogenic bacteria showing a resemblance to the mammalian tir domain. we cloned, expressed, and characterized the corresponding gene product from paracoccus denitrificans using several biophysical techniques. the protein consists of two independently folded domains. as predicted from the amino acid sequence and experimentally confirmed here, the n-terminal domain consists of a ... | 2007 | 17362878 |
| [isolation of a monocrotophos-degrading bacterial strain and characterization of enzymatic degradation]. | a monocrotophos [dimethyl (e)-1-2-methylcarbamoylvinylphosphate or mcp] -degrading strain named as m-1 was isolated from sludge collected from the wastewater treatment pool of a pesticide factory and identified as paracoccus sp. according to its morphology and biochemical properties and 16s rdna sequence analysis. using mcp as a sole carbon source, m-1 was able to degrade mcp(100 mg x l(-1)) by 92.47% in 24 h. the key enzyme(s) involved in the initial biodegradation of monocrotophos in m-1 was s ... | 2007 | 17639959 |
| phosphate removal under denitrifying conditions by brachymonas sp. strain p12 and paracoccus denitrificans pp15. | in this study, we used the denitrifying phosphorus-removing bacterium brachymonas sp. strain p12 to investigate the enhanced biologic phosphorus-removal (ebpr) mechanism involved with polyhydroxybutyrate (phb), glycogen, and phosphorus uptake in the presence of acetate under anoxic or aerobic conditions. the results showed that excess acetate concentration and aerobic cultivation can enhance phb formation efficiency and that phb formation might be stimulated by glycogenolysis of the cellular gly ... | 2007 | 17668033 |
| comparative genomics and site-directed mutagenesis support the existence of only one input channel for protons in the c-family (cbb3 oxidase) of heme-copper oxygen reductases. | oxygen reductase members of the heme-copper superfamily are terminal respiratory oxidases in mitochondria and many aerobic bacteria and archaea, coupling the reduction of molecular oxygen to water to the translocation of protons across the plasma membrane. the protons required for catalysis and pumping in the oxygen reductases are derived from the cytoplasmic side of the membrane, transferred via proton-conducting channels comprised of hydrogen bond chains containing internal water molecules alo ... | 2007 | 17676874 |
| continuous deodorization and bacterial community analysis of a biofilter treating nitrogen-containing gases from swine waste storage pits. | a biofilter inoculated with arthrobacter sp. was applied to the simultaneous elimination of trimethylamine (tma) and ammonia (nh3) from the exhaust air of swine waste storage pits. the results showed that the biofilter achieved average removal efficiencies of 96.8+/-2.5% and 97.2+/-2.3% for tma and nh3, respectively. a near-neutral ph (7.3-7.4) was maintained due to the accumulation of acid metabolites and the adsorption of alkaline nh3. low moisture demand, low pressure drop and high biofilm st ... | 2008 | 17697773 |
| electron transfer kinetics of soluble fragments indicate a direct interaction between complex iii and the caa3 oxidase in thermus thermophilus. | the extremely thermophilic bacterium thermus thermophilus expresses an aerobic respiratory chain resembling that of mitochondria and many mesophilic prokaryotes. yet, interaction modes between redox partners differ between the thermophilic and mesophilic electron transport chains. while electron transfer in mesophilic organisms such as paracoccus denitrificans follows a two-step mechanism mostly governed by long-range electrostatic interactions, the electron transfer in thermophiles is mediated ... | 2007 | 17701551 |
| activation of the heterodimeric central complex soxyz of chemotrophic sulfur oxidation is linked to a conformational change and soxy-y interprotein disulfide formation. | the central protein of the four component sulfur oxidizing (sox) enzyme system of paracoccus pantotrophus, soxyz, carries at the soxy subunit the covalently bound sulfur substrate which the other three proteins bind, oxidize, and release as sulfate. soxyz of different preparations resulted in different specific thiosulfate-oxidizing activities of the reconstituted sox enzyme system. from these preparations soxyz was activated up to 24-fold by different reductants with disodium sulfide being the ... | 2007 | 17760419 |
| the periplasmic thioredoxin soxs plays a key role in activation in vivo of chemotrophic sulfur oxidation of paracoccus pantotrophus. | the significance of the soxs gene product on chemotrophic sulfur oxidation of paracoccus pantotrophus was investigated. the thioredoxin soxs was purified, and the n-terminal amino acid sequence identified soxs as the soxs gene product. the wild-type formed thiosulfate-oxidizing activity and sox proteins during mixotrophic growth with succinate plus thiosulfate, while there was no activity, and only traces of sox proteins, under heterotrophic conditions. the homogenote mutant strain gbomegas is u ... | 2007 | 17379716 |
| a single methionine residue dictates the kinetic mechanism of interprotein electron transfer from methylamine dehydrogenase to amicyanin. | amicyanin is a type 1 copper protein that is the natural electron acceptor for the quinoprotein methylamine dehydrogenase (madh). a p52g amicyanin mutation increased the kd for complex formation and caused the normally true electron transfer (et) reaction from o-quinol madh to amicyanin to become a gated et reaction (ma, j. k., carrell, c. j., mathews, f. s., and davidson, v. l. (2006) biochemistry 45, 8284-8293). one consequence of the p52g mutation was to reposition the side chain of met51, wh ... | 2007 | 17824674 |
| voltammetric characterization of the aerobic energy-dissipating nitrate reductase of paracoccus pantotrophus: exploring the activity of a redox-balancing enzyme as a function of electrochemical potential. | paracoccus pantotrophus expresses two nitrate reductases associated with respiratory electron transport, termed napabc and narghi. both enzymes derive electrons from ubiquinol to reduce nitrate to nitrite. however, while narghi harnesses the energy of the quinol/nitrate couple to generate a transmembrane proton gradient, napabc dissipates the energy associated with these reducing equivalents. in the present paper we explore the nitrate reductase activity of purified napab as a function of electr ... | 2008 | 17900239 |
| robotized incubation system for monitoring gases (o2, no, n2o n2) in denitrifying cultures. | as genomic data for bacteria are unraveled at an increasing speed, there is a need for more efficient and refined techniques to characterize metabolic traits. the regulatory apparatus for denitrification, for instance, has been explored extensively for type strains, but we lack refined observations of how these and wild type denitrifiers respond metabolically to changing environmental conditions. there is a need for new "phenomic" approaches, and the present paper describes one; an automated inc ... | 2007 | 17904668 |
| [phylogenetic diversity of culturable bacteria in the ancient salt deposits of the yipinglang salt mine, p. r. china]. | the microbial diversity of cultivable bacteria, isolated from the ancient salt deposits from the yipinglang salt mine (ypl) in the yunnan province, p. r. china,was investigated by using conventional culture-dependent method and phylogenetic analyses based on 16s rrna gene sequence comparisons. 38 bacteria strains were isolated from the brine, halite and saline soil samples on mba (marine broth agar 2216, difco) and isp 2 (international streotomyces project medium 2) media supplemented with 0.5-3 ... | 2007 | 17944352 |
| time-resolved atr-ftir spectroscopy of the oxygen reaction in the d124n mutant of cytochrome c oxidase from paracoccus denitrificans. | real-time measurements of the cytochrome c oxidase reaction with oxygen were performed by atr-ftir spectroscopy, using a mutant with a blocked d-pathway of proton transfer (d124n, paracoccus denitrificans numbering). the complex spectrum of the ferryl-->oxidized transition together with other bands showed protonation of glu 278 with a peak position at 1743 cm-1. since our time resolution was not sufficient to follow the earlier reaction steps, the ftir spectrum of the co-inhibited fully reduced- ... | 2007 | 17949011 |
| screening and isolation of phb-producing bacteria in a polluted marine microbial mat. | the characteristics of microbial mats within the waste stream from a seafood cannery were compared to a microbial community at a pristine site near a sandy beach at puerto san carlos, baja california sur, mexico. isolation of poly-beta-hydroxybutyrate (phb)-producing bacteria, recognition of brightly refractile cytoplasmatic inclusions, lipophilic stains with sudan black and nile red, and chemical extraction of phb were used as a culture-dependent strategy for the detection of phb-producing bact ... | 2008 | 17965957 |
| activation of the cytochrome cd1 nitrite reductase from paracoccus pantotrophus. reaction of oxidized enzyme with substrate drives a ligand switch at heme c. | cytochromes cd(1) are dimeric bacterial nitrite reductases, which contain two hemes per monomer. on reduction of both hemes, the distal ligand of heme d(1) dissociates, creating a vacant coordination site accessible to substrate. heme c, which transfers electrons from donor proteins into the active site, has histidine/methionine ligands except in the oxidized enzyme from paracoccus pantotrophus where both ligands are histidine. during reduction of this enzyme, tyr(25) dissociates from the distal ... | 2007 | 17623666 |
| a new ruthenium complex to study single-electron reduction of the pulsed o(h) state of detergent-solubilized cytochrome oxidase. | the first step in the catalytic cycle of cytochrome oxidase, the one-electron reduction of the fully oxidized enzyme, was investigated using a new photoactive binuclear ruthenium complex, [ru(bipyrazine)2]2(quaterpyridine), (ru2z). the aim of the work was to examine differences in the redox kinetics resulting from pulsing the oxidase (i.e., fully reducing the enzyme followed by reoxidation) just prior to photoreduction. recent reports indicate transient changes in the redox behavior of the metal ... | 2007 | 18027981 |
| magnetic circular dichroism evidence for a weakly coupled heme-radical pair at the active site of cytochrome cd1, a nitrite reductase. | in nitrite-treated cytochrome cd1 nitrite reductase, heme d1 is electron paramagnetic resonance silent but paramagnetic. analysis of the unusual temperature dependence of the magnetic circular dichroism spectra unambiguously demonstrates that the heme d1 is not in the oxoferryl (feiv=o) state but is low-spin feiii weakly coupled to a radical species. this species could be either a protein-bound radical generated by a nitrite ion reacting with a heme group resulting in a one-electron oxidation of ... | 2007 | 18044879 |
| kinetic resolution of a tryptophan-radical intermediate in the reaction cycle of paracoccus denitrificans cytochrome c oxidase. | the catalytic mechanism, electron transfer coupled to proton pumping, of heme-copper oxidases is not yet fully understood. microsecond freeze-hyperquenching single turnover experiments were carried out with fully reduced cytochrome aa(3) reacting with o(2) between 83 micros and 6 ms. trapped intermediates were analyzed by low temperature uv-visible, x-band, and q-band epr spectroscopy, enabling determination of the oxidation-reduction kinetics of cu(a), heme a, heme a(3), and of a recently detec ... | 2007 | 17761680 |
| mesaconyl-coenzyme a hydratase, a new enzyme of two central carbon metabolic pathways in bacteria. | the coenzyme a (coa)-activated c5-dicarboxylic acids mesaconyl-coa and beta-methylmalyl-coa play roles in two as yet not completely resolved central carbon metabolic pathways in bacteria. first, these compounds are intermediates in the 3-hydroxypropionate cycle for autotrophic co2 fixation in chloroflexus aurantiacus, a phototrophic green nonsulfur bacterium. second, mesaconyl-coa and beta-methylmalyl-coa are intermediates in the ethylmalonyl-coa pathway for acetate assimilation in various bacte ... | 2008 | 18065535 |
| a pathway for protons in nitric oxide reductase from paracoccus denitrificans. | nitric oxide reductase (nor) from p. denitrificans is a membrane-bound protein complex that catalyses the reduction of no to n(2)o (2no+2e(-)+2h(+)-->n(2)o+h(2)o) as part of the denitrification process. even though no reduction is a highly exergonic reaction, and nor belongs to the superfamily of o(2)-reducing, proton-pumping heme-copper oxidases (hcuos), previous measurements have indicated that the reaction catalyzed by nor is non-electrogenic, i.e. not contributing to the proton electrochemic ... | 2007 | 17466934 |
| diversity of reed (phragmites australis) stem biofilm bacterial communities in two hungarian soda lakes. | from reed biofilm samples of kelemen-szék (kiskunság national park, knp) and nagy-vadas (hortobágy national park, hnp) altogether 260 bacterial isolates were gained after serial dilutions and plating onto different media. following a primary selection 164 strains were investigated by "traditional" phenotypic tests and clustered by numerical analysis. fifty-six representative strains were selected to ardra and 16s rdna sequence analysis for identification. strains were identified as members of ge ... | 2007 | 18088008 |
| identification of proteins involved in formaldehyde metabolism by rhodobacter sphaeroides. | formaldehyde is an intermediate formed during the metabolism of methanol or other methylated compounds. many gram-negative bacteria generate formaldehyde from methanol via a periplasmic pyrroloquinoline quinone (pqq)-dependent dehydrogenase in which the alpha subunit of an alpha(2)beta(2) tetramer has catalytic activity. the genome of the facultative formaldehyde-oxidizing bacterium rhodobacter sphaeroides encodes xoxf, a homologue of the catalytic subunit of a proposed pqq-containing dehydrogen ... | 2008 | 18174148 |
| paracoccus halophilus sp. nov., isolated from marine sediment of the south china sea, china, and emended description of genus paracoccus davis 1969. | an aerobic bacterial isolate, strain hn-182(t), was isolated from sediments of the south china sea. cells of strain hn-182(t) are coccoid to short rods, gram-negative, non-spore-forming and non-motile. strain hn-182(t) is heterotrophic and grows well on marine broth (difco 2216), and is not capable of growing autotrophically on reduced sulfur. grows at temperatures ranging from 7 to 42 degrees c (optimum at 25 degrees c), but not at 4 or 45 degrees c, and at ph 5.0-9.0 (optimum at ph 7.0), but n ... | 2008 | 18175718 |
| defining the proton entry point in the bacterial respiratory nitric-oxide reductase. | the bacterial respiratory nitric-oxide reductase (nor) is a member of the superfamily of o(2)-reducing, proton-pumping, heme-copper oxidases. even although nitric oxide reduction is a highly exergonic reaction, nor is not a proton pump and rather than taking up protons from the cytoplasmic (membrane potential-negative) side of the membrane, like the heme-copper oxidases, nor derives its substrate protons from the periplasmic (membrane potential-positive) side of the membrane. the molecular detai ... | 2008 | 18056717 |
| microbial characterisation of polyhydroxyalkanoates storing populations selected under different operating conditions using a cell-sorting rt-pcr approach. | the identity of polyhydroxyalkanoates (pha) storing bacteria selected under aerobic dynamic feeding conditions, using propionate as carbon source (reactor p), was determined by applying reverse transcriptase-polymerase chain reaction (rt-pcr) on micromanipulated cells and confirmed by fluorescence in situ hybridisation (fish). four genera, amaricoccus, azoarcus, thauera and paraccoccus were detected, the latter only rarely present. all the biomass was involved in pha storage as shown by nile blu ... | 2008 | 18193421 |
| resonance raman spectroscopy of nitric oxide reductase and cbb(3) heme-copper oxidase. | elucidating the structure and properties of the active sites in cbb3 heme-copper oxidase and in nitric oxide reductase (nor) is crucial in understanding the reaction mechanisms of oxygen and nitric oxide reduction by both enzymes. in the work here, we have applied resonance raman (rr) spectroscopy to investigate the structure and properties of the binuclear heme b3-cub center of cbb3 heme-copper oxidase from pseudomonas stutzeri and the dinuclear heme b3-feb center of nor from paracoccus denitri ... | 2008 | 18211060 |
| differential efficacy of inhibition of mitochondrial and bacterial cytochrome bc1 complexes by center n inhibitors antimycin, ilicicolin h and funiculosin. | we have compared the efficacy of inhibition of the cytochrome bc1 complexes from yeast and bovine heart mitochondria and paracoccus denitrificans by antimycin, ilicicolin h, and funiculosin, three inhibitors that act at the quinone reduction site at center n of the enzyme. although the three inhibitors have some structural features in common, they differ significantly in their patterns of inhibition. also, while the overall folding pattern of cytochrome b around center n is similar in the enzyme ... | 2008 | 18022381 |
| kinetic and physical evidence that the diheme enzyme maug tightly binds to a biosynthetic precursor of methylamine dehydrogenase with incompletely formed tryptophan tryptophylquinone. | methylamine dehydrogenase (madh) contains the protein-derived cofactor tryptophan tryptophylquinone (ttq) which is generated by the posttranslational modification of two endogenous tryptophan residues. the modifications are incorporation of two oxygens into one tryptophan side chain and the covalent cross-linking of that side chain to a second tryptophan residue. this process requires at least one accessory gene, maug. inactivation of maug in vivo results in production of an inactive 119 kda tet ... | 2008 | 18220357 |
| electron transfer kinetics between soluble modules of paracoccus denitrificans cytochrome c1 and its physiological redox partners. | the transient electron transfer (et) interactions between cytochrome c1 of the bc1-complex from paracoccus denitrificans and its physiological redox partners cytochrome c552 and cytochrome c550 have been characterized functionally by stopped-flow spectroscopy. two different soluble fragments of cytochrome c1 were generated and used together with a soluble cytochrome c552 module as a model system for interprotein et reactions. both c1 fragments lack the membrane anchor; the c1 core fragment (c1cf ... | 2008 | 18241666 |
| [research advances in aerobic denitrifiers]. | this paper reviewed the varieties and characteristics of aerobic denitrifiers, their action mechanisms, and the factors affecting aerobic denitrification. aerobic denitrifiers mainly include pseudomonas, alcaligenes, paracoccus and bacillus, which are either aerobic or facultative aerobic, and heterotrophic. they can denitrify under aerobic conditions, with the main product being n2o. they can also convert nh4+ -n to gas product. the nitrate reductase which catalyzes the denitrification is perip ... | 2007 | 18260473 |
| [isolation and identification of aerobic denitrifiers and dispose the wastewater of no3(-)-n]. | after domesticating activated sludge to enriched aerobic denitrifiers, 5 aerobic denitrifiers were isolated from it. the removal rates of tn were 90.4%, 91.2%, 94.6%, 95.6% and 97% by fl, f2, f3, f5 and f7, respectively. according to the physiological biochemical index, five strains of aerobic denitrifiers were generally identified as pseudomonas sp., paracoccus sp., respectively. the establishment of continuous flow reactor surveyed various indices. and the efficiency of nitrate nitrogen remova ... | 2007 | 18269001 |
| assessment of microbial diversity in effluent treatment plants by culture dependent and culture independent approaches. | microbial community structure of two distinct effluent treatment plants (etps) of pesticide and pharmaceutical industries was assessed and defined by (i) culture dependent and culture independent approaches on the basis of 16s rrna gene sequencing, (ii) diversity index analysis - operational taxonomic units (otus). a total of 38 and 44 bacterial otus having 85-99% similarity with the closest match in the database were detected among pharmaceutical and pesticide sludge samples, respectively. fift ... | 2008 | 18280146 |
| paracoccus marinus sp. nov., an adonixanthin diglucoside-producing bacterium isolated from coastal seawater in tokyo bay. | two novel marine, gram-negative, non-motile, catalase- and oxidase-positive, aerobic bacteria were isolated from coastal seawater in tokyo bay. analysis of almost-complete 16s rrna gene sequences showed that the two isolates are members of the genus paracoccus, sharing highest 16s rrna gene sequence similarity (96.5 %) with paracoccus aminophilus nbrc 16710(t). the dna-dna reassociation values between p. aminophilus nbrc 16710(t) and these isolates were only 10-20 %, in contrast to the high dna ... | 2008 | 18218935 |
| pseudoazurin dramatically enhances the reaction profile of nitrite reduction by paracoccus pantotrophus cytochrome cd1 and facilitates release of product nitric oxide. | cytochrome cd(1) is a respiratory nitrite reductase found in the periplasm of denitrifying bacteria. when fully reduced paracoccus pantotrophus cytochrome cd(1) is mixed with nitrite in a stopped-flow apparatus in the absence of excess reductant, a kinetically stable complex of enzyme and product forms, assigned as a mixture of cfe(ii) d(1)fe(ii)-no(+) and cfe(iii) d(1)fe(ii)-no (cd(1)-x). however, in order for the enzyme to achieve steady-state turnover, product (no) release must occur. in this ... | 2008 | 18310770 |
| spectroscopic study on the communication between a heme a3 propionate, asp399 and the binuclear center of cytochrome c oxidase from paracoccus denitrificans. | the proton pumping mechanism of cytochrome c oxidase on a molecular level is highly disputed. recently theoretical calculations and real time electron transfer measurements indicated the involvement of residues in the vicinity of the ring a propionate of heme a3, including asp399 and the cub ligands his 325, 326. in this study we probed the interaction of asp399 with the binuclear center and characterize the protonation state of its side chain. redox induced ftir difference spectra of mutations ... | 2008 | 18078804 |
| benefits of membrane electrodes in the electrochemistry of metalloproteins: mediated catalysis of paracoccus pantotrophus cytochrome c peroxidase by horse cytochrome c: a case study. | a comparative study of direct and mediated electrochemistry of metalloproteins in bulk and membrane-entrapped solutions is presented. this work reports the first electrochemical study of the electron transfer between a bacterial cytochrome c peroxidase and horse heart cytochrome c. the mediated catalysis of the peroxidase was analysed both using the membrane electrode configuration and with all proteins in solution. an apparent michaelis constant of 66 +/- 4 and 42 +/- 5 microm was determined at ... | 2008 | 18365258 |
| phylogenetic and enzymatic diversity of deep subseafloor aerobic microorganisms in organics- and methane-rich sediments off shimokita peninsula. | "a meta-enzyme approach" is proposed as an ecological enzymatic method to explore the potential functions of microbial communities in extreme environments such as the deep marine subsurface. we evaluated a variety of extra-cellular enzyme activities of sediment slurries and isolates from a deep subseafloor sediment core. using the new deep-sea drilling vessel "chikyu", we obtained 365 m of core sediments that contained approximately 2% organic matter and considerable amounts of methane from offs ... | 2008 | 18368287 |
| ultrafast ligand binding dynamics in the active site of native bacterial nitric oxide reductase. | the active site of nitric oxide reductase from paracoccus denitrificans contains heme and non-heme iron and is evolutionarily related to heme-copper oxidases. the co and no dynamics in the active site were investigated using ultrafast transient absorption spectroscopy. we find that, upon photodissociation from the active site heme, 20% of the co rebinds in 170 ps, suggesting that not all the co transiently binds to the non-heme iron. the remaining 80% does not rebind within 4 ns and likely migra ... | 2008 | 18420024 |
| the respiratory nitric oxide reductase (norbc) from paracoccus denitrificans. | the two subunit cytochrome bc complex (norbc) isolated from membranes of the model denitrifying soil bacterium paracoccus denitrificans is the best characterized example of the bacterial respiratory nitric oxide reductases. these are members of the superfamily of heme-copper oxidases and are characterized by the elemental composition of their active site, which contains nonheme iron rather than copper, at which the reductive coupling of two molecules of nitric oxide to form nitrous oxide is cata ... | 2008 | 18433624 |
| microbial degradation and metabolic pathway of pyridine by a paracoccus sp. strain bw001. | a bacterial strain using pyridine as sole carbon, nitrogen and energy source was isolated from the activated sludge of a coking wastewater treatment plant. by means of morphologic observation, physiological characteristics study and 16s rrna gene sequence analysis, the strain was identified as the species of paracoccus. the strain could degrade 2,614 mg l(-1) of pyridine completely within 49.5 h. experiment designed to track the metabolic pathway showed that pyridine ring was cleaved between the ... | 2008 | 18437507 |
| in situ monitoring of the catalytic activity of cytochrome c oxidase in a biomimetic architecture. | cytochrome c oxidase (cco) from paracoccus denitrificans was immobilized in a strict orientation via a his-tag attached to subunit i on a gold film and reconstituted in situ into a protein-tethered bilayer lipid membrane. in this orientation, the cytochrome c (cyt c) binding site is directed away from the electrode pointing to the outer side of the protein-tethered bilayer lipid membrane architecture. the cco can thus be activated by cyt c under aerobic conditions. catalytic activity was monitor ... | 2008 | 18441024 |
| calcium-dependent heme structure in the reduced forms of the bacterial cytochrome c peroxidase from paracoccus pantotrophus. | this work reports for the first time a resonance raman study of the mixed-valence and fully reduced forms of paracoccus pantotrophus bacterial cytochrome c peroxidase. the spectra of the active mixed-valence enzyme show changes in the structure of the ferric peroxidatic heme compared to the fully oxidized enzyme; these differences are observed upon reduction of the electron-transferring heme and upon full occupancy of the calcium site. for the mixed-valence form in the absence of ca(2+), the per ... | 2008 | 18442258 |
| biogenesis of cytochrome c oxidase--in vitro approaches to study cofactor insertion into a bacterial subunit i. | biogenesis of cytochrome c oxidase is a complex process involving more than 30 known accessory proteins in yeast for the regulation of transcription and translation, membrane insertion and protein processing, cofactor insertion, and subunit assembly. here, we focus on the process of cofactor insertion into subunit i of cytochrome c oxidase using the soil bacterium paracoccus denitrificans as a model organism. the use of bacterial systems facilitates biogenesis studies, as the number of required ... | 2008 | 18445471 |
| unexpected dependence on ph of no release from paracoccus pantotrophus cytochrome cd1. | a previous study of nitrite reduction by paracoccus pantotrophus cytochrome cd(1) at ph 7.0 identified early reaction intermediates. the c-heme rapidly oxidised and nitrite was reduced to no at the d(1)-heme. a slower equilibration of electrons followed, forming a stable complex assigned as 55% cfe(iii)d(1)fe(ii)-no and 45% cfe(ii)d(1)fe(ii)-no(+). no catalytically competent no release was observed. here we show that at ph 6.0, a significant proportion of the enzyme undergoes turnover and releas ... | 2008 | 18471989 |
| conformational dynamics coupled to protonation equilibrium at the cua site of thermus thermophilus: insights into the origin of thermostability. | an extremely slow ph dependent conformational equilibrium between a valence-delocalized and a valence-trapped species of the dinuclear cua domain of cytochrome c oxidase from thermus thermophilus has been identified and characterized using uv-visible absorption, circular dichroism, time-resolved fluorescence and electron paramagnetic resonance spectroscopy as well as by stopped-flow kinetic techniques. the results indicated that the nature of this ph dependent conformation change in the cua doma ... | 2008 | 18189418 |
| structural comparison of crystal and solution states of the 138 kda complex of methylamine dehydrogenase and amicyanin from paracoccus versutus. | methylamine can be used as the sole carbon source of certain methylotrophic bacteria. methylamine dehydrogenase catalyzes the conversion of methylamine into formaldehyde and donates electrons to the electron transfer protein amicyanin. the crystal structure of the complex of methylamine dehydrogenase and amicyanin from paracoccus versutus has been determined, and the rate of electron transfer from the tryptophan tryptophylquinone cofactor of methylamine dehydrogenase to the copper ion of amicyan ... | 2008 | 18512962 |
| the role of the conserved tryptophan272 of the paracoccus denitrificans cytochrome c oxidase in proton pumping. | the catalytic mechanism of heme-copper oxidases - electron transfer coupled to proton pumping - is not yet fully understood. single turnover experiments in which fully reduced cytochrome aa(3) from paracoccus denitrificans reacts with o(2) using the microsecond freeze-hyperquenching sampling technique enabled trapping of transient catalytic intermediates and analysis by low temperature uv-visible, x-band and q-band epr spectroscopy. our recent findings (wiertz et al. (2007) j. biol. chem. 282, 3 ... | 2008 | 18515062 |
| biofiltration of trimethylamine, dimethylamine, and methylamine by immobilized paracoccus sp. cp2 and arthrobacter sp. cp1. | a biofilter using granular activated carbon with immobilized paracoccus sp. cp2 was applied to the elimination of 10-250 ppm of trimethylamine (tma), dimethylamine (dma), and methylamine (ma). the results indicated that the system effectively treated ma (>93%), dma (>90%), and tma (>85%) under high loading conditions, and the maximum degradation rates were 1.4, 1.2, and 0.9g-nkg(-1) gac d(-1). among the three different amines treated, tma was the most difficult to degrade and resulted in ammonia ... | 2008 | 18331754 |
| experimental evidence for a link among cupredoxins: red, blue, and purple copper transformations in nitrous oxide reductase. | the cupredoxin fold is an important motif in numerous proteins that are central to several critical cellular processes ranging from aerobic and anaerobic respiration to catalysis and iron homeostasis. three types of copper sites have been found to date within cupredoxin folds: blue type 1 (t1) copper, red type 2 (t2) copper, and purple cu(a). although as much as 90% sequence difference has been observed among some members of this superfamily of proteins that span several kingdoms, sequence align ... | 2008 | 18535143 |
| theoretical and computational analysis of the membrane potential generated by cytochrome c oxidase upon single electron injection into the enzyme. | we have developed theory and the computational scheme for the analysis of the kinetics of the membrane potential generated by cytochrome c oxidase upon single electron injection into the enzyme. the theory allows one to connect the charge motions inside the enzyme to the membrane potential observed in the experiments by using data from the "dielectric topography" map of the enzyme that we have created. the developed theory is applied for the analysis of the potentiometric data recently reported ... | 2008 | 18541140 |
| life history of paracoccus marginatus (hemiptera: pseudococcidae) on four host plant species under laboratory conditions. | life history of the mealybug, paracoccus marginatus williams and granara de willink, on three ornamental plants [hibiscus rosa-sinensis l., acalypha wilkesiana (muell.-arg.), and plumeria rubra l.] and one weed species (parthenium hysterophorus l.) was studied under laboratory conditions. mealybugs were able to develop, survive, and reproduce on all four hosts; however, there were differences in the life history parameters. adult females that developed on acalypha and parthenium emerged approxim ... | 2008 | 18559168 |
| a catalytic di-heme bis-fe(iv) intermediate, alternative to an fe(iv)=o porphyrin radical. | high-valent iron species are powerful oxidizing agents in chemical and biological catalysis. the best characterized form of an fe(v) equivalent described in biological systems is the combination of a b-type heme with fe(iv)=o and a porphyrin or amino acid cation radical (termed compound i). this work describes an alternative natural mechanism to store two oxidizing equivalents above the ferric state for biological oxidation reactions. maug is an enzyme that utilizes two covalently bound c-type h ... | 2008 | 18562294 |
| transposable modules generated by a single copy of insertion sequence ispme1 and their influence on structure and evolution of natural plasmids of paracoccus methylutens dm12. | we demonstrated that a single copy of insertion sequence ispme1 can mobilize adjacent segments of genomic dna of paracoccus methylutens dm12, which leads to the generation of diverse transposable elements of various size and dna contents. all elements (named transposable modules [tmos]) contain ispme1 (placed at the 5' ends of the elements) and have variable 3'-end regions of between 0.5 and 5 kb. ispme1 was shown to encode an outwardly oriented promoter, which may activate the transcription of ... | 2008 | 18296518 |
| simultaneously occurring nitrification and denitrification under oxygen gradient by polyelectrolyte complex-coimmobilized nitrosomonas europaea and paracoccus denitrificans cells. | | 1988 | 18584619 |
| sulfur oxidation of paracoccus pantotrophus: the sulfur-binding protein soxyz is the target of the periplasmic thiol-disulfide oxidoreductase soxs. | the periplasmic thiol-disulfide oxidoreductase soxs is essential for chemotrophic growth of paracoccus pantotrophus with thiosulfate. to trap its periplasmic partner, the cysteine residues of the cysxaaxaacys motif of soxs (11 kda) were changed to alanine by site-directed mutagenesis. the disrupted soxs gene of the homogenote mutant g omegas was complemented with plasmids carrying the mutated soxs[c13a] or soxs[c16a] gene. strain g omegas(prd179.6[c16a](s)) displayed a marginal thiosulfate-oxidi ... | 2008 | 18599826 |
| kinetic modeling of poly(beta-hydroxybutyrate) production and consumption by paracoccus pantotrophus under dynamic substrate supply. | the objective of the research was to obtain insights into the behavior of microorganisms under feast/famine conditions as often occur in wastewater treatment processes. the response of microorganisms to such conditions is the accumulation of storage polymers like poly(beta-hydroxybutyrate). the research was performed using a pure culture of paracoccus pantotrophus lmd 94.21. a steady-state c-limited chemostat culture was switched to batch mode and a pulse of acetate was added. as long as externa ... | 1997 | 18636587 |
| microbial community of granules in expanded granular sludge bed reactor for simultaneous biological removal of sulfate, nitrate and lactate. | this study studied the cultivation of granules from an expanded granular sludge bed reactor that simultaneously transforms sulfates, nitrates, and oxygen to elementary sulfur, nitrogen gas, and carbon dioxides, respectively. the living cells accumulate at the granule outer layers, as revealed by the multicolor staining and confocal laser scanning microscope technique. the microbial community comprises sulfate-reducing bacteria (srb, desulfomicrobium sp.), heterotrophic (pseudomonas aeruginosa an ... | 2008 | 18483736 |
| high prevalence of fastidious bacteria in 1520 cases of uveitis of unknown etiology. | the etiologic evaluation of uveitis is frequently unsuccessful when noninvasive methods are used. we conducted a prospective study to evaluate systematic screening for pathogens of uveitis. all patients with uveitis referred to the participating tertiary ophthalmology departments from january 2001 to september 2007 underwent intraocular and serum specimen collection. the standardized protocol for laboratory investigations included universal polymerase chain reaction (pcr)-based detection of any ... | 2008 | 18520326 |
| very early reaction intermediates detected by microsecond time scale kinetics of cytochrome cd1-catalyzed reduction of nitrite. | paracoccus pantotrophus cytochrome cd(1) is a nitrite reductase found in the periplasm of many denitrifying bacteria. it catalyzes the reduction of nitrite to nitric oxide during the denitrification part of the biological nitrogen cycle. previous studies of early millisecond intermediates in the nitrite reduction reaction have shown, by comparison with ph 7.0, that at the optimum ph, approximately ph 6, the earliest intermediates were lost in the dead time of the instrument. access to early time ... | 2008 | 18669629 |
| thermodynamic redox behavior of the heme centers in a-type heme-copper oxygen reductases: comparison between the two subfamilies. | the study of the thermodynamic redox behavior of the hemes from two members of the a family of heme-copper oxygen reductases, paracoccus denitrificans aa3 (a1 subfamily) and rhodothermus marinus caa3 (a2 subfamily) enzymes, is presented. at different ph values, midpoint reduction potentials and interaction potentials were obtained in the framework of a pairwise model for two interacting redox centers. in both enzymes, the hemes have different reduction potentials. for the a1-type enzyme, it was ... | 2008 | 18676644 |
| an exceptionally dmso-tolerant alcohol dehydrogenase for the stereoselective reduction of ketones. | a novel short-chain alcohol dehydrogenase from paracoccus pantotrophus dsm 11072, which is applicable for hydrogen transfer, has been identified, cloned, and overexpressed in e. coli. the enzyme stereoselectively reduces several ketones in a sustainable substrate-coupled approach using 2-propanol (5% v/v) as hydrogen donor. the enzyme maintained its activity in organic co-solvents in biphasic as well as monophasic systems and was even active in micro-aqueous media (1% v/v aqueous buffer). in gen ... | 2008 | 18702138 |
| assigning vibrational spectra of ferryl-oxo intermediates of cytochrome c oxidase by periodic orbits and molecular dynamics. | complexity is inherent in biological molecules not only because of the large number of atoms but also because of their nonlinear interactions responsible for chaotic behaviours, localized motions, and bifurcation phenomena. thus, versatile spectroscopic techniques have been invented to achieve temporal and spatial resolution to minimize the uncertainties in assigning the spectra of complex molecules. can we associate spectral lines to specific chemical bonds or species in a large molecule? can e ... | 2008 | 18712866 |
| two variants of the assembly factor surf1 target specific terminal oxidases in paracoccus denitrificans. | biogenesis of cytochrome c oxidase (cox) relies on a large number of assembly proteins, one of them being surf1. in humans, the loss of surf1 function is associated with leigh syndrome, a fatal neurodegenerative disorder. in the soil bacterium paracoccus denitrificans, homologous genes specifying surf1 have been identified and located in two operons of terminal oxidases: surf1q is the last gene of the qox operon (coding for a ba(3)-type ubiquinol oxidase), and surf1c is found at the end of the c ... | 2008 | 18582433 |
| the proton donor for o-o bond scission by cytochrome c oxidase. | cytochrome c oxidase is the main catalyst of oxygen consumption in mitochondria and many aerobic bacteria. the key step in oxygen reduction is scission of the o-o bond and formation of an intermediate p(r) of the binuclear active site composed of heme a(3) and cu(b). the donor of the proton required for this reaction has been suggested to be a unique tyrosine residue (tyr-280) covalently cross-linked to one of the histidine ligands of cu(b). to test this idea we used the glu-278-gln mutant enzym ... | 2008 | 18664577 |
| cell-cell signaling and the agrobacterium tumefaciens ti plasmid copy number fluctuations. | the agrobacterium tumefaciens oncogenic ti plasmids replicate and segregate to daughter cells via repabc cassettes, in which repa and repb are plasmid partitioning genes and repc encodes the replication initiator protein. repabc cassettes are encountered in a growing number of plasmids and chromosomes of the alpha-proteobacteria, and findings from particular representatives of agrobacteria, rhizobia and paracoccus have began to shed light on their structure and functions. amongst repabc replicon ... | 2008 | 18664372 |
| electron and proton transfer in the ba(3) oxidase from thermus thermophilus. | the ba(3)-type cytochrome c oxidase from thermus thermophilus is phylogenetically very distant from the aa(3)-type cytochrome c oxidases. nevertheless, both types of oxidases have the same number of redox-active metal sites and the reduction of o(2) to water is catalysed at a haem a(3)-cu(b) catalytic site. the three-dimensional structure of the ba(3) oxidase reveals three possible proton-conducting pathways showing very low homology compared to those of the mitochondrial, rhodobacter sphaeroide ... | 2008 | 18752061 |
| molecular dynamics of amicyanin reveals a conserved dynamical core for blue copper proteins. | molecular dynamics simulation has been carried out for the blue copper protein amicyanin from two different sources, paracoccus denitrificans and paraccocus versutus, to investigate the structural and dynamical properties common to the two molecules and to identify prominent features shared with proteins of the same family, the monomeric cupredoxins. the two amicyanins have almost identical secondary and tertiary structure. in the simulation, they differ for the number of hydrogen bonds in the m ... | 2009 | 18767164 |
| interdependence of two nark domains in a fused nitrate/nitrite transporter. | nitrate uptake is essential for various bacterial processes and combines with nitrite export to form the usual initial steps of denitrification, a process that reduces nitrate to dinitrogen gas. although many bacterial species contain nark-like transporters that are proposed to function as either nitrate/proton symporters or nitrate/nitrite antiporters based on sequence homology, these transporters remain, in general, poorly characterized. several bacteria appear to contain a transporter that is ... | 2008 | 18823285 |
| identification of two inactive forms of the central sulfur cycle protein soxyz of paracoccus pantotrophus. | the central protein of the sulfur-oxidizing enzyme system of paracoccus pantotrophus, soxyz, reacts with three different sox proteins. its active site cys110(y) is on the carboxy-terminus of the soxy subunit. soxyz "as isolated" consisted mainly of the catalytically inactive soxy-y(z)(2) heterotetramer linked by a cys110(y)-cys110(y) interprotein disulfide. sulfide activated soxyz "as isolated" 456-fold, reduced the disulfide, and yielded an active soxyz heterodimer. the reductant tris(2-carboxy ... | 2008 | 18834882 |
| a d-pathway mutation decouples the paracoccus denitrificans cytochrome c oxidase by altering the side-chain orientation of a distant conserved glutamate. | asparagine 131, located near the cytoplasmic entrance of the d-pathway in subunit i of the paracoccus denitrificans aa(3) cytochrome c oxidase, is a residue crucial for proton pumping. when replaced by an aspartate, the mutant enzyme is completely decoupled: while retaining full cytochrome c oxidation activity, it does not pump protons. the same phenotype is observed for two other substitutions at this position (n131e and n131c), whereas a conservative replacement by glutamine affects both activ ... | 2008 | 18930738 |
| the protonation state of the cross-linked tyrosine during the catalytic cycle of cytochrome c oxidase. | cytochrome c oxidase is the terminal complex of the respiratory chain in mitochondria and some aerobic bacteria and is responsible for most of the o(2) consumption in biology. the key reaction in the catalysis of o(2) reduction is o-o bond scission that requires four electrons and a proton. in our recent work (gorbikova, e. a., belevich, i., wikstrom, m., and verkhovsky, m. i. (2008) proc. natl. acad. sci. u. s. a. 105, 10733-10737), it was shown that the cross-linked tyr-280 (paracoccus denitri ... | 2008 | 18931371 |
| characterization of mutations in crucial residues around the q(o) binding site of the cytochrome bc complex from paracoccus denitrificans. | the protonation state of residues around the q(o) binding site of the cytochrome bc(1) complex from paracoccus denitrificans and their interaction with bound quinone(s) was studied by a combined electrochemical and ftir difference spectroscopic approach. site-directed mutations of two groups of conserved residues were investigated: (a) acidic side chains located close to the surface and thought to participate in a water chain leading up to the heme b(l) edge, and (b) residues located in the vici ... | 2008 | 18721136 |
| biodegradation of insecticide carbofuran by paracoccus sp. ym3. | a bacterium (paracoccus sp. ym3) capable of degrading carbofuran was isolated from carbofuran-contaminated sludge. the strain was shown to metabolize carbofuran (50 mg l(-1)) to carbofuran-7-phenol in minimal salt medium within 6 days in which the pesticide was the only source of carbon. carbofuran and its main metabolite were analyzed by high performance liquid chromatography (hplc). the addition of an other carbon source led to accelerated biodegradation. the relevant degrading-enzyme was intr ... | 2008 | 18803113 |
| probing the paracoccus denitrificans cytochrome c(1)-cytochrome c(552) interaction by mutagenesis and fast kinetics. | electron transfer (et) between paracoccus denitrificans cytochrome (cyt) c(1) and cytochrome c(552) was studied using the soluble redox fragments cyt c(1cf) and cyt c(552f). a new ruthenium cyt c(552f) derivative labeled at c23 (ru(z)-23-c(552f)) was designed to measure rapid electron transfer with cyt c(1cf) in the physiological direction using flash photolysis. the bimolecular rate constant k(12) decreased rapidly with ionic strength above 40 mm, consistent with a diffusional process guided by ... | 2008 | 19006325 |
| coherent raman detected electron spin resonance spectroscopy of metalloproteins: linking electron spin resonance and magnetic circular dichroism. | the simultaneous excitation of paramagnetic molecules with optical (laser) and microwave radiation in the presence of a magnetic field can cause an amplitude, or phase, modulation of the transmitted light at the microwave frequency. the detection of this modulation indicates the presence of coupled optical and esr transitions. the phenomenon can be viewed as a coherent raman effect or, in most cases, as a microwave frequency modulation of the magnetic circular dichroism by the precessing magneti ... | 2008 | 19021521 |
| a protein-based oxygen biosensor for high-throughput monitoring of cell growth and cell viability. | fluorescently labeled hemocyanin has been previously proposed as an oxygen sensor. in this study, we explored the efficacy of this biosensor for monitoring the biological oxygen consumption of bacteria and its use in testing bacterial cell growth and viability of escherichia coli, pseudomonas aeruginosa, paracoccus denitrificans, and staphylococcus simulans. using a microwell plate, the time courses for the complete deoxygenation of samples with different initial concentrations of cells were obt ... | 2009 | 19084497 |