paracoccus denitrificans

Summary

Summary: A species of bacteria isolated from soil.

Top Publications

  1. Zharova T, Vinogradov A. Energy-dependent transformation of F0.F1-ATPase in Paracoccus denitrificans plasma membranes. J Biol Chem. 2004;279:12319-24 pubmed
    F(0).F(1)-ATP synthase in tightly coupled inside-out vesicles derived from Paracoccus denitrificans catalyzes rapid respiration-supported ATP synthesis, whereas their ATPase activity is very low...
  2. Tesarik R, Sedláček V, Plocková J, Wimmerova M, Turanek J, Kucera I. Heterologous expression and molecular characterization of the NAD(P)H:acceptor oxidoreductase (FerB) of Paracoccus denitrificans. Protein Expr Purif. 2009;68:233-8 pubmed publisher
    ..Despite somewhat lower thermal stability, the fusion protein is considered a better candidate for crystallization than the wild-type one due to a more negative value of its second optical viral coefficient. ..
  3. Mazoch J, Kunák M, Kucera I, van Spanning R. Fine-tuned regulation by oxygen and nitric oxide of the activity of a semi-synthetic FNR-dependent promoter and expression of denitrification enzymes in Paracoccus denitrificans. Microbiology. 2003;149:3405-12 pubmed
    In Paracoccus denitrificans at least three fumarate and nitrate reductase regulator (FNR)-like proteins [FnrP, nitrite and nitric oxide reductases regulator (NNR) and NarR] control the expression of several genes necessary for ..
  4. Reimann J, Flock U, Lepp H, Honigmann A, Adelroth P. A pathway for protons in nitric oxide reductase from Paracoccus denitrificans. Biochim Biophys Acta. 2007;1767:362-73 pubmed
    ..denitrificans in order to search for such a pathway. A plausible pathway, consisting of conserved protonatable residues, is suggested. ..
  5. Chen L, Doi M, Durley R, Chistoserdov A, Lidstrom M, Davidson V, et al. Refined crystal structure of methylamine dehydrogenase from Paracoccus denitrificans at 1.75 A resolution. J Mol Biol. 1998;276:131-49 pubmed
    The three-dimensional structure of the quinoprotein methylamine dehydrogenase from Paracoccus denitrificans has been refined at 1.75 A resolution utilizing the DNA-based protein sequence...
  6. Pinakoulaki E, Varotsis C. Time-resolved resonance Raman and time-resolved step-scan FTIR studies of nitric oxide reductase from Paracoccus denitrificans: comparison of the heme b3-FeB site to that of the heme-CuB in oxidases. Biochemistry. 2003;42:14856-61 pubmed
    ..The results are compared to those obtained for the aa(3)-cytochrome c oxidase from Paracoccus denitrificans. The results are compared to those obtained for the aa(3)-cytochrome c oxidase from P. denitrificans...
  7. Drosou V, Reincke B, Schneider M, Ludwig B. Specificity of the interaction between the Paracoccus denitrificans oxidase and its substrate cytochrome c: comparing the mitochondrial to the homologous bacterial cytochrome c(552), and its truncated and site-directed mutants. Biochemistry. 2002;41:10629-34 pubmed
    ..Several lines of evidence suggest that in intact membranes the heme aa(3) oxidase from Paracoccus denitrificans receives its electrons from the membrane-bound cytochrome c(552)...
  8. Siddavattam D, Karegoudar T, Mudde S, Kumar N, Baddam R, Avasthi T, et al. Genome of a novel isolate of Paracoccus denitrificans capable of degrading N,N-dimethylformamide. J Bacteriol. 2011;193:5598-9 pubmed publisher
    ..We report a de novo-assembled sequence and annotation of the genome of a novel isolate of Paracoccus denitrificans originally sourced from coal mine tailings in India...
  9. Sedláček V, Kucera I. Chromate reductase activity of the Paracoccus denitrificans ferric reductase B (FerB) protein and its physiological relevance. Arch Microbiol. 2010;192:919-26 pubmed publisher
    The homodimeric flavoprotein FerB of Paracoccus denitrificans catalyzed the reduction of chromate with NADH as electron donor. When present, oxygen was reduced concomitantly with chromate...

More Information

Publications94

  1. Li X, Feng M, Wang Y, Tachikawa H, Davidson V. Evidence for redox cooperativity between c-type hemes of MauG which is likely coupled to oxygen activation during tryptophan tryptophylquinone biosynthesis. Biochemistry. 2006;45:821-8 pubmed
    ..The structural and mechanistic implications of these findings are discussed. ..
  2. Chen L, Mathews F, Davidson V, Huizinga E, Vellieux F, Hol W. Three-dimensional structure of the quinoprotein methylamine dehydrogenase from Paracoccus denitrificans determined by molecular replacement at 2.8 A resolution. Proteins. 1992;14:288-99 pubmed
    ..The redox cofactor of MADH, tryptophan tryptophylquinone is highly unusual. It is formed from two covalently linked tryptophan side chains at positions 57 and 107 of the L subunit, one of which contains an orthoquinone. ..
  3. Anttila J, Heinonen P, Nenonen T, Pino A, Iwai H, Kauppi E, et al. Is coproporphyrin III a copper-acquisition compound in Paracoccus denitrificans?. Biochim Biophys Acta. 2011;1807:311-8 pubmed publisher
    b>Paracoccus denitrificans is a soil bacterium which can respire aerobically and also denitrify if oxygen is absent...
  4. Gao D, Maehara A, Yamane T, Ueda S. Identification of the intracellular polyhydroxyalkanoate depolymerase gene of Paracoccus denitrificans and some properties of the gene product. FEMS Microbiol Lett. 2001;196:159-64 pubmed
    b>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...
  5. Goenrich M, Bartoschek S, Hagemeier C, Griesinger C, Vorholt J. A glutathione-dependent formaldehyde-activating enzyme (Gfa) from Paracoccus denitrificans detected and purified via two-dimensional proton exchange NMR spectroscopy. J Biol Chem. 2002;277:3069-72 pubmed
    ..We describe here the discovery of an enzyme from Paracoccus denitrificans that accelerates this spontaneous condensation reaction...
  6. Roberts D, Salazar D, Fulmer J, Frerman F, Kim J. Crystal structure of Paracoccus denitrificans electron transfer flavoprotein: structural and electrostatic analysis of a conserved flavin binding domain. Biochemistry. 1999;38:1977-89 pubmed
    The crystal structure of electron transfer flavoprotein (ETF) from Paracoccus denitrificans was determined and refined to an R-factor of 19.3% at 2.6 A resolution...
  7. Kojima T, Yamane T, Nakano H. In vitro selection of DNA binding sites for transcription factor, PhaR, from Paracoccus denitrificans using genetic library on microbeads and flow cytometry. J Biosci Bioeng. 2006;101:440-4 pubmed
    We attempted the selection of a site for DNA binding to a transcription factor, PhaR, from Paracoccus denitrificans expressed by cell-free protein synthesis, from a random oligonucleotide library on microbeads that was constructed by the ..
  8. Bergaust L, van Spanning R, Frostegard A, Bakken L. Expression of nitrous oxide reductase in Paracoccus denitrificans is regulated by oxygen and nitric oxide through FnrP and NNR. Microbiology. 2012;158:826-34 pubmed publisher
    ..We investigated denitrification phenotypes of Paracoccus denitrificans mutants deficient in: (i) regulatory proteins (three FNR-type transcriptional regulators, NarR, NNR and ..
  9. Bachmann J, Bauer B, Zwicker K, Ludwig B, Anderka O. The Rieske protein from Paracoccus denitrificans is inserted into the cytoplasmic membrane by the twin-arginine translocase. FEBS J. 2006;273:4817-30 pubmed
    ..Based on the presence of two consecutive arginines, it was argued that the ISP of Paracoccus denitrificans, a Gram-negative soil bacterium, is inserted into the cytoplasmic membrane via the twin-arginine ..
  10. Sedláček V, van Spanning R, Kucera I. Characterization of the quinone reductase activity of the ferric reductase B protein from Paracoccus denitrificans. Arch Biochem Biophys. 2009;483:29-36 pubmed publisher
    The ferric reductase B (FerB) protein of Paracoccus denitrificans exhibits activity of an NAD(P)H: Fe(III) chelate, chromate and quinone oxidoreductase...
  11. Wang Y, Graichen M, Liu A, Pearson A, Wilmot C, Davidson V. MauG, a novel diheme protein required for tryptophan tryptophylquinone biogenesis. Biochemistry. 2003;42:7318-25 pubmed
    The biosynthesis of methylamine dehydrogenase (MADH) from Paracoccus denitrificans requires four genes in addition to those that encode the two structural protein subunits. None of these gene products have been previously isolated...
  12. Coby A, Picardal F. Inhibition of NO3- and NO2- reduction by microbial Fe(III) reduction: evidence of a reaction between NO2- and cell surface-bound Fe2+. Appl Environ Microbiol. 2005;71:5267-74 pubmed
    ..Previous adsorption of Fe(2+) onto Paracoccus denitrificans inhibited NO(x)(-) reduction, showing that Fe(II) can reduce rates of soluble electron acceptor ..
  13. Puustinen A, Finel M, Virkki M, Wikstrom M. Cytochrome o (bo) is a proton pump in Paracoccus denitrificans and Escherichia coli. FEBS Lett. 1989;249:163-7 pubmed
    Spheroplasts from aerobically grown wild-type Paracoccus denitrificans cells respire with succinate despite specific inhibition of the cytochrome bc1 complex by myxothiazol...
  14. De Boer A, van der Oost J, Reijnders W, Westerhoff H, Stouthamer A, Van Spanning R. Mutational analysis of the nor gene cluster which encodes nitric-oxide reductase from Paracoccus denitrificans. Eur J Biochem. 1996;242:592-600 pubmed
    The genes that encode the hc-type nitric-oxide reductase from Paracoccus denitrificans have been identified...
  15. Strohm T, Griffin B, Zumft W, Schink B. Growth yields in bacterial denitrification and nitrate ammonification. Appl Environ Microbiol. 2007;73:1420-4 pubmed
    ..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 ..
  16. Van Spanning R, Reijnders W, Stouthamer A. Integration of heterologous DNA into the genome of Paracoccus denitrificans is mediated by a family of IS1248-related elements and a second type of integrative recombination event. J Bacteriol. 1995;177:4772-8 pubmed
    All members of the IS1248 family residing in the genome of Paracoccus denitrificans have been isolated by using a set of insertion sequence entrapment vectors...
  17. Batista A, Pereira M. Sodium influence on energy transduction by complexes I from Escherichia coli and Paracoccus denitrificans. Biochim Biophys Acta. 2011;1807:286-92 pubmed publisher
    The nature of the ions that are translocated by Escherichia coli and Paracoccus denitrificans complexes I was investigated. We observed that E...
  18. Field S, Thorndycroft F, Matorin A, Richardson D, Watmough N. The respiratory nitric oxide reductase (NorBC) from Paracoccus denitrificans. Methods Enzymol. 2008;437:79-101 pubmed publisher
    ..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...
  19. Van Spanning R, Houben E, Reijnders W, Spiro S, Westerhoff H, Saunders N. Nitric oxide is a signal for NNR-mediated transcription activation in Paracoccus denitrificans. J Bacteriol. 1999;181:4129-32 pubmed
    ..of the nirI, nirS, and norC promoters were assayed in the wild type and in NNR-deficient mutants of Paracoccus denitrificans grown under various growth conditions...
  20. Shin S, Feng M, Davidson V. Mutation of Trp(93) of MauG to tyrosine causes loss of bound Ca(2+) and alters the kinetic mechanism of tryptophan tryptophylquinone cofactor biosynthesis. Biochem J. 2013;456:129-37 pubmed publisher
    ..A kinetic model is presented to explain the long pre-steady-state phase of the reaction of W93Y MauG, and the role of this conserved tryptophan residue in MauG and related dihaem enzymes is discussed. ..
  21. Lee Y, Shearer N, Spiro S. Transcription factor NNR from Paracoccus denitrificans is a sensor of both nitric oxide and oxygen: isolation of nnr* alleles encoding effector-independent proteins and evidence for a haem-based sensing mechanism. Microbiology. 2006;152:1461-70 pubmed
    The nitrite reductase and nitric oxide reductase regulator (NNR) from Paracoccus denitrificans activates transcription in response to nitric oxide (NO)...
  22. Yukl E, Goblirsch B, Davidson V, Wilmot C. Crystal structures of CO and NO adducts of MauG in complex with pre-methylamine dehydrogenase: implications for the mechanism of dioxygen activation. Biochemistry. 2011;50:2931-8 pubmed publisher
    ..Gln103 is in a position to provide a hydrogen bond to the Fe(IV)?O moiety that may account for the unusual stability of this species in MauG. ..
  23. Harms N, Ras J, Reijnders W, Van Spanning R, Stouthamer A. S-formylglutathione hydrolase of Paracoccus denitrificans is homologous to human esterase D: a universal pathway for formaldehyde detoxification?. J Bacteriol. 1996;178:6296-9 pubmed
    Downstream of flhA, the Paracoccus denitrificans gene encoding glutathione-dependent formaldehyde dehydrogenase, an open reading frame was identified and called fghA...
  24. Pearson A, De la Mora Rey T, Graichen M, Wang Y, Jones L, Marimanikkupam S, et al. Further insights into quinone cofactor biogenesis: probing the role of mauG in methylamine dehydrogenase tryptophan tryptophylquinone formation. Biochemistry. 2004;43:5494-502 pubmed
    b>Paracoccus denitrificans methylamine dehydrogenase (MADH) is an enzyme containing a quinone cofactor tryptophan tryptophylquinone (TTQ) derived from two tryptophan residues (betaTrp(57) and betaTrp(108)) within the polypeptide chain...
  25. Sukumaran S, Hauser K, Rauscher A, Mäntele W. Thermal stability of outer membrane protein porin from Paracoccus denitrificans: FT-IR as a spectroscopic tool to study lipid-protein interaction. FEBS Lett. 2005;579:2546-50 pubmed
    ..Earlier we have reported the extreme thermal stability of porin from Paracoccus denitrificans reconstituted into liposomes...
  26. Iwata S, Ostermeier C, Ludwig B, Michel H. Structure at 2.8 A resolution of cytochrome c oxidase from Paracoccus denitrificans. Nature. 1995;376:660-9 pubmed
    ..8 A resolution of the four protein subunits containing cytochrome c oxidase from the soil bacterium Paracoccus denitrificans, complexed with antibody Fv fragment, is described...
  27. Barford C, Montoya J, Altabet M, Mitchell R. Steady-state nitrogen isotope effects of N2 and N2O production in Paracoccus denitrificans. Appl Environ Microbiol. 1999;65:989-94 pubmed
    ..We developed a simple steady-state reactor to allow the measurement of denitrification isotope effects in Paracoccus denitrificans. With [dO2] between 0 and 1...
  28. Kleinschroth T, Castellani M, Trinh C, Morgner N, Brutschy B, Ludwig B, et al. X-ray structure of the dimeric cytochrome bc(1) complex from the soil bacterium Paracoccus denitrificans at 2.7-Å resolution. Biochim Biophys Acta. 2011;1807:1606-15 pubmed publisher
    ..The complex from the ?-proteobacterium Paracoccus denitrificans, a model for the medically relevant mitochondrial complexes, lacked structural characterization...
  29. Yukl E, Liu F, Krzystek J, Shin S, Jensen L, Davidson V, et al. Diradical intermediate within the context of tryptophan tryptophylquinone biosynthesis. Proc Natl Acad Sci U S A. 2013;110:4569-73 pubmed publisher
    ..This work defines a unique mechanism for radical-mediated catalysis of a protein substrate, and has broad implications in the areas of applied biocatalysis and understanding of oxidative protein modification during oxidative stress...
  30. Jasaitis A, Backgren C, Morgan J, Puustinen A, Verkhovsky M, Wikstrom M. Electron and proton transfer in the arginine-54-methionine mutant of cytochrome c oxidase from Paracoccus denitrificans. Biochemistry. 2001;40:5269-74 pubmed
    Arginine 54 in subunit I of cytochrome c oxidase from Paracoccus denitrificans interacts with the formyl group of heme a...
  31. Ras J, van Ophem P, Reijnders W, Van Spanning R, Duine J, Stouthamer A, et al. Isolation, sequencing, and mutagenesis of the gene encoding NAD- and glutathione-dependent formaldehyde dehydrogenase (GD-FALDH) from Paracoccus denitrificans, in which GD-FALDH is essential for methylotrophic growth. J Bacteriol. 1995;177:247-51 pubmed
    NAD- and glutathione-dependent formaldehyde dehydrogenase (GD-FALDH) of Paracoccus denitrificans has been purified as a tetramer with a relative molecular mass of 150 kDa...
  32. Shin S, Feng M, Chen Y, Jensen L, Tachikawa H, Wilmot C, et al. The tightly bound calcium of MauG is required for tryptophan tryptophylquinone cofactor biosynthesis. Biochemistry. 2011;50:144-50 pubmed
    ..These results are discussed in the context of the structures of MauG and heme-containing peroxidases...
  33. Kelly D, Euzéby J, Goodhew C, Wood A. Redefining Paracoccus denitrificans and Paracoccus pantotrophus and the case for a reassessment of the strains held by international culture collections. Int J Syst Evol Microbiol. 2006;56:2495-500 pubmed
    ..A definitive summary is given of the valid type strains of Paracoccus denitrificans and Paracoccus pantotrophus and of culture collection strains that can be assigned to these species...
  34. Abu Tarboush N, Shin S, Geng J, Liu A, Davidson V. Effects of the loss of the axial tyrosine ligand of the low-spin heme of MauG on its physical properties and reactivity. FEBS Lett. 2012;586:4339-43 pubmed publisher
    ..The results clarify the role of Tyr ligation of the five-coordinate heme in determining the physical and redox properties and reactivity of MauG...
  35. Van Spanning R, De Boer A, Reijnders W, Westerhoff H, Stouthamer A, van der Oost J. FnrP and NNR of Paracoccus denitrificans are both members of the FNR family of transcriptional activators but have distinct roles in respiratory adaptation in response to oxygen limitation. Mol Microbiol. 1997;23:893-907 pubmed
    The Paracoccus denitrificans fnrP gene encoding a homologue of the Escherichia coli FNR protein was localized upstream of the gene cluster that encodes the high-affinity cbb3-type oxidase...
  36. Kucera I. Interference of chlorate and chlorite with nitrate reduction in resting cells of Paracoccus denitrificans. Microbiology. 2006;152:3529-34 pubmed
    When grown anaerobically on a succinate+nitrate (SN) medium, Paracoccus denitrificans forms the membrane-bound, cytoplasmically oriented, chlorate-reducing nitrate reductase Nar, while the periplasmic enzyme Nap is expressed during ..
  37. Olkhova E, Hutter M, Lill M, Helms V, Michel H. Dynamic water networks in cytochrome C oxidase from Paracoccus denitrificans investigated by molecular dynamics simulations. Biophys J. 2004;86:1873-89 pubmed
    We present a molecular dynamics study of cytochrome c oxidase from Paracoccus denitrificans in the fully oxidized state, embedded in a fully hydrated dimyristoylphosphatidylcholine lipid bilayer membrane...
  38. Vacková L, Srb M, Stloukal R, Wanner J. Comparison of denitrification at low temperature using encapsulated Paracoccus denitrificans, Pseudomonas fluorescens and mixed culture. Bioresour Technol. 2011;102:4661-6 pubmed publisher
    ..was to compare denitrification activity of three types of encapsulated biomass containing pure culture of Paracoccus denitrificans or Pseudomonas fluorescens or mixed culture of psychrophilic denitrifiers cultivated at 5 °C from ..
  39. Morales Ríos E, de la Rosa Morales F, Mendoza Hernandez G, Rodriguez Zavala J, Celis H, Zarco Zavala M, et al. A novel 11-kDa inhibitory subunit in the F1FO ATP synthase of Paracoccus denitrificans and related alpha-proteobacteria. FASEB J. 2010;24:599-608 pubmed publisher
    The F(1)F(O) and F(1)-ATPase complexes of Paracoccus denitrificans were isolated for the first time by ion exchange, gel filtration, and density gradient centrifugation into functional native preparations...
  40. Chistoserdov A, Boyd J, Mathews F, Lidstrom M. The genetic organization of the mau gene cluster of the facultative autotroph Paracoccus denitrificans. Biochem Biophys Res Commun. 1992;184:1181-9 pubmed
    The mau gene cluster from Paracoccus denitrificans was cloned. The regions of a cloned fragment carrying genes for the small and the large subunit of the methylamine dehydrogenase were identified and sequenced...
  41. Fojt L, Strasak L, Vetterl V. Effect of electromagnetic fields on the denitrification activity of Paracoccus denitrificans. Bioelectrochemistry. 2007;70:91-5 pubmed
    Enzymatic activity (denitrification) of Paracoccus denitrificans was estimated electrochemically by reduction of duroquinone (DQ). Graphite electrodes covered with whole bacterial cells behind a dialysis membrane were used for measurement...
  42. Zharova T, Vinogradov A. Requirement of medium ADP for the steady-state hydrolysis of ATP by the proton-translocating Paracoccus denitrificans Fo.F1-ATP synthase. Biochim Biophys Acta. 2006;1757:304-10 pubmed
    Fo.F1-ATP synthase in inside-out coupled vesicles derived from Paracoccus denitrificans catalyzes Pi-dependent proton-translocating ATPase reaction if exposed to prior energization that relieves ADP.Mg2+ -induced inhibition (Zharova, T.V...
  43. Li X, Fu R, Lee S, Krebs C, Davidson V, Liu A. A catalytic di-heme bis-Fe(IV) intermediate, alternative to an Fe(IV)=O porphyrin radical. Proc Natl Acad Sci U S A. 2008;105:8597-600 pubmed publisher
    ..These findings broaden our views of how proteins can stabilize a highly reactive oxidizing species and the scope of enzyme-catalyzed posttranslational modifications...
  44. Harrenga A, Michel H. The cytochrome c oxidase from Paracoccus denitrificans does not change the metal center ligation upon reduction. J Biol Chem. 1999;274:33296-9 pubmed
    ..No ligand exchanges or other major structural changes upon reduction of the cytochrome c oxidase from Paracoccus denitrificans were observed...
  45. Maehara A, Ueda S, Nakano H, Yamane T. Analyses of a polyhydroxyalkanoic acid granule-associated 16-kilodalton protein and its putative regulator in the pha locus of Paracoccus denitrificans. J Bacteriol. 1999;181:2914-21 pubmed
    The polyhydroxyalkanoic acid (PHA) granule-associated 16-kDa protein (GA16 protein) of Paracoccus denitrificans was identified, and its corresponding gene was cloned and analyzed at the molecular level...
  46. Wunsch P, Körner H, Neese F, van Spanning R, Kroneck P, Zumft W. NosX function connects to nitrous oxide (N2O) reduction by affecting the Cu(Z) center of NosZ and its activity in vivo. FEBS Lett. 2005;579:4605-9 pubmed
    ..was investigated with an N2O-respiration negative, double mutant of the paralogous genes nosX and nirX of Paracoccus denitrificans. In spite of absence of whole-cell N2O-reducing activity, the purified reductase was catalytically active,..
  47. Zickermann V, Barquera B, Wikstrom M, Finel M. Analysis of the pathogenic human mitochondrial mutation ND1/3460, and mutations of strictly conserved residues in its vicinity, using the bacterium Paracoccus denitrificans. Biochemistry. 1998;37:11792-6 pubmed
    ..1991) Am. J. Hum. Genet. 48, 1147]. We have used a bacterial counterpart of Complex I, NDH-1 from Paracoccus denitrificans, for studying the effect of mutations in the ND1 subunit on the enzymatic activity...
  48. Sun D, Ono K, Okajima T, Tanizawa K, Uchida M, Yamamoto Y, et al. Chemical and kinetic reaction mechanisms of quinohemoprotein amine dehydrogenase from Paracoccus denitrificans. Biochemistry. 2003;42:10896-903 pubmed
    ..On the basis of these results, kinetic and chemical reaction mechanisms for QHNDH are proposed and discussed in the context of the crystal structure of the enzyme...
  49. Sambongi Y, Ferguson S. Synthesis of holo Paracoccus denitrificans cytochrome c550 requires targeting to the periplasm whereas that of holo Hydrogenobacter thermophilus cytochrome c552 does not. Implications for c-type cytochrome biogenesis. FEBS Lett. 1994;340:65-70 pubmed
    ..gene, including the codons for the N-terminal periplasmic targeting signal, for cytochrome c550 of Paracoccus denitrificans led to the formation of the holo protein in the periplasms of both P. denitrificans and Escherichia coli...
  50. Felgate H, Giannopoulos G, Sullivan M, Gates A, Clarke T, Baggs E, et al. The impact of copper, nitrate and carbon status on the emission of nitrous oxide by two species of bacteria with biochemically distinct denitrification pathways. Environ Microbiol. 2012;14:1788-800 pubmed publisher
    ..g. Paracoccus denitrificans) or a Nir that is solely dependent on copper (Cu) as a cofactor (e.g. Achromobacter xylosoxidans)...
  51. Soares C, Baptista A, Pereira M, Teixeira M. Investigation of protonatable residues in Rhodothermus marinus caa3 haem-copper oxygen reductase: comparison with Paracoccus denitrificans aa3 haem-copper oxygen reductase. J Biol Inorg Chem. 2004;9:124-34 pubmed
    ..D- and K-proton channels, with the notable exception of the helix VI glutamate residue (Glu278(I) in Paracoccus denitrificans aa(3)), being nevertheless a true oxygen reductase reducing O(2) to water, and an efficient proton pump...
  52. Brüggemann C, Denger K, Cook A, Ruff J. Enzymes and genes of taurine and isethionate dissimilation in Paracoccus denitrificans. Microbiology. 2004;150:805-16 pubmed
    Growth of the alpha-proteobacterium Paracoccus denitrificans NKNIS with taurine or isethionate as sole source of carbon involves sulfoacetaldehyde acetyltransferase (Xsc), which is presumably encoded by an xsc gene in subgroup 3, none of ..
  53. MacMillan F, Budiman K, Angerer H, Michel H. The role of tryptophan 272 in the Paracoccus denitrificans cytochrome c oxidase. FEBS Lett. 2006;580:1345-9 pubmed
    ..The significance of this finding for the catalytic function of the enzyme is discussed...
  54. Davidson V, Wilmot C. Posttranslational biosynthesis of the protein-derived cofactor tryptophan tryptophylquinone. Annu Rev Biochem. 2013;82:531-50 pubmed publisher
    ..This review addresses these highly unusual aspects of the long-range catalytic reaction mediated by MauG...
  55. Gates A, Luque Almagro V, Goddard A, Ferguson S, Roldan M, Richardson D. A composite biochemical system for bacterial nitrate and nitrite assimilation as exemplified by Paracoccus denitrificans. Biochem J. 2011;435:743-53 pubmed publisher
    The denitrifying bacterium Paracoccus denitrificans can grow aerobically or anaerobically using nitrate or nitrite as the sole nitrogen source...
  56. Low L, Mukasa T, Reed J, Pascual J. Characterization of a TIR-like protein from Paracoccus denitrificans. Biochem Biophys Res Commun. 2007;356:481-6 pubmed
    ..We cloned, expressed, and characterized the corresponding gene product from Paracoccus denitrificans using several biophysical techniques. The protein consists of two independently folded domains...
  57. Page M, Ferguson S. Paracoccus denitrificans CcmG is a periplasmic protein-disulphide oxidoreductase required for c- and aa3-type cytochrome biogenesis; evidence for a reductase role in vivo. Mol Microbiol. 1997;24:977-90 pubmed
    Cloning and sequencing of the Paracoccus denitrificans ccmG gene indicates that it codes for a periplasmic protein-disulphide oxidoreductase; the presence of the sequence Cys-Pro-Pro-Cys at the CcmG active site suggests that it may act in ..
  58. Feng M, Jensen L, Yukl E, Wei X, Liu A, Wilmot C, et al. Proline 107 is a major determinant in maintaining the structure of the distal pocket and reactivity of the high-spin heme of MauG. Biochemistry. 2012;51:1598-606 pubmed publisher
  59. Lee S, Shin S, Li X, Davidson V. Kinetic mechanism for the initial steps in MauG-dependent tryptophan tryptophylquinone biosynthesis. Biochemistry. 2009;48:2442-7 pubmed publisher
    ..This kinetic mechanism is also distinct from that of the homologous diheme cytochrome c peroxidases that require a mixed valence state for activity...
  60. Stroh A, Anderka O, Pfeiffer K, Yagi T, Finel M, Ludwig B, et al. Assembly of respiratory complexes I, III, and IV into NADH oxidase supercomplex stabilizes complex I in Paracoccus denitrificans. J Biol Chem. 2004;279:5000-7 pubmed
    ..Using the mild detergent digitonin for solubilization of Paracoccus denitrificans membranes we could isolate NADH oxidase, assembled from complexes I, III, and IV in a 1:4:4 stoichiometry...
  61. Fukami T, Yohda M, Taguchi H, Yoshida M, Miki K. Crystal structure of chaperonin-60 from Paracoccus denitrificans. J Mol Biol. 2001;312:501-9 pubmed
    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...
  62. Hederstedt L. Succinate:quinone oxidoreductase in the bacteria Paracoccus denitrificans and Bacillus subtilis. Biochim Biophys Acta. 2002;1553:74-83 pubmed
    An overview of the present knowledge about succinate:quinone oxidoreductase in Paracoccus denitrificans and Bacillus subtilis is presented. P...
  63. Jensen L, Sanishvili R, Davidson V, Wilmot C. In crystallo posttranslational modification within a MauG/pre-methylamine dehydrogenase complex. Science. 2010;327:1392-4 pubmed publisher
    ..In addition, one of the hemes has an atypical His-Tyr axial ligation. The crystalline protein complex is catalytically competent; upon addition of hydrogen peroxide, MauG-dependent TTQ synthesis occurs...
  64. Yip C, Harbour M, Jayawardena K, Fearnley I, Sazanov L. Evolution of respiratory complex I: "supernumerary" subunits are present in the alpha-proteobacterial enzyme. J Biol Chem. 2011;286:5023-33 pubmed publisher
    ..Here, we report the first purification and characterization of complex I from the ?-proteobacterium Paracoccus denitrificans. Single particle electron microscopy shows that the complex has a well defined L-shape...
  65. Kotlyar A, Borovok N. NADH oxidation and NAD+ reduction catalysed by tightly coupled inside-out vesicles from Paracoccus denitrificans. Eur J Biochem. 2002;269:4020-4 pubmed
    Tightly coupled inside-out vesicles were prepared from Paracoccus denitrificans cells (SPP, sub-Paracoccus particles) and characterized kinetically...
  66. Yano T, Sklar J, Nakamaru Ogiso E, Takahashi Y, Yagi T, Ohnishi T. Characterization of cluster N5 as a fast-relaxing [4Fe-4S] cluster in the Nqo3 subunit of the proton-translocating NADH-ubiquinone oxidoreductase from Paracoccus denitrificans. J Biol Chem. 2003;278:15514-22 pubmed
    The NADH-quinone oxidoreductase from Paracoccus denitrificans consists of 14 subunits (Nqo1-14) and contains one FMN and eight iron-sulfur clusters...
  67. Tarboush N, Jensen L, Yukl E, Geng J, Liu A, Wilmot C, et al. Mutagenesis of tryptophan199 suggests that hopping is required for MauG-dependent tryptophan tryptophylquinone biosynthesis. Proc Natl Acad Sci U S A. 2011;108:16956-61 pubmed publisher
  68. Rausch C, Lerchner A, Schiefner A, Skerra A. Crystal structure of the ?-aminotransferase from Paracoccus denitrificans and its phylogenetic relationship with other class III aminotransferases that have biotechnological potential. Proteins. 2013;81:774-87 pubmed publisher
    ..One representative is the ?-AT from Paracoccus denitrificans (PD ?-AT) which catalyzes, for example, the transamination in a novel biocatalytic process for the ..
  69. Yukl E, Williamson H, Higgins L, Davidson V, Wilmot C. Oxidative damage in MauG: implications for the control of high-valent iron species and radical propagation pathways. Biochemistry. 2013;52:9447-55 pubmed publisher
    ..That is, methionine oxidation may represent a protective mechanism that prevents the generation of reactive oxygen species by MauG in the absence of preMADH. ..
  70. Bergaust L, Mao Y, Bakken L, Frostegard A. Denitrification response patterns during the transition to anoxic respiration and posttranscriptional effects of suboptimal pH on nitrous [corrected] oxide reductase in Paracoccus denitrificans. Appl Environ Microbiol. 2010;76:6387-96 pubmed publisher
    ..we conducted an in-depth investigation of the regulation of denitrification in the model organism Paracoccus denitrificans during transition to anoxia both at pH 7 and when challenged with pHs ranging from 6 to 7.5...
  71. Mazoch J, Tesarik R, Sedláček V, Kucera I, Turanek J. Isolation and biochemical characterization of two soluble iron(III) reductases from Paracoccus denitrificans. Eur J Biochem. 2004;271:553-62 pubmed
    ..complexes by NADH, were purified to near homogeneity from the aerobically grown iron-limited culture of Paracoccus denitrificans using a combination of anion-exchange chromatography (Sepharose Q), chromatofocusing (Mono P), and gel ..
  72. Kaplan P, Kucera I. Relationship between cardiolipin content and cytochrome c oxidase activity of cytochrome aa3 in Paracoccus denitrificans. Biochem Int. 1992;28:137-42 pubmed
    Using cultivation at different oxygen tensions, the molar ratio of cardiolipin to haem a in cells of Paracoccus denitrificans was varied systematically from 30 to 300...
  73. Bouchal P, Struhárová I, Budinska E, Sedo O, Vyhlídalová T, Zdrahal Z, et al. Unraveling an FNR based regulatory circuit in Paracoccus denitrificans using a proteomics-based approach. Biochim Biophys Acta. 2010;1804:1350-8 pubmed publisher
    The switch from aerobic to anaerobic respiration in the bacterium Paracoccus denitrificans is orchestrated by the action of three FNR-type transcription regulators FnrP, NNR and NarR, which are sensors for oxygen, nitric oxide and nitrite,..
  74. Capitanio N, Palese L, Capitanio G, Martino P, Richter O, Ludwig B, et al. Allosteric interactions and proton conducting pathways in proton pumping aa(3) oxidases: heme a as a key coupling element. Biochim Biophys Acta. 2012;1817:558-66 pubmed publisher
    ..This effect appears to result from alteration of the structural/functional device, closer to the positive, opposite (P) surface, which separates pumped protons from those consumed in the reduction of O(2) to 2 H(2)O...
  75. Ind A, Porter S, Brown M, Byles E, de Beyer J, Godfrey S, et al. Inducible-expression plasmid for Rhodobacter sphaeroides and Paracoccus denitrificans. Appl Environ Microbiol. 2009;75:6613-5 pubmed publisher
    ..allows graduated levels of protein expression in the alphaproteobacteria Rhodobacter sphaeroides and Paracoccus denitrificans. pIND4 confers kanamycin resistance and combines the stable replicon of pMG160 with the lacI(q) gene from ..
  76. Okamoto A, Nakai Y, Hayashi H, Hirotsu K, Kagamiyama H. Crystal structures of Paracoccus denitrificans aromatic amino acid aminotransferase: a substrate recognition site constructed by rearrangement of hydrogen bond network. J Mol Biol. 1998;280:443-61 pubmed
    ..recognition mechanism, we determined the crystal structures of aromatic amino acid aminotransferase from Paracoccus denitrificans (pdAroAT): unliganded pdAroAT, pdAroAT in a complex with maleate as an acidic substrate analog, and ..
  77. Matsson M, Ackrell B, Cochran B, Hederstedt L. Carboxin resistance in Paracoccus denitrificans conferred by a mutation in the membrane-anchor domain of succinate:quinone reductase. Arch Microbiol. 1998;170:27-37 pubmed
    ..Carboxin is a potent inhibitor of the enzyme of certain organisms. The bacterium Paracoccus denitrificans was found to be sensitive to carboxin in vivo, and mutants that grow in the presence of 3'-methyl ..
  78. Otten M, Stork D, Reijnders W, Westerhoff H, Van Spanning R. Regulation of expression of terminal oxidases in Paracoccus denitrificans. Eur J Biochem. 2001;268:2486-97 pubmed
    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, ..
  79. Pinakoulaki E, Pfitzner U, Ludwig B, Varotsis C. Direct detection of Fe(IV)[double bond]O intermediates in the cytochrome aa3 oxidase from Paracoccus denitrificans/H2O2 reaction. J Biol Chem. 2003;278:18761-6 pubmed
    ..Raman characterization of the reaction products of both the wild-type and Y280H cytochrome aa3 from Paracoccus denitrificans indicate the formation of six-coordinate low spin species, and do not support, in contrast to previous ..
  80. Wienk H, Maneg O, Lücke C, Pristovsek P, Lohr F, Ludwig B, et al. Interaction of cytochrome c with cytochrome c oxidase: an NMR study on two soluble fragments derived from Paracoccus denitrificans. Biochemistry. 2003;42:6005-12 pubmed
    ..we investigated the molecular interaction between two components of the electron-transfer chain from Paracoccus denitrificans: the engineered, water-soluble fragment of cytochrome c(552) and the Cu(A) domain from the cytochrome c ..
  81. Lee A, Kirichenko A, Vygodina T, Siletsky S, Das T, Rousseau D, et al. Ca(2+)-binding site in Rhodobacter sphaeroides cytochrome C oxidase. Biochemistry. 2002;41:8886-98 pubmed
    ..This is similar to COX from Paracoccus denitrificans [Pfitzner, U., Kirichenko, A., Konstantinov, A. A., Mertens, M., Wittershagen, A., Kolbesen, B. O...
  82. Koepke J, Olkhova E, Angerer H, Müller H, Peng G, Michel H. High resolution crystal structure of Paracoccus denitrificans cytochrome c oxidase: new insights into the active site and the proton transfer pathways. Biochim Biophys Acta. 2009;1787:635-45 pubmed publisher
    The structure of the two-subunit cytochrome c oxidase from Paracoccus denitrificans has been refined using X-ray cryodata to 2.25 A resolution in order to gain further insights into its mechanism of action...
  83. Choi M, Shin S, Davidson V. Characterization of electron tunneling and hole hopping reactions between different forms of MauG and methylamine dehydrogenase within a natural protein complex. Biochemistry. 2012;51:6942-9 pubmed publisher
    ..These data provide insight into how the intervening protein matrix and redox potentials of the electron donor and acceptor determine whether the ET reaction proceeds via single-step tunneling or multistep hopping...
  84. Ostermeier C, Harrenga A, Ermler U, Michel H. Structure at 2.7 A resolution of the Paracoccus denitrificans two-subunit cytochrome c oxidase complexed with an antibody FV fragment. Proc Natl Acad Sci U S A. 1997;94:10547-53 pubmed
    ..cytochrome c oxidase consisting of the core subunits I and II only was isolated from the soil bacterium Paracoccus denitrificans and crystallized as complex with a monoclonal antibody Fv fragment...
  85. Kirichenko A, Pfitzner U, Ludwig B, Soares C, Vygodina T, Konstantinov A. Cytochrome c oxidase as a calcium binding protein. Studies on the role of a conserved aspartate in helices XI-XII cytoplasmic loop in cation binding. Biochemistry. 2005;44:12391-401 pubmed
    ..In the oxidases from Paracoccus denitrificans or Rhodobacter sphaeroides, the site is occupied by tightly bound calcium, whereas the mitochondrial ..