Desulfovibrio vulgaris str. Hildenborough

Summary

Alias: Desulfovibrio vulgaris subsp. vulgaris str. Hildenborough, Desulfovibrio vulgaris (STRAIN HILDENBOROUGH), Desulfovibrio vulgaris Hildenborough, Desulfovibrio vulgaris subsp. vulgaris (strain Hildenborough), Desulfovibrio vulgaris vulgaris (strain Hildenborough), Desulfovibrio vulgaris ATCC 29579, Desulfovibrio vulgaris subsp. vulgaris ATCC 29579

Top Publications

  1. Gao S, Ho J, Fan L, Nouwens A, Hoelzle R, Schulz B, et al. A comparative proteomic analysis of Desulfovibrio vulgaris Hildenborough in response to the antimicrobial agent free nitrous acid. Sci Total Environ. 2019;672:625-633 pubmed publisher
    ..Here we report the proteomic response of Desulfovibrio vulgaris Hildenborough and reveal that the antimicrobial effect of FNA is multi-targeted and dependent on the FNA levels...
  2. Zacarias S, Velez M, Pita M, De Lacey A, Matias P, Pereira I. Characterization of the [NiFeSe] hydrogenase from Desulfovibrio vulgaris Hildenborough. Methods Enzymol. 2018;613:169-201 pubmed publisher
    ..vulgaris Hildenborough and the creation of a homologous expression system for production of variant forms of the enzyme. ..
  3. Barca C, Ranava D, Bauzan M, Ferrasse J, Giudici Orticoni M, Soric A. Fermentative hydrogen production in an up-flow anaerobic biofilm reactor inoculated with a co-culture of Clostridium acetobutylicum and Desulfovibrio vulgaris. Bioresour Technol. 2016;221:526-533 pubmed publisher
    ..that an artificial consortium of two anaerobic bacteria, Clostridium acetobutylicum and Desulfovibrio vulgaris Hildenborough, may redirect metabolic fluxes and improve H2 yields...
  4. Pinck S, Xu M, Clement R, Lojou E, Jorand F, Etienne M. Influence of cytochrome charge and potential on the cathodic current of electroactive artificial biofilms. Bioelectrochemistry. 2018;124:185-194 pubmed publisher
    ..Optimal results have been obtained with c3 from Desulfovibrio vulgaris Hildenborough having an isoelectric point of 10...
  5. Neca A, Soares R, Carepo M, Pauleta S. Resonance assignment of DVU2108 that is part of the Orange Protein complex in Desulfovibrio vulgaris Hildenborough. Biomol NMR Assign. 2016;10:117-20 pubmed publisher
    We report the 94 % assignment of DVU2108, a protein belonging to the Orange Protein family, that in Desulfovibrio vulgaris Hildenborough forms a protein complex named the Orange Protein complex...
  6. Ueda Y, Shibata N, Takeuchi D, Kitamura M, Higuchi Y. Crystallization and preliminary X-ray crystallographic study of flavoredoxin from Desulfovibrio vulgaris Miyazaki F. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2008;64:851-3 pubmed publisher
    ..05 A resolution under cryogenic conditions. The space group was determined to be P3(1)21, with unit-cell parameters a = b = 53.35, c = 116.22 A. Phase determination was carried out by the SAD method using methylmercuric chloride. ..
  7. Christensen G, Zane G, Kazakov A, Li X, Rodionov D, Novichkov P, et al. Rex (encoded by DVU_0916) in Desulfovibrio vulgaris Hildenborough is a repressor of sulfate adenylyl transferase and is regulated by NADH. J Bacteriol. 2015;197:29-39 pubmed publisher
    ..In the model sulfate-reducing microbe Desulfovibrio vulgaris Hildenborough, the gene DVU_0916 was observed to resemble other known Rex proteins...
  8. Ogata M, Kondo S, Okawara N, Yagi T. Purification and characterization of ferredoxin from Desulfovibrio vulgaris Miyazaki. J Biochem. 1988;103:121-5 pubmed
  9. Matias P, Frazao C, Morais J, Coll M, Carrondo M. Structure analysis of cytochrome c3 from Desulfovibrio vulgaris Hildenborough at 1.9 A resolution. J Mol Biol. 1993;234:680-99 pubmed
    The three-dimensional X-ray structure of cytochrome c3 from sulfate-reducing bacteria Desulfovibrio vulgaris Hildenborough (DvH) (M(r) 13 kDa, 107 residues, 4 heme groups) has been determined at 1...

More Information

Publications140 found, 100 shown here

  1. Franco L, Steinbeisser S, Zane G, Wall J, Fields M. Cr(VI) reduction and physiological toxicity are impacted by resource ratio in Desulfovibrio vulgaris. Appl Microbiol Biotechnol. 2018;102:2839-2850 pubmed publisher
    ..b>Desulfovibrio vulgaris Hildenborough was grown under environmentally relevant conditions (i.e...
  2. Prickril B, Kurtz D, LeGall J, Voordouw G. Cloning and sequencing of the gene for rubrerythrin from Desulfovibrio vulgaris (Hildenborough). Biochemistry. 1991;30:11118-23 pubmed
    ..If folding of the rubredoxin-like amino acid sequence domain in rubrerythrin is similar to that in rubredoxins, then three His residues are brought into proximity.(ABSTRACT TRUNCATED AT 250 WORDS) ..
  3. deMaré F, Kurtz D, Nordlund P. The structure of Desulfovibrio vulgaris rubrerythrin reveals a unique combination of rubredoxin-like FeS4 and ferritin-like diiron domains. Nat Struct Biol. 1996;3:539-46 pubmed
    ..The four-helix bundle of rubrerythrin closely resembles those of the ferritin and bacterioferritin subunits, suggesting a relationship among these proteins-consistent with the recently demonstrated ferroxidase activity of rubrerythrin. ..
  4. Pereira A, Tavares P, Moura I, Moura J, Huynh B. Mössbauer characterization of the iron-sulfur clusters in Desulfovibrio vulgaris hydrogenase. J Am Chem Soc. 2001;123:2771-82 pubmed
    ..The results also reveal that binding of exogenous CO to the H cluster affects significantly the exchange coupling between the [4Fe-4S](H) and the [2Fe](H) subclusters. Implication of such a CO binding effect is discussed. ..
  5. Pellerin A, Anderson Trocmé L, Whyte L, Zane G, Wall J, Wing B. Sulfur isotope fractionation during the evolutionary adaptation of a sulfate-reducing bacterium. Appl Environ Microbiol. 2015;81:2676-89 pubmed publisher
    ..by studying the covariation of fitness, sulfur isotope fractionation, and growth characteristics in Desulfovibrio vulgaris Hildenborough in a microbial evolution experiment...
  6. Reynolds R, Watt W, Watenpaugh K. Structures and comparison of the Y98H (2.0 A) and Y98W (1.5 A) mutants of flavodoxin (Desulfovibrio vulgaris). Acta Crystallogr D Biol Crystallogr. 2001;57:527-35 pubmed
    ..The interaction between O61 and N5 in the flavin is discussed because of the new conformation of this loop. ..
  7. Takayama Y, Kobayashi Y, Yahata N, Saitoh T, Hori H, Ikegami T, et al. Specific binding of CO to tetraheme cytochrome c3. Biochemistry. 2006;45:3163-9 pubmed
    ..Therefore, the CO-bound cyt c(3) may play a role in maintaining electron transport pathways on accumulation of toxic CO for its utilization. ..
  8. Voordouw G, Brenner S. Cloning and sequencing of the gene encoding cytochrome c3 from Desulfovibrio vulgaris (Hildenborough). Eur J Biochem. 1986;159:347-51 pubmed
    ..This amino-terminal extension functions in the export of cytochrome c3, which is thought to reside in the periplasm of D. vulgaris. ..
  9. Krey G, Vanin E, Swenson R. Cloning, nucleotide sequence, and expression of the flavodoxin gene from Desulfovibrio vulgaris (Hildenborough). J Biol Chem. 1988;263:15436-43 pubmed
    ..vulgaris. To our knowledge, this is the first example of the expression of a foreign flavodoxin gene in E. coli using recombinant DNA methods. ..
  10. Voordouw G. Cloning of genes encoding redox proteins of known amino acid sequence from a library of the Desulfovibrio vulgaris (Hildenborough) genome. Gene. 1988;67:75-83 pubmed
    A library of 900 recombinant phages has been constructed for the genome of Desulfovibrio vulgaris Hildenborough (1.7 x 10(6) bp) by cloning size-fractionated Sau3A fragments (15-20 kb) into the replacement vector lambda-2001...
  11. He T, Guo L, Guo X, Chang C, Wang L, Zhong D. Femtosecond dynamics of short-range protein electron transfer in flavodoxin. Biochemistry. 2013;52:9120-8 pubmed publisher
    ..Such vibrationally coupled charge recombination should be a general feature of flavoproteins with similar configurations and interactions between the cofactor flavin and neighboring aromatic residues. ..
  12. Kröckel M, Trautwein A, Arendsen A, Hagen W. The prismane protein resolved--Mössbauer investigation of a 4Fe cluster with an unusual mixture of bridging ligands and metal coordinations. Eur J Biochem. 1998;251:454-61 pubmed
    ..H., Liu, M.-Y. & LeGall, J. (1992) J. Biol. Chem. 287, 4487-4496]. However, they are in full agreement with the crystal structure of the isolated protein, which, concurrent with our Mössbauer investigation, has been solved. ..
  13. Voordouw J, Voordouw G. Deletion of the rbo gene increases the oxygen sensitivity of the sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough. Appl Environ Microbiol. 1998;64:2882-7 pubmed
    The rbo gene of Desulfovibrio vulgaris Hildenborough encodes rubredoxin oxidoreductase (Rbo), a 14-kDa iron sulfur protein; forms an operon with the gene for rubredoxin; and is preceded by the gene for the oxygen-sensing protein DcrA...
  14. Dolla A, Fu R, Brumlik M, Voordouw G. Nucleotide sequence of dcrA, a Desulfovibrio vulgaris Hildenborough chemoreceptor gene, and its expression in Escherichia coli. J Bacteriol. 1992;174:1726-33 pubmed
    ..from the nucleotide sequence of the dcrA gene from the anaerobic, sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough, indicates a structure similar to the methyl-accepting chemotaxis proteins from Escherichia coli, ..
  15. Kazakov A, Rajeev L, Chen A, Luning E, Dubchak I, Mukhopadhyay A, et al. σ54-dependent regulome in Desulfovibrio vulgaris Hildenborough. BMC Genomics. 2015;16:919 pubmed publisher
    ..b>Desulfovibrio vulgaris Hildenborough, a model bacterium for sulfate reduction studies, has a high number of EBPs, more than most ..
  16. Carepo M, Carreira C, Grazina R, Zakrzewska M, Dolla A, Aubert C, et al. Orange protein from Desulfovibrio alaskensis G20: insights into the Mo-Cu cluster protein-assisted synthesis. J Biol Inorg Chem. 2016;21:53-62 pubmed publisher
    ..alaskensis G20, the orp genes are encoded by a polycistronic unit composed of six genes whereas in Desulfovibrio vulgaris Hildenborough the same genes are organized into two divergent operons, although the composition in genes is ..
  17. Dolla A, Arnoux P, Protasevich I, Lobachov V, Brugna M, Giudici Orticoni M, et al. Key role of phenylalanine 20 in cytochrome c3: structure, stability, and function studies. Biochemistry. 1999;38:33-41 pubmed
    ..In the tetraheme cytochrome c3 (Mr 13 000) from Desulfovibrio vulgaris Hildenborough, Phe20, is located between heme 1 and heme 3 with its aromatic ring close and almost parallel to ..
  18. Trousil E, Campbell L. Amino acid sequence of cytochrome c3 from Desulfovibrio vulgaris. J Biol Chem. 1974;249:386-93 pubmed
  19. Karkhoff Schweizer R, Bruschi M, Voordouw G. Expression of the gamma-subunit gene of desulfoviridin-type dissimilatory sulfite reductase and of the alpha- and beta-subunit genes is not coordinately regulated. Eur J Biochem. 1993;211:501-7 pubmed
    ..Biochemical analysis of the purified protein, expressed in E. coli, and library comparison of its sequence, have so far failed to establish the function of gamma. ..
  20. Venceslau S, Cort J, Baker E, Chu R, Robinson E, Dahl C, et al. Redox states of Desulfovibrio vulgaris DsrC, a key protein in dissimilatory sulfite reduction. Biochem Biophys Res Commun. 2013;441:732-6 pubmed publisher
    ..The oxidized state of DsrC with an intramolecular disulfide bond, which is proposed to be a key metabolic intermediate, could be successfully produced for the first time by treatment with arginine. ..
  21. Pollock W, Loutfi M, Bruschi M, Rapp Giles B, Wall J, Voordouw G. Cloning, sequencing, and expression of the gene encoding the high-molecular-weight cytochrome c from Desulfovibrio vulgaris Hildenborough. J Bacteriol. 1991;173:220-8 pubmed
    ..deoxyoligonucleotide probe designed to recognize the structural gene for cytochrome cc3 from Desulfovibrio vulgaris Hildenborough, a 3.7-kb XhoI genomic DNA fragment containing the cc3 gene was isolated...
  22. Bruschi M, Le Gall J. C-type cytochromes of Desulfovibrio vulgaris. The primary structure of cytochrome c 553. Biochim Biophys Acta. 1972;271:48-60 pubmed
  23. Morelli X, Guerlesquin F. Mapping the cytochrome c553 interacting site using 1H and 15N NMR. FEBS Lett. 1999;460:77-80 pubmed
    ..This is the first mapping of the interaction site on a c-type cytochrome, using heteronuclear NMR. ..
  24. Adman E, Sieker L, Jensen L, Bruschi M, Le Gall J. A structural model of rubredoxin from Desulfovibrio vulgaris at 2 A resolution. J Mol Biol. 1977;112:113-20 pubmed
  25. Prickril B, Czechowski M, Przybyla A, Peck H, LeGall J. Putative signal peptide on the small subunit of the periplasmic hydrogenase from Desulfovibrio vulgaris. J Bacteriol. 1986;167:722-5 pubmed
    ..Voordouw and S. Brenner, Eur. J. Biochem. 148:515-520, 1985). We suggest that this region constitutes a signal peptide based on comparison with known procaryotic signal peptides. ..
  26. Watenpaugh K, Sieker L, Jensen L, LeGall J, Dubourdieu M. Structure of the oxidized form of a flavodoxin at 2.5-Angstrom resolution: resolution of the phase ambiguity by anomalous scattering. Proc Natl Acad Sci U S A. 1972;69:3185-8 pubmed
    ..The flavin mononucleotide lies mostly buried on one side of the molecule, but the methyl groups, one edge of the flavin, and part of the ribityl are exposed at the surface. ..
  27. Van Beeumen J, Van Driessche G, Liu M, LeGall J. The primary structure of rubrerythrin, a protein with inorganic pyrophosphatase activity from Desulfovibrio vulgaris. Comparison with hemerythrin and rubredoxin. J Biol Chem. 1991;266:20645-53 pubmed
    ..This paper is the first sequence report of a protein with pyrophosphatase activity although the physiological substrate for the rubrerythrin may be not inorganic pyrophosphate. ..
  28. Jin S, Kurtz D, Liu Z, Rose J, Wang B. X-ray crystal structure of Desulfovibrio vulgaris rubrerythrin with zinc substituted into the [Fe(SCys)4] site and alternative diiron site structures. Biochemistry. 2004;43:3204-13 pubmed
  29. Morelli X, Czjzek M, Hatchikian C, Bornet O, Fontecilla Camps J, Palma N, et al. Structural model of the Fe-hydrogenase/cytochrome c553 complex combining transverse relaxation-optimized spectroscopy experiments and soft docking calculations. J Biol Chem. 2000;275:23204-10 pubmed
  30. Timóteo C, Guilherme M, Penas D, Folgosa F, Tavares P, Pereira A. Desulfovibrio vulgaris bacterioferritin uses H(2)O(2) as a co-substrate for iron oxidation and reveals DPS-like DNA protection and binding activities. Biochem J. 2012;446:125-33 pubmed publisher
    ..The use of H(2)O(2) as an oxidant, combined with the DNA binding and protection activities, seems to indicate a DPS (DNA-binding protein from starved cells)-like role for D. vulgaris Bfr. ..
  31. Sugimoto Y, Kitazumi Y, Shirai O, Nishikawa K, Higuchi Y, Yamamoto M, et al. Electrostatic roles in electron transfer from [NiFe] hydrogenase to cytochrome c3 from Desulfovibrio vulgaris Miyazaki F. Biochim Biophys Acta Proteins Proteom. 2017;1865:481-487 pubmed publisher
  32. Ozawa K, Meikari T, Motohashi K, Yoshida M, Akutsu H. Evidence for the presence of an F-type ATP synthase involved in sulfate respiration in Desulfovibrio vulgaris. J Bacteriol. 2000;182:2200-6 pubmed
    ..vulgaris Miyazaki F cells is similar to that in the Escherichia coli cells cultured aerobically. It indicates that the enzyme works as an ATP synthase in the D. vulgaris Miyazaki F cells in connection with sulfate respiration. ..
  33. Marques M, Coelho R, Pereira I, Matias P. Purification, crystallization and preliminary crystallographic analysis of the [NiFeSe] hydrogenase from Desulfovibrio vulgaris Hildenborough. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2009;65:920-2 pubmed publisher
    ..and preliminary X-ray diffraction analysis of the [NiFeSe] hydrogenase isolated from Desulfovibrio vulgaris Hildenborough are reported...
  34. Knauf M, Lohr F, Blümel M, Mayhew S, Rüterjans H. NMR investigation of the solution conformation of oxidized flavodoxin from Desulfovibrio vulgaris. Determination of the tertiary structure and detection of protein-bound water molecules. Eur J Biochem. 1996;238:423-34 pubmed
    ..The locations of these water molecules have been compared with those found in the X-ray structure. ..
  35. Mizuno N, Voordouw G, Miki K, Sarai A, Higuchi Y. Crystal structure of dissimilatory sulfite reductase D (DsrD) protein--possible interaction with B- and Z-DNA by its winged-helix motif. Structure. 2003;11:1133-40 pubmed
    The crystal structure of DsrD from Desulfovibrio vulgaris Hildenborough has been determined at 1.2 A resolution. DsrD is in a dimeric form in the crystal, and five sulfate anions were located on the surface...
  36. Bruschi M. Non-heme iron proteins. The amino acid sequence of rubredoxin from Desulfovibrio vulgaris. Biochim Biophys Acta. 1976;434:4-17 pubmed
    ..It has been shown that 20 amino acid residues occurred in identical positions. The locations of the four cysteine residues were found to be invariable. A crystallographic study of the Desulfovibrio vulgaris rubredoxin is in progress. ..
  37. Loutfi M, Guerlesquin F, Bianco P, Haladjian J, Bruschi M. Comparative studies of polyhemic cytochromes c isolated from Desulfovibrio vulgaris (Hildenborough) and Desulfovibrio desulfuricans (Norway). Biochem Biophys Res Commun. 1989;159:670-6 pubmed
    ..Absorption spectrum is similar to cytochrome c3 (Mr 13,000) and individual redox potentials have an average value of -180 mV.3 The N terminal sequence is compared with an homologous cytochrome isolated from D. desulfuricans Norway. ..
  38. Okawara N, Ogata M, Yagi T, Wakabayashi S, Matsubara H. Amino acid sequence of ferredoxin I from Desulfovibrio vulgaris Miyazaki. J Biochem. 1988;104:196-9 pubmed
    ..Fd I has 76% homology to Fd II of D. desulfuricans Norway. ..
  39. Sebban Kreuzer C, Dolla A, Guerlesquin F. The formate dehydrogenase-cytochrome c553 complex from Desulfovibrio vulgaris Hildenborough. Eur J Biochem. 1998;253:645-52 pubmed
    The electron transfer between formate dehydrogenase and cytochrome c553 from the anaerobic bacteria Desulfovibrio vulgaris Hildenborough has been investigated. Parameters of the electron transfer kinetics are reported...
  40. Messias A, Aguiar A, Brennan L, Salgueiro C, Saraiva L, Xavier A, et al. Solution structures of tetrahaem ferricytochrome c3 from Desulfovibrio vulgaris (Hildenborough) and its K45Q mutant: the molecular basis of cooperativity. Biochim Biophys Acta. 2006;1757:143-53 pubmed
    The NMR structure of the oxidised wild-type cytochrome c3 from Desulfovibrio vulgaris Hildenborough was determined in solution...
  41. Aramini J, Hamilton K, Rossi P, Ertekin A, Lee H, Lemak A, et al. Solution NMR structure, backbone dynamics, and heme-binding properties of a novel cytochrome c maturation protein CcmE from Desulfovibrio vulgaris. Biochemistry. 2012;51:3705-7 pubmed publisher
    ..Heme binding analyses of wild-type and mutant dvCcmE' demonstrate the absolute requirement of residue C127 for noncovalent heme binding in vitro. ..
  42. Stokkermans J, Pierik A, Wolbert R, Hagen W, van Dongen W, Veeger C. The primary structure of a protein containing a putative [6Fe-6S] prismane cluster from Desulfovibrio vulgaris (Hildenborough). Eur J Biochem. 1992;208:435-42 pubmed
    ..Hybridization of the cloned gene with genomic DNA of several other Desulfovibrio species indicates that homologous sequences are generally present in the genus Desulfovibrio. ..
  43. Morimoto Y, Tani T, Okumura H, Higuchi Y, Yasuoka N. Effects of amino acid substitution on three-dimensional structure: an X-ray analysis of cytochrome c3 from Desulfovibrio vulgaris Hildenborough at 2 A resolution. J Biochem. 1991;110:532-40 pubmed
    The three-dimensional structure of cytochrome c3 from Desulfovibrio vulgaris Hildenborough has been determined by use of the molecular replacement method and refined at 2.0 A resolution...
  44. Stockman B, Euvrard A, Kloosterman D, Scahill T, Swenson R. 1H and 15N resonance assignments and solution secondary structure of oxidized Desulfovibrio vulgaris flavodoxin determined by heteronuclear three-dimensional NMR spectroscopy. J Biomol NMR. 1993;3:133-49 pubmed
    ..The resonance assignments presented here can form the basis for assigning single-site mutant flavodoxins and for correlating structural differences between wild-type and mutant flavodoxins with altered redox potentials. ..
  45. Fu R, Voordouw G. ISD1, an insertion element from the sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough: structure, transposition, and distribution. Appl Environ Microbiol. 1998;64:53-61 pubmed
    ..the insertional inactivation of an introduced sacB gene, is present in two copies in the genome of Desulfovibrio vulgaris Hildenborough. Southern blot analysis indicated at least two insertion sites in the sacB gene...
  46. Sebban Kreuzer C, Blanchard L, Bersch B, Blackledge M, Marion D, Dolla A, et al. 1H-NMR study of the structural influence of Y64 substitution in Desulfovibrio vulgaris Hildenborough cytochrome c553. Eur J Biochem. 1998;251:787-94 pubmed
    Y64 has been replaced in cytochrome c553 from Desulfovibrio vulgaris Hildenborough by phenylalanine, leucine, valine, serine and alanine residues...
  47. Walsh M, McCarthy A, O Farrell P, McArdle P, Cunningham P, Mayhew S, et al. X-ray crystal structure of the Desulfovibrio vulgaris (Hildenborough) apoflavodoxin-riboflavin complex. Eur J Biochem. 1998;258:362-71 pubmed
  48. Matias P, Coelho A, Valente F, Placido D, Legall J, Xavier A, et al. Sulfate respiration in Desulfovibrio vulgaris Hildenborough. Structure of the 16-heme cytochrome c HmcA AT 2.5-A resolution and a view of its role in transmembrane electron transfer. J Biol Chem. 2002;277:47907-16 pubmed
    The crystal structure of the high molecular mass cytochrome c HmcA from Desulfovibrio vulgaris Hildenborough is described...
  49. Zhou A, Chen Y, Zane G, He Z, Hemme C, Joachimiak M, et al. Functional characterization of Crp/Fnr-type global transcriptional regulators in Desulfovibrio vulgaris Hildenborough. Appl Environ Microbiol. 2012;78:1168-77 pubmed publisher
    ..about the function of four annotated Crp/Fnr homologs (DVU0379, DVU2097, DVU2547, and DVU3111) in Desulfovibrio vulgaris Hildenborough. A systematic study using bioinformatic, transcriptomic, genetic, and physiological approaches was ..
  50. Rajeev L, Chen A, Kazakov A, Luning E, Zane G, Novichkov P, et al. Regulation of Nitrite Stress Response in Desulfovibrio vulgaris Hildenborough, a Model Sulfate-Reducing Bacterium. J Bacteriol. 2015;197:3400-8 pubmed publisher
    ..b>Desulfovibrio vulgaris Hildenborough, a model SRB, carries a cytochrome c-type nitrite reductase (nrfHA) that confers resistance to low ..
  51. Kurtz D, Prickril B. Intrapeptide sequence homology in rubrerythrin from Desulfovibrio vulgaris: identification of potential ligands to the diiron site. Biochem Biophys Res Commun. 1991;181:337-41 pubmed
    ..No propene monooxygenase activity was detected with rubrerythrin using the assay designed to test activity of methane monooxygenase component A in the absence of other protein components. ..
  52. Brumlik M, Voordouw G. Analysis of the transcriptional unit encoding the genes for rubredoxin (rub) and a putative rubredoxin oxidoreductase (rbo) in Desulfovibrio vulgaris Hildenborough. J Bacteriol. 1989;171:4996-5004 pubmed
    ..EcoRI restriction fragment upstream from the gene (rub, 162 base pairs) encoding rubredoxin from Desulfovibrio vulgaris Hildenborough indicates that it is part of a larger transcriptional unit, containing an additional 378-base-pair ..
  53. Prickril B, He S, Li C, Menon N, Choi E, Przybyla A, et al. Identification of three classes of hydrogenase in the genus, Desulfovibrio. Biochem Biophys Res Commun. 1987;149:369-77 pubmed
    ..These results, in conjunction with antibody analyses, clearly indicate that the iron, iron + nickel, and iron + nickel + selenium containing hydrogenases represent three distinct classes of hydrogenase in Desulfovibrio. ..
  54. Speich N, Dahl C, Heisig P, Klein A, Lottspeich F, Stetter K, et al. Adenylylsulphate reductase from the sulphate-reducing archaeon Archaeoglobus fulgidus: cloning and characterization of the genes and comparison of the enzyme with other iron-sulphur flavoproteins. Microbiology. 1994;140 ( Pt 6):1273-84 pubmed
    ..aprB encodes a 17.1 kDa polypeptide representing an iron-sulphur protein, seven cysteine residues of which are arranged in two clusters typical of ligands of the iron-sulphur centres in ([Fe3S4][Fe4S4]) 7-Fe ferredoxins. ..
  55. Verhagen M, Voorhorst W, Kolkman J, Wolbert R, Hagen W. On the two iron centers of desulfoferrodoxin. FEBS Lett. 1993;336:13-8 pubmed
    ..2 and pKred = 5.3. Upon reduction (Em,7.5 = +2 mV) FeA exhibits an unusually sharp S = 2 resonance in parallel-mode EPR. The second iron, FeB, has S = 5/2 and E/D = 0.33; upon reduction (Em,7.5 = +90 mV) FeB turns EPR-silent. ..
  56. Blanchard L, Marion D, Pollock B, Voordouw G, Wall J, Bruschi M, et al. Overexpression of Desulfovibrio vulgaris Hildenborough cytochrome c553 in Desulfovibrio desulfuricans G200. Evidence of conformational heterogeneity in the oxidized protein by NMR. Eur J Biochem. 1993;218:293-301 pubmed
    Plasmid pRC41, containing the cyf gene encoding cytochrome c533 from Desulfovibrio vulgaris Hildenborough, was transferred by conjugation from Escherichia coli to Desulfovibrio desulfuricans G200...
  57. Knauf M, Lohr F, Curley G, O FARRELL P, Mayhew S, Muller F, et al. Homonuclear and heteronuclear NMR studies of oxidized Desulfovibrio vulgaris flavodoxin. Sequential assignments and identification of secondary structure elements. Eur J Biochem. 1993;213:167-84 pubmed
    ..Several proton resonances of the bound flavin mononucleotide cofactor have been assigned. NOE contacts between the prosthetic group and the apoprotein have been detected. ..
  58. Lumppio H, Shenvi N, Garg R, Summers A, Kurtz D. A rubrerythrin operon and nigerythrin gene in Desulfovibrio vulgaris (Hildenborough). J Bacteriol. 1997;179:4607-15 pubmed
    ..vulgaris chromosome, and Northern analysis showed that, in contrast to rbr, ngr is not cotranscribed with other genes. Possible redox-linked functions for rubrerythrin and nigerythrin in iron homeostasis are proposed. ..
  59. Messias A, Kastrau D, Costa H, LeGall J, Turner D, Santos H, et al. Solution structure of Desulfovibrio vulgaris (Hildenborough) ferrocytochrome c3: structural basis for functional cooperativity. J Mol Biol. 1998;281:719-39 pubmed
    ..An important rearrangement in the vicinity of the propionate groups of haem I and involving the covalent linkage of haem II suggests that this is the critical region for the functional cooperativities of this protein. ..
  60. Sieker L, Holmes M, Le Trong I, Turley S, Liu M, LeGall J, et al. The 1.9 A crystal structure of the "as isolated" rubrerythrin from Desulfovibrio vulgaris: some surprising results. J Biol Inorg Chem. 2000;5:505-13 pubmed
    ..This feature/ability may give rise to some of the confusing activities ascribed to this molecule. ..
  61. Macedo S, Mitchell E, Romão C, Cooper S, Coelho R, Liu M, et al. Hybrid cluster proteins (HCPs) from Desulfovibrio desulfuricans ATCC 27774 and Desulfovibrio vulgaris (Hildenborough): X-ray structures at 1.25 A resolution using synchrotron radiation. J Biol Inorg Chem. 2002;7:514-25 pubmed
    ..Electronic supplementary material to this paper can be obtained by using the Springer Link server located at http://dx.doi.org/10.1007/s00775-001-0326-y. ..
  62. Emerson J, Cabelli D, Kurtz D. An engineered two-iron superoxide reductase lacking the [Fe(SCys)4] site retains its catalytic properties in vitro and in vivo. Proc Natl Acad Sci U S A. 2003;100:3802-7 pubmed
    ..e., destruction of the [Fe(SCys)(4)] site did not unmask latent SOD activity of the [Fe(NHis)(4)(SCys)] site. Possible alternative roles for the [Fe(SCys)(4)] site in 2Fe-SORs are considered. ..
  63. Dauter Z, Sieker L, Wilson K. Refinement of rubredoxin from Desulfovibrio vulgaris at 1.0 A with and without restraints. Acta Crystallogr B. 1992;48 ( Pt 1):42-59 pubmed
    ..339 H atoms were included at their calculated positions, which were not refined. There is clear evidence for anisotropic thermal motion. This has not been incorporated in the present model. ..
  64. Allen S, Blaschek H. Factors involved in the electroporation-induced transformation of Clostridium perfringens. FEMS Microbiol Lett. 1990;58:217-20 pubmed
    ..In addition to C. perfringens 3624A Rifr Strr, strains 13, 10543A, 3628C, NTG-4, and 3624A were successfully transformed. Nuclease does not appear to be a factor in the C. perfringens strain-specific electro-transformation protocol. ..
  65. Kwoh D, Vedvick T, McCue A, Gevertz D. Rapid comparison of the cytochrome c3 gene from nine strains of Desulfovibrio vulgaris using polymerase chain reaction amplification. Can J Microbiol. 1993;39:402-11 pubmed
    ..In contrast to the results obtained with strain NCIMB 8456, limited homology was observed between the first 20 amino acid residues of cytochrome c3 from strain DSM 1744 and strain NCIMB 8303. ..
  66. Lobo S, Brindley A, Romão C, Leech H, Warren M, Saraiva L. Two distinct roles for two functional cobaltochelatases (CbiK) in Desulfovibrio vulgaris hildenborough. Biochemistry. 2008;47:5851-7 pubmed publisher
    The sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough possesses a large number of porphyrin-containing proteins whose biosynthesis is poorly characterized...
  67. Rajeev L, Hillesland K, Zane G, Zhou A, Joachimiak M, He Z, et al. Deletion of the Desulfovibrio vulgaris carbon monoxide sensor invokes global changes in transcription. J Bacteriol. 2012;194:5783-93 pubmed publisher
  68. Gao S, Ho J, Fan L, Richardson D, Yuan Z, Bond P. Antimicrobial Effects of Free Nitrous Acid on Desulfovibrio vulgaris: Implications for Sulfide-Induced Corrosion of Concrete. Appl Environ Microbiol. 2016;82:5563-75 pubmed publisher
    ..Here, we report the multiple-targeted antimicrobial effects of FNA on the SRB Desulfovibrio vulgaris Hildenborough by determining the growth, physiological, and gene expression responses to FNA exposure...
  69. Dubourdieu M, Fox J. Amino acid sequence of Desulfovibrio vulgaris flavodoxin. J Biol Chem. 1977;252:1453-63 pubmed
    ..C., and Jensen, L.H. (1973) Proc. NAtl. Acad. Sci. U.S.A. 70, 3857-3860). Ser(10), Thr(12), Asn(14), and Thr(15) were shown to bind the phosphate of the FMN while the isoalloxazine ring is positioned between Trp(60) and Tyr(98). ..
  70. Marion D, Guerlesquin F. Sequential NMR resonance assignment and secondary structure of ferrocytochrome c553 from Desulfovibrio vulgaris Hildenborough. Biochemistry. 1992;31:8171-9 pubmed
    ..vulgaris Miyazaki. On the basis of the secondary structure element and of observed chemical shift due to the heme ring current, a structural alignment of eukaryotic and prokaryotic cytochromes c is proposed. ..
  71. Tan J, Cowan J. Coordination and redox properties of a novel triheme cytochrome from Desulfovibrio vulgaris (Hildenborough). Biochemistry. 1990;29:4886-92 pubmed
    ..The cyanide adduct gave two waves with reduction potentials of -263 (8) and -401 (8) mV. The cytochrome was found to catalyze the reduction of nitrite and hydroxylamine. ..
  72. Shimizu F, Ogata M, Yagi T, Wakabayashi S, Matsubara H. Amino acid sequence and function of rubredoxin from Desulfovibrio vulgaris Miyazaki. Biochimie. 1989;71:1171-7 pubmed
  73. Deckers H, Voordouw G. Identification of a large family of genes for putative chemoreceptor proteins in an ordered library of the Desulfovibrio vulgaris Hildenborough genome. J Bacteriol. 1994;176:351-8 pubmed
    A library of 879 recombinant lambda phages, constructed for the genome of Desulfovibrio vulgaris Hildenborough, has been ordered by restriction fingerprinting...
  74. Artali R, Bombieri G, Meneghetti F, Gilardi G, Sadeghi S, Cavazzini D, et al. Comparison of the refined crystal structures of wild-type (1.34 A) flavodoxin from Desulfovibrio vulgaris and the S35C mutant (1.44 A) at 100 K. Acta Crystallogr D Biol Crystallogr. 2002;58:1787-92 pubmed
    ..The solvent exposure of Cys35 is 43 A(2), of which 8 A(2) is for the sulfur. This is comparable to the exposure of 48 A(2) found for the wt Ser35, where that of the hydroxyl oxygen is also 8 A(2). ..
  75. Rentmeister A, Mayer G, Kuhn N, Famulok M. Secondary structures and functional requirements for thiM riboswitches from Desulfovibrio vulgaris, Erwinia carotovora and Rhodobacter spheroides. Biol Chem. 2008;389:127-34 pubmed publisher
    ..Our study shows that aptamer domains in riboswitches with high similarity in their secondary structures can communicate with a broad variety of non-related expression domains by similar mechanisms. ..
  76. Krumholz L, Wang L, Beck D, Wang T, Hackett M, Mooney B, et al. Membrane protein complex of APS reductase and Qmo is present in Desulfovibrio vulgaris and Desulfovibrio alaskensis. Microbiology. 2013;159:2162-8 pubmed publisher
    ..This interaction was recently verified in Desulfovibrio desulfuricans. Membrane proteins of Desulfovibrio vulgaris Hildenborough ?qmoABCD JW9021, a deletion mutant, were compared to the parent strain using blue-native PAGE to ..
  77. van Rooijen G, Bruschi M, Voordouw G. Cloning and sequencing of the gene encoding cytochrome c553 from Desulfovibrio vulgaris Hildenborough. J Bacteriol. 1989;171:3575-8 pubmed
    The gene encoding cytochrome c553 from Desulfovibrio vulgaris Hildenborough was cloned by using two synthetic deoxyoligonucleotide probes...
  78. Tan J, Helms L, Swenson R, Cowan J. Primary structure of the assimilatory-type sulfite reductase from Desulfovibrio vulgaris (Hildenborough): cloning and nucleotide sequence of the reductase gene. Biochemistry. 1991;30:9900-7 pubmed
    ..Lina, A. R., Moura, J. J. G., Xavier, A. V., Fauque, G., Peck, H. D., & Le Gall, J. (1986) Biochem. Biophys. Res. Commun. 141, 1032-1041]...
  79. Moura I, Tavares P, Moura J, Ravi N, Huynh B, Liu M, et al. Purification and characterization of desulfoferrodoxin. A novel protein from Desulfovibrio desulfuricans (ATCC 27774) and from Desulfovibrio vulgaris (strain Hildenborough) that contains a distorted rubredoxin center and a mononuclear ferrous center. J Biol Chem. 1990;265:21596-602 pubmed
    ..J., and Voordouw, G. (1989) J. Bacteriol. 171, 49996-50004), which was suggested to be a rubredoxin oxidoreductase. However, reduced pyridine nucleotides failed to reduce the desulforedoxin-like center of this new protein...
  80. Misaki S, Morimoto Y, Ogata M, Yagi T, Higuchi Y, Yasuoka N. Structure determination of rubredoxin from Desulfovibrio vulgaris Miyazaki F in two crystal forms. Acta Crystallogr D Biol Crystallogr. 1999;55:408-13 pubmed
    ..From this comparison, a similarity in the core region, which is composed of aromatic residues and includes the active centre, has been revealed...
  81. Jin S, Kurtz D, Liu Z, Rose J, Wang B. X-ray crystal structures of reduced rubrerythrin and its azide adduct: a structure-based mechanism for a non-heme diiron peroxidase. J Am Chem Soc. 2002;124:9845-55 pubmed
    ..On the basis of these unique structural features, a mechanism is proposed for facile reduction of hydrogen peroxide by Rbr involving a cis mu-eta(2) H2O2 diferrous intermediate...
  82. McCarthy A, Walsh M, Verma C, O Connell D, Reinhold M, Yalloway G, et al. Crystallographic investigation of the role of aspartate 95 in the modulation of the redox potentials of Desulfovibrio vulgaris flavodoxin. Biochemistry. 2002;41:10950-62 pubmed
  83. ElAntak L, Morelli X, Bornet O, Hatchikian C, Czjzek M, Dolla A, et al. The cytochrome c3-[Fe]-hydrogenase electron-transfer complex: structural model by NMR restrained docking. FEBS Lett. 2003;548:1-4 pubmed
    ..tetrahemic cytochrome is an intermediate between the [Fe]-hydrogenase and the cytochrome Hmc in Desulfovibrio vulgaris Hildenborough strain...
  84. Jin S, Kurtz D, Liu Z, Rose J, Wang B. Displacement of iron by zinc at the diiron site of Desulfovibrio vulgaris rubrerythrin: X-ray crystal structure and anomalous scattering analysis. J Inorg Biochem. 2004;98:786-96 pubmed publisher
    ..vulgaris Rbr could be due to displacement of iron from a native diiron site by adventitious zinc during isolation and/or crystallization, and that reduced diiron and dizinc sites can adopt very similar structures in Rbr...
  85. Iyer R, Silaghi Dumitrescu R, Kurtz D, Lanzilotta W. High-resolution crystal structures of Desulfovibrio vulgaris (Hildenborough) nigerythrin: facile, redox-dependent iron movement, domain interface variability, and peroxidase activity in the rubrerythrins. J Biol Inorg Chem. 2005;10:407-16 pubmed publisher
    ..The characteristic combination of iron sites together with the redox-dependent iron toggling between protein ligands can account for the selectivity of Rbrs for hydrogen peroxide over dioxygen...
  86. Bender K, Yen H, Hemme C, Yang Z, He Z, He Q, et al. Analysis of a ferric uptake regulator (Fur) mutant of Desulfovibrio vulgaris Hildenborough. Appl Environ Microbiol. 2007;73:5389-400 pubmed publisher
    ..Both the physiological and transcriptional data implicate a global regulatory role for Fur in the sulfate-reducing bacterium D. vulgaris...
  87. Shomura Y, Komori H, Miyabe N, Tomiyama M, Shibata N, Higuchi Y. Crystal structures of hydrogenase maturation protein HypE in the Apo and ATP-bound forms. J Mol Biol. 2007;372:1045-54 pubmed publisher
    ..Here, we present the crystal structures of HypE from Desulfovibrio vulgaris Hildenborough in the presence and in the absence of ATP at a resolution of 2.0 A and 2.6 A, respectively...
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    ..between intracellular iron storage and oxidative stress response in the sulfate reducing bacterium Desulfovibrio vulgaris Hildenborough, an anaerobe that is often found in oxygenated niches...
  89. Bruschi M, Bertrand P, More C, LeRoy G, Bonicel J, Haladjian J, et al. Biochemical and spectroscopic characterization of the high molecular weight cytochrome c from Desulfovibrio vulgaris Hildenborough expressed in Desulfovibrio desulfuricans G200. Biochemistry. 1992;31:3281-8 pubmed
    The gene of high molecular weight, multiheme cytochrome c (Hmc) from the sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough has been overexpressed in Desulfovibrio desulfuricans G200. The recombinant protein has been purified...
  90. Watt W, Tulinsky A, Swenson R, Watenpaugh K. Comparison of the crystal structures of a flavodoxin in its three oxidation states at cryogenic temperatures. J Mol Biol. 1991;218:195-208 pubmed
  91. Blackledge M, Medvedeva S, Poncin M, Guerlesquin F, Bruschi M, Marion D. Structure and dynamics of ferrocytochrome c553 from Desulfovibrio vulgaris studied by NMR spectroscopy and restrained molecular dynamics. J Mol Biol. 1995;245:661-81 pubmed publisher
    The solution structure of Desulfovibrio vulgaris Hildenborough (DvH) ferrocytochrome c553 has been determined by nuclear magnetic resonance spectroscopy and combined simulated annealing/high temperature restrained molecular dynamics ..
  92. Karkhoff Schweizer R, Huber D, Voordouw G. Conservation of the genes for dissimilatory sulfite reductase from Desulfovibrio vulgaris and Archaeoglobus fulgidus allows their detection by PCR. Appl Environ Microbiol. 1995;61:290-6 pubmed