Crystallization and preliminary crystallographic analysis of manganese(II)-dependent 2,3-dihydroxybiphenyl 1,2-dioxygenase from Bacillus sp. JF8.

PubWeight™: 0.75‹?›

🔗 View Article (PMC 2833037)

Published in Acta Crystallogr Sect F Struct Biol Cryst Commun on February 24, 2010

Authors

Miki Senda1, Takashi Hatta, Kazuhide Kimbara, Toshiya Senda

Author Affiliations

1: Structure Guided Drug Development Project, Research and Development Department, Japan Biological Informatics Consortium, 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan.

Articles cited by this

A short history of SHELX. Acta Crystallogr A (2007) 7339.18

Coot: model-building tools for molecular graphics. Acta Crystallogr D Biol Crystallogr (2004) 227.01

The CCP4 suite: programs for protein crystallography. Acta Crystallogr D Biol Crystallogr (1994) 187.88

Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr D Biol Crystallogr (1997) 137.43

Solvent content of protein crystals. J Mol Biol (1968) 106.07

Crystal structures of Fe2+ dioxygenase superoxo, alkylperoxo, and bound product intermediates. Science (2007) 3.03

Crystal structure of the biphenyl-cleaving extradiol dioxygenase from a PCB-degrading pseudomonad. Science (1995) 2.68

The ins and outs of ring-cleaving dioxygenases. Crit Rev Biochem Mol Biol (2006) 2.36

Three-dimensional structures of free form and two substrate complexes of an extradiol ring-cleavage type dioxygenase, the BphC enzyme from Pseudomonas sp. strain KKS102. J Mol Biol (1996) 1.98

Evolutionary relationships among extradiol dioxygenases. J Bacteriol (1996) 1.88

Crystallographic comparison of manganese- and iron-dependent homoprotocatechuate 2,3-dioxygenases. J Bacteriol (2004) 1.84

Crystal structures of the reaction intermediate and its homologue of an extradiol-cleaving catecholic dioxygenase. J Mol Biol (2002) 1.50

Swapping metals in Fe- and Mn-dependent dioxygenases: evidence for oxygen activation without a change in metal redox state. Proc Natl Acad Sci U S A (2008) 1.47

Definitive evidence for monoanionic binding of 2,3-dihydroxybiphenyl to 2,3-dihydroxybiphenyl 1,2-dioxygenase from UV resonance Raman spectroscopy, UV/Vis absorption spectroscopy, and crystallography. J Am Chem Soc (2002) 1.45

Mechanism of extradiol aromatic ring-cleaving dioxygenases. Curr Opin Struct Biol (2008) 1.43

Catechol dioxygenases from Escherichia coli (MhpB) and Alcaligenes eutrophus (MpcI): sequence analysis and biochemical properties of a third family of extradiol dioxygenases. J Bacteriol (1996) 1.22

The mechanism-based inactivation of 2,3-dihydroxybiphenyl 1,2-dioxygenase by catecholic substrates. J Biol Chem (2001) 1.17

A manganese-dependent dioxygenase from Arthrobacter globiformis CM-2 belongs to the major extradiol dioxygenase family. J Bacteriol (1995) 1.08

Development of a fully automated macromolecular crystallization/observation robotic system, HTS-80. Acta Crystallogr D Biol Crystallogr (2005) 0.91

Characterization of a novel thermostable Mn(II)-dependent 2,3-dihydroxybiphenyl 1,2-dioxygenase from a polychlorinated biphenyl- and naphthalene-degrading Bacillus sp. JF8. J Biol Chem (2003) 0.83

Articles by these authors

Structure and function of the histone chaperone CIA/ASF1 complexed with histones H3 and H4. Nature (2007) 3.19

Crystal structure of a full-length LysR-type transcriptional regulator, CbnR: unusual combination of two subunit forms and molecular bases for causing and changing DNA bend. J Mol Biol (2003) 2.02

Tertiary structure-function analysis reveals the pathogenic signaling potentiation mechanism of Helicobacter pylori oncogenic effector CagA. Cell Host Microbe (2012) 1.72

Crystal structure of the terminal oxygenase component of biphenyl dioxygenase derived from Rhodococcus sp. strain RHA1. J Mol Biol (2004) 1.62

Relationship between the structure of SET/TAF-Ibeta/INHAT and its histone chaperone activity. Proc Natl Acad Sci U S A (2007) 1.55

Crystal structures of the reaction intermediate and its homologue of an extradiol-cleaving catecholic dioxygenase. J Mol Biol (2002) 1.50

Crystal structure of a gamma-butyrolactone autoregulator receptor protein in Streptomyces coelicolor A3(2). J Mol Biol (2004) 1.44

Bacterial redox protein azurin, tumor suppressor protein p53, and regression of cancer. Proc Natl Acad Sci U S A (2002) 1.41

Crystal structure of the radical SAM enzyme catalyzing tricyclic modified base formation in tRNA. J Mol Biol (2007) 1.25

Tolerance of the Rieske-type [2Fe-2S] cluster in recombinant ferredoxin BphA3 from Pseudomonas sp. KKS102 to histidine ligand mutations. Biochem J (2005) 1.23

Crystallization and preliminary X-ray analysis of the reduced Rieske-type [2Fe-2S] ferredoxin derived from Pseudomonas sp. strain KKS102. Acta Crystallogr Sect F Struct Biol Cryst Commun (2007) 1.21

High-throughput identification and screening of novel Methylobacterium species using whole-cell MALDI-TOF/MS analysis. PLoS One (2012) 1.16

Crystallization and preliminary X-ray analysis of the Rieske-type [2Fe-2S] ferredoxin component of biphenyl dioxygenase from Pseudomonas sp. strain KKS102. Acta Crystallogr Sect F Struct Biol Cryst Commun (2006) 1.16

Structure and conservation of a polyethylene glycol-degradative operon in sphingomonads. Microbiology (2007) 1.15

Diversity of 2,3-dihydroxybiphenyl dioxygenase genes in a strong PCB degrader, Rhodococcus sp. strain RHA1. J Biosci Bioeng (2002) 1.11

Novel approach to the improvement of biphenyl and polychlorinated biphenyl degradation activity: promoter implantation by homologous recombination. Appl Environ Microbiol (2003) 1.11

Molecular mechanism of the redox-dependent interaction between NADH-dependent ferredoxin reductase and Rieske-type [2Fe-2S] ferredoxin. J Mol Biol (2007) 1.08

The bacterial redox protein azurin induces apoptosis in J774 macrophages through complex formation and stabilization of the tumor suppressor protein p53. Infect Immun (2002) 1.08

Oxygen affinity of hemoglobin regulates O2 consumption, metabolism, and physical activity. J Biol Chem (2002) 1.07

Structural basis for recognition of cognate tRNA by tyrosyl-tRNA synthetase from three kingdoms. Nucleic Acids Res (2007) 1.07

Apoptosis or growth arrest: Modulation of tumor suppressor p53's specificity by bacterial redox protein azurin. Proc Natl Acad Sci U S A (2004) 1.03

Crystallization and preliminary X-ray analysis of the electron-transfer complex of Rieske-type [2Fe-2S] ferredoxin and NADH-dependent ferredoxin reductase derived from Acidovorax sp. strain KKS102. Acta Crystallogr Sect F Struct Biol Cryst Commun (2007) 1.03

Enantioselectivity of haloalkane dehalogenases and its modulation by surface loop engineering. Angew Chem Int Ed Engl (2010) 0.98

Practical application of methanol-mediated mutualistic symbiosis between Methylobacterium species and a roof greening moss, Racomitrium japonicum. PLoS One (2012) 0.95

Structure of the histone chaperone CIA/ASF1-double bromodomain complex linking histone modifications and site-specific histone eviction. Proc Natl Acad Sci U S A (2010) 0.95

Flow cytometry analysis of changes in the DNA content of the polychlorinated biphenyl degrader Comamonas testosteroni TK102: effect of metabolites on cell-cell separation. Appl Environ Microbiol (2002) 0.95

Isolation of bacteria able to grow on both polyethylene glycol (PEG) and polypropylene glycol (PPG) and their PEG/PPG dehydrogenases. Appl Microbiol Biotechnol (2006) 0.94

Single-cell analyses revealed transfer ranges of IncP-1, IncP-7, and IncP-9 plasmids in a soil bacterial community. Appl Environ Microbiol (2013) 0.92

Induction of apoptosis in macrophages by Pseudomonas aeruginosa azurin: tumour-suppressor protein p53 and reactive oxygen species, but not redox activity, as critical elements in cytotoxicity. Mol Microbiol (2003) 0.92

The crucial role of mitochondrial regulation in adaptive aluminium resistance in Rhodotorula glutinis. Microbiology (2008) 0.90

Regulatory system of the protocatechuate 4,5-cleavage pathway genes essential for lignin downstream catabolism. J Bacteriol (2010) 0.90

Analysis of amino acid residues involved in catalysis of polyethylene glycol dehydrogenase from Sphingopyxis terrae, using three-dimensional molecular modeling-based kinetic characterization of mutants. Appl Environ Microbiol (2006) 0.90

Culturable bacteria in hydroponic cultures of moss Racomitrium japonicum and their potential as biofertilizers for moss production. J Biosci Bioeng (2011) 0.89

bph genes of the thermophilic PCB degrader, Bacillus sp. JF8: characterization of the divergent ring-hydroxylating dioxygenase and hydrolase genes upstream of the Mn-dependent BphC. Microbiology (2005) 0.89

A bacterial biosensor for oxidative stress using the constitutively expressed redox-sensitive protein roGFP2. Sensors (Basel) (2010) 0.87

The regulatory mechanism of 2,4,6-trichlorophenol catabolic operon expression by HadR in Ralstonia pickettii DTP0602. Microbiology (2013) 0.86

Biochemical and molecular characterization of a periplasmic hydrolase for oxidized polyvinyl alcohol from Sphingomonas sp. strain 113P3. Microbiology (2005) 0.85

Genes for Mn(II)-dependent NahC and Fe(II)-dependent NahH located in close proximity in the thermophilic naphthalene and PCB degrader, Bacillus sp. JF8: cloning and characterization. Microbiology (2004) 0.85

The pva operon is located on the megaplasmid of Sphingopyxis sp. strain 113P3 and is constitutively expressed, although expression is enhanced by PVA. Appl Microbiol Biotechnol (2008) 0.84

Cloning and expression of the gene for periplasmic poly(vinyl alcohol) dehydrogenase from Sphingomonas sp. strain 113P3, a novel-type quinohaemoprotein alcohol dehydrogenase. Microbiology (2006) 0.84

Proposed oxidative metabolic pathway for polypropylene glycol in Sphingobium sp. strain PW-1. Biosci Biotechnol Biochem (2008) 0.84

Purification, crystallization and preliminary X-ray diffraction analysis of human oncoprotein SET/TAF-1beta. Acta Crystallogr D Biol Crystallogr (2004) 0.84

Extensive reduction of cell viability and enhanced matrix production in Pseudomonas aeruginosa PAO1 flow biofilms treated with a D-amino acid mixture. Appl Environ Microbiol (2012) 0.83

Characterization of a novel thermostable Mn(II)-dependent 2,3-dihydroxybiphenyl 1,2-dioxygenase from a polychlorinated biphenyl- and naphthalene-degrading Bacillus sp. JF8. J Biol Chem (2003) 0.83

Crystallization of CprB, an autoregulator-receptor protein from Streptomyces coelicolor A3(2). Acta Crystallogr D Biol Crystallogr (2003) 0.83

Methylobacterium gnaphalii sp. nov., isolated from leaves of Gnaphalium spicatum. Int J Syst Evol Microbiol (2011) 0.82

Metabolic pathway of xenoestrogenic short ethoxy chain-nonylphenol to nonylphenol by aerobic bacteria, Ensifer sp. strain AS08 and Pseudomonas sp. strain AS90. Appl Microbiol Biotechnol (2006) 0.82

Dual regulation of a polyethylene glycol degradative operon by AraC-type and GalR-type regulators in Sphingopyxis macrogoltabida strain 103. Microbiology (2006) 0.82

Direct observation of protein microcrystals in crystallization buffer by atmospheric scanning electron microscopy. Int J Mol Sci (2012) 0.82

Theoretical framework for the histone modification network: modifications in the unstructured histone tails form a robust scale-free network. Genes Cells (2009) 0.82

Crystallization and preliminary crystallographic analysis of a haloalkane dehalogenase, DbjA, from Bradyrhizobium japonicum USDA110. Acta Crystallogr Sect F Struct Biol Cryst Commun (2007) 0.81

Pandoraea oxalativorans sp. nov., Pandoraea faecigallinarum sp. nov. and Pandoraea vervacti sp. nov., isolated from oxalate-enriched culture. Int J Syst Evol Microbiol (2010) 0.81

Prophenol oxidase A3 in Drosophila melanogaster: activation and the PCR-based cDNA sequence. Biochem Genet (2003) 0.81

Xenoestrogenic short ethoxy chain nonylphenol is oxidized by a flavoprotein alcohol dehydrogenase from Ensifer sp. strain AS08. Appl Microbiol Biotechnol (2006) 0.80

Complete Genome Sequence of the Thermophilic Polychlorinated Biphenyl Degrader Geobacillus sp. Strain JF8 (NBRC 109937). Genome Announc (2014) 0.80

Crystal structure of a zinc-dependent D-serine dehydratase from chicken kidney. J Biol Chem (2011) 0.80

Rapid assessment of the physiological status of the polychlorinated biphenyl degrader Comamonas testosteroni TK102 by flow cytometry. Appl Environ Microbiol (2002) 0.79

Single-turnover kinetics of 2,3-dihydroxybiphenyl 1,2-dioxygenase reacting with 3-formylcatechol. Biochem Biophys Res Commun (2005) 0.79

Methylobacterium oxalidis sp. nov., isolated from leaves of Oxalis corniculata. Int J Syst Evol Microbiol (2011) 0.79

Crystallization of the terminal oxygenase component of biphenyl dioxygenase derived from Rhodococcus sp. strain RHA1. Protein Pept Lett (2003) 0.79

Crystal structure of Methanococcus jannaschii TATA box-binding protein. Genes Cells (2008) 0.78

Multifunctionalization of alkenes via aerobic oxynitration and sp3 C-H oxidation. Chem Commun (Camb) (2013) 0.78

Method for assessment of viability and morphological changes of bacteria in the early stage of colony formation on a simulated natural environment. Appl Environ Microbiol (2006) 0.78

Assessment of change in biofilm architecture by nutrient concentration using a multichannel microdevice flow system. J Biosci Bioeng (2012) 0.77

Purification and crystallization of a LysR-type transcriptional regulator CBNR from Ralstonia eutropha NH9. Protein Pept Lett (2003) 0.77

Amino acids in positions 48, 52, and 73 differentiate the substrate specificities of the highly homologous chlorocatechol 1,2-dioxygenases CbnA and TcbC. J Bacteriol (2005) 0.77

Genes involved in novel adaptive aluminum resistance in Rhodotorula glutinis. J Biosci Bioeng (2010) 0.77

Crystallization and preliminary crystallographic analysis of D-serine dehydratase from chicken kidney. Acta Crystallogr Sect F Struct Biol Cryst Commun (2010) 0.77

Polyethylene glycol (PEG)-carboxylate-CoA synthetase is involved in PEG metabolism in Sphingopyxis macrogoltabida strain 103. Arch Microbiol (2007) 0.77

Three-dimensional structure of the ternary complex of yeast tyrosyl-tRNA synthetase. Nucleic Acids Symp Ser (Oxf) (2004) 0.77

Crystallization and preliminary crystallographic analysis of gallate dioxygenase DesB from Sphingobium sp. SYK-6. Acta Crystallogr Sect F Struct Biol Cryst Commun (2009) 0.77

Structural basis of the γ-lactone-ring formation in ascorbic acid biosynthesis by the senescence marker protein-30/gluconolactonase. PLoS One (2013) 0.76

Roles of histone chaperone CIA/Asf1 in nascent DNA elongation during nucleosome replication. Genes Cells (2011) 0.76

Crystallization and preliminary crystallographic analysis of D-aspartate oxidase from porcine kidney. Acta Crystallogr Sect F Struct Biol Cryst Commun (2012) 0.75

Effect of leucine-to-methionine substitutions on the diffraction quality of histone chaperone SET/TAF-Ibeta/INHAT crystals. Acta Crystallogr Sect F Struct Biol Cryst Commun (2008) 0.75

Crystallization and preliminary crystallographic analysis of DtsR1, a carboxyltransferase subunit of acetyl-CoA carboxylase from Corynebacterium glutamicum. Acta Crystallogr Sect F Struct Biol Cryst Commun (2007) 0.75

Iodine-mediated α-acetoxylation of 2,3-disubstituted indoles. Org Lett (2012) 0.75

Flow cytometry-based method for isolating live bacteria with meta-cleavage activity on dihydroxy compounds of biphenyl. J Biosci Bioeng (2009) 0.75

Crystallization and preliminary crystallographic analysis of the catechol 2,3-dioxygenase PheB from Bacillus stearothermophilus BR219. Acta Crystallogr Sect F Struct Biol Cryst Commun (2006) 0.75

Complete Genome Sequence of Ralstonia pickettii DTP0602, a 2,4,6-Trichlorophenol Degrader. Genome Announc (2013) 0.75

Cell surface structure enhancing uptake of polyvinyl alcohol (PVA) is induced by PVA in the PVA-utilizing Sphingopyxis sp. strain 113P3. Arch Microbiol (2007) 0.75

Rapid and multiple in situ identification and analyses of physiological status of specific bacteria based on fluorescent in situ hybridization. J Biosci Bioeng (2010) 0.75

Characterization of a cryptic plasmid, pSM103mini, from polyethylene-glycol degrading Sphingopyxis macrogoltabida strain 103. Biosci Biotechnol Biochem (2011) 0.75

Purification, crystallization and preliminary X-ray analysis of Methanococcus jannaschii TATA box-binding protein (TBP). Acta Crystallogr D Biol Crystallogr (2004) 0.75

[Immuno-EM in solution using atmospheric scanning electron microscope (ASEM) applicable to various antibodies]. Seikagaku (2014) 0.75

[Mechanism of nucleosome assembly/disassembly mediated by histone chaperone CIA; implications for nucleosome semi-conservative replication]. Seikagaku (2007) 0.75

Complete pyridine-nucleotide-specific conversion of an NADH-dependent ferredoxin reductase. Biochem J (2014) 0.75

Involvement of PEG-carboxylate dehydrogenase and glutathione S-transferase in PEG metabolism by Sphingopyxis macrogoltabida strain 103. Appl Microbiol Biotechnol (2008) 0.75

Cation-driven Optical Properties of Artificial Luciferases. Anal Sci (2015) 0.75