Crystallization and preliminary crystallographic analysis of gallate dioxygenase DesB from Sphingobium sp. SYK-6.

PubWeight™: 0.77‹?›

🔗 View Article (PMC 2777051)

Published in Acta Crystallogr Sect F Struct Biol Cryst Commun on October 30, 2009

Authors

Keisuke Sugimoto1, Yoshihiro Yamamoto, Siswanto Antoni, Miki Senda, Daisuke Kasai, Eiji Masai, Masao Fukuda, Toshiya Senda

Author Affiliations

1: Department of Materials Chemistry, Asahikawa National College of Technology, Shunko-dai, Asahikawa, Hokkaido, Japan.

Articles cited by this

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

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

Biodegradation of lignocellulosics: microbial, chemical, and enzymatic aspects of the fungal attack of lignin. Int Microbiol (2005) 2.80

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

Versatility of biological non-heme Fe(II) centers in oxygen activation reactions. Nat Chem Biol (2008) 2.64

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

Genetic and biochemical investigations on bacterial catabolic pathways for lignin-derived aromatic compounds. Biosci Biotechnol Biochem (2007) 1.93

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

A bacterial enzyme degrading the model lignin compound beta-etherase is a member of the glutathione-S-transferase superfamily. FEBS Lett (1993) 1.52

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

Cloning of a Sphingomonas paucimobilis SYK-6 gene encoding a novel oxygenase that cleaves lignin-related biphenyl and characterization of the enzyme. Appl Environ Microbiol (1998) 1.45

Cloning and sequencing of the gene for a Pseudomonas paucimobilis enzyme that cleaves beta-aryl ether. J Bacteriol (1991) 1.44

Lignin primary structures and dirigent sites. Curr Opin Biotechnol (2005) 1.34

Roles of the enantioselective glutathione S-transferases in cleavage of beta-aryl ether. J Bacteriol (2003) 1.29

Crystal structure of an aromatic ring opening dioxygenase LigAB, a protocatechuate 4,5-dioxygenase, under aerobic conditions. Structure (1999) 1.27

Characterization of the meta-cleavage compound hydrolase gene involved in degradation of the lignin-related biphenyl structure by Sphingomonas paucimobilis SYK-6. Appl Environ Microbiol (1999) 1.09

Identification and analysis of a bottleneck in PCB biodegradation. Nat Struct Biol (2002) 1.08

Identification of three alcohol dehydrogenase genes involved in the stereospecific catabolism of arylglycerol-beta-aryl ether by Sphingobium sp. strain SYK-6. Appl Environ Microbiol (2009) 1.00

Characterization of the gallate dioxygenase gene: three distinct ring cleavage dioxygenases are involved in syringate degradation by Sphingomonas paucimobilis SYK-6. J Bacteriol (2005) 0.98

Characterization of the 3-O-methylgallate dioxygenase gene and evidence of multiple 3-O-methylgallate catabolic pathways in Sphingomonas paucimobilis SYK-6. J Bacteriol (2004) 0.98

Coexistence of two different O demethylation systems in lignin metabolism by Sphingomonas paucimobilis SYK-6: cloning and sequencing of the lignin biphenyl-specific O-demethylase (LigX) gene. Appl Environ Microbiol (2000) 0.88

Articles by these authors

Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110. Mol Syst Biol (2006) 5.20

The complete genome of Rhodococcus sp. RHA1 provides insights into a catabolic powerhouse. Proc Natl Acad Sci U S A (2006) 4.18

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

Genetic and biochemical investigations on bacterial catabolic pathways for lignin-derived aromatic compounds. Biosci Biotechnol Biochem (2007) 1.93

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

Efficacy of linezolid against Panton-Valentine leukocidin (PVL)-positive meticillin-resistant Staphylococcus aureus (MRSA) in a mouse model of haematogenous pulmonary infection. Int J Antimicrob Agents (2009) 1.52

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

Roles of the enantioselective glutathione S-transferases in cleavage of beta-aryl ether. J Bacteriol (2003) 1.29

Polymorphisms of the TNF gene and the TNF receptor superfamily member 1B gene are associated with susceptibility to ulcerative colitis and Crohn's disease, respectively. Immunogenetics (2002) 1.25

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

A novel tetrahydrofolate-dependent O-demethylase gene is essential for growth of Sphingomonas paucimobilis SYK-6 with syringate. J Bacteriol (2004) 1.17

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

A novel telomerase template antagonist (GRN163) as a potential anticancer agent. Cancer Res (2003) 1.15

Cloning and characterization of linR, involved in regulation of the downstream pathway for gamma-hexachlorocyclohexane degradation in Sphingomonas paucimobilis UT26. Appl Environ Microbiol (2002) 1.14

A tetrahydrofolate-dependent O-demethylase, LigM, is crucial for catabolism of vanillate and syringate in Sphingomonas paucimobilis SYK-6. J Bacteriol (2005) 1.14

Identification and characterization of genes involved in the downstream degradation pathway of gamma-hexachlorocyclohexane in Sphingomonas paucimobilis UT26. J Bacteriol (2005) 1.13

Functional characterization of a catabolic plasmid from polychlorinated- biphenyl-degrading Rhodococcus sp. strain RHA1. J Bacteriol (2004) 1.12

Crystal structure of γ-hexachlorocyclohexane Dehydrochlorinase LinA from Sphingobium japonicum UT26. J Mol Biol (2010) 1.12

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

Novel 2,4-dichlorophenoxyacetic acid degradation genes from oligotrophic Bradyrhizobium sp. strain HW13 isolated from a pristine environment. J Bacteriol (2002) 1.11

Daily intake of heat-killed Lactobacillus plantarum L-137 augments acquired immunity in healthy adults. J Nutr (2006) 1.08

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

Diagnostic significance of Aspergillus species isolated from respiratory samples in an adult pneumology ward. Med Mycol (2011) 1.05

Cloning and characterization of the ferulic acid catabolic genes of Sphingomonas paucimobilis SYK-6. Appl Environ Microbiol (2002) 1.04

IL18 polymorphism is associated with an increased risk of Crohn's disease. J Gastroenterol (2002) 1.04

Potency of SMP-601, a novel carbapenem, in hematogenous murine bronchopneumonia caused by methicillin-resistant and vancomycin-intermediate Staphylococcus aureus. Antimicrob Agents Chemother (2008) 1.04

Spatial localization of mono-and diphosphorylated myosin II regulatory light chain at the leading edge of motile HeLa cells. Cell Struct Funct (2002) 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

Characterization of the 4-carboxy-4-hydroxy-2-oxoadipate aldolase gene and operon structure of the protocatechuate 4,5-cleavage pathway genes in Sphingomonas paucimobilis SYK-6. J Bacteriol (2003) 1.01

Identification of three alcohol dehydrogenase genes involved in the stereospecific catabolism of arylglycerol-beta-aryl ether by Sphingobium sp. strain SYK-6. Appl Environ Microbiol (2009) 1.00

Roles of calcineurin and Crz1 in antifungal susceptibility and virulence of Candida glabrata. Antimicrob Agents Chemother (2010) 1.00

Severe pulmonary tuberculosis complicating Ileocecal intussusception due to intestinal tuberculosis: a case report. Ann Clin Microbiol Antimicrob (2008) 1.00

Enhancement of hemocompatibility of the MERA monopivot centrifugal pump: toward medium-term use. Artif Organs (2012) 0.99

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

Characterization of the gallate dioxygenase gene: three distinct ring cleavage dioxygenases are involved in syringate degradation by Sphingomonas paucimobilis SYK-6. J Bacteriol (2005) 0.98

Sustained high levels of serum interferon-γ during HIV-1 infection: a specific trend different from other cytokines. Viral Immunol (2010) 0.98

Identification and characterization of the Escherichia coli envC gene encoding a periplasmic coiled-coil protein with putative peptidase activity. FEMS Microbiol Lett (2002) 0.98

Antifungal susceptibilities of Aspergillus fumigatus clinical isolates obtained in Nagasaki, Japan. Antimicrob Agents Chemother (2011) 0.98

A combination of caffeine, arginine, soy isoflavones, and L-carnitine enhances both lipolysis and fatty acid oxidation in 3T3-L1 and HepG2 cells in vitro and in KK mice in vivo. J Nutr (2007) 0.98

Characterization of the 3-O-methylgallate dioxygenase gene and evidence of multiple 3-O-methylgallate catabolic pathways in Sphingomonas paucimobilis SYK-6. J Bacteriol (2004) 0.98

Characterization of the 5-carboxyvanillate decarboxylase gene and its role in lignin-related biphenyl catabolism in Sphingomonas paucimobilis SYK-6. Appl Environ Microbiol (2002) 0.97

Characterization of the protocatechuate 4,5-cleavage pathway operon in Comamonas sp. strain E6 and discovery of a novel pathway gene. Appl Environ Microbiol (2010) 0.97

2-Hydroxypenta-2,4-dienoate metabolic pathway genes in a strong polychlorinated biphenyl degrader, Rhodococcus sp. strain RHA1. Appl Environ Microbiol (2003) 0.97

Characterization of the terephthalate degradation genes of Comamonas sp. strain E6. Appl Environ Microbiol (2006) 0.96

Complete genome sequence of Sphingobium sp. strain SYK-6, a degrader of lignin-derived biaryls and monoaryls. J Bacteriol (2012) 0.96

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

Multilocus sequence typing of Cryptococcus neoformans in non-HIV associated cryptococcosis in Nagasaki, Japan. Med Mycol (2012) 0.95

DNA barcoding reveals 24 distinct lineages as cryptic bird species candidates in and around the Japanese Archipelago. Mol Ecol Resour (2014) 0.95

Isolation and characterization of Streptomyces, Actinoplanes, and Methylibium strains that are involved in degradation of natural rubber and synthetic poly(cis-1,4-isoprene). Enzyme Microb Technol (2011) 0.95

Oral administration of heat-killed Lactobacillus plantarum L-137 enhances protection against influenza virus infection by stimulation of type I interferon production in mice. Int Immunopharmacol (2009) 0.94

In vivo efficacy and pharmacokinetics of tomopenem (CS-023), a novel carbapenem, against Pseudomonas aeruginosa in a murine chronic respiratory tract infection model. J Antimicrob Chemother (2008) 0.94

Multiple lung abscesses caused by Actinomyces graevenitzii mimicking acute pulmonary coccidioidomycosis. J Clin Microbiol (2012) 0.94

Characterization of FerC, a MarR-type transcriptional regulator, involved in transcriptional regulation of the ferulate catabolic operon in Sphingobium sp. strain SYK-6. FEMS Microbiol Lett (2012) 0.93

Characterization of transcriptional regulatory genes for biphenyl degradation in Rhodococcus sp. strain RHA1. J Bacteriol (2004) 0.93

Usefulness of the oximetry test for the diagnosis of sleep apnea syndrome in Japan. Am J Med Sci (2006) 0.93

Roles of ring-hydroxylating dioxygenases in styrene and benzene catabolism in Rhodococcus jostii RHA1. J Bacteriol (2007) 0.92

A nonradioisotope, enzymatic assay for 2-deoxyglucose uptake in L6 skeletal muscle cells cultured in a 96-well microplate. Anal Biochem (2006) 0.92

Characterization of the isophthalate degradation genes of Comamonas sp. strain E6. Appl Environ Microbiol (2009) 0.92

Role of the Slt2 mitogen-activated protein kinase pathway in cell wall integrity and virulence in Candida glabrata. FEMS Yeast Res (2010) 0.91

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