Mode of DNA binding by SopA protein of Escherichia coli F plasmid.

Abstract:

:The binding of SopA to the promoter region of its own gene, in which four copies of SopA's recognition sequence, 5'-CTTTGC-3', are arrayed asymmetrically, was examined in vitro. Titration using electrophoretic mobility shift assay showed that the stoichiometry of SopA protomers to the promoter-region DNA is 4 and that the binding is highly co-operative. The co-operativity was corroborated by EMSA and DNase I footprinting for a number of mutant DNA fragments in which 5'-CTTTGC-3' was changed to 5'-CTTACG-3'. EMSA in the style of circular permutation showed that SopA bends DNA. Mutation at either outermost binding site had a different effect on DNA bending by SopA, reflecting the asymmetry in the arrangement of the binding sites, for which the results of DNase I footprinting were in agreement. Gel filtration chromatography and analytical ultracentrifugation of free SopA showed that the protein can exist as a monomer and oligomers in the absence of ATP. Hence, the results indicate that the co-operativity in SopA's DNA binding is based on its intrinsic protein-protein interaction modified by DNA interaction.

journal_name

J Biochem

journal_title

Journal of biochemistry

authors

Komai M,Umino M,Hanai R

doi

10.1093/jb/mvq151

subject

Has Abstract

pub_date

2011-04-01 00:00:00

pages

455-61

issue

4

eissn

0021-924X

issn

1756-2651

pii

mvq151

journal_volume

149

pub_type

杂志文章
  • The structure and function of acid proteases. V. Comparative studies on the specific inhibition of acid proteases by diazoacetyl-DL-norleucine methyl ester, 1,2-epoxy-3-(p-nitrophenoxy) propane and pepstatin.

    abstract::Comparative studies have been made on the effects of diazoacetyl-DL-norleucine methyl ester (DAN), 1,2-epoxy-3-(p-nitrophenoxy)propane (EPNP) and pepstatin on acid proteases, including those from Acrocylindrium sp., Aspergillus niger, Aspergillus saitoi, Mucor pusillus, Paecilomyces varioti, Rhizopus chinensis, and Tr...

    journal_title:Journal of biochemistry

    pub_type: 杂志文章

    doi:10.1093/oxfordjournals.jbchem.a131304

    authors: Takahashi K,Chang WJ

    更新日期:1976-09-01 00:00:00

  • Significance of highly conserved aromatic residues in Micrococcus luteus B-P 26 undecaprenyl diphosphate synthase.

    abstract::Undecaprenyl diphosphate synthase catalyzes the sequential condensation of eight molecules of isopentenyl diphosphate (IPP) in the cis-configuration into farnesyl diphosphate (FPP) to produce undecaprenyl diphosphate (UPP), which is indispensable for the biosynthesis of the bacterial cell wall. This cis-type prenyltra...

    journal_title:Journal of biochemistry

    pub_type: 杂志文章

    doi:10.1093/jb/mvg207

    authors: Kharel Y,Zhang YW,Fujihashi M,Miki K,Koyama T

    更新日期:2003-12-01 00:00:00

  • Fluorometric studies on the light chains of skeletal muscle myosin. III. Effect of Ca2+ on the reactivity of two SH groups of DTNB light chain in myosin and in the isolated state.

    abstract::We studied the effect of Ca2+ on the reactivities of two SH groups of DTNB light chain (Cys 128 and Cys 157) using a fluorogenic thiol reagent. It was found that a Ca2+-induced change in reactivity occurred only with Cys 128 when the light chain was in an isolated state, whereas it occurred with both Cys 128 and Cys 1...

    journal_title:Journal of biochemistry

    pub_type: 杂志文章

    doi:10.1093/oxfordjournals.jbchem.a132727

    authors: Yamamoto K,Honjo R,Sekine T

    更新日期:1980-01-01 00:00:00

  • High concentration of glucitol in fetal serum and glucitol permeable cells.

    abstract::We found that the glucitol concentration was extraordinarily high in bovine fetal serum, which is routinely used for cell culture in laboratories: it was as much as two orders of magnitude higher than that reported for human adult serum. We also confirmed that the serum glucitol concentration in new born babies was on...

    journal_title:Journal of biochemistry

    pub_type: 杂志文章

    doi:10.1093/oxfordjournals.jbchem.a124133

    authors: Mizuno H,Akanuma H

    更新日期:1993-07-01 00:00:00

  • Cloning and sequence analysis of cDNA for a possible DNA-binding protein 5E5 in the nervous system.

    abstract::Monoclonal antibody 5E5 recognized an intranuclear antigen of neurons in the rat. We isolated 5E5cDNA and determined its nucleotide and deduced amino acid sequences. The 5E5cDNA had an open reading frame of 825 amino acids and its amino acid sequence showed no significant homology to any protein or to any DNA binding ...

    journal_title:Journal of biochemistry

    pub_type: 杂志文章

    doi:10.1093/oxfordjournals.jbchem.a124866

    authors: Suzuki E,Kojima N,Yoshimura K,Uyemura K,Obata K,Akagawa K

    更新日期:1995-07-01 00:00:00

  • Fatty acids bound to recombinant tear lipocalin and their role in structural stabilization.

    abstract::A variant of human tear lipocalin was expressed in Escherichia coli, and the bound fatty acids were analysed by gas chromatography, mass spectroscopy and nuclear magnetic resonance spectroscopy. Five major fatty acids were identified as hexadecanoic acid (palmitic acid, PA), cis-9-hexadecenoic acid (palmitoleic acid),...

    journal_title:Journal of biochemistry

    pub_type: 杂志文章

    doi:10.1093/jb/mvp076

    authors: Tsukamoto S,Fujiwara K,Ikeguchi M

    更新日期:2009-09-01 00:00:00

  • Growth hormone has dual stage-specific effects on the differentiation of 3T3-L1 preadipocytes.

    abstract::Reports vary on the role of growth hormone (GH) in adipocyte differentiation. In this study, we showed that GH exerted dual effects depending on the stage of differentiation, using a serum-free culture of 3T3-L1 preadipocytes. GH promoted the differentiation when added to the medium during differentiation-inducing tre...

    journal_title:Journal of biochemistry

    pub_type: 杂志文章

    doi:10.1093/oxfordjournals.jbchem.a003301

    authors: Tominaga S,Morikawa M,Osumi T

    更新日期:2002-12-01 00:00:00

  • Effects of salts on thermolysin: activation of hydrolysis and synthesis of N-carbobenzoxy-L-aspartyl-L-phenylalanine methyl ester, and a unique change in the absorption spectrum of thermolysin.

    abstract::It has been reported that neutral salts such as NaCl activate the thermolysin-catalyzed hydrolysis of substrates containing glycine at the P1 position (carboxylic side of the cleavage bond) [Holmquist, B. & Vallee, B.L. (1976) Biochemistry 15, 101-107]. In this paper, we demonstrate that high concentrations (1-4 M) of...

    journal_title:Journal of biochemistry

    pub_type: 杂志文章

    doi:10.1093/oxfordjournals.jbchem.a123901

    authors: Inouye K

    更新日期:1992-09-01 00:00:00

  • Studies on the serine proteases associated with rat liver chromatin.

    abstract::The chromatin fraction of rat liver exhibited proteolytic activity caused by serine proteases, with maximal activity at pH 8 or 10. They were analyzed by affinity labeling with [3H]diisopropylfluorophosphate followed by SDS-polyacrylamide gel electrophoresis, and partially purified by gel filtration through Sepharose ...

    journal_title:Journal of biochemistry

    pub_type: 杂志文章

    doi:10.1093/oxfordjournals.jbchem.a134061

    authors: Tsurugi K,Ogata K

    更新日期:1982-11-01 00:00:00

  • Expression of inter-alpha-trypsin inhibitor light chain (bikunin) in human pancreas.

    abstract::Expression of inter-alpha-trypsin inhibitor light chain (ITI-LC, also known as bikunin or urinary trypsin inhibitor) was examined in various human tissues. By reverse-transcription polymerase chain reaction, the mRNA was detected not only in the liver, a known site of ITI-LC production, but also in the kidney, heart, ...

    journal_title:Journal of biochemistry

    pub_type: 杂志文章

    doi:10.1093/oxfordjournals.jbchem.a021409

    authors: Itoh H,Tomita M,Kobayashi T,Uchino H,Maruyama H,Nawa Y

    更新日期:1996-08-01 00:00:00

  • Purification and characterization of the Proteus vulgaris BlaA protein, the activator of the beta-lactamase gene.

    abstract::Induction of the expression of the beta-lactamase gene, blaB, is regulated by the blaA gene located just upstream of blaB in the opposite direction in Proteus vulgaris. The expression of the blaA gene is negatively autoregulated by its own product BlaA, the activator of the blaB gene. The P. vulgaris BlaA protein shar...

    journal_title:Journal of biochemistry

    pub_type: 杂志文章

    doi:10.1093/oxfordjournals.jbchem.a021399

    authors: Ishiguro K,Sugimoto K

    更新日期:1996-07-01 00:00:00

  • One- and two-dimensional 1H-NMR characterization of two series of sulfated disaccharides prepared from chondroitin sulfate and heparan sulfate/heparin by bacterial eliminase digestion.

    abstract::The 1H-NMR spectra of eight unsaturated disaccharides obtained by bacterial eliminase digestion of chondroitin sulfate and of heparan sulfate/heparin were recorded in order to construct an NMR data base of sulfated oligosaccharides and to investigate the effects of sulfation on the proton chemical shifts. These shifts...

    journal_title:Journal of biochemistry

    pub_type: 杂志文章

    doi:10.1093/oxfordjournals.jbchem.a123919

    authors: Yamada S,Yoshida K,Sugiura M,Sugahara K

    更新日期:1992-10-01 00:00:00

  • Studies on cellulases of a phytopathogenic fungus, Pyricularia oryzae Cavara. IV. Kinetic studies on beta-glucosidases.

    abstract::Kinetic studies of the two beta-glucosidase isozymes, GB-1 and GB-2, which were from the culture filtrate of a phytopathogenic fungus Pyricularia oryzae, revaled that the latter isozyme was an allosteric protein with two substrate binding sites. The homotropic effects of o- and m-nitrophenyl-beta-D-glucosides on GB-2 ...

    journal_title:Journal of biochemistry

    pub_type: 杂志文章

    doi:

    authors: Hirayama T,Nagayama H,Matsuda K

    更新日期:1980-04-01 00:00:00

  • Enhancement of the frequency of initiation by a stimulatory protein of RNA polymerase II.

    abstract::By use of purified RNA polymerase II, it was demonstrated that S-II, a stimulatory protein of RNA polymerase II, enhanced the frequency of initiation of transcription from discrete sites on the promoter region of the silk fibroin gene integrated in a supercoiled plasmid DNA in the presence of manganese. In the absence...

    journal_title:Journal of biochemistry

    pub_type: 杂志文章

    doi:10.1093/oxfordjournals.jbchem.a135020

    authors: Sekimizu K,Horikoshi M,Natori S

    更新日期:1984-12-01 00:00:00

  • Characterization of monoclonal antibodies against human prorenin profragment and identification of active prorenins in plasma.

    abstract::Monoclonal antibodies were raised against a synthetic peptide (43 amino acid residues) that corresponds to the complete profragment of human prorenin. Seven monoclonal antibodies were chosen for further characterization. Two antibodies, 2-X-C1 and 4-X-E1, reacted with the middle region and C-terminus of the profragmen...

    journal_title:Journal of biochemistry

    pub_type: 杂志文章

    doi:10.1093/oxfordjournals.jbchem.a122869

    authors: Ishizuka Y,Iizumi S,Akiyama F,Hori H,Poorman RA,Lobl TJ,Murakami K

    更新日期:1989-09-01 00:00:00

  • Role of 67 kDa cell surface laminin binding protein of Leishmania donovani in pathogenesis.

    abstract::The role that interaction with laminin may play in Leishmania donovani infection was investigated. Binding of (125)I-radiolabeled laminin, in a liquid-phase assay, by the parasite was rapid, saturable, specific, reversible, and of high affinity. Using a Western blotting procedure, a 67 kDa laminin-binding protein (LBP...

    journal_title:Journal of biochemistry

    pub_type: 杂志文章

    doi:10.1093/oxfordjournals.jbchem.a002953

    authors: Bandyopadhyay K,Karmakar S,Ghosh A,Das PK

    更新日期:2001-07-01 00:00:00

  • On the minor gangliosides of erythrocyte membranes of Japanese cats.

    abstract::Seven ganglioside species were isolated and purified from erythrocyte membranes of Japanese cats by DEAE-Sephadex and Iatrobeads column chromatographies. The structures of these gangliosides were determined as Gmi(NeuGc), Gm3(NeuAc), GM3(NeuGc), GD3(NeuGc), GD3(NeuGc comes from NeuAc), GT3(NeuGc), and another GM3 cont...

    journal_title:Journal of biochemistry

    pub_type: 杂志文章

    doi:10.1093/oxfordjournals.jbchem.a133775

    authors: Ando N,Yamakawa T

    更新日期:1982-03-01 00:00:00

  • Detection and isolation of a 30 kDa abnormal protein in avian dystrophic muscle.

    abstract::We have studied the protein composition of the pectoralis superficialis muscle of genetically dystrophic (New Hampshire line 413) and normal control (line 412) chickens by one- and two-dimensional gel electrophoresis. A protein, referred to hereafter as the 30 kDa abnormal protein, was specifically detected in the aff...

    journal_title:Journal of biochemistry

    pub_type: 杂志文章

    doi:10.1093/oxfordjournals.jbchem.a123010

    authors: Kobayashi R,Toyoshima I,Masamune O,Tashima Y

    更新日期:1990-01-01 00:00:00

  • Structure, expression, and evolution of guinea pig serum amyloid P component and C-reactive protein.

    abstract::The structure and expression of the pentraxins, serum amyloid P component (SAP), and C-reactive protein (CRP), have been investigated in the guinea pig. Northern blot analysis of hepatic RNA from animals in which acute inflammation had been induced by intraperitoneal injection of thioglycollate established that neithe...

    journal_title:Journal of biochemistry

    pub_type: 杂志文章

    doi:10.1093/oxfordjournals.jbchem.a124039

    authors: Rubio N,Sharp PM,Rits M,Zahedi K,Whitehead AS

    更新日期:1993-03-01 00:00:00

  • Opening of mitochondrial ATP-sensitive potassium channels evokes oxygen radical generation in rabbit heart slices.

    abstract::The purpose of this study was to determine whether ATP-sensitive potassium channel (K(ATP) channel) activation generates oxygen free radicals in the rabbit heart. We assayed malondialdehyde (MDA) in rabbit heart slices in vitro as an indicator of oxygen free radical generation. The K(ATP) channel openers, pinacidil an...

    journal_title:Journal of biochemistry

    pub_type: 杂志文章

    doi:10.1093/oxfordjournals.jbchem.a003157

    authors: Han J,Kim N,Park J,Seog DH,Joo H,Kim E

    更新日期:2002-05-01 00:00:00

  • Macrophage activation by PAF incorporated into dipalmitoylphosphatidylcholine-cholesterol liposomes.

    abstract::The phospholipid mediator, platelet activating factor (PAF: 1-O-alkyl-2-O-acetyl-sn-glycero-3-phosphocholine), was recently reported to activate macrophage-monocyte cells as well as neutrophils or platelets. PAF was incorporated into dipalmitoylphosphatidylcholine-cholesterol liposomes, and their effect on guinea pig ...

    journal_title:Journal of biochemistry

    pub_type: 杂志文章

    doi:10.1093/oxfordjournals.jbchem.a135172

    authors: Hayashi H,Kudo I,Inoue K,Nomura H,Nojima S

    更新日期:1985-04-01 00:00:00

  • Effect of dietary protein content on the activity of rat liver asparagine synthetase.

    abstract::The activity of rat liver asparagine synthetase [EC 6.3.1.1]increased when animals maintained on 25% protein diet were placed on 15% or 6% protein diet. The enzyme activity level rose within one day, reached a maximum in 7 or 10 days after switching the diet and thereafter dropped gradually. During the purification of...

    journal_title:Journal of biochemistry

    pub_type: 杂志文章

    doi:10.1093/oxfordjournals.jbchem.a132537

    authors: Hongo S,Matsumoto T,Suzuki I,Sato T

    更新日期:1979-08-01 00:00:00

  • A rapid vapor-phase acid (hydrochloric acid and trifluoroacetic acid) hydrolysis of peptide and protein.

    abstract::A new method for the acid hydrolysis of protein is presented. Peptide bonds are cleaved by the action of an HCl/trifluoroacetic acid (TFA) vapor mixture. Contamination for the hydrolysis mixture is reduced to low levels (1-3 pmol). Recovery of hydrophobic amino acid is improved. Short reaction times are achieved and r...

    journal_title:Journal of biochemistry

    pub_type: 杂志文章

    doi:10.1093/oxfordjournals.jbchem.a122209

    authors: Tsugita A,Uchida T,Mewes HW,Ataka T

    更新日期:1987-12-01 00:00:00

  • In vitro yeast reconstituted translation system reveals function of eIF5A for synthesis of long polypeptide.

    abstract::We have recently developed an in vitro yeast reconstituted translation system, which is capable of synthesizing long polypeptides. Utilizing the system, we examined the role of eIF5A and its hypusine modification in translating polyproline sequence within long open reading frames. We found that polyproline motif inser...

    journal_title:Journal of biochemistry

    pub_type: 杂志文章

    doi:10.1093/jb/mvaa022

    authors: Abe T,Nagai R,Shimazaki S,Kondo S,Nishimura S,Sakaguchi Y,Suzuki T,Imataka H,Tomita K,Takeuchi-Tomita N

    更新日期:2020-05-01 00:00:00

  • Studies on D-tetrose metabolism. VI. Crystallization and some properties of D-erythrulose reducatase from beef liver.

    abstract::D-Erythrulose reductase of beef liver was crystallized from ammonium sulfate solution at pH 8.17. The crystals are needle-shaped. The enzyme protein contains 851 amino acid residues per mole of the enzyme: Lys28, His11, Arg52, Asp79, Thr58, Ser56, Glu68, Pro20, Gly80, Ala107, Val112, Met24, Ile31, Leu88, Tyr7, Phe22, ...

    journal_title:Journal of biochemistry

    pub_type: 杂志文章

    doi:10.1093/oxfordjournals.jbchem.a130936

    authors: Uehara K,Tanimoto T

    更新日期:1975-09-01 00:00:00

  • Midkine (MK) expression in extraembryonic tissues, amniotic fluid, and cerebrospinal fluid during mouse embryogenesis.

    abstract::Midkine (MK) and pleiotrophin (PTN) constitute a new family of heparin-binding growth factors. Extraembryonic membranes and the placenta of the mouse expressed MK mRNA at 11.5 days gestation. While the MK mRNA level in extraembryonic membranes decreased during embryogenesis, that in the placenta remained unchanged. Im...

    journal_title:Journal of biochemistry

    pub_type: 杂志文章

    doi:10.1093/oxfordjournals.jbchem.a124896

    authors: Obama H,Tsutsui J,Ozawa M,Yoshida H,Yoshida Y,Osame M,Muramatsu T

    更新日期:1995-07-01 00:00:00

  • Feedback inhibition by methionine and S-adenosylmethionine, and desensitization of homoserine O-acetyltransferase in Brevibacterium flavum.

    abstract::Homoserine O-acetyltransferase [EC 2.3.1.31] partially purified from Brevibacterium flavum was found to be specifically inhibited by the metabolic end products methionine and S-adenosylmethionine only when the enzymatic reaction was performed in the presence of cysteine or dithiothreitol, or after the preincubation of...

    journal_title:Journal of biochemistry

    pub_type: 杂志文章

    doi:10.1093/oxfordjournals.jbchem.a133342

    authors: Shiio I,Ozaki H

    更新日期:1981-05-01 00:00:00

  • The effects of mutations at position 253 on the thermostability of the Bacillus subtilis 3-isopropylmalate dehydrogenase subunit interface.

    abstract::3-Isopropylmalate dehydrogenase (IPMDH) is a dimeric enzyme with a strongly hydrophobic core that is composed of residues from four alpha-helices. We replaced Glu253, which is found in the hydrophobic core and is part of the subunit interface of the Bacillus subtilis (Bs) IPMDH, with several other amino acids to probe...

    journal_title:Journal of biochemistry

    pub_type: 杂志文章

    doi:10.1093/jb/mvm082

    authors: Ohkuri T,Yamagishi A

    更新日期:2007-06-01 00:00:00

  • Characterization of a human placental fructose-6-phosphate, 2-kinase/fructose-2,6-bisphosphatase.

    abstract::A full-length cDNA, which encodes a human placental fructose-6-phosphate,2-kinase/ fructose-2,6-bisphosphatase, was constructed and expressed in Escherichia coli. The expressed protein, purified to homogeneity, showed a molecular weight of 58,000 by gel electrophoresis under denaturing conditions, compared to the dedu...

    journal_title:Journal of biochemistry

    pub_type: 杂志文章

    doi:10.1093/oxfordjournals.jbchem.a021719

    authors: Sakakibara R,Kato M,Okamura N,Nakagawa T,Komada Y,Tominaga N,Shimojo M,Fukasawa M

    更新日期:1997-07-01 00:00:00

  • A sulfated polysaccharide produced by an Arthrobacter species.

    abstract::A new sulfated polysaccharide was isolated from the culture supernatant of a strain of Arthrobacter sp. The polysaccharide purified with quaternary ammonium salts consists of D-galactose, D-glucose, sulfate, phosphorus, glucosamine, muramic acid, alanine, glutamic acid, glycine, and LL-diaminopimelic acid in a molar r...

    journal_title:Journal of biochemistry

    pub_type: 杂志文章

    doi:10.1093/oxfordjournals.jbchem.a134107

    authors: Inoue K,Korenaga H,Kadoya S

    更新日期:1982-12-01 00:00:00