EcoliWiki - User contributions [en]

PMID:9917404

2014-08-10T16:58:20Z

54.87.37.196: Fill PMID: Page!

{{RightTOC}}


{| id="L53e7a4ac7d9de" class=" tableEdit PMID_info_table"

|-
!align=left |Citation
||
'''Loris, R, Dao-Thi, MH, Bahassi, EM, Van Melderen, L, Poortmans, F, Liddington, R, Couturier, M and Wyns, L''' (1999) Crystal structure of CcdB, a topoisomerase poison from E. coli. ''J. Mol. Biol.'' '''285''':1667-77
|-
!align=left |Abstract
||
The crystal structure of CcdB, a protein that poisons Escherichia coli gyrase, was determined in three crystal forms. The protein consists of a five-stranded antiparallel beta-pleated sheet followed by a C-terminal alpha-helix. In one of the loops of the sheet, a second small three-stranded antiparallel beta-sheet is inserted that sticks out of the molecule as a wing. This wing contains the LysC proteolytic cleavage site that is protected by CcdA and, therefore, forms a likely CcdA recognition site. A dimer is formed by sheet extension and by extensive hydrophobic contacts involving three of the five methionine residues and the C terminus of the alpha-helix. The surface of the dimer on the side of the alpha-helix is overall negatively charged, while the opposite side as well as the wing sheet is dominated by positive charges. We propose that the CcdB dimer binds into the central hole of the 59 kDa N-terminal fragment of GyrA, after disruption of the head dimer interface of GyrA.
|-
!align=left |Links
||
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=9917404 PubMed]
Online version:[http://dx.doi.org/10.1006/jmbi.1998.2395 10.1006/jmbi.1998.2395]
|-
!align=left |Keywords
||
Amino Acid Sequence; Bacterial Proteins/chemistry; Bacterial Proteins/genetics; Bacterial Proteins/metabolism; Bacterial Toxins/chemistry; Bacterial Toxins/genetics; Crystallography, X-Ray; DNA Gyrase; DNA, Bacterial/metabolism; Dimerization; Escherichia coli/chemistry; Escherichia coli/enzymology; Escherichia coli/genetics; Hydrogen Bonding; Macromolecular Substances; Models, Molecular; Molecular Sequence Data; Mutation; Plasmids/genetics; Protein Conformation; Protein Structure, Secondary; Topoisomerase II Inhibitors

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.183727.L53e7a4ac7d9de&page=183727&pagename={{FULLPAGENAMEE}}&type=1&template=PMID_info_table edit table] ||
|}


==Significance {{HelpIcon|Help:Literature}} ==
{{LitSignificance}}

== Useful Materials and Methods {{HelpIcon|Help:Literature}}==
{{LitMaterials}}

==Annotations {{HelpIcon|Help:Literature}}==
<annotationlinks/>

==EcoliWiki Links {{HelpIcon|Help:Literature}} ==
{{LitLinks}}

==See also==

==References==
{{RefHelp}}
<references/>

PMID:9917404

2014-08-10T16:58:20Z

54.87.37.196: New PMID: Page!

PMID on Demand placeholder

PMID:9324241

2014-08-08T19:39:39Z

54.87.37.196: Fill PMID: Page!

{{RightTOC}}


{| id="P53e5277a8775f" class=" tableEdit PMID_info_table"

|-
!align=left |Citation
||
'''Obuchowski, M, Shotland, Y, Koby, S, Giladi, H, Gabig, M, Wegrzyn, G and Oppenheim, AB''' (1997) Stability of CII is a key element in the cold stress response of bacteriophage lambda infection. ''J. Bacteriol.'' '''179''':5987-91
|-
!align=left |Abstract
||
Bacteria are known to adapt to environmental changes such as temperature fluctuations. It was found that temperature affects the lysis-lysogeny decision of lambda such that at body temperature (37 degrees C) the phage can select between the lytic and lysogenic pathways, while at ambient temperature (20 degrees C) the lytic pathway is blocked. This temperature-dependent discriminatory developmental pathway is governed mainly by the phage CII activity as a transcriptional activator. Mutations in cII or point mutations at the pRE promoter lead to an over-1,000-fold increase in mature-phage production at low temperature while mutations in cI cause a smaller increase in phage production. Interference with CII activity can restore lytic growth at low temperature. We found that at low temperature the stability of CII in vivo is greatly increased. It was also found that phage DNA replication is blocked at 20 degrees C but can be restored by supplying O and P in trans. It is proposed that CII hampers transcription of the rightward pR promoter, thus reducing the levels of the lambda O and P proteins, which are necessary for phage DNA replication. Our results implicate CII itself or host proteins affecting CII stability as a "molecular thermometer".
|-
!align=left |Links
||
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=9324241 PubMed] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC179497 PMC179497]

|-
!align=left |Keywords
||
Bacteriophage lambda/genetics; Bacteriophage lambda/physiology; Cold Temperature; DNA Replication; DNA-Directed RNA Polymerases/genetics; DNA-Directed RNA Polymerases/metabolism; Lysogeny; Mutation; Promoter Regions, Genetic; Temperature; Transcription Factors/genetics; Transcription Factors/physiology; Transcription, Genetic; Viral Proteins/physiology; Virus Replication

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.183720.P53e5277a8775f&page=183720&pagename={{FULLPAGENAMEE}}&type=1&template=PMID_info_table edit table] ||
|}


==Significance {{HelpIcon|Help:Literature}} ==
{{LitSignificance}}

== Useful Materials and Methods {{HelpIcon|Help:Literature}}==
{{LitMaterials}}

==Annotations {{HelpIcon|Help:Literature}}==
<annotationlinks/>

==EcoliWiki Links {{HelpIcon|Help:Literature}} ==
{{LitLinks}}

==See also==

==References==
{{RefHelp}}
<references/>

PMID:9324241

2014-08-08T19:39:38Z

54.87.37.196: New PMID: Page!

PMID on Demand placeholder

PMID:16963775

2014-08-04T15:09:09Z

54.87.37.196: Fill PMID: Page!

{{RightTOC}}


{| id="V53dfa21560262" class=" tableEdit PMID_info_table"

|-
!align=left |Citation
||
'''Smith, AB and Maxwell, A''' (2006) A strand-passage conformation of DNA gyrase is required to allow the bacterial toxin, CcdB, to access its binding site. ''Nucleic Acids Res.'' '''34''':4667-76
|-
!align=left |Abstract
||
DNA gyrase is the only topoisomerase able to introduce negative supercoils into DNA. Absent in humans, gyrase is a successful target for antibacterial drugs. However, increasing drug resistance is a serious problem and new agents are urgently needed. The naturally-produced Escherichia coli toxin CcdB has been shown to target gyrase by what is predicted to be a novel mechanism. CcdB has been previously shown to stabilize the gyrase 'cleavage complex', but it has not been shown to inhibit the catalytic reactions of gyrase. We present data showing that CcdB does indeed inhibit the catalytic reactions of gyrase by stabilization of the cleavage complex and that the GyrA C-terminal DNA-wrapping domain and the GyrB N-terminal ATPase domain are dispensable for CcdB's action. We further investigate the role of specific GyrA residues in the action of CcdB by site-directed mutagenesis; these data corroborate a model for CcdB action based on a recent crystal structure of a CcdB-GyrA fragment complex. From this work, we are now able to present a model for CcdB action that explains all previous observations relating to CcdB-gyrase interaction. CcdB action requires a conformation of gyrase that is only revealed when DNA strand passage is taking place.
|-
!align=left |Links
||
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16963775 PubMed] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1635281 PMC1635281]
Online version:[http://dx.doi.org/10.1093/nar/gkl636 10.1093/nar/gkl636]
|-
!align=left |Keywords
||
Anti-Bacterial Agents/chemistry; Anti-Bacterial Agents/pharmacology; Bacterial Proteins/chemistry; Bacterial Proteins/pharmacology; Bacterial Toxins/chemistry; Bacterial Toxins/pharmacology; Binding Sites; Ciprofloxacin/pharmacology; DNA Gyrase/chemistry; DNA Gyrase/genetics; DNA Gyrase/metabolism; DNA, Superhelical/metabolism; Inhibitory Concentration 50; Models, Biological; Mutagenesis, Site-Directed; Nucleotides/metabolism; Protein Structure, Tertiary

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.183714.V53dfa21560262&page=183714&pagename={{FULLPAGENAMEE}}&type=1&template=PMID_info_table edit table] ||
|}


==Significance {{HelpIcon|Help:Literature}} ==
{{LitSignificance}}

== Useful Materials and Methods {{HelpIcon|Help:Literature}}==
{{LitMaterials}}

==Annotations {{HelpIcon|Help:Literature}}==
<annotationlinks/>

==EcoliWiki Links {{HelpIcon|Help:Literature}} ==
{{LitLinks}}

==See also==

==References==
{{RefHelp}}
<references/>

PMID:16963775

2014-08-04T15:09:09Z

54.87.37.196: New PMID: Page!

PMID on Demand placeholder

PMID:2848243

2014-08-04T14:21:08Z

54.87.37.196: Fill PMID: Page!

{{RightTOC}}


{| id="V53df96d3c5b9b" class=" tableEdit PMID_info_table"

|-
!align=left |Citation
||
'''Yang, Y and Ames, GF''' (1988) DNA gyrase binds to the family of prokaryotic repetitive extragenic palindromic sequences. ''Proc. Natl. Acad. Sci. U.S.A.'' '''85''':8850-4
|-
!align=left |Abstract
||
A family of repetitive extragenic palindromic (REP) sequences is composed of hundreds of copies distributed throughout the chromosome. Their palindromic nature and conservation suggested that they are specifically recognized by a protein(s). We have identified DNA gyrase [DNA topoisomerase (ATP-hydrolysing), EC 5.99.1.3] as one of the REP-binding proteins. Gyrase has at least a 10-fold higher affinity for DNA containing REP sequences than for DNA not containing REP sequences. Binding effectiveness correlates directly with the number of REP sequences in the DNA. DNase I footprinting shows that gyrase protects 205 base pairs on a REP-containing DNA fragment enclosing the REP sequences. In agreement with the above results, a comparison of the REP consensus sequence with the sequence of previously identified pBR322 "strong" gyrase cleavage sites reveals a high degree of homology. Because REP sequences are numerous and found throughout the genome, we suggest they have physiological functions mediated through their interaction with gyrase, such as being sites of action for the maintenance of DNA supercoiling. In addition, we speculate that these interactions may be of a structural nature, such as involvement in the higher-order structure of the bacterial chromosome.
|-
!align=left |Links
||
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=2848243 PubMed] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC282604 PMC282604]

|-
!align=left |Keywords
||
Base Sequence; DNA Topoisomerases, Type II/metabolism; Escherichia coli/enzymology; Kinetics; Molecular Sequence Data; Repetitive Sequences, Nucleic Acid; Substrate Specificity

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.183711.V53df96d3c5b9b&page=183711&pagename={{FULLPAGENAMEE}}&type=1&template=PMID_info_table edit table] ||
|}


==Significance {{HelpIcon|Help:Literature}} ==
{{LitSignificance}}

== Useful Materials and Methods {{HelpIcon|Help:Literature}}==
{{LitMaterials}}

==Annotations {{HelpIcon|Help:Literature}}==
<annotationlinks/>

==EcoliWiki Links {{HelpIcon|Help:Literature}} ==
{{LitLinks}}

==See also==

==References==
{{RefHelp}}
<references/>

PMID:2848243

2014-08-04T14:21:07Z

54.87.37.196: New PMID: Page!

PMID on Demand placeholder

PMID:4275917

2014-07-31T15:47:25Z

54.87.37.196: Fill PMID: Page!

{{RightTOC}}


{| id="M53da650c489b5" class=" tableEdit PMID_info_table"

|-
!align=left |Citation
||
'''Sakaki, Y, Karu, AE, Linn, S and Echols, H''' (1973) Purification and properties of the gamma-protein specified by bacteriophage lambda: an inhibitor of the host RecBC recombination enzyme. ''Proc. Natl. Acad. Sci. U.S.A.'' '''70''':2215-9
|-
!align=left |Abstract
||
Previous experiments have indicated that the gam gene of bacteriophage lambda is responsible for an inhibition of the RecBC DNase-an enzyme that is essential for the major host pathway of genetic recombination. We report here experiments that define the inhibitor as the protein product of the gam gene ("gamma-protein") and that characterize the inhibition reaction with highly purified preparations of gamma-protein and RecBC DNase. Genetic characterization was performed with partially purified fractions prepared from cells infected with various lambda mutants. An activity that inhibits RecBC DNase was absent in extracts prepared after infection by phage that carry nonsense or deletion mutations in the gam gene; this activity was highly thermolabile in an extract prepared after infection by phage that carry a temperature-sensitive mutation in the gam gene. For biochemical characterization, the gamma-protein has been purified more than 800-fold. This highly purified preparation inhibited all of the known catalytic activities associated with the RecBC enzyme, but exhibited no detectable DNase or ATPase activities by itself. These findings are discussed in terms of their implications for regulation of genetic recombination and bacteriophage lambda development.
|-
!align=left |Links
||
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=4275917 PubMed] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC433704 PMC433704]

|-
!align=left |Keywords
||
Adenosine Triphosphatases/antagonists & inhibitors; Centrifugation, Density Gradient; Chromatography; Chromatography, DEAE-Cellulose; Chromatography, Gel; Coliphages/analysis; Coliphages/metabolism; DNA, Bacterial/metabolism; DNA, Circular/metabolism; DNA, Viral/metabolism; Deoxyribonucleases/antagonists & inhibitors; Escherichia coli/enzymology; Exonucleases/antagonists & inhibitors; Mutation; Recombination, Genetic; Viral Proteins/biosynthesis; Viral Proteins/isolation & purification; Viral Proteins/pharmacology

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.183705.M53da650c489b5&page=183705&pagename={{FULLPAGENAMEE}}&type=1&template=PMID_info_table edit table] ||
|}


==Significance {{HelpIcon|Help:Literature}} ==
{{LitSignificance}}

== Useful Materials and Methods {{HelpIcon|Help:Literature}}==
{{LitMaterials}}

==Annotations {{HelpIcon|Help:Literature}}==
<annotationlinks/>

==EcoliWiki Links {{HelpIcon|Help:Literature}} ==
{{LitLinks}}

==See also==

==References==
{{RefHelp}}
<references/>

PMID:4275917

2014-07-31T15:47:24Z

54.87.37.196: New PMID: Page!

PMID on Demand placeholder

PMID:16885328

2014-07-24T04:32:49Z

54.87.37.196: Fill PMID: Page!

{{RightTOC}}


{| id="G53d08c711a8dd" class=" tableEdit PMID_info_table"

|-
!align=left |Citation
||
'''Beekwilder, J, Wolswinkel, R, Jonker, H, Hall, R, de Vos, CH and Bovy, A''' (2006) Production of resveratrol in recombinant microorganisms. ''Appl. Environ. Microbiol.'' '''72''':5670-2
|-
!align=left |Abstract
||
Resveratrol production in Saccharomyces cerevisiae was compared to that in Escherichia coli. In both systems, 4-coumarate:coenzyme A ligase from tobacco and stilbene synthase from grapes were expressed. When p-coumaric acid was used as the precursor, resveratrol accumulations in the culture medium were observed to be comparable in E. coli (16 mg/liter) and yeast (6 mg/liter).
|-
!align=left |Links
||
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16885328 PubMed] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1538726 PMC1538726]
Online version:[http://dx.doi.org/10.1128/AEM.00609-06 10.1128/AEM.00609-06]
|-
!align=left |Keywords
||
Acyltransferases/genetics; Acyltransferases/metabolism; Biotechnology/methods; Coenzyme A Ligases/genetics; Coenzyme A Ligases/metabolism; Coumaric Acids/metabolism; Escherichia coli/enzymology; Escherichia coli/genetics; Escherichia coli/metabolism; Recombination, Genetic; Saccharomyces cerevisiae/enzymology; Saccharomyces cerevisiae/genetics; Saccharomyces cerevisiae/metabolism; Stilbenes/metabolism; Tobacco/enzymology; Tobacco/genetics; Vitis/genetics; Vitis/metabolism

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.183693.G53d08c711a8dd&page=183693&pagename={{FULLPAGENAMEE}}&type=1&template=PMID_info_table edit table] ||
|}


==Significance {{HelpIcon|Help:Literature}} ==
{{LitSignificance}}

== Useful Materials and Methods {{HelpIcon|Help:Literature}}==
{{LitMaterials}}

==Annotations {{HelpIcon|Help:Literature}}==
<annotationlinks/>

==EcoliWiki Links {{HelpIcon|Help:Literature}} ==
{{LitLinks}}

==See also==

==References==
{{RefHelp}}
<references/>

PMID:16885328

2014-07-24T04:32:48Z

54.87.37.196: New PMID: Page!

PMID on Demand placeholder

PMID:1958130

2014-07-18T18:32:22Z

54.87.37.196: Fill PMID: Page!

{{RightTOC}}


{| id="W53c9683620c6a" class=" tableEdit PMID_info_table"

|-
!align=left |Citation
||
'''Seidel, W, Künkel, F, Geisler, B, Garten, W, Herrmann, B, Döhner, L and Klenk, HD''' (1991) Intraepidemic variants of influenza virus H3 hemagglutinin differing in the number of carbohydrate side chains. ''Arch. Virol.'' '''120''':289-96
|-
!align=left |Abstract
||
During the epidemic outbreak in the region of Greifswald in the winter 1974/75, we found influenza virus variants which showed differences in the electrophoretic mobility of HA. Among the 25 isolates 13 were of slower and 12 of higher mobility. HA1 of 6 isolates was studied by determining the number of the carbohydrate side chains and by direct sequencing of vRNA. Evidence is presented that variants showing a slower electrophoretic mobility of HA1 had consistently acquired a seventh carbohydrate side chain at Asn 126 in epitope A. All the isolates differed from the reference strain A/Port Chalmers/1/73 by the loss of the oligosaccharide at Asn 81. The field strain A/Dresden/3/71 possessed only 5 oligosaccharides in HA1. These results suggest that changes in glycosylation are an important mechanism in the structural variation underlying antigenic drift of HA.
|-
!align=left |Links
||
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=1958130 PubMed]

|-
!align=left |Keywords
||
Antigenic Variation; Disease Outbreaks; Electrophoresis, Polyacrylamide Gel; Glycosylation; Hemagglutinin Glycoproteins, Influenza Virus; Hemagglutinins, Viral/chemistry; Hemagglutinins, Viral/genetics; Hemagglutinins, Viral/immunology; Humans; Influenza A virus/genetics; Influenza A virus/immunology; Influenza, Human/epidemiology; Influenza, Human/microbiology; Oligosaccharides/analysis

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.183685.W53c9683620c6a&page=183685&pagename={{FULLPAGENAMEE}}&type=1&template=PMID_info_table edit table] ||
|}


==Significance {{HelpIcon|Help:Literature}} ==
{{LitSignificance}}

== Useful Materials and Methods {{HelpIcon|Help:Literature}}==
{{LitMaterials}}

==Annotations {{HelpIcon|Help:Literature}}==
<annotationlinks/>

==EcoliWiki Links {{HelpIcon|Help:Literature}} ==
{{LitLinks}}

==See also==

==References==
{{RefHelp}}
<references/>

PMID:1958130

2014-07-18T18:32:21Z

54.87.37.196: New PMID: Page!

PMID on Demand placeholder

PMID:8635474

2014-07-16T04:26:05Z

54.87.37.196: Fill PMID: Page!

{{RightTOC}}


{| id="T53c5fedccbb8b" class=" tableEdit PMID_info_table"

|-
!align=left |Citation
||
'''Lewis, RJ, Singh, OM, Smith, CV, Skarzynski, T, Maxwell, A, Wonacott, AJ and Wigley, DB''' (1996) The nature of inhibition of DNA gyrase by the coumarins and the cyclothialidines revealed by X-ray crystallography. ''EMBO J.'' '''15''':1412-20
|-
!align=left |Abstract
||
This study describes the first crystal structures of a complex between a DNA topoisomerase and a drug. We present the structures of a 24 kDa N-terminal fragment of the Escherichia coli DNA gyrase B protein in complexes with two different inhibitors of the ATPase activity of DNA gyrase, namely the coumarin antibiotic, novobiocin, and GR122222X, a member of the cyclothialidine family. These structures are compared with the crystal structure of the complex with an ATP analogue, adenylyl-beta-gamma-imidodiphosphate (ADPNP). The likely mechanism, by which mutant gyrase B proteins become resistant to inhibition by novobiocin are discussed in light of these comparisons. The three ligands are quite dissimilar in chemical structure and bind to the protein in very different ways, but their binding is competitive because of a small degree of overlap of their binding sites. These crystal structures consequently describe a chemically well characterized ligand binding surface and provide useful information to assist in the design of novel ligands.
|-
!align=left |Links
||
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=8635474 PubMed] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC450046 PMC450046]

|-
!align=left |Keywords
||
Adenylyl Imidodiphosphate/chemistry; Crystallography, X-Ray; DNA Gyrase; DNA Topoisomerases, Type II/chemistry; Enzyme Inhibitors/chemistry; Escherichia coli/chemistry; Escherichia coli/enzymology; Models, Molecular; Novobiocin/chemistry; Peptide Fragments/chemistry; Peptides, Cyclic/chemistry; Topoisomerase II Inhibitors

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.183682.T53c5fedccbb8b&page=183682&pagename={{FULLPAGENAMEE}}&type=1&template=PMID_info_table edit table] ||
|}


==Significance {{HelpIcon|Help:Literature}} ==
{{LitSignificance}}

== Useful Materials and Methods {{HelpIcon|Help:Literature}}==
{{LitMaterials}}

==Annotations {{HelpIcon|Help:Literature}}==
<annotationlinks/>

==EcoliWiki Links {{HelpIcon|Help:Literature}} ==
{{LitLinks}}

==See also==

==References==
{{RefHelp}}
<references/>

PMID:8635474

2014-07-16T04:26:04Z

54.87.37.196: New PMID: Page!

PMID on Demand placeholder

PMID:6296055

2014-07-13T07:43:12Z

54.87.37.196: Fill PMID: Page!

{{RightTOC}}


{| id="S53c2388fafdfa" class=" tableEdit PMID_info_table"

|-
!align=left |Citation
||
'''Higgins, CF, Hardie, MM, Jamieson, D and Powell, LM''' (1983) Genetic map of the opp (Oligopeptide permease) locus of Salmonella typhimurium. ''J. Bacteriol.'' '''153''':830-6
|-
!align=left |Abstract
||
The uptake of peptides by Salmonella typhimurium is mediated by three apparently independent transport systems. One of these systems, the oligopeptide permease, is encoded by a genetic locus (opp) which has been mapped at 34 min on the S. typhimurium chromosomal map. We accurately mapped the location of opp by cotransduction frequencies and by deletion analysis and show that the gene order for this region of the chromosome is cysB-trp-tonB-opp-galU-tdk. All opp mutants, independently isolated by a variety of means, mapped at this one locus, between tonB and galU. Spontaneous and transposon Tn10-generated deletions were used to construct a fine-structure genetic map of opp. Evidence is presented which indicates that opp covers a 5- to 6-kb segment of DNA and is therefore likely to consist of more than one gene.
|-
!align=left |Links
||
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=6296055 PubMed] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC221702 PMC221702]

|-
!align=left |Keywords
||
Bacterial Proteins; Chromosome Mapping; Chromosomes, Bacterial; DNA Transposable Elements; Genes, Bacterial; Membrane Transport Proteins/genetics; Mutation; Oligopeptides; Salmonella typhimurium/enzymology; Salmonella typhimurium/genetics; Transduction, Genetic

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.183679.S53c2388fafdfa&page=183679&pagename={{FULLPAGENAMEE}}&type=1&template=PMID_info_table edit table] ||
|}


==Significance {{HelpIcon|Help:Literature}} ==
{{LitSignificance}}

== Useful Materials and Methods {{HelpIcon|Help:Literature}}==
{{LitMaterials}}

==Annotations {{HelpIcon|Help:Literature}}==
<annotationlinks/>

==EcoliWiki Links {{HelpIcon|Help:Literature}} ==
{{LitLinks}}

==See also==

==References==
{{RefHelp}}
<references/>

PMID:6296055

2014-07-13T07:43:11Z

54.87.37.196: New PMID: Page!

PMID on Demand placeholder

PMID:16223508

2014-07-12T21:11:24Z

54.87.37.196: Fill PMID: Page!

{{RightTOC}}


{| id="V53c1a47b7742d" class=" tableEdit PMID_info_table"

|-
!align=left |Citation
||
'''Sissi, C, Marangon, E, Chemello, A, Noble, CG, Maxwell, A and Palumbo, M''' (2005) The effects of metal ions on the structure and stability of the DNA gyrase B protein. ''J. Mol. Biol.'' '''353''':1152-60
|-
!align=left |Abstract
||
The effects of mono- and divalent metal ions on the DNA gyrase B subunit, on its 43 kDa and 47 kDa domains, and on two mutants in the Toprim domain (D498A and D500C) were investigated by means of circular dichroism and protein melting experiments. Both types of metal ion, with the notable exception of Mn2+, did not affect the conformational properties of the enzyme subunit at room temperature, but were able to produce selective and differential effects on protein stability. In particular, monovalent (K+) ions increased the stability of the gyrase B structure, whereas destabilising effects were most prominent using Mn2+ as the metal ion. Ca2+ and Mg2+ produced comparable changes in the gyrase B melting profile. Additionally, we found that monovalent (K+) ions were more effective in the 43 kDa N-terminal domain where ATP binding occurs, whereas divalent ions caused large modifications in the conformational stability of the 47 kDa C-terminal domain. Our results on gyrase B mutants indicate that D498 interacts with Mn2+, whereas it has little effect on the binding of the other ions tested. A D500C mutation, in contrast, effectively impairs Mg2+ affinity, suggesting effective contacts between this ion and D500 in the wild-type enzyme. Hence, the sites of metal ion complexation within the Toprim domain are modulated by the nature of the ion species. These results suggest a double role played by metal ions in the catalytic steps involving DNA gyrase B. One has to do with direct involvement of cations complexed to the Toprim domain in the DNA cutting-rejoining process, the other, until now overlooked, is connected to the dramatic changes in protein flexibility produced by ion binding, which reduces the energy required for the huge conformational changes essential for the catalytic cycle to occur.
|-
!align=left |Links
||
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16223508 PubMed]
Online version:[http://dx.doi.org/10.1016/j.jmb.2005.09.043 10.1016/j.jmb.2005.09.043]
|-
!align=left |Keywords
||
Binding Sites; Catalysis; Cations, Divalent/pharmacology; Cations, Monovalent/pharmacology; Circular Dichroism; DNA Gyrase/chemistry; DNA Gyrase/genetics; Enzyme Stability/drug effects; Escherichia coli Proteins/chemistry; Hot Temperature; Metals/pharmacology; Mutation, Missense; Protein Conformation/drug effects; Protein Denaturation; Thermodynamics

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.183675.V53c1a47b7742d&page=183675&pagename={{FULLPAGENAMEE}}&type=1&template=PMID_info_table edit table] ||
|}


==Significance {{HelpIcon|Help:Literature}} ==
{{LitSignificance}}

== Useful Materials and Methods {{HelpIcon|Help:Literature}}==
{{LitMaterials}}

==Annotations {{HelpIcon|Help:Literature}}==
<annotationlinks/>

==EcoliWiki Links {{HelpIcon|Help:Literature}} ==
{{LitLinks}}

==See also==

==References==
{{RefHelp}}
<references/>

PMID:16223508

2014-07-12T21:11:23Z

54.87.37.196: New PMID: Page!

PMID on Demand placeholder

PMID:8631672

2014-07-09T02:39:48Z

54.87.37.196: Fill PMID: Page!

{{RightTOC}}


{| id="Z53bcab737e02e" class=" tableEdit PMID_info_table"

|-
!align=left |Citation
||
'''Pettigrew, DW, Liu, WZ, Holmes, C, Meadow, ND and Roseman, S''' (1996) A single amino acid change in Escherichia coli glycerol kinase abolishes glucose control of glycerol utilization in vivo. ''J. Bacteriol.'' '''178''':2846-52
|-
!align=left |Abstract
||
Escherichia coli glycerol kinase (EC 2.7.1.30; ATP:glycerol 3-phosphotransferase) is a key element in glucose control of glycerol metabolism. Its catalytic activity is inhibited allosterically by the glycolytic intermediate, fructose 1,6-biphosphate, and by the phosphotransferase system phosphocarrier protein, IIIGlc (also known as IIAGlc). These inhibitors provide mechanisms by which glucose blocks glycerol utilization in vivo. We report here the cloning and sequencing of the glpK22 gene isolated from E. C. C. Lin strain 43, a strain that shows the loss of glucose control of glycerol utilization. DNA sequencing shows a single missense mutation that translates to the amino acid change Gly-304 to Ser (G-304-S) in glycerol kinase. The effects of this substitution on the functional and physical properties of the purified mutant enzyme were determined. Neither of the allosteric ligands inhibits it under conditions that produce strong inhibition of the wild-type enzyme, which is sufficient to explain the phenotype of strain 43. However, IIIGlc activates the mutant enzyme, which could not be predicted from the phenotype. In the wild-type enzyme, G-304 is located 1.3 nm from the active site and 2.5 nm from the IIIGlc binding site (M. Feese, D. W. Pettigrew, N. D. Meadow, S. Roseman, and S. J. Remington, Proc. Natl. Acad. Sci. USA 91:3544-3548, 1994). It is located in the same region as amino acid substitutions in the related protein DnaK which alter its catalytic and regulatory properties and which are postulated to interfere with a domain closure motion (A. S. Kamath-Loeb, C. Z. Lu, W.-C. Suh, M. A. Lonetto, and C. A. Gross, J. Biol. Chem. 270:30051-30059, 1995). The global effect of the G-304-S substitution on the conformation and catalytic and regulatory properties of glycerol kinase is consistent with a role for the domain closure motion in the molecular mechanism for glucose control of glycerol utilization.
|-
!align=left |Links
||
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=8631672 PubMed] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC178019 PMC178019]

|-
!align=left |Keywords
||
Allosteric Regulation; Cloning, Molecular; Dose-Response Relationship, Drug; Escherichia coli/drug effects; Escherichia coli/enzymology; Escherichia coli/genetics; Fructosediphosphates/pharmacology; Glucose/pharmacology; Glycerol/metabolism; Glycerol Kinase/chemistry; Glycerol Kinase/drug effects; Glycerol Kinase/genetics; Glycerol Kinase/metabolism; Models, Molecular; Molecular Sequence Data; Mutation; Protein Conformation; Sequence Analysis, DNA; Species Specificity

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.183668.Z53bcab737e02e&page=183668&pagename={{FULLPAGENAMEE}}&type=1&template=PMID_info_table edit table] ||
|}


==Significance {{HelpIcon|Help:Literature}} ==
{{LitSignificance}}

== Useful Materials and Methods {{HelpIcon|Help:Literature}}==
{{LitMaterials}}

==Annotations {{HelpIcon|Help:Literature}}==
<annotationlinks/>

==EcoliWiki Links {{HelpIcon|Help:Literature}} ==
{{LitLinks}}

==See also==

==References==
{{RefHelp}}
<references/>

PMID:8631672

2014-07-09T02:39:47Z

54.87.37.196: New PMID: Page!

PMID on Demand placeholder

PMID:3157679

2014-07-01T03:28:11Z

54.87.37.196: Fill PMID: Page!

{{RightTOC}}


{| id="A53b22acb52a98" class=" tableEdit PMID_info_table"

|-
!align=left |Citation
||
'''Garrett, S, Taylor, RK, Silhavy, TJ and Berman, ML''' (1985) Isolation and characterization of delta ompB strains of Escherichia coli by a general method based on gene fusions. ''J. Bacteriol.'' '''162''':840-4
|-
!align=left |Abstract
||
We isolated a series of delta ompR delta envZ mutants by inducing a strain carrying a lambda prophage in the closely linked gene malP and screening the bacterial survivors for loss of the major outer membrane porins OmpF and OmpC. Characterization of these deletion strains showed that both OmpR and EnvZ were necessary for transcription of ompF and ompC and that neither gene was essential for cell viability. Moreover, the deletion strains did not exhibit the pleiotropic membrane protein deficiency observed with certain envZ mutants. The method described should allow the simple isolation of deletions in any region of the chromosome.
|-
!align=left |Links
||
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=3157679 PubMed] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC218932 PMC218932]

|-
!align=left |Keywords
||
Bacterial Outer Membrane Proteins/genetics; Bacteriophage lambda/genetics; Chromosome Deletion; DNA, Bacterial/genetics; DNA, Recombinant; Escherichia coli/genetics

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.183644.A53b22acb52a98&page=183644&pagename={{FULLPAGENAMEE}}&type=1&template=PMID_info_table edit table] ||
|}


==Significance {{HelpIcon|Help:Literature}} ==
{{LitSignificance}}

== Useful Materials and Methods {{HelpIcon|Help:Literature}}==
{{LitMaterials}}

==Annotations {{HelpIcon|Help:Literature}}==
<annotationlinks/>

==EcoliWiki Links {{HelpIcon|Help:Literature}} ==
{{LitLinks}}

==See also==

==References==
{{RefHelp}}
<references/>

PMID:3157679

2014-07-01T03:28:11Z

54.87.37.196: New PMID: Page!

PMID on Demand placeholder

PMID:6338493

2014-07-01T03:17:56Z

54.87.37.196: Fill PMID: Page!

{{RightTOC}}


{| id="L53b228634d4f4" class=" tableEdit PMID_info_table"

|-
!align=left |Citation
||
'''Joachimiak, A, Kelley, RL, Gunsalus, RP, Yanofsky, C and Sigler, PB''' (1983) Purification and characterization of trp aporepressor. ''Proc. Natl. Acad. Sci. U.S.A.'' '''80''':668-72
|-
!align=left |Abstract
||
We have isolated homogeneous trp aporepressor from an overproducing strain of Escherichia coli carrying a plasmid containing trpR preceded by tandem trp operon promoters. Dye-affinity and ion-exchange chromatography were used in conjunction with a gel electrophoresis assay in which the repressor, when bound to the trp operator, protects an Rsa I restriction site from endonuclease cleavage. Crystals suitable for x-ray diffraction studies were grown from a variety of concentrated salt solutions. Hydrodynamic properties and electrophoretic analysis of unmodified and covalently crosslinked aporepressor show that the free aporepressor has an isoelectric point of 5.9 and is a dimer containing two identical 12.5-kilodalton subunits in the presence or absence of L-tryptophan. The repressor . operator complex binds poorly to nitrocellulose filters, but restriction-site protection studies indicate that, in the presence of tryptophan, one dimer is bound to the operator site with an apparent dissociation constant less than 2 X 10(-9) M. Preliminary equilibrium dialysis experiments suggest that tryptophan binds to the aporepressor with a dissociation constant of 1.6 X 10(-5) M.
|-
!align=left |Links
||
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=6338493 PubMed] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC393440 PMC393440]

|-
!align=left |Keywords
||
Amino Acid Sequence; Apoproteins/isolation & purification; Crystallography; Escherichia coli/genetics; Gene Expression Regulation; Isoelectric Point; Molecular Weight; Operon; Protein Binding; Repressor Proteins/isolation & purification; Repressor Proteins/metabolism; Spectrum Analysis; Transcription Factors/isolation & purification; Tryptophan/genetics; Tryptophan/metabolism

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.183643.L53b228634d4f4&page=183643&pagename={{FULLPAGENAMEE}}&type=1&template=PMID_info_table edit table] ||
|}


==Significance {{HelpIcon|Help:Literature}} ==
{{LitSignificance}}

== Useful Materials and Methods {{HelpIcon|Help:Literature}}==
{{LitMaterials}}

==Annotations {{HelpIcon|Help:Literature}}==
<annotationlinks/>

==EcoliWiki Links {{HelpIcon|Help:Literature}} ==
{{LitLinks}}

==See also==

==References==
{{RefHelp}}
<references/>

PMID:6338493

2014-07-01T03:17:55Z

54.87.37.196: New PMID: Page!

PMID on Demand placeholder

PMID:6207302

2014-06-20T05:05:04Z

54.87.37.196: Fill PMID: Page!

{{RightTOC}}


{| id="M53a3c0ff85d99" class=" tableEdit PMID_info_table"

|-
!align=left |Citation
||
'''Yoshimura, M, Inokuchi, H and Ozeki, H''' (1984) Identification of transfer RNA suppressors in Escherichia coli. IV. Amber suppressor Su+6 a double mutant of a new species of leucine tRNA. ''J. Mol. Biol.'' '''177''':627-44
|-
!align=left |Abstract
||
An Escherichia coli DNA fragment containing an Su+6 amber suppressor gene (supP) was cloned into a lambda gt lambda Ch vector by the shotgun method, selecting a Su+6 transducing phage lambda pSu+6. Through prophage integration followed by induction occurring at the transducing region of the lambda pSu+6 in Su- E. coli, a counterpart transducing phage carrying the wild-type allele (Su degrees 6) was isolated (lambda pSu degrees 6). The fingerprint of a tRNA encoded by lambda pSu degrees 6 was identical to that of an unidentified tRNAE previously reported (Ikemura & Ozeki, 1977). The cloverleaf structure of this tRNA was determined by combining the results of tRNA analysis and DNA sequencing of the gene. Judging from the anticodon of 5'-CAA-3', Su degrees 6 tRNA was identified as a new type of leucine isoacceptor in E. coli. Unlike other suppressors analyzed, Su+6 tRNA differed by two nucleotides from Su degrees 6 tRNA; one at the anticodon (CAA to CUA) and the other at the junction of D- and anticodon-stem (A27 to G27). DNA sequence analysis revealed that a single stretch of tRNA is flanked by the putative sequences of promoter and terminator. Thus a single copy of the Su degrees 6 tRNA gene constitutes a solitary tRNA transcription unit. Southern blotting showed only one copy of Su degrees 6 tRNA gene per haploid genome of E. coli. Since this single gene can mutate to the Su+6 suppressor, the Su degrees 6 leucine tRNA may be accounted as a dispensable species among the leucine isoacceptor tRNAs. Two possible open reading frames are found immediately following the Su degrees 6 tRNA gene.
|-
!align=left |Links
||
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=6207302 PubMed]

|-
!align=left |Keywords
||
Bacteriophage lambda/genetics; Bacteriophage lambda/isolation & purification; Base Sequence; Cloning, Molecular; DNA, Bacterial; Electrophoresis, Agar Gel; Escherichia coli/genetics; Genes, Bacterial; Mutation; RNA, Bacterial/genetics; RNA, Transfer/genetics; RNA, Transfer, Amino Acyl/genetics; Suppression, Genetic; Transduction, Genetic

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.183585.M53a3c0ff85d99&page=183585&pagename={{FULLPAGENAMEE}}&type=1&template=PMID_info_table edit table] ||
|}


==Significance {{HelpIcon|Help:Literature}} ==
{{LitSignificance}}

== Useful Materials and Methods {{HelpIcon|Help:Literature}}==
{{LitMaterials}}

==Annotations {{HelpIcon|Help:Literature}}==
<annotationlinks/>

==EcoliWiki Links {{HelpIcon|Help:Literature}} ==
{{LitLinks}}

==See also==

==References==
{{RefHelp}}
<references/>

PMID:6207302

2014-06-20T05:03:17Z

54.87.37.196: New PMID: Page!

PMID on Demand placeholder

PMID:786731

2014-06-20T03:43:52Z

54.87.37.196: Fill PMID: Page!

{{RightTOC}}


{| id="H53a3adf804336" class=" tableEdit PMID_info_table"

|-
!align=left |Citation
||
'''Wittmann-Liebold, B, Marzinzig, E and Lehmann, A''' (1976) Primary structure of protein S20 from the small ribosomal subunit of Escherichia coli. ''FEBS Lett.'' '''68''':110-4
|-
!align=left |Abstract
||
No abstract in PubMed
|-
!align=left |Links
||
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=786731 PubMed]

|-
!align=left |Keywords
||
Amino Acid Sequence; Escherichia coli; Peptide Fragments/analysis; Peptide Hydrolases; Ribosomal Proteins; Thermolysin; Trypsin

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.183584.H53a3adf804336&page=183584&pagename={{FULLPAGENAMEE}}&type=1&template=PMID_info_table edit table] ||
|}


==Significance {{HelpIcon|Help:Literature}} ==
{{LitSignificance}}

== Useful Materials and Methods {{HelpIcon|Help:Literature}}==
{{LitMaterials}}

==Annotations {{HelpIcon|Help:Literature}}==
<annotationlinks/>

==EcoliWiki Links {{HelpIcon|Help:Literature}} ==
{{LitLinks}}

==See also==

==References==
{{RefHelp}}
<references/>

PMID:786731

2014-06-20T03:43:51Z

54.87.37.196: New PMID: Page!

PMID on Demand placeholder

PMID:19589130

2014-06-16T15:50:48Z

54.87.37.196: Fill PMID: Page!

{{RightTOC}}


{| id="Y539f1257c22ba" class=" tableEdit PMID_info_table"

|-
!align=left |Citation
||
'''Heermann, R, Lippert, ML and Jung, K''' (2009) Domain swapping reveals that the N-terminal domain of the sensor kinase KdpD in Escherichia coli is important for signaling. ''BMC Microbiol.'' '''9''':133
|-
!align=left |Abstract
||
The KdpD/KdpE two-component system of Escherichia coli regulates expression of the kdpFABC operon encoding the high affinity K+ transport system KdpFABC. The input domain of KdpD comprises a domain that belongs to the family of universal stress proteins (Usp). It has been previously demonstrated that UspC binds to this domain, resulting in KdpD/KdpE scaffolding under salt stress. However the mechanistic significance of this domain for signaling remains unclear. Here, we employed a "domain swapping" approach to replace the KdpD-Usp domain with four homologous domains or with the six soluble Usp proteins of E. coli.
|-
!align=left |Links
||
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=19589130 PubMed] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2714519 PMC2714519]
Online version:[http://dx.doi.org/10.1186/1471-2180-9-133 10.1186/1471-2180-9-133]
|-
!align=left |Keywords
||
Amino Acid Sequence; Binding Sites; Escherichia coli/genetics; Escherichia coli/metabolism; Escherichia coli Proteins/genetics; Escherichia coli Proteins/metabolism; Heat-Shock Proteins/genetics; Heat-Shock Proteins/metabolism; Molecular Sequence Data; Phosphorylation; Potassium/metabolism; Protein Interaction Domains and Motifs; Protein Kinases/genetics; Protein Kinases/metabolism; Protein Structure, Tertiary; Recombinant Proteins/genetics; Recombinant Proteins/metabolism; Sequence Alignment; Signal Transduction; Sodium Chloride/metabolism; Stress, Physiological

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.183578.Y539f1257c22ba&page=183578&pagename={{FULLPAGENAMEE}}&type=1&template=PMID_info_table edit table] ||
|}


==Significance {{HelpIcon|Help:Literature}} ==
{{LitSignificance}}

== Useful Materials and Methods {{HelpIcon|Help:Literature}}==
{{LitMaterials}}

==Annotations {{HelpIcon|Help:Literature}}==
<annotationlinks/>

==EcoliWiki Links {{HelpIcon|Help:Literature}} ==
{{LitLinks}}

==See also==

==References==
{{RefHelp}}
<references/>

PMID:19589130

2014-06-16T15:50:47Z

54.87.37.196: New PMID: Page!

PMID on Demand placeholder

PMID:460428

2014-06-14T03:45:47Z

54.87.37.196: Fill PMID: Page!

{{RightTOC}}


{| id="E539bc56b02e63" class=" tableEdit PMID_info_table"

|-
!align=left |Citation
||
'''Meager, A, Graves, H, Burke, DC and Swallow, DM''' (1979) Involvement of a gene on chromosome 9 in human fibroblast interferon production. ''Nature'' '''280''':493-5
|-
!align=left |Abstract
||
No abstract in PubMed
|-
!align=left |Links
||
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=460428 PubMed]

|-
!align=left |Keywords
||
Animals; Cell Fusion; Cell Line; Chromosomes, Human, 6-12 and X; Fibroblasts/metabolism; Humans; Interferons/biosynthesis; Interferons/genetics; Mice

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.183559.E539bc56b02e63&page=183559&pagename={{FULLPAGENAMEE}}&type=1&template=PMID_info_table edit table] ||
|}


==Significance {{HelpIcon|Help:Literature}} ==
{{LitSignificance}}

== Useful Materials and Methods {{HelpIcon|Help:Literature}}==
{{LitMaterials}}

==Annotations {{HelpIcon|Help:Literature}}==
<annotationlinks/>

==EcoliWiki Links {{HelpIcon|Help:Literature}} ==
{{LitLinks}}

==See also==

==References==
{{RefHelp}}
<references/>

PMID:460428

2014-06-14T03:45:46Z

54.87.37.196: New PMID: Page!

PMID on Demand placeholder

PMID:365698

2014-06-14T01:54:22Z

54.87.37.196: Fill PMID: Page!

{{RightTOC}}


{| id="Z539bab4def640" class=" tableEdit PMID_info_table"

|-
!align=left |Citation
||
'''Allen, G and Wittmann-Liebold, B''' (1978) The amino acid sequence of the ribosomal protein S8 of Escherichia coli. ''Hoppe-Seyler's Z. Physiol. Chem.'' '''359''':1509-25
|-
!align=left |Abstract
||
The primary structure of protein S8 from the 30S subunit of Escherichia coli ribosomes has been determined by sequencing the peptides derived from tryptic, chymotryptic, thermolytic and staphylococcal protease digestion of the protein. Protein S8 has 129 amino acid residues which result in a molecular weight of 13996. The N-terminal part of the sequence up to position 68 is in complete agreement with the reported sequence data[1,2]. However, differences exist in the C-terminal half, where an additional hydrophobic tryptic peptide has been found.
|-
!align=left |Links
||
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=365698 PubMed]

|-
!align=left |Keywords
||
Amino Acid Sequence; Chymotrypsin; Escherichia coli/analysis; Molecular Weight; Peptide Fragments/analysis; Ribosomal Proteins/isolation & purification; Thermolysin; Trypsin

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.183556.Z539bab4def640&page=183556&pagename={{FULLPAGENAMEE}}&type=1&template=PMID_info_table edit table] ||
|}


==Significance {{HelpIcon|Help:Literature}} ==
{{LitSignificance}}

== Useful Materials and Methods {{HelpIcon|Help:Literature}}==
{{LitMaterials}}

==Annotations {{HelpIcon|Help:Literature}}==
<annotationlinks/>

==EcoliWiki Links {{HelpIcon|Help:Literature}} ==
{{LitLinks}}

==See also==

==References==
{{RefHelp}}
<references/>

PMID:365698

2014-06-14T01:54:21Z

54.87.37.196: New PMID: Page!

PMID on Demand placeholder

PMID:126327

2014-06-13T18:08:34Z

54.87.37.196: Fill PMID: Page!

{{RightTOC}}


{| id="X539b3e21f2ba4" class=" tableEdit PMID_info_table"

|-
!align=left |Citation
||
'''Nashimoto, H and Uchida, H''' (1975) Late steps in the assembly of 30 S ribosomal proteins in vivo in a spectinomycin-resistant mutant of Escherichia coli. ''J. Mol. Biol.'' '''96''':443-53
|-
!align=left |Abstract
||
No abstract in PubMed
|-
!align=left |Links
||
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=126327 PubMed]

|-
!align=left |Keywords
||
Cold Temperature; Diploidy; Drug Resistance, Microbial; Escherichia coli/drug effects; Escherichia coli/metabolism; Genetic Linkage; Mutation; Ribosomal Proteins/biosynthesis; Ribosomes/drug effects; Ribosomes/metabolism; Species Specificity; Spectinomycin/pharmacology

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.183553.X539b3e21f2ba4&page=183553&pagename={{FULLPAGENAMEE}}&type=1&template=PMID_info_table edit table] ||
|}


==Significance {{HelpIcon|Help:Literature}} ==
{{LitSignificance}}

== Useful Materials and Methods {{HelpIcon|Help:Literature}}==
{{LitMaterials}}

==Annotations {{HelpIcon|Help:Literature}}==
<annotationlinks/>

==EcoliWiki Links {{HelpIcon|Help:Literature}} ==
{{LitLinks}}

==See also==

==References==
{{RefHelp}}
<references/>

PMID:126327

2014-06-13T18:08:33Z

54.87.37.196: New PMID: Page!

PMID on Demand placeholder

PMID:6365894

2014-06-13T02:06:43Z

54.87.37.196: Fill PMID: Page!

{{RightTOC}}


{| id="Q539a5cb31bb06" class=" tableEdit PMID_info_table"

|-
!align=left |Citation
||
'''Magota, K, Otsuji, N, Miki, T, Horiuchi, T, Tsunasawa, S, Kondo, J, Sakiyama, F, Amemura, M, Morita, T and Shinagawa, H''' (1984) Nucleotide sequence of the phoS gene, the structural gene for the phosphate-binding protein of Escherichia coli. ''J. Bacteriol.'' '''157''':909-17
|-
!align=left |Abstract
||
phoS is the structural gene for the phosphate-binding protein, which is localized in periplasm and involved in active transport of phosphate in Escherichia coli. It is also a negative regulatory gene for the pho regulon, and the gene expression is inducible by phosphate starvation. The complete nucleotide sequence of the phoS gene was determined by the method of Maxam and Gilbert (A. M. Maxam and W. Gilbert, Methods Enzymol. 65:499-560, 1980). The amino acid sequences at the amino termini of the pre-PhoS and PhoS proteins and at the carboxy terminus of the PhoS protein were determined by using the purified proteins. Furthermore, the amino acid sequence of enzymatically digested peptide fragments of the PhoS protein was determined. The combined data established the nucleotide sequence of the coding region and the amino acid sequence of the pre-PhoS and the PhoS proteins. The pre-PhoS protein contains an extension of peptide composed of 25 amino acid residues at the amino terminus of the PhoS protein, which has the general characteristics of a signal peptide. The mature PhoS protein is composed of 321 amino acid residues, with a calculated molecular weight of 34,422, and lacks the disulfide bond and methionine. The regulatory region of phoS contains a characteristic Shine-Dalgarno sequence at an appropriate position preceding the translational initiation site, as well as three possible Pribnow boxes and one -35 sequence. the nucleotide sequence of the regulatory region of phoS was compared with those of phoA and phoE, the genes constituting the pho regulon.
|-
!align=left |Links
||
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=6365894 PubMed] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC215345 PMC215345]

|-
!align=left |Keywords
||
Amino Acid Sequence; Bacterial Proteins/genetics; Base Sequence; Carrier Proteins/genetics; Chromosome Mapping; Chromosomes, Bacterial; Escherichia coli/genetics; Escherichia coli/metabolism; Genes; Genes, Bacterial; Genes, Regulator; Phosphate-Binding Proteins; Phosphates/metabolism; Protein Biosynthesis; Transcription, Genetic

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.183548.Q539a5cb31bb06&page=183548&pagename={{FULLPAGENAMEE}}&type=1&template=PMID_info_table edit table] ||
|}


==Significance {{HelpIcon|Help:Literature}} ==
{{LitSignificance}}

== Useful Materials and Methods {{HelpIcon|Help:Literature}}==
{{LitMaterials}}

==Annotations {{HelpIcon|Help:Literature}}==
<annotationlinks/>

==EcoliWiki Links {{HelpIcon|Help:Literature}} ==
{{LitLinks}}

==See also==

==References==
{{RefHelp}}
<references/>

PMID:6365894

2014-06-13T02:06:43Z

54.87.37.196: New PMID: Page!

PMID on Demand placeholder

PMID:1100506

2014-06-13T01:57:07Z

54.87.37.196: Fill PMID: Page!

{{RightTOC}}


{| id="T539a5a72a263a" class=" tableEdit PMID_info_table"

|-
!align=left |Citation
||
'''Bitar, KG and Wittmann-Liebold, B''' (1975) The primary structure of the 5s rRNA binding protein L25 of Escherichia coli ribosomes. ''Hoppe-Seyler's Z. Physiol. Chem.'' '''356''':1343-52
|-
!align=left |Abstract
||
The primary structure of protein L25 from the large subunit of Escherichia coli ribosomes was determined by isolation and analysis of peptides obtained after cleavage of the protein with trypsin, thermolysin and Staphylococcus protease as well as by Edman degradation of the intact protein and of a CNBr peptide. The complete amino acid sequence is shown in Fig. 4. There are sequence homologies within protein L25 (Table 6) as well as between protein L25 and other ribosomal proteins (Table 5).
|-
!align=left |Links
||
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=1100506 PubMed]

|-
!align=left |Keywords
||
Amino Acid Sequence; Amino Acids/analysis; Escherichia coli/analysis; Peptide Fragments/analysis; Protein Binding; RNA, Ribosomal; Ribosomal Proteins/analysis; Ribosomes/analysis; Thermolysin; Trypsin

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.183547.T539a5a72a263a&page=183547&pagename={{FULLPAGENAMEE}}&type=1&template=PMID_info_table edit table] ||
|}


==Significance {{HelpIcon|Help:Literature}} ==
{{LitSignificance}}

== Useful Materials and Methods {{HelpIcon|Help:Literature}}==
{{LitMaterials}}

==Annotations {{HelpIcon|Help:Literature}}==
<annotationlinks/>

==EcoliWiki Links {{HelpIcon|Help:Literature}} ==
{{LitLinks}}

==See also==

==References==
{{RefHelp}}
<references/>

PMID:1100506

2014-06-13T01:57:06Z

54.87.37.196: New PMID: Page!

PMID on Demand placeholder

PMID:6263858

2014-06-12T18:03:28Z

54.87.37.196: Fill PMID: Page!

{{RightTOC}}


{| id="O5399eb705ca0a" class=" tableEdit PMID_info_table"

|-
!align=left |Citation
||
'''Sclafani, RA and Wechsler, JA''' (1981) dnaB125, a dnaB nonsense mutation. ''J. Bacteriol.'' '''146''':1170-3
|-
!align=left |Abstract
||
A temperature-sensitive dnaB mutation, dnaB125, was shown to be a suppressed amber mutation. The effects of inserting different amino acids at the mutated site via amber suppressors were examined for both Escherichia coli and bacteriophage gamma growth. In addition, the dnaB125 amber allele was shown to be different from the previously described dnaB amber allele, dnaB266. The extent of residual deoxyribonucleic acid synthesis observed in a supF(Ts) dnaB125 strain at high temperature revealed that the dnaB protein was present in excess and that deoxyribonucleic acid synthesis could continue for several generation equivalents without further production of dnaB protein.
|-
!align=left |Links
||
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=6263858 PubMed] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC216976 PMC216976]

|-
!align=left |Keywords
||
Alleles; Bacterial Proteins/genetics; DNA, Bacterial/biosynthesis; Escherichia coli/genetics; Mutation; Temperature

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.183543.O5399eb705ca0a&page=183543&pagename={{FULLPAGENAMEE}}&type=1&template=PMID_info_table edit table] ||
|}


==Significance {{HelpIcon|Help:Literature}} ==
{{LitSignificance}}

== Useful Materials and Methods {{HelpIcon|Help:Literature}}==
{{LitMaterials}}

==Annotations {{HelpIcon|Help:Literature}}==
<annotationlinks/>

==EcoliWiki Links {{HelpIcon|Help:Literature}} ==
{{LitLinks}}

==See also==

==References==
{{RefHelp}}
<references/>

PMID:6263858

2014-06-12T18:03:28Z

54.87.37.196: New PMID: Page!

PMID on Demand placeholder

PMID:13791860

2014-06-08T02:07:32Z

54.87.37.196: Fill PMID: Page!

{{RightTOC}}


{| id="T5393c564a8191" class=" tableEdit PMID_info_table"

|-
!align=left |Citation
||
'''ADELBERG, EA and BURNS, SN''' (1960) Genetic variation in the sex factor of Escherichia coli. ''J. Bacteriol.'' '''79''':321-30
|-
!align=left |Abstract
||
No abstract in PubMed
|-
!align=left |Links
||
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=13791860 PubMed] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC278688 PMC278688]

|-
!align=left |Keywords
||
Escherichia coli/genetics

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.183516.T5393c564a8191&page=183516&pagename={{FULLPAGENAMEE}}&type=1&template=PMID_info_table edit table] ||
|}


==Significance {{HelpIcon|Help:Literature}} ==
{{LitSignificance}}

== Useful Materials and Methods {{HelpIcon|Help:Literature}}==
{{LitMaterials}}

==Annotations {{HelpIcon|Help:Literature}}==
<annotationlinks/>

==EcoliWiki Links {{HelpIcon|Help:Literature}} ==
{{LitLinks}}

==See also==

==References==
{{RefHelp}}
<references/>

PMID:13791860

2014-06-08T02:07:32Z

54.87.37.196: New PMID: Page!

PMID on Demand placeholder

PMID:17257049

2014-06-07T14:08:35Z

54.87.37.196: Fill PMID: Page!

{{RightTOC}}


{| id="M53931ce30525e" class=" tableEdit PMID_info_table"

|-
!align=left |Citation
||
'''Wei, Y, Ringe, D, Wilson, MA and Ondrechen, MJ''' (2007) Identification of functional subclasses in the DJ-1 superfamily proteins. ''PLoS Comput. Biol.'' '''3''':e10
|-
!align=left |Abstract
||
Genomics has posed the challenge of determination of protein function from sequence and/or 3-D structure. Functional assignment from sequence relationships can be misleading, and structural similarity does not necessarily imply functional similarity. Proteins in the DJ-1 family, many of which are of unknown function, are examples of proteins with both sequence and fold similarity that span multiple functional classes. THEMATICS (theoretical microscopic titration curves), an electrostatics-based computational approach to functional site prediction, is used to sort proteins in the DJ-1 family into different functional classes. Active site residues are predicted for the eight distinct DJ-1 proteins with available 3-D structures. Placement of the predicted residues onto a structural alignment for six of these proteins reveals three distinct types of active sites. Each type overlaps only partially with the others, with only one residue in common across all six sets of predicted residues. Human DJ-1 and YajL from Escherichia coli have very similar predicted active sites and belong to the same probable functional group. Protease I, a known cysteine protease from Pyrococcus horikoshii, and PfpI/YhbO from E. coli, a hypothetical protein of unknown function, belong to a separate class. THEMATICS predicts a set of residues that is typical of a cysteine protease for Protease I; the prediction for PfpI/YhbO bears some similarity. YDR533Cp from Saccharomyces cerevisiae, of unknown function, and the known chaperone Hsp31 from E. coli constitute a third group with nearly identical predicted active sites. While the first four proteins have predicted active sites at dimer interfaces, YDR533Cp and Hsp31 both have predicted sites contained within each subunit. Although YDR533Cp and Hsp31 form different dimers with different orientations between the subunits, the predicted active sites are superimposable within the monomer structures. Thus, the three predicted functional classes form four different types of quaternary structures. The computational prediction of the functional sites for protein structures of unknown function provides valuable clues for functional classification.
|-
!align=left |Links
||
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=17257049 PubMed] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1782040 PMC1782040]
Online version:[http://dx.doi.org/10.1371/journal.pcbi.0030010 10.1371/journal.pcbi.0030010]
|-
!align=left |Keywords
||
Algorithms; Amino Acid Sequence; Binding Sites; Computer Simulation; Intracellular Signaling Peptides and Proteins/chemistry; Intracellular Signaling Peptides and Proteins/classification; Models, Chemical; Models, Molecular; Molecular Sequence Data; Oncogene Proteins/chemistry; Oncogene Proteins/classification; Oncogene Proteins/ultrastructure; Protein Binding; Protein Conformation; Sequence Analysis, Protein/methods

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.183515.M53931ce30525e&page=183515&pagename={{FULLPAGENAMEE}}&type=1&template=PMID_info_table edit table] ||
|}


==Significance {{HelpIcon|Help:Literature}} ==
{{LitSignificance}}

== Useful Materials and Methods {{HelpIcon|Help:Literature}}==
{{LitMaterials}}

==Annotations {{HelpIcon|Help:Literature}}==
<annotationlinks/>

==EcoliWiki Links {{HelpIcon|Help:Literature}} ==
{{LitLinks}}

==See also==

==References==
{{RefHelp}}
<references/>

PMID:17257049

2014-06-07T14:08:34Z

54.87.37.196: New PMID: Page!

PMID on Demand placeholder