EcoliWiki - User contributions [en]

PMID:6750604

2014-09-28T05:27:43Z

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'''Smiley, BL, Lupski, JR, Svec, PS, McMacken, R and Godson, GN''' (1982) Sequences of the Escherichia coli dnaG primase gene and regulation of its expression. ''Proc. Natl. Acad. Sci. U.S.A.'' '''79''':4550-4
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!align=left |Abstract
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The nucleotide sequence of a cloned section of the Escherichia coli chromosome containing the dnaG primase gene [Lupski, J., Smiley, B., Blattner, F. & Godson, G. N. (1982) Mol. Gen, Genet. 185, 120--128] has been determined. The region coding for the dnaG primase has been identified by NH2-terminal and tryptic peptide amino acid analysis of the dnaG protein. The coding region is 1,740 base pairs long (580 amino acids) and is preceded by an unusual ribosome-binding site sequence (G-G-G-G). The dnaG gene is read in the same direction as the adjacent rpoD gene, but no obvious promoter sequences can be found for either gene within several hundred nucleotides upstream. Other unusual features of the dnaG gene that may explain the maintenance of its product at low copy number are the presence of a RNA polymerase terminator 31 nucleotides upstream from the ATG initiator codon and greater use (3--10 times) of certain condons that occur infrequently in other E. coli genes. The nucleotide sequence has also been correlated with data from transposon Tn5 insertional inactivation mapping.
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[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=6750604 PubMed] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC346712 PMC346712]

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!align=left |Keywords
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Amino Acid Sequence; Bacterial Proteins/genetics; Base Sequence; Codon; DNA Primase; DNA, Bacterial/genetics; Escherichia coli/genetics; Gene Expression Regulation; Genes, Bacterial; Nucleic Acid Conformation; Peptide Fragments/analysis; RNA Nucleotidyltransferases/genetics

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PMID:6750604

2014-09-28T05:27:41Z

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PMID:17419738

2014-09-09T02:18:01Z

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'''Christensen, O, Harvat, EM, Thöny-Meyer, L, Ferguson, SJ and Stevens, JM''' (2007) Loss of ATP hydrolysis activity by CcmAB results in loss of c-type cytochrome synthesis and incomplete processing of CcmE. ''FEBS J.'' '''274''':2322-32
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The proteins CcmA and CcmB have long been known to be essential for cytochrome c maturation in Escherichia coli. We have purified a complex of these proteins, and found it to have ATP hydrolysis activity. CcmA, which has the features of a soluble ATP hydrolysis subunit, is found in a membrane-bound complex only when CcmB is present in the membrane. Mutation of the Walker A motif in CcmA(K40D) results in loss of the in vitro ATPase activity and in loss of cytochrome c biogenesis in vivo. The same mutation does not prevent covalent attachment of heme to the heme chaperone CcmE, but holo-CcmE is, for some unidentified reason, incompetent for heme transfer to an apocytochrome c or for release into the periplasm as a soluble variant. Addition of exogenous heme to heme-permeable E. coli with a ccmA deletion did not restore cytochrome c production. Our results suggest a role for CcmAB in the handling of heme by CcmE, which is chemically complex and involves an unusual histidine-heme covalent bond.
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[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=17419738 PubMed]
Online version:[http://dx.doi.org/10.1111/j.1742-4658.2007.05769.x 10.1111/j.1742-4658.2007.05769.x]
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!align=left |Keywords
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ATP-Binding Cassette Transporters/biosynthesis; ATP-Binding Cassette Transporters/chemistry; ATP-Binding Cassette Transporters/genetics; ATP-Binding Cassette Transporters/metabolism; Adenosine Triphosphate/metabolism; Amino Acid Motifs/genetics; Aspartic Acid/genetics; Bacterial Outer Membrane Proteins/biosynthesis; Bacterial Outer Membrane Proteins/chemistry; Bacterial Outer Membrane Proteins/genetics; Bacterial Outer Membrane Proteins/metabolism; Cytochromes c/biosynthesis; Cytochromes c/genetics; Cytochromes c/metabolism; Escherichia coli/enzymology; Escherichia coli/genetics; Escherichia coli Proteins/biosynthesis; Escherichia coli Proteins/genetics; Escherichia coli Proteins/metabolism; Heme/metabolism; Hemeproteins/biosynthesis; Hemeproteins/genetics; Hemeproteins/metabolism; Histidine/metabolism; Hydrolysis; Lysine/genetics; Mutagenesis, Site-Directed; Protein Processing, Post-Translational/genetics; Protein Subunits/chemistry; Protein Subunits/genetics; Protein Subunits/metabolism; Sequence Deletion

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PMID:17419738

2014-09-09T02:18:00Z

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PMID:7021852

2014-08-30T21:05:04Z

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'''Sauer, B, Ow, D, Ling, L and Calendar, R''' (1981) Mutants of satellite bacteriophage P4 that are defective in the suppression of transcriptional polarity. ''J. Mol. Biol.'' '''145''':29-46
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No abstract in PubMed
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[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=7021852 PubMed]

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Bacteriolysis; Coliphages/genetics; Escherichia coli; Gene Expression; Mutation; Protein Biosynthesis; Suppression, Genetic; Viral Proteins/biosynthesis

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PMID:7021852

2014-08-30T21:05:03Z

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PMID:24224554

2014-08-24T15:07:34Z

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'''Garland, AF and Brookman-Frazee, L''' (2013) Therapists and researchers: Advancing collaboration. ''Psychother Res'' ''''''
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Abstract Collaborative partnerships between community-based clinicians and academic researchers have the potential to improve the relevance, utility, and feasibility of research, as well as the effectiveness of practice. Collaborative partnership research from a variety of fields can inform the development and maintenance of effective partnerships. In this paper we present a conceptual model of research-community practice partnership derived from literature across disciplines and then illustrate application of this model to one case example. The case example is a multi-year partnership between an interdisciplinary group of community-based psychotherapists and a team of mental health researchers. This partnership was initiated to support federally funded research on community-based outpatient mental health care for children with disruptive behavior problems, but it has evolved to drive and support new intervention studies with different clinical foci. Lessons learned from this partnership process will be shared and interpreted in the context of the presented research-practice partnership model.
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[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=24224554 PubMed]
Online version:[http://dx.doi.org/10.1080/10503307.2013.838655 10.1080/10503307.2013.838655]
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PMID:24224554

2014-08-24T15:07:33Z

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PMID:378403

2014-08-10T15:30:23Z

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'''Morrison, A and Cozzarelli, NR''' (1979) Site-specific cleavage of DNA by E. coli DNA gyrase. ''Cell'' '''17''':175-84
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!align=left |Abstract
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E. coli DNA gyrase, which catalyzes the supercoiling of DNA, cleaves DNA site-specifically when oxolinic acid and sodium dodecylsulfate are added to the reaction. We studied the structure of the gyrasecleaved DNA because of its implications for the reaction mechanism and biological role of gyrase. Gyrase made a staggered cut, creating DNA termini with a free 3' hydroxyl and a 5' extension that provided a template primer for DNA polymerase. The cleaved DNA was resistant to labeling with T4 polynucleotide kinase even after treatment with proteinase K. Thus the denatured enzyme that remains attached to cleaved DNA is covalently bonded to both 5' terminal extensions. The 5' extensions of many gyrase cleavage fragments from phi X174, SV40 and Col E1 DNA were partially sequenced using repair with E. coli DNA polymerase I. No unique sequence existed within the cohesive ends, but G was the predominant first base incorporated by DNA polymerase I. The cohesive and sequences of four gyrase sites were determined, and they demonstrated a four base 5' extension. The dinucleotide TG, straddling the gyrase cut on one DNA strand, provided the only common bases within a 100 bp region surrounding the cleavage sites. Analysis of other cleavage fragments showed that cutting between a TG doublet is common to most, or all, gyrase cleavages. Other bases common to some of the sequenced sites were clustered nonrandomly around the TG doublet, and may be variable components of the cleavage sequence. This diverse recognition sequence with common elements is a pattern shared with several other specific nucleic acid-protein interactions.
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[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=378403 PubMed]

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!align=left |Keywords
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Base Sequence; Coliphages; DNA Polymerase I/metabolism; DNA Replication; DNA, Superhelical/metabolism; DNA, Viral; Escherichia coli/enzymology

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PMID:378403

2014-08-10T15:30:22Z

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PMID:9278055

2014-08-04T14:41:52Z

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'''Morais Cabral, JH, Jackson, AP, Smith, CV, Shikotra, N, Maxwell, A and Liddington, RC''' (1997) Crystal structure of the breakage-reunion domain of DNA gyrase. ''Nature'' '''388''':903-6
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!align=left |Abstract
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DNA gyrase is a type II DNA topoisomerase from bacteria that introduces supercoils into DNA. It catalyses the breakage of a DNA duplex (the G segment), the passage of another segment (the T segment) through the break, and then the reunification of the break. This activity involves the opening and dosing of a series of molecular 'gates' which is coupled to ATP hydrolysis. Here we present the crystal structure of the 'breakage-reunion' domain of the gyrase at 2.8 A resolution. Comparison of the structure of this 59K (relative molecular mass, 59,000) domain with that of a 92K fragment of yeast topoisomerase II reveals a very different quaternary organization, and we propose that the two structures represent two principal conformations that participate in the enzymatic pathway. The gyrase structure reveals a new dimer contact with a grooved concave surface for binding the G segment and a cluster of conserved charged residues surrounding the active-site tyrosines. It also shows how breakage of the G segment can occur and, together with the topoisomerase II structure, suggests a pathway by which the T segment can be released through the second gate of the enzyme. Mutations that confer resistance to the quinolone antibacterial agents cluster at the new dimer interface, indicating how these drugs might interact with the gyrase-DNA complex.
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[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=9278055 PubMed]
Online version:[http://dx.doi.org/10.1038/42294 10.1038/42294]
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!align=left |Keywords
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Amino Acid Sequence; Crystallography, X-Ray; DNA/chemistry; DNA Topoisomerases, Type II/chemistry; Escherichia coli/enzymology; Models, Molecular; Molecular Sequence Data; Protein Conformation; Saccharomyces cerevisiae/enzymology; Sequence Homology, Amino Acid

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PMID:9278055

2014-08-04T14:41:51Z

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PMID:17973909

2014-07-26T01:04:18Z

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'''Barre, FX''' (2007) FtsK and SpoIIIE: the tale of the conserved tails. ''Mol. Microbiol.'' '''66''':1051-5
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During Bacillus subtilis sporulation, the SpoIIIE DNA translocase moves a trapped chromosome across the sporulation septum into the forespore. The preferential assembly of SpoIIIE complexes in the mother cell provided the idea that SpoIIIE functioned as a DNA exporter, which ensured translocation orientation. In this issue of Molecular Microbiology, Becker and Pogliano reinvestigate the molecular mechanisms that orient the activity of SpoIIIE. Their findings indicate that SpoIIIE reads the polarity of DNA like its Escherichia coli homologue, FtsK.
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[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=17973909 PubMed]
Online version:[http://dx.doi.org/10.1111/j.1365-2958.2007.05981.x 10.1111/j.1365-2958.2007.05981.x]
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!align=left |Keywords
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Bacillus subtilis/genetics; Bacillus subtilis/physiology; Bacterial Proteins/genetics; Bacterial Proteins/physiology; Conserved Sequence; Escherichia coli/genetics; Escherichia coli/physiology; Escherichia coli Proteins/genetics; Escherichia coli Proteins/physiology; Membrane Proteins/genetics; Membrane Proteins/physiology; Protein Structure, Tertiary

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PMID:17973909

2014-07-26T01:04:17Z

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PMID:6154685

2014-07-22T07:05:15Z

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'''Fairweather, NF, Orr, E and Holland, IB''' (1980) Inhibition of deoxyribonucleic acid gyrase: effects on nucleic acid synthesis and cell division in Escherichia coli K-12. ''J. Bacteriol.'' '''142''':153-61
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!align=left |Abstract
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Mutants of Escherichia coli resistant to the antibiotic clorobiocin are also coumermycin resistant, and the mutation to resistance in at least one mutant was mapped near gyrB. We conclude, therefore, that clorobiocin inhibits deoxyribonucleic acid gyrase, and the drug was used to probe the role of this enzyme in vivo. Deozyribonucleic acid synthesis was preferentially inhibited but not completely blocked by the antibiotic. Transcription and cell division were also markedly affected. However, unlike other inhibitors of deoxyribonucleic acid synthesis, clorobiocin failed to induce the synthesis of protein X, the recA gene product. In mutants resistant to clorobiocin the replication velocity was unaffected, but initiation of deoxyribonucleic acid synthesis appeared to be delayed. We conclude that deoxyribonucleic acid gyrase, and hence the supercoiled structure of the chromosome, is important for transcription, normal initiation of deoxyribonucleic acid replication, and cell division. The possible role of deoxyribonucleic acid gyrase in the elongation of replication forks is also discussed.
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[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=6154685 PubMed] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC293920 PMC293920]

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!align=left |Keywords
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Bacterial Proteins/biosynthesis; Cell Division/drug effects; DNA, Bacterial/biosynthesis; Drug Resistance, Microbial; Escherichia coli/drug effects; Escherichia coli/enzymology; Escherichia coli/metabolism; Mutation; Novobiocin/analogs & derivatives; Novobiocin/pharmacology; RNA, Bacterial/biosynthesis; Topoisomerase II Inhibitors

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PMID:6154685

2014-07-22T07:05:14Z

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PMID:6255421

2014-07-12T21:13:36Z

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{| id="B53c1a4ffa4a41" class=" tableEdit PMID_info_table"

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'''Sugino, A, Higgins, NP and Cozzarelli, NR''' (1980) DNA gyrase subunit stoichiometry and the covalent attachment of subunit A to DNA during DNA cleavage. ''Nucleic Acids Res.'' '''8''':3865-74
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!align=left |Abstract
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Escherichia coli DNA gyrase contains a 1:1 ratio of protomers coded by the genes gyrA and gyrB. This along with previous results shows that the enzyme has two copies of each protomer and thus a molecular weight of 400,000. Abortion of the gyrase reaction results in double-strand breakage of the DNA and covalent attachment of both gyrA protomers to the 5'-cut ends. We conclude that the gyrA protomer contains a critical part of the active site for the concerted breakage and reunion reaction of gyrase, the topoisomerase activity of the enzyme.
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!align=left |Links
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[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=6255421 PubMed] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC324200 PMC324200]

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!align=left |Keywords
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Binding Sites; DNA Topoisomerases, Type II/metabolism; DNA, Bacterial/metabolism; Escherichia coli/enzymology; Genes; Macromolecular Substances; Molecular Weight; Operon; Protein Binding

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PMID:6255421

2014-07-12T21:13:35Z

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PMID:16207917

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'''Madhusudan, S, Paukner, A, Klingen, Y and Schnetz, K''' (2005) Independent regulation of H-NS-mediated silencing of the bgl operon at two levels: upstream by BglJ and LeuO and downstream by DnaKJ. ''Microbiology (Reading, Engl.)'' '''151''':3349-59
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!align=left |Abstract
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Silencing of the Escherichia coli bgl operon by the histone-like nucleoid-structuring protein H-NS occurs at two levels. Binding of H-NS upstream of the promoter represses transcription initiation, whilst binding within the coding region is also proposed to repress transcription elongation. The latter, downstream level of repression is counteracted by the protease Lon and, thus, silencing of the bgl operon is more effective in lon mutants. Transposon-mutagenesis screens for suppression of this lon phenotype on bgl were performed and insertion mutations disrupting rpoS and crl were obtained, as well as mutations mapping upstream of the open reading frames of bglJ, leuO and dnaK. In rpoS and crl mutants, bgl promoter activity is known to be higher. Likewise, as shown here, bgl promoter activity is increased in the bglJ and leuO mutants, which express BglJ and LeuO constitutively. However, BglJ and LeuO have no impact on downstream repression. A dnaKJ mutant was isolated for the first time in the context of the bgl operon. The mutant expresses lower levels of DnaK than the wild-type. Interestingly, in this dnaKJ : : miniTn10 mutant, downstream repression of bgl by H-NS is less effective, whilst upstream repression by H-NS remains unaffected. Together, the data show that the two levels of bgl silencing by H-NS are regulated independently.
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[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16207917 PubMed]
Online version:[http://dx.doi.org/10.1099/mic.0.28080-0 10.1099/mic.0.28080-0]
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!align=left |Keywords
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Bacterial Proteins/genetics; Bacterial Proteins/metabolism; DNA Transposable Elements; DNA-Binding Proteins/genetics; DNA-Binding Proteins/metabolism; Escherichia coli/genetics; Escherichia coli/metabolism; Escherichia coli Proteins/genetics; Escherichia coli Proteins/metabolism; Gene Expression Regulation, Bacterial; Gene Silencing; Glucosides/metabolism; HSP70 Heat-Shock Proteins/genetics; HSP70 Heat-Shock Proteins/metabolism; Mutagenesis, Insertional; Operon; Trans-Activators/genetics; Trans-Activators/metabolism; Transcription Factors/genetics; Transcription Factors/metabolism

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

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

PMID:16207917

2014-07-12T14:33:08Z

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PMID:18953042

2014-07-09T11:49:11Z

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{| id="Y53bd2c370f5fb" class=" tableEdit PMID_info_table"

|-
!align=left |Citation
||
'''Guillier, M and Gottesman, S''' (2008) The 5' end of two redundant sRNAs is involved in the regulation of multiple targets, including their own regulator. ''Nucleic Acids Res.'' '''36''':6781-94
|-
!align=left |Abstract
||
Small RNAs are widespread regulators of gene expression in numerous organisms. This study describes the mode of action of two redundant Escherichia coli sRNAs, OmrA and OmrB, that downregulate the expression of multiple targets, most of which encode outer membrane proteins. Our results show that both sRNAs directly interact with at least two of these target mRNAs, ompT and cirA, in the vicinity of the translation initiation region, consistent with control of these targets being dependent on both Hfq and RNase E. Interestingly, these interactions depend on short stretches of complementarity and involve the conserved 5' end of OmrA/B. A mutation in this region abolishes control of all OmrA/B targets tested thus far, thereby highlighting the crucial role of the OmrA/B 5' end. This allowed us, by looking for mRNA sequences complementary to the OmrA/B 5' end, to identify ompR as an additional direct target of these two sRNAs. Since the OmpR transcriptional regulator activates expression of both omrA and omrB genes, this newly identified control should result in an autoregulatory loop limiting the amount of OmrA/B sRNAs.
|-
!align=left |Links
||
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=18953042 PubMed] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2588501 PMC2588501]
Online version:[http://dx.doi.org/10.1093/nar/gkn742 10.1093/nar/gkn742]
|-
!align=left |Keywords
||
5' Untranslated Regions; Bacterial Outer Membrane Proteins/genetics; Bacterial Outer Membrane Proteins/metabolism; Bacterial Proteins/genetics; Bacterial Proteins/metabolism; Base Pairing; Endoribonucleases/metabolism; Escherichia coli/enzymology; Escherichia coli/genetics; Escherichia coli/metabolism; Escherichia coli Proteins/genetics; Escherichia coli Proteins/metabolism; Gene Expression Regulation, Bacterial; Peptide Hydrolases/genetics; Peptide Hydrolases/metabolism; Protein Biosynthesis; RNA, Messenger/chemistry; RNA, Messenger/metabolism; RNA, Untranslated/biosynthesis; RNA, Untranslated/chemistry; Receptors, Cell Surface/genetics; Receptors, Cell Surface/metabolism; Trans-Activators/genetics; Trans-Activators/metabolism

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|}


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

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

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<annotationlinks/>

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

==See also==

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

PMID:18953042

2014-07-09T11:49:10Z

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PMID:3900671

2014-07-09T02:45:30Z

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{| id="V53bcacc9e4ba2" class=" tableEdit PMID_info_table"

|-
!align=left |Citation
||
'''Postma, PW and Lengeler, JW''' (1985) Phosphoenolpyruvate:carbohydrate phosphotransferase system of bacteria. ''Microbiol. Rev.'' '''49''':232-69
|-
!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=3900671 PubMed] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC373035 PMC373035]

|-
!align=left |Keywords
||
Bacteria/enzymology; Bacteria/genetics; Bacteria/metabolism; Bacterial Physiological Phenomena; Biological Evolution; Carbohydrate Metabolism; Chemotaxis; Chromosome Mapping; Diffusion; Enzyme Activation; Enzyme Induction; Enzyme Repression; Genes, Bacterial; Genes, Regulator; Membrane Potentials; Mutation; Operon; Phosphoenolpyruvate Sugar Phosphotransferase System/genetics; Phosphoenolpyruvate Sugar Phosphotransferase System/metabolism; Phosphorylation; Suppression, Genetic

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.183669.V53bcacc9e4ba2&page=183669&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:3900671

2014-07-09T02:45:29Z

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PMID:18977760

2014-07-08T20:06:25Z

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{| id="X53bc4f40a8566" class=" tableEdit PMID_info_table"

|-
!align=left |Citation
||
'''Su'etsugu, M, Nakamura, K, Keyamura, K, Kudo, Y and Katayama, T''' (2008) Hda monomerization by ADP binding promotes replicase clamp-mediated DnaA-ATP hydrolysis. ''J. Biol. Chem.'' '''283''':36118-31
|-
!align=left |Abstract
||
ATP-DnaA is the initiator of chromosomal replication in Escherichia coli, and the activity of DnaA is regulated by the regulatory inactivation of the DnaA (RIDA) system. In this system, the Hda protein promotes DnaA-ATP hydrolysis to produce inactive ADP-DnaA in a mechanism that is mediated by the DNA-loaded form of the replicase sliding clamp. In this study, we first revealed that hda translation uses an unusual initiation codon, CUG, located downstream of the annotated initiation codon. The CUG initiation codon could be used for restricting the Hda level, as this initiation codon has a low translation efficiency, and the cellular Hda level is only approximately 100 molecules per cell. Hda translated using the correct reading frame was purified and found to have a high RIDA activity in vitro. Moreover, we found that Hda has a high affinity for ADP but not for other nucleotides, including ATP. ADP-Hda was active in the RIDA system in vitro and stable in a monomeric state, whereas apo-Hda formed inactive homomultimers. Both ADP-Hda and apo-Hda could form complexes with the DNA-loaded clamp; however, only ADP-Hda-DNA-clamp complexes were highly functional in the following interaction with DnaA. Formation of ADP-Hda was also observed in vivo, and mutant analysis suggested that ADP binding is crucial for cellular Hda activity. Thus, we propose that ADP is a crucial Hda ligand that promotes the activated conformation of the protein. ADP-dependent monomerization might enable the arginine finger of the Hda AAA+ domain to be accessible to ATP bound to the DnaA AAA+ domain.
|-
!align=left |Links
||
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=18977760 PubMed] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2662290 PMC2662290]
Online version:[http://dx.doi.org/10.1074/jbc.M803158200 10.1074/jbc.M803158200]
|-
!align=left |Keywords
||
Adenosine Diphosphate/chemistry; Adenosine Triphosphatases/metabolism; Adenosine Triphosphate/chemistry; Amino Acid Sequence; Arginine/chemistry; Bacterial Proteins/metabolism; Base Sequence; Codon; Codon, Initiator; DNA/chemistry; DNA-Binding Proteins/metabolism; DNA-Directed DNA Polymerase/metabolism; Escherichia coli Proteins/metabolism; Hydrolysis; Ligands; Open Reading Frames; Protein Binding; Protein Conformation; Protein Structure, Tertiary

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|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.183666.X53bc4f40a8566&page=183666&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:18977760

2014-07-08T20:06:24Z

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PMID:1593632

2014-07-04T17:04:03Z

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{| id="J53b6de83749b1" class=" tableEdit PMID_info_table"

|-
!align=left |Citation
||
'''von Heijne, G''' (1992) Membrane protein structure prediction. Hydrophobicity analysis and the positive-inside rule. ''J. Mol. Biol.'' '''225''':487-94
|-
!align=left |Abstract
||
A new strategy for predicting the topology of bacterial inner membrane proteins is proposed on the basis of hydrophobicity analysis, automatic generation of a set of possible topologies and ranking of these according to the positive-inside rule. A straightforward implementation with no attempts at optimization predicts the correct topology for 23 out of 24 inner membrane proteins with experimentally determined topologies, and correctly identifies 135 transmembrane segments with only one overprediction.
|-
!align=left |Links
||
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=1593632 PubMed]

|-
!align=left |Keywords
||
Bacterial Proteins/chemistry; Hydrogen-Ion Concentration; Membrane Proteins/chemistry; Protein Conformation; Water

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.183660.J53b6de83749b1&page=183660&pagename={{FULLPAGENAMEE}}&type=1&template=PMID_info_table edit table] ||
|}


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

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

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<annotationlinks/>

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

==See also==

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

PMID:1593632

2014-07-04T17:04:03Z

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PMID on Demand placeholder

Category:GO:0006323 ! DNA packaging

2014-07-02T20:00:02Z

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{{GO term stub|GO:0006323_!_DNA_packaging}}

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

PMID:2381886

2014-06-29T16:31:34Z

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{| id="N53b03f65b97de" class=" tableEdit PMID_info_table"

|-
!align=left |Citation
||
'''Hindle, WH''' (1990) Breast masses. In-office evaluation with diagnostic triad. ''Postgrad Med'' '''88''':85-7, 90-4
|-
!align=left |Abstract
||
Using the diagnostic triad of clinical breast examination, fine-needle aspiration, and mammography, primary care physicians can make an in-office definitive diagnosis in 90% of women presenting with a dominant breast mass. The remaining 10% should undergo open surgical biopsy. This diagnostic-triad approach is accurate, efficient, and cost-effective, and it does not require additional lengthy training, expensive equipment, or complex technology. In the case of breast cancer, the woman and her family can be immediately counseled and quickly prepared for consulting appointments and appropriate treatment options.
|-
!align=left |Links
||
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=2381886 PubMed]

|-
!align=left |Keywords
||
Adult; Biopsy, Needle/methods; Breast Diseases/diagnosis; Breast Diseases/pathology; Breast Diseases/psychology; Female; Humans; Mammography; Middle Aged; Palpation; Primary Health Care/methods

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.183642.N53b03f65b97de&page=183642&pagename={{FULLPAGENAMEE}}&type=1&template=PMID_info_table edit table] ||
|}


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

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

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<annotationlinks/>

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{{LitLinks}}

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

PMID:2381886

2014-06-29T16:31:33Z

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PMID on Demand placeholder

Category:GO:0045892 ! negative regulation of cellular transcription, DNA-dependent

2014-06-23T18:13:42Z

130.185.139.213: New GO term category page

{{GO term stub|GO:0045892_!_negative_regulation_of_cellular_transcription,_DNA-dependent}}

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

PMID:12139617

2014-06-19T03:51:46Z

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{| id="K53a25e51b053c" class=" tableEdit PMID_info_table"

|-
!align=left |Citation
||
'''Chamnongpol, S, Dodson, W, Cromie, MJ, Harris, ZL and Groisman, EA''' (2002) Fe(III)-mediated cellular toxicity. ''Mol. Microbiol.'' '''45''':711-9
|-
!align=left |Abstract
||
Because it can undergo reversible changes in oxidation state, iron is an excellent biocatalyst but also a potentially deleterious metal. Iron-mediated toxicity has been ascribed to Fe(II), which reacts with oxygen to generate free radicals that damage macromolecules and cause cell death. However, we now report that Fe(III) exhibits microbicidal activity towards strains of Salmonella enterica, Escherichia coli and Klebsiella pneumoniae defective in the Fe(III)-responding PmrA/PmrB signal transduction system. Fe(III) bound to a pmrA Salmonella mutant more effectively than to the isogenic wild-type strain and exerted its microbicidal activity even under anaerobic conditions. Moreover, Fe(III) permeabilized the outer membrane of the pmrA mutant, rendering it susceptible to vancomycin, which is normally non-toxic to Gram-negative species. On the other hand, Fe(III) did not affect the viability of a mutant defective in Fur, the major regulator of cytosolic iron homeostasis, which is hypersensitive to Fe(II)-mediated toxicity. A functional pmrA gene was necessary for bacterial survival in soil. Our results indicate that Fe(III) exerts its microbicidal activity by a mechanism that is oxygen independent and different from that mediated by Fe(II).
|-
!align=left |Links
||
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=12139617 PubMed]

|-
!align=left |Keywords
||
Bacterial Proteins/genetics; Bacterial Proteins/metabolism; Ferric Compounds/pharmacology; Ferrous Compounds/pharmacology; Gene Expression Regulation, Bacterial/drug effects; Gene Expression Regulation, Bacterial/genetics; Iron-Binding Proteins; Oxygen/metabolism; Salmonella/drug effects; Salmonella/metabolism; Signal Transduction/drug effects; Soil Microbiology; Transcription Factors/genetics; Transcription Factors/metabolism

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|}


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

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

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<annotationlinks/>

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

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

PMID:12139617

2014-06-19T03:51:45Z

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PMID:4611426

2014-06-15T19:16:57Z

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{| id="B539df1298884d" class=" tableEdit PMID_info_table"

|-
!align=left |Citation
||
'''Okuyama, A, Yoshikawa, M and Tanaka, N''' (1974) Alteration of ribosomal protein S2 in kasugamycin-resistant mutant derived from Escherichia coli AB312. ''Biochem. Biophys. Res. Commun.'' '''60''':1163-9
|-
!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=4611426 PubMed]

|-
!align=left |Keywords
||
Aminoglycosides; Anti-Bacterial Agents; Bacterial Proteins/isolation & purification; Carbon Radioisotopes; Drug Resistance, Microbial; Electrophoresis, Polyacrylamide Gel; Escherichia coli/metabolism; Genes; Inositol; Mutation; Peptide Initiation Factors; Polynucleotides; Ribosomes/metabolism; Valine/metabolism

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|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.183571.B539df1298884d&page=183571&pagename={{FULLPAGENAMEE}}&type=1&template=PMID_info_table edit table] ||
|}


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

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<annotationlinks/>

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{{LitLinks}}

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

PMID:4611426

2014-06-15T19:16:57Z

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PMID:4573678

2014-06-14T14:50:57Z

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{| id="B539c61513610e" class=" tableEdit PMID_info_table"

|-
!align=left |Citation
||
'''Terhorst, C, Möller, W, Laursen, R and Wittmann-Liebold, B''' (1973) The primary structure of an acidic protein from 50-S ribosomes of Escherichia coli which is involved in GTP hydrolysis dependent on elongation factors G and T. ''Eur. J. Biochem.'' '''34''':138-52
|-
!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=4573678 PubMed]

|-
!align=left |Keywords
||
Amino Acid Sequence; Autoanalysis; Bacterial Proteins/analysis; Binding Sites; Carboxypeptidases; Chromatography, Ion Exchange; Chromatography, Paper; Chymotrypsin; Electrophoresis, Paper; Electrophoresis, Polyacrylamide Gel; Escherichia coli/analysis; Guanosine Triphosphate; Hydrolysis; Leucyl Aminopeptidase; Pancreatic Elastase; Peptide Elongation Factors; Ribosomes/analysis; Trypsin

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.183564.B539c61513610e&page=183564&pagename={{FULLPAGENAMEE}}&type=1&template=PMID_info_table edit table] ||
|}


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

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{{LitMaterials}}

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<annotationlinks/>

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

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

PMID:4573678

2014-06-14T14:50:57Z

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PMID:18455185

2014-06-14T14:20:02Z

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{| id="Q539c5a122b5ca" class=" tableEdit PMID_info_table"

|-
!align=left |Citation
||
'''Kim, IK, Yim, HS, Kim, MK, Kim, DW, Kim, YM, Cha, SS and Kang, SO''' (2008) Crystal structure of a new type of NADPH-dependent quinone oxidoreductase (QOR2) from Escherichia coli. ''J. Mol. Biol.'' '''379''':372-84
|-
!align=left |Abstract
||
Escherichia coli QOR2 [NAD(P)H-dependent quinone oxidoreductase; a ytfG gene product], which catalyzes two-electron reduction of methyl-1,4-benzoquinone, is a new type of quinone-reducing enzyme with distinct primary sequence and oligomeric conformation from previously known quinone oxidoreductases. The crystal structures of native QOR2 and the QOR2-NADPH (nicotinamide adenine dinucleotide phosphate, reduced form) complex reveal that QOR2 consists of two domains (N-domain and C-domain) resembling those of NmrA, a negative transcriptional regulator that belongs to the short-chain dehydrogenase/reductase family. The N-domain, which adopts the Rossmann fold, provides a platform for NADPH binding, whereas the C-domain, which contains a hydrophobic pocket connected to the NADPH-binding site, appears to play important roles in substrate binding. Asn143 near the NADPH-binding site has been identified to be involved in substrate binding and catalysis from structural and mutational analyses. Moreover, compared with wild-type strain, the qor2-overexpressing strain shows growth retardation and remarkable decrease in several enzymes involved in carbon metabolism, suggesting that QOR2 could play some physiological roles in addition to quinone reduction.
|-
!align=left |Links
||
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=18455185 PubMed]
Online version:[http://dx.doi.org/10.1016/j.jmb.2008.04.003 10.1016/j.jmb.2008.04.003]
|-
!align=left |Keywords
||
Amino Acid Sequence; Crystallography, X-Ray; DNA Mutational Analysis; Escherichia coli/enzymology; Escherichia coli Proteins/chemistry; Escherichia coli Proteins/genetics; Escherichia coli Proteins/metabolism; Fungal Proteins/chemistry; Fungal Proteins/genetics; Fungal Proteins/metabolism; Models, Molecular; Molecular Sequence Data; Mutagenesis, Site-Directed; NADP/chemistry; NADP/metabolism; Oxidation-Reduction; Protein Structure, Secondary; Protein Structure, Tertiary; Quinone Reductases/chemistry; Quinone Reductases/genetics; Quinone Reductases/metabolism; Recombinant Proteins/chemistry; Recombinant Proteins/genetics; Recombinant Proteins/metabolism; Repressor Proteins/chemistry; Repressor Proteins/genetics; Repressor Proteins/metabolism; Sequence Alignment

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|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.183563.Q539c5a122b5ca&page=183563&pagename={{FULLPAGENAMEE}}&type=1&template=PMID_info_table edit table] ||
|}


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

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

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<annotationlinks/>

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{{LitLinks}}

==See also==

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

PMID:18455185

2014-06-14T14:20:02Z

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PMID:1100394

2014-06-14T14:19:29Z

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{| id="C539c59f1715e0" class=" tableEdit PMID_info_table"

|-
!align=left |Citation
||
'''Schiltz, E and Reinbolt, J''' (1975) Determination of the complete amino-acid sequence of protein S4 from Escherichia coli ribosomes. ''Eur. J. Biochem.'' '''56''':467-81
|-
!align=left |Abstract
||
After digestion of protein S4 with trypsin, all 32 tryptic peptides were isolated. Their amino acid compositions were analyzed and the sequence of the amino acids within the tryptic peptides was determined by means of a solid-phase peptide sequenator and by exopeptidases. Alignment of the tryptic peptides was established by analyzing and partially sequencing peptides isolated after digestion of the S4 protein with chymotrypsin, thermolysin and a glutamic-acid-specific protease. Further information about the alignment of peptides came from treatment of S4 with CNBr and with a lysine-modifying reagent.
|-
!align=left |Links
||
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=1100394 PubMed]

|-
!align=left |Keywords
||
Amino Acid Sequence; Bacterial Proteins/analysis; Chymotrypsin; Cyanogen Bromide; Escherichia coli/analysis; Peptide Fragments/analysis; Ribosomal Proteins/analysis; Trypsin

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.183562.C539c59f1715e0&page=183562&pagename={{FULLPAGENAMEE}}&type=1&template=PMID_info_table edit table] ||
|}


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

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

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<annotationlinks/>

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{{LitLinks}}

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

PMID:1100394

2014-06-14T14:19:29Z

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PMID:2846509

2014-06-13T17:41:08Z

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{| id="J539b37b3e1583" class=" tableEdit PMID_info_table"

|-
!align=left |Citation
||
'''Forst, S, Delgado, J, Ramakrishnan, G and Inouye, M''' (1988) Regulation of ompC and ompF expression in Escherichia coli in the absence of envZ. ''J. Bacteriol.'' '''170''':5080-5
|-
!align=left |Abstract
||
The expression of the genes encoding the major outer membrane porin proteins OmpF and OmpC in Escherichia coli is regulated by ompR, which encodes the transcriptional activator protein OmpR, and envZ, which encodes a receptorlike protein located in the inner membrane. To examine the role of EnvZ in the expression of the osmoregulated porin genes, we analyzed the production of OmpF and OmpC in cells that lack envZ function. We show that EnvZ is required for the maximal production of OmpC in cells grown in minimal medium but is not essential for the efficient induction of OmpC that occurs during a shift to a high-osmolarity medium. In contrast, the production of OmpF in cells that lack envZ function was similar to that of the parent strain, whereas OmpF repression during a shift to a high-osmolarity medium was incomplete in the absence of EnvZ. These results are discussed in the context of the putative role of EnvZ in the expression of ompF and ompC.
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[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=2846509 PubMed] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC211574 PMC211574]

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!align=left |Keywords
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Bacterial Outer Membrane Proteins/biosynthesis; Bacterial Outer Membrane Proteins/genetics; Bacterial Outer Membrane Proteins/isolation & purification; Escherichia coli/genetics; Gene Expression Regulation; Genes; Genes, Bacterial; Plasmids; Porins; Transcription, Genetic

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PMID:2846509

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'''Manning, PA and Reeves, P''' (1976) Outer membrane of Escherichia coli K-12: TSX mutants (resistant to bacteriophage T6 and colicin K) lack an outer membrane protein. ''Biochem. Biophys. Res. Commun.'' '''71''':466-71
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!align=left |Abstract
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No abstract in PubMed
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!align=left |Links
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[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=786287 PubMed]

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!align=left |Keywords
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Bacterial Proteins/deficiency; Bacterial Proteins/metabolism; Cell Membrane/metabolism; Colicins/pharmacology; Coliphages/metabolism; Drug Resistance, Microbial; Escherichia coli/drug effects; Escherichia coli/metabolism; Mutation; Species Specificity

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

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<annotationlinks/>

==EcoliWiki Links {{HelpIcon|Help:Literature}} ==
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==References==
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PMID:786287

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PMID:9079899

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'''Moukadiri, I, Armero, J, Abad, A, Sentandreu, R and Zueco, J''' (1997) Identification of a mannoprotein present in the inner layer of the cell wall of Saccharomyces cerevisiae. ''J. Bacteriol.'' '''179''':2154-62
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!align=left |Abstract
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Cell wall extracts from the double-mutant mnn1 mnn9 strain were used as the immunogen to obtain a monoclonal antibody (MAb), SAC A6, that recognizes a specific mannoprotein--which we have named Icwp--in the walls of cells of Saccharomyces cerevisiae. Icwp runs as a polydisperse band of over 180 kDa in sodium dodecyl sulfate-polyacrylamide gel electrophoresis analysis of Zymolyase extracts of cell walls, although an analysis of the secretory pattern of the mannoprotein shows that at the level of secretory vesicles, it behaves like a discrete band of 140 kDa. Immunofluorescence analysis with the MAb showed that Icwp lies at the inner layer of the cell wall, being accessible to the antibody only after the outer layer of mannoproteins is disturbed by treatment with tunicamycin. The screening of a lambda gt11 expression library enabled us to identify the open reading frame (ORF) coding for Icwp. ICWP (EMBL accession number YLR391w, frame +3) codes for 238 amino acids, of which over 40% are serine or threonine, and contains a putative N-glycosylation site and a putative glycosylphosphatidylinositol attachment signal. Both disruption and overexpression of the ORF caused increased sensitivities to calcofluor white and Congo red, while the disruption caused an increased sensitivity to Zymolyase digestion, suggesting for Icwp a structural role in association with glucan.
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[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=9079899 PubMed] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC178950 PMC178950]

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!align=left |Keywords
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Antibodies, Monoclonal/immunology; Antigens, Fungal/genetics; Base Sequence; Cell Wall/chemistry; DNA, Complementary/genetics; Fungal Proteins/genetics; Genes, Fungal; Glycosylphosphatidylinositols; Membrane Glycoproteins/genetics; Membrane Glycoproteins/immunology; Membrane Glycoproteins/metabolism; Molecular Sequence Data; Mutagenesis, Insertional; Saccharomyces cerevisiae/chemistry; Saccharomyces cerevisiae/genetics; Saccharomyces cerevisiae/immunology; Saccharomyces cerevisiae Proteins

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PMID:9079899

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'''Lesnyak, DV, Sergiev, PV, Bogdanov, AA and Dontsova, OA''' (2006) Identification of Escherichia coli m2G methyltransferases: I. the ycbY gene encodes a methyltransferase specific for G2445 of the 23 S rRNA. ''J. Mol. Biol.'' '''364''':20-5
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!align=left |Abstract
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N2-methylguanosine 2445 of the 23 S rRNA is located in a cluster of modified nucleotides concentrated at the peptidyl transferase center of the ribosome. Here we describe the identification of a gene, ycbY, as encoding an enzyme responsible for methylation of G2445. Knock-out of the ycbY gene leads to loss of modification at G2445 as revealed by reverse transcription. The modification is restored in the ycbY knock-out strain if co-transformed with a plasmid expressing the ycbY gene product. Recombinant YcbY protein is able to methylate 23 S rRNA purified from the ycbY knock-out strain in vitro, assembled 50 S subunits are not a substrate for the methylase. Knock-out of the ycbY gene leads to growth retardation. Growth competition with the parental wild-type strain leads to a gradual decrease in the knock-out strain cells proportion in the media. It is likely that the G2445 modification is necessary for prevention of non-functional secondary or tertiary structure formation at the peptidyl transferase center. Based on these results we suggest that YcbY be renamed to RlmL in accordance with the accepted nomenclature for rRNA methyltransferases.
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[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=17010378 PubMed]
Online version:[http://dx.doi.org/10.1016/j.jmb.2006.09.009 10.1016/j.jmb.2006.09.009]
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!align=left |Keywords
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Base Sequence; Escherichia coli/enzymology; Escherichia coli/genetics; Escherichia coli Proteins/genetics; Escherichia coli Proteins/metabolism; Guanine/metabolism; Methyltransferases/genetics; Methyltransferases/metabolism; Molecular Structure; RNA, Ribosomal, 23S/genetics; RNA, Ribosomal, 23S/metabolism; Recombinant Proteins/genetics; Recombinant Proteins/metabolism

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

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PMID:17010378

2014-06-11T07:00:30Z

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