EcoliWiki - User contributions [en]

PMID:2254312

2008-02-07T23:35:30Z

165.91.10.100: New PMID: Page!

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 '''Gavini, N and Davidson, BE''' (1990) pheAo mutants of Escherichia coli have a defective pheA attenuator.''J. Biol. Chem.'' '''265''':21532-5

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|{{TableHeadingColor}} |'''Abstract''' || Two classes of mutants affecting the regulation of pheA expression in Escherichia coli have been reported previously: trans-acting mutants involving the locus pheR, and cis-acting mutants involving the locus pheAo. The effects of these mutants have been found to be mediated through one regulatory mechanism. The gene pheR has been shown to encode tRNA(Phe) (Gavini, N., and Davidson, B. E. (1990) J. Biol. Chem. 265, 21527-21531). In this paper we report the cloning and nucleotide sequencing of the promoter-attenuator regions from two of the cis-acting mutants pheAo351 and pheAo352. Both pheAo351 and pheAo352 contained a G:C to A:T base pair transition, at different positions in the 3:4 stem of the pheA attenuator terminator. Since these changes would destabilize the G:C stem of the attenuator terminator we propose that the enhanced expression of pheA observed in the pheAo mutants is due to increased transcription readthrough at the defective attenuator terminator.
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|{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=2254312 PubMed]
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!Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status
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PMID:11035800

2008-02-07T23:35:24Z

165.91.10.100: New PMID: Page!

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 '''Mohanty, BK and Kushner, SR''' (2000) Polynucleotide phosphorylase functions both as a 3' right-arrow 5' exonuclease and a poly(A) polymerase in Escherichia coli.''Proc. Natl. Acad. Sci. U.S.A.'' '''97''':11966-71

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|{{TableHeadingColor}} |'''Abstract''' || In vitro, polynucleotide phosphorylase of Escherichia coli can both synthesize RNA by using nucleotide diphosphates as precursors and exonucleolytically degrade RNA in the presence of inorganic phosphate. However, because of the high in vivo concentration of inorganic phosphate in exponentially growing cells, it has been assumed that the enzyme works exclusively as an exonuclease. Here we demonstrate that, contrary to this prediction, polynucleotide phosphorylase not only synthesizes long, highly heteropolymeric tails in vivo, but also accounts for all of the observed residual polyadenylylation in poly(A) polymerase I deficient strains. In addition, the enzyme is responsible for adding the C and U residues that are found in poly(A) tails in exponentially growing cultures of wild type E. coli.
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|{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11035800 PubMed]
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{|class = 'sortable' {{Prettytable}} id='241072'
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PMID:11090620

2008-02-07T23:35:19Z

165.91.10.100: New PMID: Page!

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 '''Cromie, GA and Leach, DR''' (2000) Control of crossing over.''Mol. Cell'' '''6''':815-26

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|{{TableHeadingColor}} |'''Abstract''' || The Holliday junction is a central intermediate in homologous recombination. It consists of a four-way structure that can be resolved by cleavage to give either the crossover or noncrossover products observed. We show here that the formation of these products is controlled by the E. coli resolvasome (RuvABC) in such way that double-strand break repair (DSBR) leads to crossing over and single-strand gap repair (SSGR) does not lead to crossing over. We argue that the positioning of the RuvABC complex and its consequent direction of junction-cleavage is not random. In fact, the action of the RuvABC complex avoids crossing over in the most commonly predicted situations where Holliday junctions are encountered in DNA replication and repair. Our observations suggest that the positioning of the resolvasome may provide a general biochemical mechanism by which cells can control crossing over in recombination.
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|{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11090620 PubMed]
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PMID:11092872

2008-02-07T23:35:13Z

165.91.10.100: New PMID: Page!

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 '''Egan, SM, Pease, AJ, Lang, J, Li, X, Rao, V, Gillette, WK, Ruiz, R, Ramos, JL and Wolf, RE''' (2000) Transcription activation by a variety of AraC/XylS family activators does not depend on the class II-specific activation determinant in the N-terminal domain of the RNA polymerase alpha subunit.''J. Bacteriol.'' '''182''':7075-7

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|{{TableHeadingColor}} |'''Abstract''' || The N-terminal domain of the RNA polymerase alpha subunit (alpha-NTD) was tested for a role in transcription activation by a variety of AraC/XylS family members. Based on substitutions at residues 162 to 165 and an extensive genetic screen we conclude that alpha-NTD is not an activation target for these activators.
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|{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11092872 PubMed]
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PMID:11377793

2008-02-07T23:34:58Z

165.91.10.100: New PMID: Page!

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 '''Aguilera, A''' (2001) Double-strand break repair: are Rad51/RecA--DNA joints barriers to DNA replication?''Trends Genet.'' '''17''':318-21

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|{{TableHeadingColor}} |'''Abstract''' || The central step of homologous recombination is the DNA strand exchange reaction catalyzed by bacterial RecA or eukaryotic Rad51. Besides Rad51-mediated synthesis-dependent strand annealing (SDSA), DNA ends can promote replication in Escherichia coli (recombination-dependent replication, RDR) and yeast (break-induced replication, BIR). However, what causes a DNA end to be repaired via SDSA or via BIR/RDR? I propose that Rad51/RecA--DNA plectonemic joints act as barriers to DNA replication and that BIR/RDR is only possible when the DNA polymerase that synthesizes DNA from the invading 3' end does not encounter RecA/Rad51--DNA joints in its path.
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|{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11377793 PubMed]
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PMID:11336819

2008-02-07T23:34:53Z

165.91.10.100: New PMID: Page!

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 '''Sargent, F''' (2001) A marriage of bacteriology with cell biology results in twin arginines.''Trends Microbiol.'' '''9''':196-8

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|{{TableHeadingColor}} |'''Abstract''' || The Tat apparatus is a remarkable molecular machine required for the transmembrane translocation of folded proteins. Recent studies have identified jellyfish green fluorescent protein as an excellent reporter protein for the bacterial Tat pathway. Although the genetics of the Tat system are reasonably well-defined in Escherichia coli, the utilization of heterologous proteins as transport substrates promises to facilitate further mechanistic and structural characterization of this system.
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|{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11336819 PubMed]
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PMID:11318649

2008-02-07T23:34:47Z

165.91.10.100: New PMID: Page!

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 '''Rothery, RA, Blasco, F and Weiner, JH''' (2001) Electron transfer from heme bL to the [3Fe-4S] cluster of Escherichia coli nitrate reductase A (NarGHI).''Biochemistry'' '''40''':5260-8

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|{{TableHeadingColor}} |'''Abstract''' || We have investigated the functional relationship between three of the prosthetic groups of Escherichia coli nitrate reductase A (NarGHI): the two hemes of the membrane anchor subunit (NarI) and the [3Fe-4S] cluster of the electron-transfer subunit (NarH). In two site-directed mutants (NarGHI(H56R) and NarGHI(H205Y)) that lack the highest potential heme of NarI (heme b(H)), a large negative DeltaE(m,7) is elicited on the NarH [3Fe-4S] cluster, suggesting a close juxtaposition of these two centers in the holoenzyme. In a mutant retaining heme b(H), but lacking heme b(L) (NarGHI(H66Y)), there is no effect on the NarH [3Fe-4S] cluster redox properties. These results suggest a role for heme b(H) in electron transfer to the [3Fe-4S] cluster. Studies of the pH dependence of the [3Fe-4S] cluster, heme b(H), and heme b(L) E(m) values suggest that significant deprotonation is only observed during oxidation of the latter heme (a pH dependence of -36 mV pH(-1)). In NarI expressed in the absence of NarGH [NarI(DeltaGH)], apparent exposure of heme b(H) to the aqueous milieu results in both it and heme b(L) having E(m) values with pH dependencies of approximately -30 mV pH(-1). These results are consistent with heme b(H) being isolated from the aqueous milieu and pH effects in the holoenzyme. Optical spectroscopy indicates that inhibitors such as HOQNO and stigmatellin bind and inhibit oxidation of heme b(L) but do not inhibit oxidation of heme b(H). Fluorescence quench titrations indicate that HOQNO binds with higher affinity to the reduced form of NarGHI than to the oxidized form. Overall, the data support the following model for electron transfer through the NarI region of NarGHI: Q(P) site --> heme b(L) --> heme b(H) --> [3Fe-4S] cluster.
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|{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11318649 PubMed]
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!Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status
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PMID:11341995

2008-02-07T23:34:41Z

165.91.10.100: New PMID: Page!

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 '''Walker, GC and Bridges, B''' (2001) Bryn Bridges and mutagenesis: exploring the intellectual space.''Mutat. Res.'' '''485''':69-81

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|{{TableHeadingColor}} |'''Abstract''' || The products of the SOS-regulated umuDC genes are required for most UV and chemical mutagenesis in Escherichia coli. Recently it has been recognized that UmuC is the founding member of a superfamily of novel DNA polymerases found in all three kingdoms of life. Key findings leading to these insights are reviewed, placing a particular emphasis on contributions made by Bryn Bridges and on his interest in the importance of interactions between the umuDC gene products and the replicative DNA polymerase.
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|{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11341995 PubMed]
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PMID:11350160

2008-02-07T23:34:35Z

165.91.10.100: New PMID: Page!

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 '''Falke, S, Fisher, MT and Gogol, EP''' (2001) Structural changes in GroEL effected by binding a denatured protein substrate.''J. Mol. Biol.'' '''308''':569-77

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|{{TableHeadingColor}} |'''Abstract''' || In the absence of nucleotides or cofactors, the Escherichia coli chaperonin GroEL binds select proteins in non-native conformations, such as denatured glutamine synthetase (GS) monomers, preventing their aggregation and spontaneous renaturation. The nature of the GroEL-GS complexes thus formed, specifically the effect on the conformation of the GroEL tetradecamer, has been examined by electron microscopy. We find that specimens of GroEL-GS are visibly heterogeneous, due to incomplete loading of GroEL with GS. Images contain particles indistinguishable from GroEL alone, and also those with consistent identifiable differences. Side-views of the modified particles reveal additional protein density at one end of the GroEL-GS complex, and end-views display chirality in the heptameric projection not seen in the unliganded GroEL. The coordinate appearance of these two projection differences suggests that binding of GS, as representative of a class of protein substrates, induces or stabilizes a conformation of GroEL that differs from the unliganded chaperonin. Three-dimensional reconstruction of the GroEL-GS complex reveals the location of the bound protein substrate, as well as complex conformational changes in GroEL itself, both cis and trans with respect to the bound GS. The most apparent structural alterations are inward movements of the apical domains of both GroEL heptamers, protrusion of the substrate protein from the cavity of the cis ring, and a narrowing of the unoccupied opening of the trans ring.
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|{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11350160 PubMed]
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!Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status
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PMID:11472091

2008-02-07T23:34:29Z

165.91.10.100: New PMID: Page!

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 '''Falke, S, Fisher, MT and Gogol, EP''' Classification and reconstruction of a heterogeneous set of electron microscopic images: a case study of GroEL-substrate complexes.''J. Struct. Biol.'' '''133''':203-13

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|{{TableHeadingColor}} |'''Abstract''' || Image analysis methods were used to separate images of a large macromolecular complex, the chaperonin GroEL, in a preparation in which it is partially liganded to a nonnative protein substrate, glutamine synthetase. The relatively small difference ( approximately 6%) in size between the chaperonin in its free and complexed forms, and the absence of gross changes in overall conformation, made separation of the two types of particles challenging. Different approaches were evaluated and used for alignment and classification of images, both in two common projections and in three dimensions, yielding 2D averages and a 3D reconstruction. The results of 3D analysis describe the conformational changes effected by binding of this particular protein substrate and demonstrate the utility of 2D analysis as an indicator of structural change in this system.
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|{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11472091 PubMed]
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!Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status
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PMID:11078742

2008-02-07T23:34:24Z

165.91.10.100: New PMID: Page!

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 '''Gao, D and McHenry, CS''' (2001) Tau binds and organizes Escherichia coli replication proteins through distinct domains. Domain III, shared by gamma and tau, binds delta delta ' and chi psi.''J. Biol. Chem.'' '''276''':4447-53

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|{{TableHeadingColor}} |'''Abstract''' || The DnaX complex of the DNA polymerase holoenzyme assembles the beta(2) processivity factor onto the primed template enabling highly processive replication. The key ATPases within this complex are tau and gamma, alternative frameshift products of the dnaX gene. Of the five domains of tau, I-III are shared with gamma In vivo, gamma binds the auxiliary subunits deltadelta' and chipsi (Glover, B. P., and McHenry, C. S. (2000) J. Biol. Chem. 275, 3017-3020). To localize deltadelta' and chipsi binding domains within gamma domains I-III, we measured the binding of purified biotin-tagged DnaX proteins lacking specific domains to deltadelta' and chipsi by surface plasmon resonance. Fusion proteins containing either DnaX domains I-III or domains III-V bound deltadelta' and chipsi subunits. A DnaX protein only containing domains I and II did not bind deltadelta' or chipsi. The binding affinity of chipsi for DnaX domains I-III and domains III-V was the same as that of chipsi for full-length tau, indicating that domain III contained all structural elements required for chipsi binding. Domain III of tau also contained deltadelta' binding sites, although the interaction between deltadelta' and domains III-V of tau was 10-fold weaker than the interaction between deltadelta' and full length tau. The presence of both delta and chipsi strengthened the delta'-C(0)tau interaction by at least 15-fold. Domain III was the only domain common to all of tau fusion proteins whose interaction with delta' was enhanced in the presence of delta and chipsi. Thus, domain III of the DnaX proteins not only contains the deltadelta' and chipsi binding sites but also contains the elements required for the positive cooperative assembly of the DnaX complex.
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|{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11078742 PubMed]
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!Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status
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PMID:11350161

2008-02-07T23:34:18Z

165.91.10.100: New PMID: Page!

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 '''German, GJ and Misra, R''' (2001) The TolC protein of Escherichia coli serves as a cell-surface receptor for the newly characterized TLS bacteriophage.''J. Mol. Biol.'' '''308''':579-85

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|{{TableHeadingColor}} |'''Abstract''' || The TolC protein of Escherichia coli is implicated in a variety of diverse cellular functions, including antibiotic efflux and alpha-hemolysin secretion. An incidental role of TolC is to facilitate the entry of the bacteriophage TLS and colicin E1 into the bacterial cell. Despite the resolution of TolC's atomic structure, the roles of specific residues in its diverse functions are unknown. Here, we describe a genetic strategy for isolating missense tolC mutations that abolish the bacteriophage receptor activity of the TolC protein without influencing its role in antibiotic efflux. These spontaneous mutations affected two regions of the TolC protein and included base-pair substitutions, insertions, and deletions. Comparison of the TolC sequence with those of its homologues revealed two hypervariable stretches that were predicted to represent loops. Interestingly, all but one of the TolC alterations preventing phage binding were located in these two hypervariable regions, which are likely to be exposed on the cell surface. This was substantiated by the recently solved three-dimensional structure of TolC. Curiously, all the phage-resistant TolC mutants showed varying degrees of resistance to colicin E1, suggesting the involvement of overlapping regions of TolC in colicin E1 import and phage binding.The phage used in this study, TLS, was earlier reported as a strain of U3. However, we show here that, unlike the previously reported lipopolysaccharide-specific U3 phage, this phage displays a distinctly different host range and discrete morphological features and, in addition to utilizing TolC as receptor, it requires the inner core of a lipopolysaccharide.
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|{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11350161 PubMed]
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<protect>

{|class = 'sortable' {{Prettytable}} id='241062'
|- {{table heading style}}
!Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status
|-class='sortbottom'
|[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.0.X47ab957a2434b&page=0&pagename={{FULLPAGENAMEE}} edit table] || || || || || || || ||
|}
</protect>

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

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

PMID:11459954

2008-02-07T23:34:12Z

165.91.10.100: New PMID: Page!

<protect>
{{RightTOC}}

 '''McCool, JD and Sandler, SJ''' (2001) Effects of mutations involving cell division, recombination, and chromosome dimer resolution on a priA2::kan mutant.''Proc. Natl. Acad. Sci. U.S.A.'' '''98''':8203-10

{|{{Prettytable}} align = 'center' width= '70%'
|-
|{{TableHeadingColor}} |'''Abstract''' || Recombinational repair of replication forks can occur either to a crossover (XO) or noncrossover (non-XO) depending on Holliday junction resolution. Once the fork is repaired by recombination, PriA is important for restarting these forks in Escherichia coli. PriA mutants are Rec(-) and UV sensitive and have poor viability and 10-fold elevated basal levels of SOS expression. PriA sulB mutant cells and their nucleoids were studied by differential interference contrast and fluorescence microscopy of 4',6-diamidino-2-phenylindole-stained log phase cells. Two populations of cells were seen. Eighty four percent appeared like wild type, and 16% of the cells were filamented and had poorly partitioned chromosomes (Par(-)). To probe potential mechanisms leading to the two populations of cells, mutations were added to the priA sulB mutant. Mutating sulA or introducing lexA3 decreased, but did not eliminate filamentation or defects in partitioning. Mutating either recA or recB virtually eliminated the Par(-) phenotype. Filamentation in the recB mutant decreased to 3%, but increased to 28% in the recA mutant. The ability to resolve and/or branch migrate Holliday junctions also appeared crucial in the priA mutant because removing either recG or ruvC was lethal. Lastly, it was tested whether the ability to resolve chromosome dimers caused by XOs was important in a priA mutant by mutating dif and the C-terminal portion of ftsK. Mutation of dif showed no change in phenotype whereas ftsK1cat was lethal with priA2kan. A model is proposed where the PriA-independent pathway of replication restart functions at forks that have been repaired to non-XOs.
</noinclude>
|-
|{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11459954 PubMed]
|}
</protect>
==Significance {{HelpIcon|Help:Literature}} ==
{{LitSignificance}}

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

==Annotations {{HelpIcon|Help:Literature}}==
<protect>

{|class = 'sortable' {{Prettytable}} id='241061'
|- {{table heading style}}
!Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status
|-class='sortbottom'
|[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.0.S47ab957461378&page=0&pagename={{FULLPAGENAMEE}} edit table] || || || || || || || ||
|}
</protect>

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

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

PMID:15954614

2008-02-07T23:34:06Z

165.91.10.100: New PMID: Page!

<protect>
{{RightTOC}}

 '''Vandedrinck, S, Deschamps, G, Sablon, E and Vandamme, EJ''' (2001) Metabolic engineering of Escherichia coli: construction and characterization of a gltA (citrate synthase) knockout mutant.''Meded Rijksuniv Gent Fak Landbouwkd Toegep Biol Wet'' '''66''':333-6

{|{{Prettytable}} align = 'center' width= '70%'
|-
|{{TableHeadingColor}} |'''Abstract''' || E. coli is one of the most important host organisms for recombinant protein production. However, growth and recombinant protein production can be limited by acetate accumulation during high-cell-density fermentations. Some of the strategies used to overcome this problem are based on the alteration of the genotype of the host. This paper discusses the construction and characterization of an E. coli gltA- knockout mutant. The knockout of the gene was confirmed by the loss of citrate synthase activity in an enzyme assay. Also the growth rate of the mutant on Luria Broth and Luria Broth + acetate was reduced.
</noinclude>
|-
|{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15954614 PubMed]
|}
</protect>
==Significance {{HelpIcon|Help:Literature}} ==
{{LitSignificance}}

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

==Annotations {{HelpIcon|Help:Literature}}==
<protect>

{|class = 'sortable' {{Prettytable}} id='241060'
|- {{table heading style}}
!Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status
|-class='sortbottom'
|[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.0.A47ab956ea330e&page=0&pagename={{FULLPAGENAMEE}} edit table] || || || || || || || ||
|}
</protect>

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

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

PMID:11714930

2008-02-07T23:33:55Z

165.91.10.100: New PMID: Page!

<protect>
{{RightTOC}}

 '''Weaver, LH, Kwon, K, Beckett, D and Matthews, BW''' (2001) Competing protein:protein interactions are proposed to control the biological switch of the E coli biotin repressor.''Protein Sci.'' '''10''':2618-22

{|{{Prettytable}} align = 'center' width= '70%'
|-
|{{TableHeadingColor}} |'''Abstract''' || A model is suggested for the complex between the biotin repressor of Escherichia coli, BirA, and BCCP, the biotin carboxyl carrier protein to which BirA transfers biotin. The model is consistent with prior physical and biochemical studies. Measurement of transfer rates for variants of BirA with single-site mutations in the proposed BirA:BCCP interface region also provides support. The unique feature of the proposed interaction between BirA and BCCP is that it uses the same beta-sheet region on the surface of BirA that the protein uses for homodimerization into a form competent to bind DNA. The resulting mutually exclusive protein:protein interfaces explain the novel feature of the BirA regulatory system, namely, that transcription of the genes involved in biotin synthesis is not determined by the level of biotin, per se, but by the level of unmodified BCCP. The model also provides a role for the C-terminal domain of BirA that is structurally similar to an SH3 domain.
</noinclude>
|-
|{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11714930 PubMed]
|}
</protect>
==Significance {{HelpIcon|Help:Literature}} ==
{{LitSignificance}}

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

==Annotations {{HelpIcon|Help:Literature}}==
<protect>

{|class = 'sortable' {{Prettytable}} id='241059'
|- {{table heading style}}
!Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status
|-class='sortbottom'
|[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.0.T47ab9563a13bb&page=0&pagename={{FULLPAGENAMEE}} edit table] || || || || || || || ||
|}
</protect>

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

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

PMID:11120740

2008-02-07T23:33:50Z

165.91.10.100: New PMID: Page!

<protect>
{{RightTOC}}

 '''Schurmann, M and Sprenger, GA''' (2001) Fructose-6-phosphate aldolase is a novel class I aldolase from Escherichia coli and is related to a novel group of bacterial transaldolases.''J. Biol. Chem.'' '''276''':11055-61

{|{{Prettytable}} align = 'center' width= '70%'
|-
|{{TableHeadingColor}} |'''Abstract''' || We have cloned an open reading frame from the Escherichia coli K-12 chromosome that had been assumed earlier to be a transaldolase or a transaldolase-related protein, termed MipB. Here we show that instead a novel enzyme activity, fructose-6-phosphate aldolase, is encoded by this open reading frame, which is the first report of an enzyme that catalyzes an aldol cleavage of fructose 6-phosphate from any organism. We propose the name FSA (for fructose-six phosphate aldolase; gene name fsa). The recombinant protein was purified to apparent homogeneity by anion exchange and gel permeation chromatography with a yield of 40 mg of protein from 1 liter of culture. By using electrospray tandem mass spectroscopy, a molecular weight of 22,998 per subunit was determined. From gel filtration a size of 257,000 (+/- 20,000) was calculated. The enzyme most likely forms either a decamer or dodecamer of identical subunits. The purified enzyme displayed a V(max) of 7 units mg(-)1 of protein for fructose 6-phosphate cleavage (at 30 degrees C, pH 8.5 in 50 mm glycylglycine buffer). For the aldolization reaction a V(max) of 45 units mg(-)1 of protein was found; K(m) values for the substrates were 9 mm for fructose 6-phosphate, 35 mm for dihydroxyacetone, and 0.8 mm for glyceraldehyde 3-phosphate. FSA did not utilize fructose, fructose 1-phosphate, fructose 1,6-bisphosphate, or dihydroxyacetone phosphate. FSA is not inhibited by EDTA which points to a metal-independent mode of action. The lysine 85 residue is essential for its action as its exchange to arginine (K85R) resulted in complete loss of activity in line with the assumption that the reaction mechanism involves a Schiff base formation through this lysine residue (class I aldolase). Another fsa-related gene, talC of Escherichia coli, was shown to also encode fructose-6-phosphate aldolase activity and not a transaldolase as proposed earlier.
</noinclude>
|-
|{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11120740 PubMed]
|}
</protect>
==Significance {{HelpIcon|Help:Literature}} ==
{{LitSignificance}}

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

==Annotations {{HelpIcon|Help:Literature}}==
<protect>

{|class = 'sortable' {{Prettytable}} id='241058'
|- {{table heading style}}
!Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status
|-class='sortbottom'
|[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.0.S47ab955dd4436&page=0&pagename={{FULLPAGENAMEE}} edit table] || || || || || || || ||
|}
</protect>

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

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

PMID:11318871

2008-02-07T23:33:42Z

165.91.10.100: New PMID: Page!

<protect>
{{RightTOC}}

 '''Yamanaka, K and Inouye, M''' (2001) Induction of CspA, an E. coli major cold-shock protein, upon nutritional upshift at 37 degrees C.''Genes Cells'' '''6''':279-90

{|{{Prettytable}} align = 'center' width= '70%'
|-
|{{TableHeadingColor}} |'''Abstract''' || BACKGROUND: The synthesis of CspA, the major cold-shock protein of Escherichia coli, is dramatically induced upon cold shock. It was recently reported that there is massive presence of CspA under nonstress conditions, and it is thus claimed that CspA as the cold-shock protein is a misnomer. RESULTS: Here, we re-examined and confirmed that CspA is induced upon culture dilution at 37 degrees C. However, its induction level is one-sixth of the cold-shock-induced level, clearly indicating that the major stress that induces CspA is cold shock. It was further found that CspA induction can be achieved not only by culture dilution but also by the simple addition of nutrients, and that it was almost completely abolished in the presence of rifampicin or nalidixic acid. Nutritional upshift causes the induction of only CspA but not other cold-shock-inducible CspA homologues. The amount of cspA mRNA rapidly and transiently increased by culture dilution, but its stability was not significantly changed. CONCLUSIONS: These results suggest that CspA is a nutritional-upshift stress protein as well as a cold-shock stress protein, and that CspA induction following nutritional upshift may be due to transcriptional activation.
</noinclude>
|-
|{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11318871 PubMed]
|}
</protect>
==Significance {{HelpIcon|Help:Literature}} ==
{{LitSignificance}}

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

==Annotations {{HelpIcon|Help:Literature}}==
<protect>

{|class = 'sortable' {{Prettytable}} id='241057'
|- {{table heading style}}
!Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status
|-class='sortbottom'
|[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.0.N47ab955636ddb&page=0&pagename={{FULLPAGENAMEE}} edit table] || || || || || || || ||
|}
</protect>

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

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

PMID:11459953

2008-02-07T23:33:36Z

165.91.10.100: New PMID: Page!

<protect>
{{RightTOC}}

 '''Courcelle, J and Hanawalt, PC''' (2001) Participation of recombination proteins in rescue of arrested replication forks in UV-irradiated Escherichia coli need not involve recombination.''Proc. Natl. Acad. Sci. U.S.A.'' '''98''':8196-202

{|{{Prettytable}} align = 'center' width= '70%'
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|{{TableHeadingColor}} |'''Abstract''' || Alternative reproductive cycles make use of different strategies to generate different reproductive products. In Escherichia coli, recA and several other rec genes are required for the generation of recombinant genomes during Hfr conjugation. During normal asexual reproduction, many of these same genes are needed to generate clonal products from UV-irradiated cells. However, unlike conjugation, this latter process also requires the function of the nucleotide excision repair genes. Following UV irradiation, the recovery of DNA replication requires uvrA and uvrC, as well as recA, recF, and recR. The rec genes appear to be required to protect and maintain replication forks that are arrested at DNA lesions, based on the extensive degradation of the nascent DNA that occurs in their absence. The products of the recJ and recQ genes process the blocked replication forks before the resumption of replication and may affect the fidelity of the recovery process. We discuss a model in which several rec gene products process replication forks arrested by DNA damage to facilitate the repair of the blocking DNA lesions by nucleotide excision repair, thereby allowing processive replication to resume with no need for strand exchanges or recombination. The poor survival of cellular populations that depend on recombinational pathways (compared with that in their excision repair proficient counterparts) suggests that at least some of the rec genes may be designed to function together with nucleotide excision repair in a common and predominant pathway by which cells faithfully recover replication and survive following UV-induced DNA damage.
</noinclude>
|-
|{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11459953 PubMed]
|}
</protect>
==Significance {{HelpIcon|Help:Literature}} ==
{{LitSignificance}}

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

==Annotations {{HelpIcon|Help:Literature}}==
<protect>

{|class = 'sortable' {{Prettytable}} id='241056'
|- {{table heading style}}
!Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status
|-class='sortbottom'
|[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.0.E47ab955070ce4&page=0&pagename={{FULLPAGENAMEE}} edit table] || || || || || || || ||
|}
</protect>

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

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

PMID:11391469

2008-02-07T23:33:30Z

165.91.10.100: New PMID: Page!

<protect>
{{RightTOC}}

 '''Ammons, D and Rampersad, J''' (2001) An E. coli 5S rRNA deletion mutant useful for the study of 5S rRNA structure/function relationships.''Curr. Microbiol.'' '''43''':89-92

{|{{Prettytable}} align = 'center' width= '70%'
|-
|{{TableHeadingColor}} |'''Abstract''' || We report on the construction of a novel strain of E. coli that can be useful for studies on the structure/function relationship of 5S rRNAs. The bacterial strain is deficient in six of the eight naturally occurring 5S rRNA genes (operons B, D, H, G, E) and demonstrates a greatly reduced growth rate that can be compensated by the plasmid-encoded expression of 5S rRNA. The relatively large difference in growth rate between compensated and non-compensated mutants provides the basis for a quick and simple assaying system for both the evaluation and mass screening of divergent 5S rRNA sequences for function. We describe the construction of the 5S rRNA deletion mutant BDHGE and characterize the usefulness and limitations of the system for evaluating structure/function relationships of 5S rRNA sequence.
</noinclude>
|-
|{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11391469 PubMed]
|}
</protect>
==Significance {{HelpIcon|Help:Literature}} ==
{{LitSignificance}}

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

==Annotations {{HelpIcon|Help:Literature}}==
<protect>

{|class = 'sortable' {{Prettytable}} id='241055'
|- {{table heading style}}
!Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status
|-class='sortbottom'
|[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.0.X47ab954aae25e&page=0&pagename={{FULLPAGENAMEE}} edit table] || || || || || || || ||
|}
</protect>

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

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

PMID:11257015

2008-02-07T23:33:25Z

165.91.10.100: New PMID: Page!

<protect>
{{RightTOC}}

 '''Apfel, CM, Evers, S, Hubschwerlen, C, Pirson, W, Page, MG and Keck, W''' (2001) Peptide deformylase as an antibacterial drug target: assays for detection of its inhibition in Escherichia coli cell homogenates and intact cells.''Antimicrob. Agents Chemother.'' '''45''':1053-7

{|{{Prettytable}} align = 'center' width= '70%'
|-
|{{TableHeadingColor}} |'''Abstract''' || An assay was developed to determine the activity of peptide deformylase (PDF) inhibitors under conditions as close as possible to the physiological situation. The assay principle is the detection of N-terminal [35S]methionine labeling of a protein that contains no internal methionine. If PDF is active, the deformylation of the methionine renders the peptide a substrate for methionine aminopeptidase, resulting in the removal of the N-terminal methionine label. In the presence of a PDF inhibitor, the deformylation is blocked so that the N-formylated peptide is not processed and the label is detected. Using this assay, it is possible to determine the PDF activity under near-physiological conditions in a cell-free transcription-translation system as well as in intact bacterial cells.
</noinclude>
|-
|{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11257015 PubMed]
|}
</protect>
==Significance {{HelpIcon|Help:Literature}} ==
{{LitSignificance}}

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

==Annotations {{HelpIcon|Help:Literature}}==
<protect>

{|class = 'sortable' {{Prettytable}} id='241054'
|- {{table heading style}}
!Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status
|-class='sortbottom'
|[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.0.G47ab954501938&page=0&pagename={{FULLPAGENAMEE}} edit table] || || || || || || || ||
|}
</protect>

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

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

PMID:11695827

2008-02-07T23:33:19Z

165.91.10.100: New PMID: Page!

<protect>
{{RightTOC}}

 '''Steuber, J''' (2001) The Na+-translocating NADH:quinone oxidoreductase (NDH I) from Klebsiella pneumoniae and Escherichia coli: implications for the mechanism of redox-driven cation translocation by complex I.''J. Bioenerg. Biomembr.'' '''33''':179-86

{|{{Prettytable}} align = 'center' width= '70%'
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|{{TableHeadingColor}} |'''Abstract''' || Eukaryotic complex I integrated into the respiratory chain transports at least 4 H+ per NADH oxidized. Recent results indicate that the cation selectivity is altered to Na+ in complex I (NDH I) isolated from the enterobacteria Escherichia coli and Klebsiella pneumoniae. A sequence analysis illustrates the characteristic differences of the enterobacterial, Na+-translocating NDH I compared to the H+-translocating complex I from mitochondria. Special attention is given to the membranous NuoL (ND5, Nqo12) subunits that possess striking sequence similarities to secondary Na+/H+ antiporters and are proposed to participate in Na+ transport. A model of redox-linked Na+ (or H+) transport by complex I is discussed based on the ion-pair formation of a negatively charged ubisemiquinone anion with a positively charged Na+ (or H+).
</noinclude>
|-
|{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11695827 PubMed]
|}
</protect>
==Significance {{HelpIcon|Help:Literature}} ==
{{LitSignificance}}

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

==Annotations {{HelpIcon|Help:Literature}}==
<protect>

{|class = 'sortable' {{Prettytable}} id='241053'
|- {{table heading style}}
!Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status
|-class='sortbottom'
|[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.0.P47ab953f3fea0&page=0&pagename={{FULLPAGENAMEE}} edit table] || || || || || || || ||
|}
</protect>

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

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

PMID:12762053

2008-02-07T23:33:13Z

165.91.10.100: New PMID: Page!

<protect>
{{RightTOC}}

 '''Agafonov, DE, Kolb, VA and Spirin, AS''' (2001) A novel stress-response protein that binds at the ribosomal subunit interface and arrests translation.''Cold Spring Harb. Symp. Quant. Biol.'' '''66''':509-14

{|{{Prettytable}} align = 'center' width= '70%'
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|{{TableHeadingColor}} |'''Abstract''' || No abstract in PubMed
</noinclude>
|-
|{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=12762053 PubMed]
|}
</protect>
==Significance {{HelpIcon|Help:Literature}} ==
{{LitSignificance}}

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

==Annotations {{HelpIcon|Help:Literature}}==
<protect>

{|class = 'sortable' {{Prettytable}} id='241052'
|- {{table heading style}}
!Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status
|-class='sortbottom'
|[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.0.S47ab953972b32&page=0&pagename={{FULLPAGENAMEE}} edit table] || || || || || || || ||
|}
</protect>

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

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

PMID:11601855

2008-02-07T23:33:07Z

165.91.10.100: New PMID: Page!

<protect>
{{RightTOC}}

 '''Leeds, JA, Boyd, D, Huber, DR, Sonoda, GK, Luu, HT, Engelman, DM and Beckwith, J''' (2001) Genetic selection for and molecular dynamic modeling of a protein transmembrane domain multimerization motif from a random Escherichia coli genomic library.''J. Mol. Biol.'' '''313''':181-95

{|{{Prettytable}} align = 'center' width= '70%'
|-
|{{TableHeadingColor}} |'''Abstract''' || In order to identify new transmembrane helix packing motifs in naturally occurring proteins, we have selected transmembrane domains from a library of random Escherichia coli genomic DNA fragments and screened them for homomultimerization via their abilities to dimerize the bacteriophage lambda cI repressor DNA-binding domain. Sequences were isolated using a modified lambda cI headpiece dimerization assay system, which was shown previously to measure transmembrane helix-helix association in the E. coli inner membrane. Screening resulted in the identification of several novel sequences that appear to mediate helix-helix interactions. One sequence, representing the predicted sixth transmembrane domain (TM6) of the E. coli protein YjiO, was chosen for further analysis. Using site-directed mutagenesis and molecular dynamics, a small set of models for YjiO TM6 multimerization interface interactions were generated. This work demonstrates the utility of combining in vivo genetic tools with computational systems for understanding membrane protein structure and assembly.
</noinclude>
|-
|{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11601855 PubMed]
|}
</protect>
==Significance {{HelpIcon|Help:Literature}} ==
{{LitSignificance}}

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

==Annotations {{HelpIcon|Help:Literature}}==
<protect>

{|class = 'sortable' {{Prettytable}} id='241051'
|- {{table heading style}}
!Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status
|-class='sortbottom'
|[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.0.E47ab9533a9d84&page=0&pagename={{FULLPAGENAMEE}} edit table] || || || || || || || ||
|}
</protect>

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

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

PMID:11513803

2008-02-07T23:33:01Z

165.91.10.100: New PMID: Page!

<protect>
{{RightTOC}}

 '''Nachliel, E and Gutman, M''' (2001) Probing of the substrate binding domain of lactose permease by a proton pulse.''Biochim. Biophys. Acta'' '''1514''':33-50

{|{{Prettytable}} align = 'center' width= '70%'
|-
|{{TableHeadingColor}} |'''Abstract''' || The lactose permease of Escherichia coli coupled proton transfer across the bacterial inner membrane with the uptake of beta-galactosides. In the present study we have used the cysteine-less C148 mutant that was selectively labeled by fluorescein maleimide on the C148 residue, which is an active component of the substrate transporting cavity. Measurements of the protonation dynamics of the bound pH indicator in the time resolved domain allowed us to probe the binding site by a free diffusing proton. The measured signal was reconstructed by numeric integration of differential rate equations that comply with the detailed balance principle and account for all proton transfer reactions taking place in the reaction mixture. This analysis yields the rate constants and pK values of all residues participating in the fast proton transfer reaction between the bulk and the protein's surface, revealing the exposed residues that react with free protons in a diffusion controlled reaction and how they transfer protons among themselves. The magnitudes of these rate constants were finally evaluated by comparison with the rate predicted by the Debye-Smoluchowski equation. The analysis of the kinetic and pK values indicated that the protein-fluorescein adduct assumes two conformation states. One is dominant above pH 7.4, while the other exists only below 7.1. In the high pH range, the enzyme assumes a constrained configuration and the rate constant of the reaction of a free diffusing proton with the bound dye is 10 times slower than a diffusion controlled reaction. In this state, the carboxylate moiety of residue E126 is in close proximity to the dye and exchanges a proton with it at a very fast rate. Below pH 7.1, the substrate binding domain is in a relaxed configuration and freely accessed by bulk protons, and the rate of proton exchange between the dye and E126 is 100,000 times slower. The relevance of these observations to the catalytic cycle is discussed.
</noinclude>
|-
|{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11513803 PubMed]
|}
</protect>
==Significance {{HelpIcon|Help:Literature}} ==
{{LitSignificance}}

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

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<protect>

{|class = 'sortable' {{Prettytable}} id='241050'
|- {{table heading style}}
!Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status
|-class='sortbottom'
|[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.0.J47ab952d592ef&page=0&pagename={{FULLPAGENAMEE}} edit table] || || || || || || || ||
|}
</protect>

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

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

PMID:11495922

2008-02-07T23:32:55Z

165.91.10.100: New PMID: Page!

<protect>
{{RightTOC}}

 '''Cronan, JE''' (2001) The biotinyl domain of Escherichia coli acetyl-CoA carboxylase. Evidence that the "thumb" structure id essential and that the domain functions as a dimer.''J. Biol. Chem.'' '''276''':37355-64

{|{{Prettytable}} align = 'center' width= '70%'
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|{{TableHeadingColor}} |'''Abstract''' || Biotin carboxyl carrier protein (BCCP) is the small biotinylated subunit of Escherichia coli acetyl-CoA carboxylase (ACC), the enzyme that catalyzes the first committed step of fatty acid synthesis. Similar proteins are found in other bacteria and in chloroplasts. E. coli BCCP is a member of a large family of protein domains modified by covalent attachment of biotin to a specific lysine residue. However, the BCCP biotinyl domain differs from many of these proteins in that an eight-amino acid residue insertion is present upstream of the biotinylated lysine. X-ray crystallographic and multidimensional NMR studies show that these residues constitute a structure that has the appearance of an extended thumb that protrudes from the otherwise highly symmetrical domain structure. I report that expression of two mutant BCCPs lacking the thumb residues fails to restore growth and fatty acid synthesis to a temperature-sensitive E. coli strain that lacks BCCP when grown at nonpermissive temperature. Alignment of BCCPs from various organisms shows that only two of the eight thumb residues are strictly conserved, and amino acid substitution of either residue results in proteins giving only weak growth of the temperature-sensitive E. coli strain. Therefore, the thumb structure is essential for the function of BCCP in the ACC reaction and provides a useful motif for distinguishing the biotinylated proteins of multisubunit ACCs from those of enzymes catalyzing other biotin-dependent reactions. An unexpected result was that expression of a mutant BCCP in which the biotinylated lysine residue was substituted with cysteine was able to partially restore growth and fatty acid synthesis to the temperature-sensitive E. coli strain. This complementation was shown to be specific to BCCPs having native structure (excepting the biotinylated lysine) and is interpreted in terms of dimerization of the BCCP biotinyl domain during the ACC reaction.
</noinclude>
|-
|{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11495922 PubMed]
|}
</protect>
==Significance {{HelpIcon|Help:Literature}} ==
{{LitSignificance}}

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{{LitMaterials}}

==Annotations {{HelpIcon|Help:Literature}}==
<protect>

{|class = 'sortable' {{Prettytable}} id='241049'
|- {{table heading style}}
!Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status
|-class='sortbottom'
|[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.0.A47ab952793b40&page=0&pagename={{FULLPAGENAMEE}} edit table] || || || || || || || ||
|}
</protect>

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

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

PMID:11717276

2008-02-07T23:32:50Z

165.91.10.100: New PMID: Page!

<protect>
{{RightTOC}}

 '''Seaver, LC and Imlay, JA''' (2001) Alkyl hydroperoxide reductase is the primary scavenger of endogenous hydrogen peroxide in Escherichia coli.''J. Bacteriol.'' '''183''':7173-81

{|{{Prettytable}} align = 'center' width= '70%'
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|{{TableHeadingColor}} |'''Abstract''' || Hydrogen peroxide is generated during aerobic metabolism and is capable of damaging critical biomolecules. However, mutants of Escherichia coli that are devoid of catalase typically exhibit no adverse phenotypes during growth in aerobic media. We discovered that catalase mutants retain the ability to rapidly scavenge H(2)O(2) whether it is formed internally or provided exogenously. Analysis of candidate genes revealed that the residual activity is due to alkyl hydroperoxide reductase (Ahp). Mutants that lack both Ahp and catalase could not scavenge H(2)O(2). These mutants excreted substantial amounts of H(2)O(2), and they grew poorly in air. Ahp is kinetically a more efficient scavenger of trace H(2)O(2) than is catalase and therefore is likely to be the primary scavenger of endogenous H(2)O(2). Accordingly, mutants that lack Ahp accumulated sufficient hydrogen peroxide to induce the OxyR regulon, whereas the OxyR regulon remained off in catalase mutants. Catalase still has an important role in wild-type cells, because the activity of Ahp is saturated at a low (10(-5) M) concentration of H(2)O(2). In contrast, catalase has a high K(m), and it therefore becomes the predominant scavenger when H(2)O(2) concentrations are high. This arrangement is reasonable because the cell cannot provide enough NADH for Ahp to rapidly degrade large amounts of H(2)O(2). In sum, E. coli does indeed generate substantial H(2)O(2), but damage is averted by the scavenging activity of Ahp.
</noinclude>
|-
|{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11717276 PubMed]
|}
</protect>
==Significance {{HelpIcon|Help:Literature}} ==
{{LitSignificance}}

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

==Annotations {{HelpIcon|Help:Literature}}==
<protect>

{|class = 'sortable' {{Prettytable}} id='241048'
|- {{table heading style}}
!Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status
|-class='sortbottom'
|[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.0.O47ab9521d398f&page=0&pagename={{FULLPAGENAMEE}} edit table] || || || || || || || ||
|}
</protect>

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

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

PMID:11315567

2008-02-07T23:32:44Z

165.91.10.100: New PMID: Page!

<protect>
{{RightTOC}}

 '''Högbom, M, Andersson, ME and Nordlund, P''' (2001) Crystal structures of oxidized dinuclear manganese centres in Mn-substituted class I ribonucleotide reductase from Escherichia coli: carboxylate shifts with implications for O2 activation and radical generation.''J. Biol. Inorg. Chem.'' '''6''':315-23

{|{{Prettytable}} align = 'center' width= '70%'
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|{{TableHeadingColor}} |'''Abstract''' || The di-iron carboxylate proteins constitute a diverse class of non-heme iron enzymes performing a multitude of redox reactions. These reactions usually involve high-valent Fe-oxo species and are thought to be controlled by carboxylate shifts. Owing to their short lifetime, the intermediate structures have so far escaped structural characterization by X-ray crystallography. In an attempt to map the carboxylate conformations available to the protein during different redox states and different ligand environments, we have studied metal-substituted forms of the R2 protein of ribonucleotide reductase from Escherichia coli. In the present work we have solved the crystal structures of Mn-substituted R2 oxidized in two different ways. Oxidation was performed using either nitric oxide or a combination of hydrogen peroxide and hydroxylamine. The two structures are virtually identical, indicating that the oxidation states are the same, most likely a mixed-valent MnII-MnIII centre. One of the carboxylate ligands (D84) adopts a new, so far unseen, conformation, which could participate in the mechanism for radical generation in R2. E238 adopts a bridging-chelating conformation proposed to be important for proper O2 activation but not previously observed in the wild-type enzyme. Probable catalase activity was also observed during the oxidation with H2O2, indicating mechanistic similarities to the di-Mn catalases.
</noinclude>
|-
|{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11315567 PubMed]
|}
</protect>
==Significance {{HelpIcon|Help:Literature}} ==
{{LitSignificance}}

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

==Annotations {{HelpIcon|Help:Literature}}==
<protect>

{|class = 'sortable' {{Prettytable}} id='241047'
|- {{table heading style}}
!Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status
|-class='sortbottom'
|[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.0.Y47ab951c211a5&page=0&pagename={{FULLPAGENAMEE}} edit table] || || || || || || || ||
|}
</protect>

==EcoliWiki Links {{HelpIcon|Help:Literature}} ==
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==References==
{{RefHelp}}
<references/>

PMID:11344330

2008-02-07T23:32:38Z

165.91.10.100: New PMID: Page!

<protect>
{{RightTOC}}

 '''Fox, JD, Kapust, RB and Waugh, DS''' (2001) Single amino acid substitutions on the surface of Escherichia coli maltose-binding protein can have a profound impact on the solubility of fusion proteins.''Protein Sci.'' '''10''':622-30

{|{{Prettytable}} align = 'center' width= '70%'
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|{{TableHeadingColor}} |'''Abstract''' || Proteins are commonly fused to Escherichia coli maltose-binding protein (MBP) to enhance their yield and facilitate their purification. In addition, the stability and solubility of a passenger protein can often be improved by fusing it to MBP. In a previous comparison with two other highly soluble fusion partners, MBP was decidedly superior at promoting the solubility of a range of aggregation-prone proteins. To explain this observation, we proposed that MBP could function as a general molecular chaperone in the context of a fusion protein by binding to aggregation-prone folding intermediates of passenger proteins and preventing their self-association. The ligand-binding cleft in MBP was considered a likely site for peptide binding because of its hydrophobic nature. We tested this hypothesis by systematically replacing hydrophobic amino acid side chains in and around the cleft with glutamic acid. None of these mutations affected the yield or solubility of MBP in its unfused state. Each MBP was then tested for its ability to promote solubility when fused to three passenger proteins: green fluorescent protein, p16, and E6. Mutations within the maltose-binding cleft (W62E, A63E, Y155E, W230E, and W340E) had little or no effect on the solubility of the fusion proteins. In contrast, three mutations near one end of the cleft (W232E, Y242E, and I317E) dramatically reduced the solubility of the same fusion proteins. The mutations with the most profound effect on solubility were shown to reduce the global stability of MBP.
</noinclude>
|-
|{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11344330 PubMed]
|}
</protect>
==Significance {{HelpIcon|Help:Literature}} ==
{{LitSignificance}}

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{{LitMaterials}}

==Annotations {{HelpIcon|Help:Literature}}==
<protect>

{|class = 'sortable' {{Prettytable}} id='241046'
|- {{table heading style}}
!Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status
|-class='sortbottom'
|[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.0.Q47ab95166409a&page=0&pagename={{FULLPAGENAMEE}} edit table] || || || || || || || ||
|}
</protect>

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

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

PMID:11544193

2008-02-07T23:32:32Z

165.91.10.100: New PMID: Page!

<protect>
{{RightTOC}}

 '''Tsoka, S and Ouzounis, CA''' (2001) Functional versatility and molecular diversity of the metabolic map of Escherichia coli.''Genome Res.'' '''11''':1503-10

{|{{Prettytable}} align = 'center' width= '70%'
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|{{TableHeadingColor}} |'''Abstract''' || We have analyzed the known metabolic enzymes of Escherichia coli in relation to their biochemical reaction properties and their involvement in biochemical pathways. All enzymes involved in small-molecule metabolism and their corresponding protein sequences have been extracted from the EcoCyc database. These 548 metabolic enzymes are clustered into 405 protein families according to sequence similarity. In this study, we examine the functional versatility within enzyme families in terms of their reaction capabilities and pathway participation. In addition, we examine the molecular diversity of reactions and pathways according to their presence across enzyme families. These complex, many-to-many relationships between protein sequence and biochemical function reveal a significant degree of correlation between enzyme families and reactions. Pathways, however, appear to require more than one enzyme type to perform their complex biochemical transformations. Finally, the distribution of enzyme family members across different pathways provides support for the "recruitment" hypothesis of biochemical pathway evolution.
</noinclude>
|-
|{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11544193 PubMed]
|}
</protect>
==Significance {{HelpIcon|Help:Literature}} ==
{{LitSignificance}}

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{{LitMaterials}}

==Annotations {{HelpIcon|Help:Literature}}==
<protect>

{|class = 'sortable' {{Prettytable}} id='241045'
|- {{table heading style}}
!Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status
|-class='sortbottom'
|[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.0.C47ab95109cf52&page=0&pagename={{FULLPAGENAMEE}} edit table] || || || || || || || ||
|}
</protect>

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

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

PMID:11988630

2008-02-07T23:32:27Z

165.91.10.100: New PMID: Page!

<protect>
{{RightTOC}}

 '''Unniraman, S and Nagaraja, V''' (2001) Axial distortion as a sensor of supercoil changes: a molecular model for the homeostatic regulation of DNA gyrase.''J. Genet.'' '''80''':119-24

{|{{Prettytable}} align = 'center' width= '70%'
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|{{TableHeadingColor}} |'''Abstract''' || Negative supercoiling stimulates transcription of many genes. In contrast, transcription of the genes coding for DNA gyrase is subject to a novel mechanism of autoregulation, wherein relaxation of the template DNA stimulates their transcription. Since DNA gyrase is the sole supercoiling activity in the eubacterial cell, relaxation-stimulated transcription (RST) could reflect an autoregulatory mechanism to maintain supercoil levels within the cell. Extensive deletion and mutational analyses of Escherichia coli gyrA promoter have shown that the -10 region is essential for RST; however, a molecular model has proved to be elusive. We find a strong bend centre immediately downstream of the -10 region in the gyrA promoter. On the basis of analysis of various mutants in the -10 region, we propose a model where axial distortion acts as a sensor of topological changes in DNA. Our model is consistent with earlier data with E. coli gyrA anmd gyrB promoters. We also extrapolate the model to explain the phenomenon of RST of gyr promoters in other organisms and contrast it with promoters induced by supercoiling.
</noinclude>
|-
|{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11988630 PubMed]
|}
</protect>
==Significance {{HelpIcon|Help:Literature}} ==
{{LitSignificance}}

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{{LitMaterials}}

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<protect>

{|class = 'sortable' {{Prettytable}} id='241044'
|- {{table heading style}}
!Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status
|-class='sortbottom'
|[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.0.Z47ab950ae25df&page=0&pagename={{FULLPAGENAMEE}} edit table] || || || || || || || ||
|}
</protect>

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

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

PMID:11593750

2008-02-07T23:32:21Z

165.91.10.100: New PMID: Page!

<protect>
{{RightTOC}}

 '''Mori, H, Horiuchi, T, Isono, K, Wada, C, Kanaya, S, Kitagawa, M, Ara, T and Ohshima, H''' (2001) [Post sequence genome analysis of Escherichia coli]''Tanpakushitsu Kakusan Koso'' '''46''':1977-85

{|{{Prettytable}} align = 'center' width= '70%'
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|{{TableHeadingColor}} |'''Abstract''' || No abstract in PubMed
</noinclude>
|-
|{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11593750 PubMed]
|}
</protect>
==Significance {{HelpIcon|Help:Literature}} ==
{{LitSignificance}}

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{{LitMaterials}}

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<protect>

{|class = 'sortable' {{Prettytable}} id='241043'
|- {{table heading style}}
!Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status
|-class='sortbottom'
|[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.0.Q47ab950532b6d&page=0&pagename={{FULLPAGENAMEE}} edit table] || || || || || || || ||
|}
</protect>

==EcoliWiki Links {{HelpIcon|Help:Literature}} ==
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==References==
{{RefHelp}}
<references/>

PMID:11707277

2008-02-07T23:32:15Z

165.91.10.100: New PMID: Page!

<protect>
{{RightTOC}}

 '''Nouwen, N, van der Laan, M and Driessen, AJ''' (2001) SecDFyajC is not required for the maintenance of the proton motive force.''FEBS Lett.'' '''508''':103-6

{|{{Prettytable}} align = 'center' width= '70%'
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|{{TableHeadingColor}} |'''Abstract''' || SecDFyajC of Escherichia coli is required for efficient export of proteins in vivo. However, the functional role of SecDFyajC in protein translocation is unclear. We evaluated the postulated function of SecDFyajC in the maintenance of the proton motive force. As previously reported, inner membrane vesicles (IMVs) lacking SecDFyajC are defective in the generation of a stable proton motive force when energized with succinate. This phenomenon is, however, not observed when NADH is used as an electron donor. Moreover, the proton motive force generated in SecDFyajC-depleted vesicles stimulated translocation to the same extent as seen with IMVs containing SecDFyajC. Further analysis demonstrates that the reduced proton motive force with succinate in IMVs lacking SecDFyajC is due to a lower amount of the enzyme succinate dehydrogenase. The expression of this enzyme complex is repressed by growth on glucose media, the condition used to deplete SecDFyajC. These results demonstrate that SecDFyajC is not required for proton motive force-driven protein translocation.
</noinclude>
|-
|{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11707277 PubMed]
|}
</protect>
==Significance {{HelpIcon|Help:Literature}} ==
{{LitSignificance}}

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{{LitMaterials}}

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<protect>

{|class = 'sortable' {{Prettytable}} id='241042'
|- {{table heading style}}
!Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status
|-class='sortbottom'
|[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.0.N47ab94ff64503&page=0&pagename={{FULLPAGENAMEE}} edit table] || || || || || || || ||
|}
</protect>

==EcoliWiki Links {{HelpIcon|Help:Literature}} ==
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==References==
{{RefHelp}}
<references/>

PMID:11583550

2008-02-07T23:32:09Z

165.91.10.100: New PMID: Page!

<protect>
{{RightTOC}}

 '''Kim, MY, Maier, CS, Reed, DJ and Deinzer, ML''' (2001) Site-specific amide hydrogen/deuterium exchange in E. coli thioredoxins measured by electrospray ionization mass spectrometry.''J. Am. Chem. Soc.'' '''123''':9860-6

{|{{Prettytable}} align = 'center' width= '70%'
|-
|{{TableHeadingColor}} |'''Abstract''' || Mass spectrometry as an analytical tool to study protein folding and structure by hydrogen/deuterium exchange is a relatively new approach. In this study, site-specific amide deuterium content was measured in oxidized and reduced E. coli thioredoxins by using the b(n) ions in electrospray ionization CID MS/MS experiments after 20-s incubation in D(2)O phosphate-buffered solution (pH 5.7). The deuterium levels correlated well with reported NMR-determined H/D exchange rate constants. The deuterium measured by y(n) ions, however, showed much less reliable correlation with rate exchange data. In general, residues in alpha helices and beta sheets, when measured by b(n) ions, showed low incorporation of deuterium while loops and turns had high deuterium levels. Most amide sites in the two protein forms showed similar deuterium levels consistent with the expected similarity of their structures, but there were some differences. The turn consisting of residues 18-22 in particular showed more variability in deuterium content consistent with reported structural differences in the two forms. The deuterium uptake by thioredoxins alkylated at Cys-32 by S-(2-chloroethyl)glutathione and S-(2-chloroethyl)cysteine, in peptides 1-24 and 45-58, was similar to that observed for oxidized and reduced thioredoxins, but several residues, particularly Leu-53 and Thr-54, showed slightly elevated deuterium levels, suggesting that structural changes had occurred from alkylation of the protein at Cys-32. It is concluded that b(n) ions are reliable for determining the extent of site-specific amide hydrogen isotope exchange and that mass spectrometry is useful as a complementary technique to NMR and other analytical methods for probing regional structural characteristics of proteins.
</noinclude>
|-
|{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11583550 PubMed]
|}
</protect>
==Significance {{HelpIcon|Help:Literature}} ==
{{LitSignificance}}

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{{LitMaterials}}

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<protect>

{|class = 'sortable' {{Prettytable}} id='241041'
|- {{table heading style}}
!Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status
|-class='sortbottom'
|[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.0.E47ab94f999f28&page=0&pagename={{FULLPAGENAMEE}} edit table] || || || || || || || ||
|}
</protect>

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

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

PMID:11698387

2008-02-07T23:32:04Z

165.91.10.100: New PMID: Page!

<protect>
{{RightTOC}}

 '''Lövgren, JM and Wikström, PM''' (2001) The rlmB gene is essential for formation of Gm2251 in 23S rRNA but not for ribosome maturation in Escherichia coli.''J. Bacteriol.'' '''183''':6957-60

{|{{Prettytable}} align = 'center' width= '70%'
|-
|{{TableHeadingColor}} |'''Abstract''' || In Saccharomyces cerevisiae, the rRNA Gm2270 methyltransferase, Pet56p, has an essential role in the maturation of the mitochondrial large ribosomal subunit that is independent of its methyltransferase activity. Here we show that the proposed Escherichia coli ortholog, RlmB (formerly YjfH), indeed is essential for the formation of Gm in position 2251 of 23S rRNA. However, a DeltarlmB mutant did not show any ribosome assembly defects and was not outgrown by a wild-type strain even after 120 cell mass doublings. Thus, RlmB has no important role in ribosome assembly or function in E. coli.
</noinclude>
|-
|{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11698387 PubMed]
|}
</protect>
==Significance {{HelpIcon|Help:Literature}} ==
{{LitSignificance}}

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{{LitMaterials}}

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<protect>

{|class = 'sortable' {{Prettytable}} id='241040'
|- {{table heading style}}
!Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status
|-class='sortbottom'
|[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.0.N47ab94f3d821e&page=0&pagename={{FULLPAGENAMEE}} edit table] || || || || || || || ||
|}
</protect>

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

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

PMID:11673421

2008-02-07T23:31:58Z

165.91.10.100: New PMID: Page!

<protect>
{{RightTOC}}

 '''Yang, X and Ishiguro, EE''' (2001) Involvement of the N terminus of ribosomal protein L11 in regulation of the RelA protein of Escherichia coli.''J. Bacteriol.'' '''183''':6532-7

{|{{Prettytable}} align = 'center' width= '70%'
|-
|{{TableHeadingColor}} |'''Abstract''' || Amino acid-deprived rplK (previously known as relC) mutants of Escherichia coli cannot activate (p)ppGpp synthetase I (RelA) and consequently exhibit relaxed phenotypes. The rplK gene encodes ribosomal protein L11, suggesting that L11 is involved in regulating the activity of RelA. To investigate the role of L11 in the stringent response, a derivative of rplK encoding L11 lacking the N-terminal 36 amino acids (designated 'L11) was constructed. Bacteria overexpressing 'L11 exhibited a relaxed phenotype, and this was associated with an inhibition of RelA-dependent (p)ppGpp synthesis during amino acid deprivation. In contrast, bacteria overexpressing normal L11 exhibited a typical stringent response. The overexpressed 'L11 was incorporated into ribosomes and had no effect on the ribosome-binding activity of RelA. By several methods (yeast two-hybrid, affinity blotting, and copurification), no direct interaction was observed between the C-terminal ribosome-binding domain of RelA and L11. To determine whether the proline-rich helix of L11 was involved in RelA regulation, the Pro-22 residue was replaced with Leu by site-directed mutagenesis. The overexpression of the Leu-22 mutant derivative of L11 resulted in a relaxed phenotype. These results indicate that the proline-rich helix in the N terminus of L11 is involved in regulating the activity of RelA.
</noinclude>
|-
|{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11673421 PubMed]
|}
</protect>
==Significance {{HelpIcon|Help:Literature}} ==
{{LitSignificance}}

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{{LitMaterials}}

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<protect>

{|class = 'sortable' {{Prettytable}} id='241039'
|- {{table heading style}}
!Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status
|-class='sortbottom'
|[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.0.X47ab94ee1bda7&page=0&pagename={{FULLPAGENAMEE}} edit table] || || || || || || || ||
|}
</protect>

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{{LitLinks}}

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

PMID:11669613

2008-02-07T23:31:52Z

165.91.10.100: New PMID: Page!

<protect>
{{RightTOC}}

 '''Price, AC, Zhang, YM, Rock, CO and White, SW''' (2001) Structure of beta-ketoacyl-[acyl carrier protein] reductase from Escherichia coli: negative cooperativity and its structural basis.''Biochemistry'' '''40''':12772-81

{|{{Prettytable}} align = 'center' width= '70%'
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|{{TableHeadingColor}} |'''Abstract''' || The structure of beta-ketoacyl-[acyl carrier protein] reductase (FabG) from Escherichia coli was determined via the multiwavelength anomalous diffraction technique using a selenomethionine-labeled crystal containing 88 selenium sites in the asymmetric unit. The comparison of the E. coli FabG structure with the homologous Brassica napus FabG.NADP(+) binary complex reveals that cofactor binding causes a substantial conformational change in the protein. This conformational change puts all three active-site residues (Ser 138, Tyr 151, and Lys 155) into their active configurations and provides a structural mechanism for allosteric communication between the active sites in the homotetramer. FabG exhibits negative cooperative binding of NADPH, and this effect is enhanced by the presence of acyl carrier protein (ACP). NADPH binding also increases the affinity and decreases the maximum binding of ACP to FabG. Thus, unlike other members of the short-chain dehydrogenase/reductase superfamily, FabG undergoes a substantial conformational change upon cofactor binding that organizes the active-site triad and alters the affinity of the other substrate-binding sites in the tetrameric enzyme.
</noinclude>
|-
|{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11669613 PubMed]
|}
</protect>
==Significance {{HelpIcon|Help:Literature}} ==
{{LitSignificance}}

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{{LitMaterials}}

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<protect>

{|class = 'sortable' {{Prettytable}} id='241038'
|- {{table heading style}}
!Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status
|-class='sortbottom'
|[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.0.P47ab94e85fffd&page=0&pagename={{FULLPAGENAMEE}} edit table] || || || || || || || ||
|}
</protect>

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

PMID:11886566

2008-02-07T23:31:46Z

165.91.10.100: New PMID: Page!

<protect>
{{RightTOC}}

 '''Maisnier-Patin, S, Nordström, K and Dasgupta, S''' (2001) Replication arrests during a single round of replication of the Escherichia coli chromosome in the absence of DnaC activity.''Mol. Microbiol.'' '''42''':1371-82

{|{{Prettytable}} align = 'center' width= '70%'
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|{{TableHeadingColor}} |'''Abstract''' || We used a flow cytometric assay to determine the frequency of replication fork arrests during a round of chromosome replication in Escherichia coli. After synchronized initiation from oriC in a dnaC(Ts) strain, non-permissive conditions were imposed, such that active DnaC was not available during elongation. Under these conditions, about 18% of the cells failed to complete chromosome replication. The sites of replication arrests were random and occurred on either arm of the bidirectionally replicating chromosome, as stalled forks accumulated at the terminus from both directions. The forks at the terminal Ter sites disappeared in the absence of Tus protein, as the active forks could then pass through the terminus to reach the arrest site, and the unfinished rounds of replication would be completed without DnaC. In a dnaC2(Ts)rep double mutant, almost all cells failed to complete chromosome replication in the absence of DnaC activity. As inactivation of Rep helicase (the rep gene product) has been shown to cause frequent replication arrests inducing double-strand breaks (DSBs) in a replicating chromosome, DnaC activity appears to be essential for replication restart from DSBs during elongation.
</noinclude>
|-
|{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11886566 PubMed]
|}
</protect>
==Significance {{HelpIcon|Help:Literature}} ==
{{LitSignificance}}

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{{LitMaterials}}

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<protect>

{|class = 'sortable' {{Prettytable}} id='241037'
|- {{table heading style}}
!Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status
|-class='sortbottom'
|[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.0.L47ab94e2a3818&page=0&pagename={{FULLPAGENAMEE}} edit table] || || || || || || || ||
|}
</protect>

==EcoliWiki Links {{HelpIcon|Help:Literature}} ==
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==References==
{{RefHelp}}
<references/>

PMID:11478886

2008-02-07T23:31:41Z

165.91.10.100: New PMID: Page!

<protect>
{{RightTOC}}

 '''Gerratana, B, Cleland, WW and Frey, PA''' (2001) Mechanistic roles of Thr134, Tyr160, and Lys 164 in the reaction catalyzed by dTDP-glucose 4,6-dehydratase.''Biochemistry'' '''40''':9187-95

{|{{Prettytable}} align = 'center' width= '70%'
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|{{TableHeadingColor}} |'''Abstract''' || Escherichia coli dTDP-glucose 4,6-dehydratase and UDP-galactose 4-epimerase are members of the short-chain dehydrogenase/reductase SDR family. A highly conserved triad consisting of Ser/Thr, Tyr, and Lys is present in the active sites of these enzymes as well in other SDR proteins. Ser124, Tyr149, and Lys153 in the active site of UDP-galactose 4-epimerase are located in similar positions as the corresponding Thr134, Tyr160, and Lys164, in the active site of dTDP-glucose 4,6-dehydratase. The role of these residues in the first hydride transfer step of the dTDP-glucose 4,6-dehydratase mechanism has been studied by mutagenesis and steady-state kinetic analysis. In all mutants except T134S, the k(cat) values are more than 2 orders of magnitude lower than of wild-type enzyme. The substrate analogue, dTDP-xylose, was used to investigate the effects of the mutations on rate of the first hydride transfer step. The first step becomes significantly rate limiting upon mutation of Tyr160 to Phe and only partly rate limiting in the reaction catalyzed by K164M and T134A dehydratases. The pH dependence of k(cat), the steady-state NADH level, and the fraction of NADH formed with saturating dTDP-xylose show shifts in the pK(a) assigned to Tyr160 to more basic values by mutation of Lys164 and Thr134. The pK(a) of Tyr160, as determined by the pH dependence of NADH formation by dTDP-xylose, is 6.41. Lys164 and Thr134 are believed to play important roles in the stabilization of the anion of Tyr160 in a fashion similar to the roles of the corresponding residues in UDP-galactose 4-epimerase, which facilitate the ionization of Tyr149 in that enzyme [Liu, Y., et al. (1997) Biochemistry 35, 10675--10684]. Tyr160 is presumably the base for the first hydride transfer step, while Thr134 may relay a proton from the sugar to Tyr160.
</noinclude>
|-
|{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11478886 PubMed]
|}
</protect>
==Significance {{HelpIcon|Help:Literature}} ==
{{LitSignificance}}

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{{LitMaterials}}

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<protect>

{|class = 'sortable' {{Prettytable}} id='241036'
|- {{table heading style}}
!Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status
|-class='sortbottom'
|[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.0.H47ab94dcdfcfa&page=0&pagename={{FULLPAGENAMEE}} edit table] || || || || || || || ||
|}
</protect>

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

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

PMID:11532150

2008-02-07T23:31:35Z

165.91.10.100: New PMID: Page!

<protect>
{{RightTOC}}

 '''Cromie, GA and Leach, DR''' (2001) Recombinational repair of chromosomal DNA double-strand breaks generated by a restriction endonuclease.''Mol. Microbiol.'' '''41''':873-83

{|{{Prettytable}} align = 'center' width= '70%'
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|{{TableHeadingColor}} |'''Abstract''' || DNA double-strand break repair can be accomplished by homologous recombination when a sister chromatid or a homologous chromosome is available. However, the study of sister chromatid double-strand break repair in prokaryotes is complicated by the difficulty in targeting a break to only one copy of two essentially identical DNA sequences. We have developed a system using the Escherichia coli chromosome and the restriction enzyme EcoKI, in which double-strand breaks can be introduced into only one sister chromatid. We have shown that the components of the RecBCD and RecFOR 'pathways' are required for the recombinational repair of these breaks. Furthermore, we have shown a requirement for SbcCD, the prokaryotic homologue of Rad50/Mre11. This is the first demonstration that, like Rad50/Mre11, SbcCD is required for recombination in a wild-type cell. Our work suggests that the SbcCD-Rad50/Mre11 family of proteins, which have two globular domains separated by a long coiled-coil linker, is specifically required for the co-ordination of double-strand break repair reactions in which two DNA ends are required to recombine at one target site.
</noinclude>
|-
|{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11532150 PubMed]
|}
</protect>
==Significance {{HelpIcon|Help:Literature}} ==
{{LitSignificance}}

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{{LitMaterials}}

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<protect>

{|class = 'sortable' {{Prettytable}} id='241035'
|- {{table heading style}}
!Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status
|-class='sortbottom'
|[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.0.U47ab94d72c564&page=0&pagename={{FULLPAGENAMEE}} edit table] || || || || || || || ||
|}
</protect>

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

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

PMID:11286560

2008-02-07T23:31:29Z

165.91.10.100: New PMID: Page!

<protect>
{{RightTOC}}

 '''Todd, AE, Orengo, CA and Thornton, JM''' (2001) Evolution of function in protein superfamilies, from a structural perspective.''J. Mol. Biol.'' '''307''':1113-43

{|{{Prettytable}} align = 'center' width= '70%'
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|{{TableHeadingColor}} |'''Abstract''' || The recent growth in protein databases has revealed the functional diversity of many protein superfamilies. We have assessed the functional variation of homologous enzyme superfamilies containing two or more enzymes, as defined by the CATH protein structure classification, by way of the Enzyme Commission (EC) scheme. Combining sequence and structure information to identify relatives, the majority of superfamilies display variation in enzyme function, with 25 % of superfamilies in the PDB having members of different enzyme types. We determined the extent of functional similarity at different levels of sequence identity for 486,000 homologous pairs (enzyme/enzyme and enzyme/non-enzyme), with structural and sequence relatives included. For single and multi-domain proteins, variation in EC number is rare above 40 % sequence identity, and above 30 %, the first three digits may be predicted with an accuracy of at least 90 %. For more distantly related proteins sharing less than 30 % sequence identity, functional variation is significant, and below this threshold, structural data are essential for understanding the molecular basis of observed functional differences. To explore the mechanisms for generating functional diversity during evolution, we have studied in detail 31 diverse structural enzyme superfamilies for which structural data are available. A large number of variations and peculiarities are observed, at the atomic level through to gross structural rearrangements. Almost all superfamilies exhibit functional diversity generated by local sequence variation and domain shuffling. Commonly, substrate specificity is diverse across a superfamily, whilst the reaction chemistry is maintained. In many superfamilies, the position of catalytic residues may vary despite playing equivalent functional roles in related proteins. The implications of functional diversity within supefamilies for the structural genomics projects are discussed. More detailed information on these superfamilies is available at http://www.biochem.ucl.ac.uk/bsm/FAM-EC/.
</noinclude>
|-
|{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11286560 PubMed]
|}
</protect>
==Significance {{HelpIcon|Help:Literature}} ==
{{LitSignificance}}

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{{LitMaterials}}

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<protect>

{|class = 'sortable' {{Prettytable}} id='241034'
|- {{table heading style}}
!Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status
|-class='sortbottom'
|[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.0.W47ab94d16e7a8&page=0&pagename={{FULLPAGENAMEE}} edit table] || || || || || || || ||
|}
</protect>

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

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

PMID:12183225

2008-02-07T23:31:23Z

165.91.10.100: New PMID: Page!

<protect>
{{RightTOC}}

 '''Hackbarth, CJ, Chen, DZ, Lewis, JG, Clark, K, Mangold, JB, Cramer, JA, Margolis, PS, Wang, W, Koehn, J, Wu, C, Lopez, S, Withers, G, Gu, H, Dunn, E, Kulathila, R, Pan, SH, Porter, WL, Jacobs, J, Trias, J, Patel, DV, Weidmann, B, White, RJ and Yuan, Z''' (2002) N-alkyl urea hydroxamic acids as a new class of peptide deformylase inhibitors with antibacterial activity.''Antimicrob. Agents Chemother.'' '''46''':2752-64

{|{{Prettytable}} align = 'center' width= '70%'
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|{{TableHeadingColor}} |'''Abstract''' || Peptide deformylase (PDF) is a prokaryotic metalloenzyme that is essential for bacterial growth and is a new target for the development of antibacterial agents. All previously reported PDF inhibitors with sufficient antibacterial activity share the structural feature of a 2-substituted alkanoyl at the P(1)' site. Using a combination of iterative parallel synthesis and traditional medicinal chemistry, we have identified a new class of PDF inhibitors with N-alkyl urea at the P(1)' site. Compounds with MICs of <or=4 micro g/ml against gram-positive and gram-negative pathogens, including Staphylococcus aureus, Streptococcus pneumoniae, and Haemophilus influenzae, have been identified. The concentrations needed to inhibit 50% of enzyme activity (IC(50)s) for Escherichia coli Ni-PDF were <or=0.1 micro M, demonstrating the specificity of the inhibitors. In addition, these compounds were very selective for PDF, with IC(50)s of consistently >200 micro M for matrilysin and other mammalian metalloproteases. Structure-activity relationship analysis identified preferred substitutions resulting in improved potency and decreased cytotoxity. One of the compounds (VRC4307) was cocrystallized with PDF, and the enzyme-inhibitor structure was determined at a resolution of 1.7 A. This structural information indicated that the urea compounds adopt a binding position similar to that previously determined for succinate hydroxamates. Two compounds, VRC4232 and VRC4307, displayed in vivo efficacy in a mouse protection assay, with 50% protective doses of 30.8 and 17.9 mg/kg of body weight, respectively. These N-alkyl urea hydroxamic acids provide a starting point for identifying new PDF inhibitors that can serve as antimicrobial agents.
</noinclude>
|-
|{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=12183225 PubMed]
|}
</protect>
==Significance {{HelpIcon|Help:Literature}} ==
{{LitSignificance}}

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{{LitMaterials}}

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<protect>

{|class = 'sortable' {{Prettytable}} id='241033'
|- {{table heading style}}
!Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status
|-class='sortbottom'
|[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.0.Y47ab94cbb1439&page=0&pagename={{FULLPAGENAMEE}} edit table] || || || || || || || ||
|}
</protect>

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

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

PMID:12457697

2008-02-07T23:31:18Z

165.91.10.100: New PMID: Page!

<protect>
{{RightTOC}}

 '''Buddelmeijer, N and Beckwith, J''' (2002) Assembly of cell division proteins at the E. coli cell center.''Curr. Opin. Microbiol.'' '''5''':553-7

{|{{Prettytable}} align = 'center' width= '70%'
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|{{TableHeadingColor}} |'''Abstract''' || Cell division in Escherichia coli requires the coordinated action of at least ten proteins. In recent years, substantial progress has been made in understanding the assembly of these proteins at the cell septum. These findings suggest a largely stepwise appearance of cell division proteins at the centre of the cell.
</noinclude>
|-
|{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=12457697 PubMed]
|}
</protect>
==Significance {{HelpIcon|Help:Literature}} ==
{{LitSignificance}}

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{{LitMaterials}}

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<protect>

{|class = 'sortable' {{Prettytable}} id='241032'
|- {{table heading style}}
!Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status
|-class='sortbottom'
|[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.0.Y47ab94c605945&page=0&pagename={{FULLPAGENAMEE}} edit table] || || || || || || || ||
|}
</protect>

==EcoliWiki Links {{HelpIcon|Help:Literature}} ==
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{{RefHelp}}
<references/>

PMID:12500533

2008-02-07T23:31:12Z

165.91.10.100: New PMID: Page!

<protect>
{{RightTOC}}

 '''Vasil'eva, IuM and Garber, MB''' [The regulatory role of the Hfq protein in bacterial cells]''Mol. Biol. (Mosk.)'' '''36''':970-7

{|{{Prettytable}} align = 'center' width= '70%'
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|{{TableHeadingColor}} |'''Abstract''' || Hfq (HF1) is a polyfunctional translational regulator of numerous bacterial mRNAs. Its physico-chemical properties, possible mechanisms regulating bacterial translation, and the effect of Hfq on transcription of several mRNAs are considered. A similarity of Hfq and eukaryotic mRNA splicing proteins is discussed. Data are reviewed on the roles of Hfq in poly(A) metabolism and formation of the bacterial nucleoid and on the Hfq interaction with untranslated regulatory RNAs.
</noinclude>
|-
|{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=12500533 PubMed]
|}
</protect>
==Significance {{HelpIcon|Help:Literature}} ==
{{LitSignificance}}

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<protect>

{|class = 'sortable' {{Prettytable}} id='241031'
|- {{table heading style}}
!Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status
|-class='sortbottom'
|[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.0.A47ab94c04505e&page=0&pagename={{FULLPAGENAMEE}} edit table] || || || || || || || ||
|}
</protect>

==EcoliWiki Links {{HelpIcon|Help:Literature}} ==
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<references/>

PMID:12364333

2008-02-07T23:31:01Z

165.91.10.100: New PMID: Page!

<protect>
{{RightTOC}}

 '''Zuo, Y and Deutscher, MP''' (2002) Mechanism of action of RNase T. II. A structural and functional model of the enzyme.''J. Biol. Chem.'' '''277''':50160-4

{|{{Prettytable}} align = 'center' width= '70%'
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|{{TableHeadingColor}} |'''Abstract''' || A detailed structural and functional model of E. coli RNase T was generated based on sequence analysis, homology modeling, and experimental observation. In the accompanying article, three short sequence segments (nucleic acid binding sequences (NBS)) important for RNase T substrate binding were identified. In the model, these segments cluster to form a positively charged surface patch. However, this patch is on the face of the RNase T monomer opposite the DEDD catalytic center. We propose that by dimerization, the NBS patch from one subunit is brought to the vicinity of the DEDD center of the second monomer to form a fully functional RNase T active site. In support of this model, mutagenetic studies show that one NBS1 residue, Arg(13), sits at the catalytic center despite being on the opposite side of the monomer. Second, the complementarity of the RNase T subunits through the formation of homodimers was demonstrated by reconstitution of partial RNase T activity from monomers derived from two inactive mutant proteins, one defective in catalysis and one in substrate binding. These data explain why RNase T must dimerize to function. The model provides a detailed framework on which to explain the mechanism of action of RNase T.
</noinclude>
|-
|{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=12364333 PubMed]
|}
</protect>
==Significance {{HelpIcon|Help:Literature}} ==
{{LitSignificance}}

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{{LitMaterials}}

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<protect>

{|class = 'sortable' {{Prettytable}} id='241030'
|- {{table heading style}}
!Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status
|-class='sortbottom'
|[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.0.U47ab94b543554&page=0&pagename={{FULLPAGENAMEE}} edit table] || || || || || || || ||
|}
</protect>

==EcoliWiki Links {{HelpIcon|Help:Literature}} ==
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<references/>

PMID:11956202

2008-02-07T23:30:54Z

165.91.10.100: New PMID: Page!

<protect>
{{RightTOC}}

 '''Cronan, JE''' (2002) Interchangeable enzyme modules. Functional replacement of the essential linker of the biotinylated subunit of acetyl-CoA carboxylase with a linker from the lipoylated subunit of pyruvate dehydrogenase.''J. Biol. Chem.'' '''277''':22520-7

{|{{Prettytable}} align = 'center' width= '70%'
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|{{TableHeadingColor}} |'''Abstract''' || Biotin carboxyl carrier protein (BCCP) is the small biotinylated subunit of Escherichia coli acetyl-CoA carboxylase, the enzyme that catalyzes the first committed step of fatty acid synthesis. E. coli BCCP is a member of a large family of protein domains modified by covalent attachment of biotin. In most biotinylated proteins, the biotin moiety is attached to a lysine residue located about 35 residues from the carboxyl terminus of the protein, which lies in the center of a strongly conserved sequence that forms a tightly folded anti-parallel beta-barrel structure. Located upstream of the conserved biotinoyl domain sequence are proline/alanine-rich sequences of varying lengths, which have been proposed to act as flexible linkers. In E. coli BCCP, this putative linker extends for about 42 residues with over half of the residues being proline or alanine. I report that deletion of the 30 linker residues located adjacent to the biotinoyl domain resulted in a BCCP species that was defective in function in vivo, although it was efficiently biotinylated. Expression of this BCCP species failed to restore normal growth and fatty acid synthesis to a temperature-sensitive E. coli strain that lacks BCCP when grown at nonpermissive temperatures. In contrast, replacement of the deleted BCCP linker with a linker derived from E. coli pyruvate dehydrogenase gave a chimeric BCCP species that had normal in vivo function. Expression of BCCPs having deletions of various segments of the linker region of the chimeric protein showed that some deletions of up to 24 residues had significant or full biological activity, whereas others had very weak or no activity. The inactive deletion proteins all lacked an APAAAAA sequence located adjacent to the tightly folded biotinyl domain, whereas deletions that removed only upstream linker sequences remained active. Deletions within the linker of the wild type BCCP protein also showed that the residues adjacent to the tightly folded domain play an essential role in protein function, although in this case some proteins with deletions within this region retained activity. Retention of activity was due to fusion of the domain to upstream sequences. These data provide new evidence for the functional and structural similarities of biotinylated and lipoylated proteins and strongly support a common evolutionary origin of these enzyme subunits.
</noinclude>
|-
|{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11956202 PubMed]
|}
</protect>
==Significance {{HelpIcon|Help:Literature}} ==
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<protect>

{|class = 'sortable' {{Prettytable}} id='241029'
|- {{table heading style}}
!Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status
|-class='sortbottom'
|[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.0.H47ab94addbedc&page=0&pagename={{FULLPAGENAMEE}} edit table] || || || || || || || ||
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PMID:12065579

2008-02-07T23:30:48Z

165.91.10.100: New PMID: Page!

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 '''Geanacopoulos, M and Adhya, S''' (2002) Genetic analysis of GalR tetramerization in DNA looping during repressosome assembly.''J. Biol. Chem.'' '''277''':33148-52

{|{{Prettytable}} align = 'center' width= '70%'
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|{{TableHeadingColor}} |'''Abstract''' || The Gal repressosome is a nucleoprotein complex consisting of 2 GalR dimers, 1 HU, and 1 DNA loop, which represses the transcription of the gal operon. We have adopted a structure-based genetic approach to complement ongoing physical studies of the complex. Homology-based and subsequent alanine-scanning mutageneses suggest that five residues in the DNA-distal subdomain of GalR dimer are important for repressosome formation. A further analysis of these and intragenic suppressors of looping-defective GalR mutants as well as gain-of-function mutants that permit repressosome assembly in the absence of HU show that GalR dimers contact each other in the repressosome in a partially stacked configuration.
</noinclude>
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|{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=12065579 PubMed]
|}
</protect>
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<protect>

{|class = 'sortable' {{Prettytable}} id='241028'
|- {{table heading style}}
!Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status
|-class='sortbottom'
|[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.0.Z47ab94a82e0fc&page=0&pagename={{FULLPAGENAMEE}} edit table] || || || || || || || ||
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PMID:11931566

2008-02-07T23:30:42Z

165.91.10.100: New PMID: Page!

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 '''Wagner, R''' (2002) Regulation of ribosomal RNA synthesis in E. coli: effects of the global regulator guanosine tetraphosphate (ppGpp).''J. Mol. Microbiol. Biotechnol.'' '''4''':331-40

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|{{TableHeadingColor}} |'''Abstract''' || The global regulatory nucleotides (p)ppGpp are major effectors for the control of ribosomal RNA in bacteria. The effector molecules accumulate to different cellular levels at amino acid deprivation or during different growth rates. They change the activity of RNA polymerase to transcribe from sensitive promoters (e.g. ribosomal RNA promoters). Sensitive promoters are characterized by a GC-rich discriminator element in addition to further structural requirements not completely understood. ppGpp must also be regarded as a mediator for growth rate control although it appears that ppGpp-independent regulatory mechanisms exist. Inhibition occurs at various steps during initiation but also during elongation where RNA polymerase pausing is observed. From the existing data a mechanistic model for the action of ppGpp is suggested considering structural details of RNA polymerase obtained at high resolution.
</noinclude>
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|{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11931566 PubMed]
|}
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{|class = 'sortable' {{Prettytable}} id='241027'
|- {{table heading style}}
!Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status
|-class='sortbottom'
|[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.0.D47ab94a25fb44&page=0&pagename={{FULLPAGENAMEE}} edit table] || || || || || || || ||
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PMID:11755084

2008-02-07T23:30:36Z

165.91.10.100: New PMID: Page!

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 '''Gentschev, I, Dietrich, G and Goebel, W''' (2002) The E. coli alpha-hemolysin secretion system and its use in vaccine development.''Trends Microbiol.'' '''10''':39-45

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|{{TableHeadingColor}} |'''Abstract''' || Many Gram-negative bacteria use a type I secretion system to translocate proteins, including pore-forming toxins, proteases, lipases and S-layer proteins, across both the inner and outer membranes into the extracellular surroundings. The Escherichia coli alpha-hemolysin (HlyA) secretion system is the prototypical and best characterized type I secretion system. The structure and function of the components of the HlyA secretion apparatus, HlyB, HlyD and TolC, have been studied in great detail. The functional characteristics of this secretion system enable it to be used in a variety of different applications, including the presentation of heterologous antigens in live-attenuated bacterial vaccines. Such vaccines can be an effective delivery system for heterologous antigens, and the use of a type I secretion system allows the antigens to be actively exported from the cytoplasm of the bacterial carrier rather than only becoming accessible to the host immune system after bacterial disintegration.
</noinclude>
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|{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11755084 PubMed]
|}
</protect>
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<protect>

{|class = 'sortable' {{Prettytable}} id='241026'
|- {{table heading style}}
!Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status
|-class='sortbottom'
|[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.0.R47ab949ca8129&page=0&pagename={{FULLPAGENAMEE}} edit table] || || || || || || || ||
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PMID:11952238

2008-02-07T23:30:31Z

165.91.10.100: New PMID: Page!

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 '''Engel, A and Stahlberg, H''' (2002) Aquaglyceroporins: channel proteins with a conserved core, multiple functions, and variable surfaces.''Int. Rev. Cytol.'' '''215''':75-104

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|{{TableHeadingColor}} |'''Abstract''' || Membrane channels for water and small nonionic solutes are required for osmoregulation in bacteria, plants, and animals. Aquaporin-1, the water channel of human erythrocytes, is the first channel demonstrated to conduct water, by expression in Xenopus oocytes. Phylogenetic analyses reveal the existence of two clusters of subfamilies, the aquaporins (AQPs) and glycerol facilitators (GLPs). Sequence-based structure prediction provided a model comprising six membrane-spanning helices, while sequence analyses suggested strategic residues that are important for structure and function. The surface topography of several AQPs has been mapped by atomic force microscopy, revealing different features that correlate with differences in the loops connecting transmembrane helices. The 3D structures of AQP1 and GlpF have been determined by electron cryomicroscopy. The 3.8-A density map allowed the first atomic model of AQP1 to be built, taking into account data from sequence analyses. This model provides some insight into the permeation of water through a channel that blocks the passage of protons. GIpF has been resolved to 6.9 A, revealing helices that are similar to those of AQP1. Homology modeling shows the channel region of these distant aquaglyceroporins to be similar, as confirmed by the 2.2-A structure of GlpF from X-ray crystallography.
</noinclude>
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|{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11952238 PubMed]
|}
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<protect>

{|class = 'sortable' {{Prettytable}} id='241025'
|- {{table heading style}}
!Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status
|-class='sortbottom'
|[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.0.L47ab9496e02d4&page=0&pagename={{FULLPAGENAMEE}} edit table] || || || || || || || ||
|}
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PMID:11931550

2008-02-07T23:30:25Z

165.91.10.100: New PMID: Page!

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 '''Hantke, K''' (2002) Members of the Fur protein family regulate iron and zinc transport in E. coli and characteristics of the Fur-regulated fhuF protein.''J. Mol. Microbiol. Biotechnol.'' '''4''':217-22

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|{{TableHeadingColor}} |'''Abstract''' || The regulator Fur represses with Fe2+ as cofactor iron uptake genes. The fhuF gene reacts very sensitive to minor changes of Fe2+ and Fur. It is assumed that FhuF helps in the mobilisation of iron out of the hydroxamate siderophores transported into the cell. Analysis of the protein revealed an unusual [2Fe-2S] cluster bound to a Cys-Cys-X10-Cys-X2-Cys motif in FhuF. suf genes responsible for the synthesis of the iron sulfur center were identified. The Zur protein shows 27% identity to the Fur protein of E. coli. It regulates as a repressor the high affinity uptake system znuACB. Only two additional Zur binding sites in the promoter region of genes with unknown function were found. Properties of Zur and Fur proteins from different bacteria are compared.
</noinclude>
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|{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11931550 PubMed]
|}
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{|class = 'sortable' {{Prettytable}} id='241024'
|- {{table heading style}}
!Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status
|-class='sortbottom'
|[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.0.L47ab949125a3c&page=0&pagename={{FULLPAGENAMEE}} edit table] || || || || || || || ||
|}
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